(:OCELOT-KB :NAME ECOBASE :PACKAGE "ECOCYC" :WRITE-DATE
"15:23:52 on Wed Jul 26, 2006" :WRITE-UTIME 3362941432 :USER "kaipa")
(--TRANS-ACENAPHTHENE-12-DIOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |keseler|)
(:CREATION-DATE 3352662491)
(COMMON-NAME "(+-)-trans-acenaphthene-1,2-diol")
(SYNONYMS "trans-1,2-acenaphthylene glycol")
(DBLINKS (PUBCHEM "440245" NIL |hopkinso| 3317065769 NIL NIL))
(STRUCTURE-ATOMS C C C C C C C C C C C C O O H H H H H H H H H H)
(DISPLAY-COORDS-2D (5.5321d0 1.6354d0) (2.0d0 1.6562d0) (4.666d0 2.1354d0)
(2.9061d0 2.1701d0) (5.5321d0 0.6354d0) (2.0d0 0.6146d0) (3.8d0 1.6354d0)
(4.666d0 0.1354d0) (2.9061d0 0.1007d0) (3.8d0 0.6354d0) (4.4568d0 -0.8364d0)
(3.4681d0 -0.9395d0) (5.1247d0 -1.5807d0) (2.9681d0 -1.8055d0)
(6.069d0 1.9454d0) (1.4643d0 1.9683d0) (4.666d0 2.7554d0) (2.9132d0 2.79d0)
(6.069d0 0.3254d0) (1.4643d0 0.3025d0) (4.2339d0 -1.415d0)
(3.8056d0 -1.4596d0) (4.9321d0 -2.1701d0) (2.3481d0 -1.8055d0))
(STRUCTURE-BONDS (14 24 1) (13 23 1) (12 22 1) (11 21 1) (6 20 1) (5 19 1)
(4 18 1) (3 17 1) (2 16 1) (1 15 1) (12 14 1 :DOWN) (11 13 1 :UP) (11 12 1)
(9 12 1) (9 10 :AROMATIC) (8 11 1) (8 10 :AROMATIC) (10 7 :AROMATIC)
(6 9 :AROMATIC) (5 8 :AROMATIC) (7 4 :AROMATIC) (7 3 :AROMATIC)
(2 6 :AROMATIC) (4 2 :AROMATIC) (1 5 :AROMATIC) (3 1 :AROMATIC))
(COMMENT-INTERNAL "This structure was imported from PubChem on Feb-15-2005")
(CHEMICAL-FORMULA (C 12) (H 10) (O 2))
(MOLECULAR-WEIGHT 186.21d0)
(AROMATIC-RINGS (6 2 4 7 10 9) (3 7 10 8 5 1)) )
NIL)
(|1-4-alpha-D-galacturonosyl| T (
(OCELOT-GFP::PARENTS |Pectin|)
(MOLECULAR-WEIGHT 546.392d0)
(CHEMICAL-FORMULA (C 18) (H 26) (O 19))
(DISPLAY-COORDS-2D (-0.5895d0 0.6812d0) (-0.5895d0 1.5063d0)
(0.125d0 1.9188d0) (0.8395d0 1.5063d0) (0.8395d0 0.6812d0)
(0.125d0 0.2687d0) (1.5539d0 1.9188d0) (0.125d0 2.7438d0)
(-1.3039d0 1.9188d0) (-1.3039d0 0.2687d0) (-1.3039d0 -0.5563d0)
(-2.0184d0 0.6812d0) (1.5539d0 0.2687d0) (2.2684d0 -0.1438d0)
(2.2684d0 -0.9688d0) (2.9829d0 0.2688d0) (3.6973d0 -0.1438d0)
(3.6973d0 -0.9688d0) (1.5539d0 -1.3813d0) (2.9829d0 -1.3813d0)
(1.5539d0 -2.2063d0) (0.8395d0 -0.9688d0) (2.9829d0 1.0938d0)
(4.4118d0 0.2687d0) (4.4118d0 -1.3813d0) (5.1775d0 -1.7198d0)
(5.1775d0 -2.5448d0) (5.8919d0 -1.3073d0) (6.6064d0 -1.7198d0)
(6.6064d0 -2.5448d0) (4.463d0 -2.9573d0) (4.463d0 -3.7823d0)
(3.7485d0 -2.5448d0) (5.8919d0 -0.4823d0) (7.3209d0 -1.3073d0)
(7.3209d0 -2.9573d0) (5.8919d0 -2.9573d0))
(STRUCTURE-BONDS (31 32 1) (31 33 2) (28 34 1 :UP) (29 35 1 :DOWN)
(30 36 1 :DOWN) (27 31 1 :UP) (29 30 1) (28 29 1) (37 30 1) (37 27 1)
(26 28 1) (27 26 1) (26 25 1 :UP) (19 21 1) (19 22 2) (16 23 1 :UP)
(17 24 1 :DOWN) (18 25 1 :DOWN) (15 19 1 :UP) (17 18 1) (16 17 1) (20 18 1)
(20 15 1) (14 16 1) (15 14 1) (14 13 1 :UP) (10 12 2) (10 11 1) (1 10 1 :UP)
(2 9 1 :UP) (3 8 1 :UP) (4 7 1 :DOWN) (5 13 1 :DOWN) (4 5 1) (3 4 1) (2 3 1)
(1 2 1) (6 5 1) (6 1 1))
(STRUCTURE-ATOMS C C C C C O O O O C O O O C C C C C C O O O O O O C C C C C
C O O O O O O)
(COMMON-NAME "1,4-α-D-galacturonosyl")
(SYNONYMS "1,4-α-poly-D-galacturonate" "homogalacturonan")
(SCHEMA? T)
(OVERVIEW-NODE-SHAPE :SQUARE)
(N-NAME "(1,4-alpha-D-galacturonosyl)(N)")
(N+1-NAME "(1,4-α-D-galacturonosyl)(n+1)")
(:CREATOR |paley|)
(:CREATION-DATE 3276359851) )
NIL)
(|1-4-alpha-D-Glucan| T (
(OCELOT-GFP::PARENTS |Glycogens|)
(N-1-NAME "(1,4-α-D-glucosyl)(n-1)")
(APPEARS-IN-RIGHT-SIDE-OF MALTODEXGLUCOSID-RXN GLYCOGENSYN-RXN)
(APPEARS-IN-LEFT-SIDE-OF MALTODEXGLUCOSID-RXN GLYCOGENSYN-RXN ALPHA-AMYL-RXN
GLYCOGEN-BRANCH-RXN)
(N-NAME "(1,4-α-D-glucosyl)(N)")
(N+1-NAME "(1,4-α-D-glucosyl)(n+1)")
(SYNONYMS "1,4-α-D-glucan" "amylose" "β-amylase"
"(1,4-α-D-glucosyl)(n)"
"(1,4-α-D-glucosyl)(n+1)"
"(1,4-α-D-glucosyl)(n-1)")
(COMMON-NAME "a 1,4-α-D-glucan")
(:CREATION-DATE 3114278946)
(:CREATOR |kr|) )
NIL)
(|1-4-beta-D-Glucan| T (
(OCELOT-GFP::PARENTS |Beta-D-Glucans|)
(DBLINKS (CAS "9004-34-6"))
(COMMON-NAME "a 1,4-β-D-glucan")
(N-1-NAME "(1,4-β-D-glucosyl)(n-1)")
(N+1-NAME "(1,4-β-D-glucosyl)(n+1)")
(N-NAME "(1,4-β-D-glucosyl)(N)")
(SYNONYMS "(1,4-β-D-glucosyl)(n)"
"(1,4-β-D-glucosyl)(n+1)"
"(1,4-β-D-glucosyl)(n-1)")
(COMMENT "This compound class stands for 1,4-β-D-glucosyl polymers.")
(:CREATOR |kr|)
(:CREATION-DATE 3266169523) )
NIL)
(|1-6-alpha-D-glucan| T (
(OCELOT-GFP::PARENTS |Dextrins|)
(N-1-NAME "(1,6-α-D-glucosyl)(m-1)")
(COMMON-NAME "a 1-6-α-D-glucan")
(N+1-NAME "(1,6-α-D-glucosyl)(m+1)")
(N-NAME "(1,6-α-D-glucosyl)(m)")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(|1-Acylglycero-Phosphocholines| T (
(OCELOT-GFP::PARENTS |Lysolecithins|)
(DISPLAY-COORDS-2D (12.2718d0 -4.933d0) (12.9724d0 -3.3915d0)
(10.2258d0 -4.8769d0) (2.1265d0 -6.2032d0) (7.4787d0 -2.5786d0)
(3.4182d0 -1.3235d0) (7.4787d0 0.0d0) (0.0d0 -5.0378d0) (9.3567d0 -2.3263d0)
(10.5899d0 -2.3263d0) (3.4721d0 -3.7478d0) (5.5446d0 -2.4889d0)
(2.0725d0 -3.779d0) (8.7118d0 -1.2331d0) (6.2175d0 -1.2612d0)
(1.3997d0 -5.0067d0) (4.145d0 -2.5201d0) (11.2067d0 -3.3915d0)
(7.4787d0 -1.2331d0))
(COMMON-NAME "a 1-acylglycerophosphocholine")
(CHEMICAL-FORMULA (C 9) (H 19) (N 1) (O 7) (R 1) (P 1))
(ATOM-CHARGES (18 1) (7 -1))
(SYNONYMS "a 2-lysolecithin" "a 2-lysophosphatidylcholine"
"an α'-acylglycerophosphocholine" "an L-2-lysolecithin")
(STRUCTURE-BONDS (15 19 1) (14 19 1) (13 16 1) (12 17 1) (12 15 1) (11 17 1)
(11 13 1) (10 18 1) (9 14 1) (9 10 1) (8 16 1) (7 19 1) (6 17 1) (5 19 2)
(4 16 2) (3 18 1) (2 18 1) (1 18 1))
(STRUCTURE-ATOMS C C C O O O O R C C C C O O O C C N P)
(SCHEMA? T)
(NAMES "L-1-lysolecithin" "1-lysolecithin" "1-Acylglycerophosphocholine"
"alpha-Acylglycerophosphocholine" "1-Lysophosphatidylcholine")
(:CREATOR |kr|)
(:CREATION-DATE 3267207960) )
NIL)
(1-ACYLGLYCEROL-3-P-ACYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH ACP)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(ALTERNATIVE-SUBSTRATES
(ACYL-SN-GLYCEROL-3P PALMITYL-COA "PALMITOYL-ACP" PALMITOLEOYL-ACP
"CIS-VACCENOYL-ACP"))
(REACTION 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN)
(COMMENT "1-acylglycerol-3-phosphate acyltransferase catalyzes the
second step in phospholipid biosynthesis, and is thought to function
in close proximity to the first catalyzed reaction. The enzyme can
utilize either acyl-acyl carrier protein or acyl-CoA as the fatty acyl
donor. Fatty acids that are endogenously synthesized are attached to
ACP and exogenously added fatty acids are attached to coenzyme-A. It
is also believed that this enzyme determines which fatty acid,
saturated or unsaturated, will be incorporated into the sn-2 position
of glycerophospholipids, if acyl-CoA is the fatty acyl donor. |CITS:
[92212294]| The favored chain lengths are 16 and 18 with one
unsaturation. |CITS: [Mathews&vanHolde]|")
(ENZYME 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER)
(SYNONYMS "1-acylglycerol-3-phosphate O-acyltransferase"
"1-acyl-sn-glycerol-3-phosphate acyltransferase"
"1-acylglycerolphosphate acyltransferase"
"acyl-CoA:1-acyl-sn-glycerol-3-phosphate 2-O-acyltransferase"
"1-acylglycerol-3-phosphate-O-acyltransferase")
(COMMON-NAME "1-acylglycerol-3-phosphate acyltransferase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/plsC.template")
(:CREATION-DATE 3001089035)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH ACP COMMENT "Free ACP exerted a selective effect in that
it was a more potent inhibitor of acyl transfer from palmitoyl-CoA
than from palmitoyl-ACP. |CITS: [81094037]|")
(ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[81094037]")))
(1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3018" "ParF" "PlsC")
(DBLINKS (MODBASE "P26647" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF01553" IN-FAMILY |pkarp| 3346700383 NIL NIL)
(REFSEQ "NP_417490" NIL NIL NIL NIL NIL) (UNIPROT "P26647"))
(CATALYZES 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-ENZRXN)
(PI 9.76d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 27.453115000000004d0)
(GENE EG11377)
(CITATIONS "[92212294]" "[91009154]")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/plsC.template")
(:CREATION-DATE 3001089035)
(:CREATOR |mriley|) )
NIL)
(1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(IN-PATHWAY PHOSLIPSYN-PWY)
(ENZYMATIC-REACTION 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-ENZRXN)
(RIGHT L-PHOSPHATIDATE ACP)
(LEFT ACYL-SN-GLYCEROL-3P ACYL-ACP)
(EC-NUMBER "2.3.1.51")
(COMMENT "This is the second step in de novo phospholipid biosynthesis
in which a second fatty acid is esterified at C2 of the glycerol
moiety.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/plsC.template")
(:CREATION-DATE 3001089035)
(:CREATOR |mriley|) )
NIL)
(|1-Alkenyl-2-acyl-glyceroPethamines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(CHEMICAL-FORMULA (C 9) (H 16) (N 1) (O 7) (R1 1) (R2 1) (P 1))
(STRUCTURE-BONDS (18 20 1) (17 19 2) (17 18 1) (16 17 1) (1 2 1) (1 6 1)
(2 11 1) (11 7 1) (7 10 1) (7 8 2) (7 9 1) (10 3 1) (3 4 1) (4 16 1) (4 5 1)
(5 12 1) (12 13 1) (13 14 2) (14 15 1))
(DISPLAY-COORDS-2D (-3.6875d0 -1.0625d0) (-2.973d0 -1.475d0)
(-0.1151d0 -1.475d0) (0.5993d0 -1.8875d0) (1.3138d0 -1.475d0)
(-4.402d0 -1.475d0) (-1.5441d0 -1.475d0) (-1.9566d0 -2.1895d0)
(-1.1316d0 -0.7605d0) (-0.8296d0 -1.8875d0) (-2.2586d0 -1.0625d0)
(2.0283d0 -1.8875d0) (2.7427d0 -1.475d0) (3.4572d0 -1.8875d0)
(4.1717d0 -1.475d0) (0.5993d0 -2.7125d0) (-0.1152d0 -3.125d0)
(-0.1152d0 -3.95d0) (-0.8296d0 -2.7125d0) (-0.8296d0 -4.3625d0))
(STRUCTURE-ATOMS C C C C C N P O O O O O C C R1 O C C O R2)
(COMMON-NAME "a 1-alkenyl-2-acylglycerophosphoethanolamine")
(:CREATOR |paley|)
(:CREATION-DATE 3330790565) )
NIL)
(|1-Alkenylglycerophosphoethanolamines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(CHEMICAL-FORMULA (C 7) (H 15) (N 1) (O 6) (R1 1) (P 1))
(STRUCTURE-BONDS (15 16 1) (14 15 2) (13 14 1) (5 13 1) (4 5 1) (4 12 1)
(3 4 1) (10 3 1) (7 9 1) (7 8 2) (7 10 1) (11 7 1) (2 11 1) (1 6 1) (1 2 1))
(DISPLAY-COORDS-2D (-3.6875d0 -1.0625d0) (-2.973d0 -1.475d0)
(-0.1151d0 -1.475d0) (0.5993d0 -1.8875d0) (1.3138d0 -1.475d0)
(-4.402d0 -1.475d0) (-1.5441d0 -1.475d0) (-1.9566d0 -2.1895d0)
(-1.1316d0 -0.7605d0) (-0.8296d0 -1.8875d0) (-2.2586d0 -1.0625d0)
(0.5993d0 -2.7125d0) (2.0283d0 -1.8875d0) (2.7427d0 -1.475d0)
(3.4572d0 -1.8875d0) (4.1717d0 -1.475d0))
(STRUCTURE-ATOMS C C C C C N P O O O O O O C C R1)
(COMMON-NAME "a 1-alkenylglycerophosphoethanolamine")
(:CREATOR |paley|)
(:CREATION-DATE 3330790565) )
NIL)
(|1-Alkyl-2-acetyl-sn-glycero-3-phosphates| T (
(OCELOT-GFP::PARENTS |Diacylglycerides|)
(CHEMICAL-FORMULA (C 5) (H 10) (O 7) (R1 1) (P 1))
(STRUCTURE-BONDS (1 6 1) (1 2 1) (2 3 1) (3 9 1) (2 7 1) (6 14 1) (7 4 1)
(4 5 1) (4 8 2) (13 11 1) (13 12 1) (13 10 2) (9 13 1))
(DISPLAY-COORDS-2D (-3.4062d0 -1.9063d0) (-3.4062d0 -1.0813d0)
(-4.1207d0 -0.6688d0) (-1.9773d0 -1.0813d0) (-1.2628d0 -0.6688d0)
(-2.6918d0 -2.3188d0) (-2.6918d0 -0.6688d0) (-1.9773d0 -1.9063d0)
(-4.1207d0 0.1562d0) (-2.9668d0 -0.1082d0) (-2.6648d0 1.0188d0)
(-3.7918d0 1.3207d0) (-3.3793d0 0.6063d0) (-2.6918d0 -3.1438d0))
(STRUCTURE-ATOMS C C C C C O O O O O O O P R1)
(COMMON-NAME "a 1-alkyl-2-acetyl-sn-glycero-3-phosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|1-Alkyl-2-acetyl-sn-glycerols| T (
(OCELOT-GFP::PARENTS |Diacylglycerides|)
(CHEMICAL-FORMULA (C 5) (H 9) (O 4) (R1 1))
(STRUCTURE-BONDS (1 9 1) (2 9 2) (3 5 1) (4 7 1) (5 10 1) (6 7 1) (6 10 1)
(8 9 1) (8 10 1))
(DISPLAY-COORDS-2D (2.8579d0 -0.4125d0) (3.5723d0 -1.65d0) (2.1434d0 0.0d0)
(0.0d0 -2.8875d0) (1.4289d0 -0.4125d0) (0.7144d0 -1.65d0)
(0.7144d0 -2.475d0) (2.1434d0 -1.65d0) (2.8579d0 -1.2375d0)
(1.4289d0 -1.2375d0))
(STRUCTURE-ATOMS C O O R1 C C O O C C)
(COMMON-NAME "a 1-alkyl-2-acetyl-sn-glycerol")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|1-Alkyl-sn-glycero-3-phosphocholines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "a 1-alkyl-sn-glycero-3-phosphocholine")
(CHEMICAL-FORMULA (C 8) (H 20) (N 1) (O 6) (R1 1) (P 1))
(ATOM-CHARGES (16 1))
(STRUCTURE-BONDS (1 16 1) (2 16 1) (3 16 1) (4 17 2) (5 15 1) (6 17 1)
(7 12 1) (8 9 1) (8 13 1) (9 16 1) (10 12 1) (10 15 1) (11 14 1) (11 15 1)
(13 17 1) (14 17 1))
(DISPLAY-COORDS-2D (5.5182d0 -0.7083d0) (4.2667d0 -0.0172d0) (5.0902d0 0.0d0)
(2.246d0 -1.3571d0) (0.0d0 -3.5957d0) (2.2426d0 -3.007d0)
(2.2557d0 -4.4192d0) (3.4718d0 -1.4646d0) (4.2966d0 -1.4466d0)
(0.8268d0 -4.4222d0) (0.8271d0 -2.7722d0) (1.5422d0 -4.8331d0)
(3.061d0 -2.1801d0) (1.411d0 -2.1893d0) (0.825d0 -3.5972d0)
(4.6934d0 -0.7233d0) (2.2359d0 -2.1821d0))
(STRUCTURE-ATOMS C C C O O O R1 C C C C O O O C N P)
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|1-Alkyl-sn-glycerol-3-phosphates| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "a 1-alkyl-sn-glycerol-3-phosphate")
(CHEMICAL-FORMULA (C 3) (H 8) (O 6) (R1 1) (P 1))
(STRUCTURE-BONDS (1 8 1) (1 5 1) (2 6 1) (4 6 1) (5 6 1) (7 3 1) (9 8 1)
(9 3 1) (10 6 2) (11 8 1))
(DISPLAY-COORDS-2D (-0.6058d0 0.5551d0) (0.8095d0 0.3309d0)
(-1.3289d0 -1.492d0) (1.6345d0 1.1559d0) (-0.0153d0 1.1559d0)
(0.8095d0 1.1559d0) (-1.9909d0 -1.9909d0) (-0.6058d0 -0.2698d0)
(-1.3289d0 -0.667d0) (0.8095d0 1.9808d0) (-0.0153d0 -0.8503d0))
(STRUCTURE-ATOMS C O O O O P R1 C C O O)
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(1-AMINO-PROPAN-2-OL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (CAS "78-96-6"))
(:CREATION-DATE 3073857204)
(APPEARS-IN-LEFT-SIDE-OF AMINOPROPDEHYDROG-RXN)
(GIBBS-0 -46.5d0)
(SYNONYMS "(R)-1-aminopropan-2-ol" "D-1-amino-2-propanol"
"D-1-aminopropan-2-ol")
(MOLECULAR-WEIGHT 75.11d0)
(CHEMICAL-FORMULA (C 3) (H 9) (N 1) (O 1))
(DISPLAY-COORDS-2D (0.99666d0 -0.61937d0) (0.33222d0 -1.0d0)
(-0.33556d0 0.15192d0) (-0.33556d0 -0.61269d0) (-1.0d0 -0.99332d0))
(STRUCTURE-BONDS (5 4 1) (4 2 1) (3 4 1) (2 1 1))
(STRUCTURE-ATOMS N C O C C)
(COMMON-NAME "1-amino-propan-2-ol") )
((GIBBS-0 -46.5d0 CITATIONS "GibbsGroups97")))
(1-AMINO-PROPAN-2-ONE-3-PHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (-0.34397167d0 -0.6524823d0) (-0.34397167d0 -1.0d0)
(-0.6808511d0 -0.42553192d0) (-1.0d0 -0.6595745d0)
(0.64893615d0 -0.42907804d0) (0.64893615d0 -0.77304965d0)
(0.9964539d0 -0.42907804d0) (0.64893615d0 -0.08156031d0)
(0.35106373d0 -0.42907804d0) (-0.014184415d0 -0.42907804d0))
(CHEMICAL-FORMULA (C 3) (H 8) (N 1) (O 5) (P 1))
(MOLECULAR-WEIGHT 169.074d0)
(STRUCTURE-BONDS (10 9 1) (9 5 1) (5 8 1) (5 7 1) (5 6 2) (4 3 1) (3 1 1)
(1 10 1) (1 2 2))
(STRUCTURE-ATOMS C O C N P O O O O C)
(APPEARS-IN-LEFT-SIDE-OF PDXJ-RXN)
(APPEARS-IN-RIGHT-SIDE-OF PDXA-RXN)
(COMMON-NAME "1-amino-propan-2-one-3-phosphate")
(:CREATION-DATE 3122903700)
(:CREATOR |ptoole|) )
NIL)
(1-CHLORO-24-DINITROBENZENE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "CDNB")
(CHEMICAL-FORMULA (C 6) (H 3) (N 2) (O 4) (CL 1))
(MOLECULAR-WEIGHT 202.554d0)
(ATOM-CHARGES (1 1) (2 -1) (10 1) (13 -1))
(DISPLAY-COORDS-2D (3.7321d0 1.75d0) (4.5981d0 2.25d0) (2.866d0 2.25d0)
(3.7321d0 0.75d0) (4.5981d0 0.25d0) (2.866d0 0.25d0) (4.5981d0 -0.75d0)
(2.0d0 0.75d0) (2.866d0 -0.75d0) (5.4641d0 -1.25d0) (3.732d0 -1.25d0)
(5.4641d0 -2.25d0) (6.3301d0 -0.75d0))
(DBLINKS (NCI "6292" NIL |caspi| 3305664998 NIL NIL))
(STRUCTURE-BONDS (1 2 1) (1 3 2) (1 4 1) (4 5 2) (4 6 1) (5 7 1) (6 8 1)
(6 9 2) (7 10 1) (7 11 2) (10 12 2) (10 13 1) (9 11 1))
(STRUCTURE-ATOMS N O O C C C C CL C N C O O)
(APPEARS-IN-LEFT-SIDE-OF GST-RXN)
(COMMON-NAME "1-chloro-2,4-dinitrobenzene")
(:CREATION-DATE 3103396492)
(:CREATOR |ptoole|) )
NIL)
(1-DEOXYXYLONOJIRIMYCIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-6121)
(COMMON-NAME "1-deoxyxylonojirimycin")
(:CREATOR |keseler|)
(:CREATION-DATE 3337364692) )
NIL)
(1-ETHYLADENINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(AROMATIC-RINGS (14 3 1 7 5 10) (13 9 4 3 14))
(DISPLAY-COORDS-2D (-0.5947137d0 -1.0d0) (0.9955946d0 -0.7180617d0)
(-0.18942738d0 -0.7048458d0) (0.493392d0 -0.7048458d0)
(-1.0d0 -0.31277537d0) (-0.9295154d0 0.7268722d0) (-1.0d0 -0.72687227d0)
(-0.34801763d0 0.7268722d0) (0.493392d0 -0.3259912d0)
(-0.5947137d0 -0.07048464d0) (0.77973557d0 -0.79735684d0)
(-0.5947137d0 0.39647567d0) (0.15418494d0 -0.08370048d0)
(-0.18942738d0 -0.31277537d0))
(CHEMICAL-FORMULA (C 7) (H 9) (N 5))
(MOLECULAR-WEIGHT 163.182d0)
(STRUCTURE-BONDS (14 10 :AROMATIC) (14 3 :AROMATIC) (13 14 :AROMATIC)
(12 10 1) (10 5 :AROMATIC) (9 13 :AROMATIC) (8 12 1) (7 1 :AROMATIC)
(6 12 1) (5 7 :AROMATIC) (4 11 1) (4 9 :AROMATIC) (3 4 :AROMATIC) (2 11 1)
(1 3 :AROMATIC))
(STRUCTURE-ATOMS N C C N N H C H C C C N N C)
(APPEARS-IN-LEFT-SIDE-OF RXN0-986)
(COMMON-NAME "1-ethyladenine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3258925607) )
NIL)
(|1-Haloalkanes| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "a 1-haloalkane")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(1-KETO-2-METHYLVALERATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C06007" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3073857204)
(COMMENT-INTERNAL
"kr98-07-30: changed name and synonym. also, the frame ID is very wacky. a cpd with this name could not exist. how did this get here ? the structure looks ok.")
(GIBBS-0 -158.2d0)
(COMMON-NAME "2,3-dihydroxy-3-methylvalerate")
(APPEARS-IN-LEFT-SIDE-OF DIHYDROXYMETVALDEHYDRAT-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ACETOOHBUTREDUCTOISOM-RXN)
(MOLECULAR-WEIGHT 148.158d0)
(CHEMICAL-FORMULA (C 6) (H 12) (O 4))
(DISPLAY-COORDS-2D (-0.62927d0 -0.55122d0) (-0.21301d0 0.13496d0)
(0.19675d0 -0.55122d0) (0.99675d0 -0.53496d0) (0.6065d0 0.13496d0)
(0.6065d0 -0.31382d0) (-1.0d0 -0.29431d0) (-0.21301d0 -0.7626d0)
(-0.21301d0 -0.31382d0) (0.19675d0 -1.0d0))
(STRUCTURE-BONDS (10 3 1) (9 3 1) (8 9 1) (7 1 1) (6 3 1) (5 6 2) (4 6 1)
(2 9 1) (1 9 1))
(STRUCTURE-ATOMS C C C O O C C O C O)
(SYNONYMS "(R)-2,3-Dihydroxy-3-methylpentanoate"
"(R)-2,3-Dihydroxy-3-methylvalerate" "2,3-dihydroxy-3-methylpentanoate") )
((GIBBS-0 -158.2d0 CITATIONS "GibbsGroups97")))
(1-L-MYO-INOSITOL-1-P NIL (
(OCELOT-GFP::PARENTS |Myo-inositol-monophosphates|)
(ATOM-CHARGES (10 -1))
(COMMENT "There are two isomers of myo-inositol-1-phosphate:
1L-myo-inositol 1-phosphate is the compound formed from glucose 6-phosphate in the biosynthesis of inositol.
1D-myo-inositol 1-phosphate is the constituent of phospholipids and inositol polyphosphates.
Please note that 1L-myo-inositol 1-phosphate is also called 1D-myo-inositol 3-phosphate.
Additional information on the nomenclature of myo-inositol compounds can be found in the document
Numbering of atoms in myo-inositol, by the Nomenclature Committee of the International Union of Biochemistry
(NC-IUB). The document can be found at http://www.chem.qmul.ac.uk/iupac/cyclitol/myo.html")
(APPEARS-IN-LEFT-SIDE-OF |MYO-INOSITOL-1(OR-4)-MONOPHOSPHATASE-RXN|)
(:CREATOR |ptoole|)
(:CREATION-DATE 3172323276)
(GIBBS-0 -226.3d0)
(MOLECULAR-WEIGHT 259.129d0)
(CHEMICAL-FORMULA (C 6) (H 12) (O 9) (P 1))
(DISPLAY-COORDS-2D (-1.6725d0 0.8751d0) (-1.6428d0 -0.9101d0)
(-0.2033d0 -1.7444d0) (1.2499d0 -0.9388d0) (1.2201d0 0.7704d0)
(-0.2042d0 1.6586d0) (0.1665d0 2.5018d0) (0.9827d0 2.7797d0)
(-0.6043d0 2.8165d0) (0.2894d0 3.375d0) (-0.25d0 0.7937d0)
(0.4644d0 0.3813d0) (0.4644d0 -0.4437d0) (-0.25d0 -0.8562d0)
(-0.9644d0 -0.4437d0) (-0.9644d0 0.3813d0))
(STRUCTURE-BONDS (16 1 1 :UP) (15 2 1 :UP) (11 6 1 :UP) (12 5 1 :DOWN)
(13 4 1 :UP) (14 3 1 :DOWN) (15 16 1) (14 15 1) (13 14 1) (12 13 1)
(11 16 1) (11 12 1) (7 10 1) (7 9 1) (7 8 2) (6 7 1))
(STRUCTURE-ATOMS O O O O O O P O O O C C C C C C)
(COMMON-NAME "D-myo-inositol (3)-monophosphate")
(SYNONYMS "1-L-myo-inositol-1-p" "L-myo-inositol 1-phosphate"
"inositol 1-phosphate" "myo-inositol 1-phosphate"
"1D-myo-inositol 3-phosphate" "Ins(3)P1"
"1D-myo-inositol 3-monophosphate"
"myo-inositol 1-monophosphate" "Ins3P"
"1L-myo-inositol 1-phosphate" "myo-inositol phosphate") )
((GIBBS-0 -226.3d0 CITATIONS "GibbsGroups97")))
(1-PFK NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 1PFRUCTPHOSPHN-ENZRXN)
(CITATIONS "[91164390]")
(COMPONENTS 1-PFK-MONOMER)
(COMMENT "fruK had significant sequence similarities to the minor form
of 6-phosphofructokinase(pfkB) but not the major form
6-phosphofructokinase(pfkA) |CITS: [91164390]|")
(:CREATION-DATE 2945288005)
(:CREATOR |mriley|) )
((COMPONENTS 1-PFK-MONOMER COEFFICIENT 2)))
(1-PFK-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P0AEW9" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF00294" IN-FAMILY |pkarp| 3346700353 NIL NIL)
(UNIPROT "P0AEW9" NIL |pkarp| 3343984415 NIL NIL)
(REFSEQ "NP_416673" NIL NIL NIL NIL NIL))
(COMPONENT-OF 1-PFK)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 33.75563499999997d0)
(GENE EG10337)
(SYNONYMS "B2168" "Fpk" "FruF" "FruK" "phosphofructokinase monomer"
"fructose-1-phosphate kinase monomer")
(COMMON-NAME "1-phosphofructokinase monomer")
(:CREATION-DATE 2945288005)
(:CREATOR |mriley|) )
((GENE EG10337 COMMENT
"Fructose is taken up from the medium by protein specified by fruA. It appears
inside the cell as fructose-1-phospate. The phosphate moiety of this product is
derived from PEP and is transferred to the hexose as it is translocated across
the plasma membrane via a membrane associated protein fruF. All of these fru
genes are coordinately transcribed as an operon from the promoter region (p)
located next to fruF, the order being P-fruF-fruK-fruA. The fruFKA operon is
regulated through a repressor specified by fruR |CITS:[91164390]|.
")))
(1.1.1.215-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(IN-PATHWAY KETOGLUCONMET-PWY)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN-63)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3051657468)
(:CREATOR |kr|)
(EC-NUMBER "1.1.1.215")
(RIGHT CPD-377 NADPH)
(LEFT NADP GLUCONATE)
(SYNONYMS "2-KETO-D-GLUCONATE REDUCTASE") )
NIL)
(1.1.1.271-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(IN-PATHWAY COLANSYN-PWY)
(ENZYMATIC-REACTION ENZRXN0-6061)
(:CREATOR |keseler|)
(:CREATION-DATE 3336420030)
(COMMON-NAME "GDP-L-fucose synthase")
(SYNONYMS "GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase")
(LEFT NADP GUANOSINE_DIPHOSPHATE_FUCOSE)
(RIGHT NADPH GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE)
(EC-NUMBER "1.1.1.271")
(BALANCE-STATE :BALANCED) )
NIL)
(1.1.1.274-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(IN-PATHWAY KETOGLUCONMET-PWY)
(ENZYMATIC-REACTION ENZRXN-64 ENZRXN0-280)
(:CREATOR |ptoole| |keseler|)
(:CREATION-DATE 3154800778 3332776402)
(COMMON-NAME "2,5-didehydrogluconate reductase")
(SYNONYMS "2,5-diketo-D-gluconate reductase")
(LEFT NADPH 25-DIDEHYDRO-D-GLUCONATE)
(RIGHT CPD-377 NADP)
(EC-NUMBER "1.1.1.274")
(OFFICIAL-EC? T)
(BALANCE-STATE :BALANCED) )
NIL)
(1.1.1.283-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(EC-NUMBER "1.1.1.283")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY METHGLYUT-PWY)
(COMMENT
"This reaction converts methylglyoxal into lactaldehyde. Together with the lactaldehyde dehydrogenase reaction, it provides an alternate route for the breakdown of methylglyoxal to lactate.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "~ecocyc/templates/new/meth2/methylglyred.template")
(ENZYMATIC-REACTION METHYLGLYREDUCT-ENZRXN)
(:CREATION-DATE 3047338781)
(LEFT LACTALD NADP)
(RIGHT METHYL-GLYOXAL NADPH PROTON) )
NIL)
(1.13.11.16-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.13.11)
(IN-PATHWAY HCAMHPDEG-PWY)
(COMMON-NAME "3-carboxyethylcatechol 2,3-dioxygenase")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(COMMENT "This reaction is where the branched meta-cleavage
degradation pathway for 3-phenylpropionate and
3-(3-hydroxyphenyl)propionate meet.")
(:CREATOR |caspi| |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/phenylprodeg/mhpB.template")
(ENZYMATIC-REACTION DHPDIOXYGEN-ENZRXN)
(EC-NUMBER "1.13.11.16")
(:CREATION-DATE 3343408206 3041279021)
(LEFT 2-3-DIHYDROXYPHENYL-PROPIONATE OXYGEN-MOLECULE)
(RIGHT CPD-157) )
NIL)
(1.3.1.2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.3.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2760 ENZRXN0-2758)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3284153213)
(SYNONYMS "Dihydrothymine dehydrogenase"
"Dihydrouracil dehydrogenase (NADP+)")
(COMMON-NAME "Dihydropyrimidine dehydrogenase (NADP+)")
(EC-NUMBER "1.3.1.2")
(RIGHT NADPH URACIL)
(LEFT NADP DI-H-URACIL) )
NIL)
(1.5.1.20-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.5.1)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY 1CMET2-PWY)
(ENZYMATIC-REACTION METHYLENETHFREDUCT-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3324141636)
(LEFT 5-METHYL-THF |NAD(P)|)
(RIGHT METHYLENE-THF |NAD(P)H| PROTON)
(EC-NUMBER "1.5.1.20")
(COMMON-NAME "Methylenetetrahydrofolate reductase (NADPH)")
(SYNONYMS "MTHFR")
(OFFICIAL-EC? T) )
NIL)
(1.5.1.34-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-244 DIHYDROPTERIREDUCT-ENZRXN)
(RIGHT 67-DIHYDROPTERIDINE |NAD(P)H|)
(LEFT 5678-TETRAHYDROPTERIDINE |NAD(P)|)
(EC-NUMBER "1.5.1.34")
(COMMENT "This reaction is part of central intermediary metabolism.
It regenerates a cofactor, dihydrobiopterin. This cofactor is used by
many organisms, but not E. coli, in the hydroxylation of aromatic
amino acids.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/dprA.template")
(:CREATION-DATE 3016372622)
(:CREATOR |mriley|) )
NIL)
(1.6.1.2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY NADPHOS-DEPHOS-PWY)
(COMMENT "In the
course of the reaction (left to right) one H atom is transferred from
inside the cell to outside. This reaction is an important redox exchange reaction,
functioning as a proton pump across the inner membrane.")
(ENZYMATIC-REACTION PYRNUTRANSHYDROGEN-ENZRXN)
(EC-NUMBER "1.6.1.2")
(RIGHT NADH NADP)
(LEFT NAD NADPH)
(SYNONYMS "PYRIDINE NUCLEOTIDE TRANSHYDROGENASE" "TRANSHYDROGENASE") )
NIL)
(1.7.2.3-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions| EC-1.7.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ANARESPACC-PWY)
(ENZYMATIC-REACTION TMAOREDUCTI-ENZRXN ENZRXN-42)
(:CREATOR |keseler|)
(:CREATION-DATE 3322848346)
(COMMON-NAME "Trimethylamine-N-oxide reductase (cytochrome c)")
(SYNONYMS "TMAO reductase" "TOR")
(LEFT TRIMETHYLAMINE |Cytochromes-C| WATER)
(RIGHT TRIMENTHLAMINE-N-O |Cytochromes-C-Reduced| PROTON)
(EC-NUMBER "1.7.2.3") )
((RIGHT PROTON COEFFICIENT 2) (RIGHT |Cytochromes-C-Reduced| COEFFICIENT 2)
(LEFT |Cytochromes-C| COEFFICIENT 2)))
(1.7.7.2-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions| EC-1.7.7)
(IN-PATHWAY ANARESPACC-PWY)
(EC-NUMBER "1.7.7.2")
(COMMENT
"The NrfB cytochrome C and NrfA cytochrome C552 transfer electrons in the formate-dependent reduction of nitrite to ammonia.")
(OFFICIAL-EC? T)
(:CREATION-DATE 3057674142)
(RIGHT NITRITE |Cytochromes-C552-Red| PROTON)
(LEFT AMMONIA |Cytochromes-C552-Ox| WATER)
(REACTION-PRESENT-IN-E-COLI? Y)
(COMMON-NAME "nitrite reductase complex")
(ENZYMATIC-REACTION ENZRXN0-1261 NRFMULTI-ENZRXN) )
((RIGHT PROTON COEFFICIENT 7) (LEFT WATER COEFFICIENT 2)
(RIGHT |Cytochromes-C552-Red| COEFFICIENT 6)
(LEFT |Cytochromes-C552-Ox| COEFFICIENT 6)))
(1.8.4.8-RXN NIL (
(OCELOT-GFP::PARENTS EC-1.8.4 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY SO4ASSIM-PWY)
(ENZYMATIC-REACTION PAPSSULFOTRANS-ENZRXN)
(RIGHT PAPS |Red-Thioredoxin|)
(LEFT PAP SO3 |Ox-Thioredoxin|)
(EC-NUMBER "1.8.4.8")
(COMMENT "The third reaction in converting sulfate to sulfide.
The first reaction in the reduction of sulfate to sulfite
in the pathway leading to cysteine synthesis.
Note: Reaction E.C. 1.8.99.4 was transferred to E.C 1.8.4.8 in 2000.")
(:CREATION-DATE 2974150778)
(:CREATOR |mriley|) )
NIL)
(1.97.1.4-A-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions| EC-1.97.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION PFLACTENZ-ENZRXN)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3051657452)
(:CREATOR |kr|)
(EC-NUMBER "1.97.1.4")
(COMMENT
"This reaction activates pyruvate formate-lyase under anaerobic conditions.
A single glycine residue in pyruvate formate-lyase is oxidized to the
corresponding radical glycine.")
(RIGHT CH33ADO MET PYRUVFORMLY-CPLX |Oxidized-flavodoxins|)
(LEFT PYRUVFORMLY-INACTIVE-CPLX |Reduced-flavodoxins| S-ADENOSYLMETHIONINE) )
NIL)
(10-FORMYL-THF NIL (
(OCELOT-GFP::PARENTS FORMYL-THF-GLU-N)
(INHIBITORS-COMPETITIVE-OF METHENYLTHFCYCLOHYDRO-ENZRXN)
(INHIBITORS-UNKMECH-OF METHYLENETHFDEHYDROG-NADP-ENZRXN)
(DBLINKS (LIGAND-CPD "C00234" NIL |kr| 3346617701 NIL NIL) (CAS "2800-34-2"))
(:CREATION-DATE 3067881497)
(GIBBS-0 -171.4d0)
(APPEARS-IN-LEFT-SIDE-OF METHIONYL-TRNA-FORMYLTRANSFERASE-RXN RXN0-1862
FORMYLTHFDEFORMYL-RXN AICARTRANSFORM-RXN GART-RXN)
(APPEARS-IN-RIGHT-SIDE-OF METHENYLTHFCYCLOHYDRO-RXN FORMATETHFLIG-RXN)
(AROMATIC-RINGS (13 11 27 12 14 28) (26 19 29 30 31 35))
(COMMON-NAME "N10-formyl-THF")
(SYNONYMS "10-formyl-tetrahydrofolate"
"n10-formyltetrahydrofolate"
"N10-formyl-H4F" "10-formyl-THF"
"10-formyl-H4PteGlu1")
(STRUCTURE-ATOMS H N O O O O O O O C C C C C C C C C N N N N C C C C C C C C
C C C N N)
(STRUCTURE-BONDS (35 31 :AROMATIC) (31 30 :AROMATIC) (30 29 :AROMATIC)
(28 34 1) (26 35 :AROMATIC) (25 27 1) (24 33 1) (22 32 1) (22 30 1)
(21 33 1) (21 25 1) (20 29 1) (29 19 :AROMATIC) (19 26 :AROMATIC) (18 34 1)
(32 18 1 :UP) (17 32 1) (17 20 1) (33 16 1 :UP) (15 23 1) (15 16 1)
(28 14 :AROMATIC) (13 28 :AROMATIC) (12 27 :AROMATIC) (14 12 :AROMATIC)
(27 11 :AROMATIC) (11 13 :AROMATIC) (10 34 1) (9 24 1) (8 23 1) (7 31 2)
(6 25 2) (5 24 2) (4 23 2) (3 10 2) (2 26 1) (1 35 1))
(DISPLAY-COORDS-2D (0.0d0 -2.8472d0) (0.1036d0 0.0d0) (6.8601d0 -7.9031d0)
(15.1047d0 -9.7079d0) (14.8614d0 -2.6586d0) (12.2754d0 -2.9027d0)
(2.372d0 -4.244d0) (17.1537d0 -8.464d0) (16.9829d0 -3.8538d0)
(6.2019d0 -6.6344d0) (10.3733d0 -6.3177d0) (10.3733d0 -3.9511d0)
(8.9578d0 -6.3177d0) (9.0312d0 -3.9511d0) (15.0321d0 -7.3174d0)
(15.6417d0 -6.1956d0) (5.9577d0 -0.8537d0) (6.7628d0 -3.561d0)
(2.372d0 -0.146d0) (4.8111d0 -0.146d0) (13.6661d0 -5.0977d0)
(4.8111d0 -2.8532d0) (15.7638d0 -8.464d0) (15.593d0 -3.8538d0)
(12.2754d0 -4.3174d0) (1.2254d0 -0.8537d0) (11.0315d0 -5.1464d0)
(8.2995d0 -5.1225d0) (3.6159d0 -0.8537d0) (3.6159d0 -2.1702d0)
(2.372d0 -2.8532d0) (5.9577d0 -2.1702d0) (14.934d0 -5.0977d0)
(6.7628d0 -5.1225d0) (1.2254d0 -2.1702d0))
(CHEMICAL-FORMULA (C 20) (H 23) (N 7) (O 7))
(MOLECULAR-WEIGHT 473.444d0) )
((GIBBS-0 -171.4d0 CITATIONS "GibbsGroups97")))
(|11-Beta-Hydroxysteroids1| T (
(OCELOT-GFP::PARENTS |Hydroxysteroids|)
(CHEMICAL-FORMULA (C 19) (H 31) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(14 19 1) (13 20 1) (13 14 1) (12 21 1) (11 18 1) (10 17 1) (9 16 1)
(9 10 1) (8 15 1) (8 11 1) (7 16 1) (6 12 1) (5 7 1) (5 6 1) (4 15 1)
(14 3 1 :UP) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (2.4249d0 -4.9d0)
(7.8263d0 -5.9641d0) (0.0d0 -0.7d0) (0.0d0 -2.1d0) (1.2124d0 0.0d0)
(8.2166d0 -3.5d0) (3.6373d0 0.0d0) (4.8497d0 -0.7d0) (7.3937d0 -2.3674d0)
(1.2124d0 -2.8d0) (4.8497d0 -4.9d0) (3.6373d0 -4.2d0) (7.3937d0 -4.6326d0)
(2.4249d0 -0.7d0) (4.8497d0 -2.1d0) (6.0622d0 -2.8d0) (3.6373d0 -2.8d0)
(6.0622d0 -4.2d0) (2.4249d0 -2.1d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "an 11-β-hydroxysteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790567) )
NIL)
(|11-Oxosteroids| T (
(OCELOT-GFP::PARENTS |Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(14 19 1) (13 20 1) (13 14 1) (12 21 1) (11 18 1) (10 17 1) (9 16 1)
(9 10 1) (8 15 1) (8 11 1) (7 16 1) (6 12 1) (5 7 1) (5 6 1) (4 15 1)
(3 14 2) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (2.4249d0 -4.9d0)
(7.8263d0 -5.9641d0) (0.0d0 -0.7d0) (0.0d0 -2.1d0) (1.2124d0 0.0d0)
(8.2166d0 -3.5d0) (3.6373d0 0.0d0) (4.8497d0 -0.7d0) (7.3937d0 -2.3674d0)
(1.2124d0 -2.8d0) (4.8497d0 -4.9d0) (3.6373d0 -4.2d0) (7.3937d0 -4.6326d0)
(2.4249d0 -0.7d0) (4.8497d0 -2.1d0) (6.0622d0 -2.8d0) (3.6373d0 -2.8d0)
(6.0622d0 -4.2d0) (2.4249d0 -2.1d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "an 11-oxosteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(110-PHENANTHROLINE-MONOHYDROCHLORIDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-6153)
(COMMON-NAME "1,10-phenanthroline monohydrochloride")
(:CREATOR |keseler|)
(:CREATION-DATE 3344354920) )
NIL)
(|12-apo-Carotenals| T (
(OCELOT-GFP::PARENTS |carotenoids|)
(COMMON-NAME "a 12'-apo-carotenal")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(12-EPOXYPROPANE T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(MOLECULAR-WEIGHT 58.08d0)
(CHEMICAL-FORMULA (C 3) (H 6) (O 1))
(STRUCTURE-BONDS (4 5 1) (4 3 1) (4 2 1) (1 4 1) (2 1 1))
(DISPLAY-COORDS-2D (-1.5834d0 -0.7916d0) (-1.125d0 -1.5d0)
(-0.3459d0 -0.0772d0) (-0.7584d0 -0.7916d0) (0.0385d0 -0.5781d0))
(STRUCTURE-ATOMS C O C C H)
(COMMON-NAME "a 1,2-epoxypropane")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(15-DIDEOXY-15-IMINO-D-GALACTITOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF BETAGALACTOSID-ENZRXN ALPHAGALACTOSID-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979755)
(COMMON-NAME "1,5-dideoxy-1,5-imino-D-galactitol")
(STRUCTURE-ATOMS O O O O C C N C C C C)
(DISPLAY-COORDS-2D (0.0d0 -5.6d0) (4.8497d0 -1.4d0) (2.4249d0 0.0d0)
(0.0d0 -1.4d0) (0.0d0 -4.2d0) (3.6373d0 -3.5d0) (2.4249d0 -4.2d0)
(3.6373d0 -2.1d0) (2.4249d0 -1.4d0) (1.2124d0 -2.1d0) (1.2124d0 -3.5d0))
(STRUCTURE-BONDS (10 11 1) (9 10 1) (8 9 1) (7 11 1) (6 8 1) (6 7 1)
(11 5 1 :UP) (10 4 1 :UP) (9 3 1 :UP) (8 2 1 :DOWN) (1 5 1))
(CHEMICAL-FORMULA (C 6) (H 13) (N 1) (O 4))
(MOLECULAR-WEIGHT 163.173d0) )
NIL)
(|16-a-D-Man-16-a-D-Man-Oligosac| T (
(OCELOT-GFP::PARENTS |Oligosaccharides|)
(COMMON-NAME "a 1,6-α-D-mannose-1,6-α-D-mannosyl-oligosaccharide")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(|16-alpha-D-Mannosyloligosaccharides| T (
(OCELOT-GFP::PARENTS |Oligosaccharides|)
(COMMON-NAME "a 1,6-α-D-mannosyloligosaccharide")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(|16S-rRNAs| T (
(OCELOT-GFP::PARENTS |rRNAs|)
(:CREATOR |kr|)
(:CREATION-DATE 3266259236) )
NIL)
(|17-Alpha-Hydroxysteroids| T (
(OCELOT-GFP::PARENTS |Hydroxysteroids|)
(MOLECULAR-WEIGHT 292.461d0)
(CHEMICAL-FORMULA (C 19) (H 32) (O 2))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 21 1) (16 19 1) (16 18 1) (15 20 1)
(13 20 1) (12 21 1) (11 17 1) (11 14 1) (10 19 1) (10 13 1) (9 18 1)
(8 14 1) (8 12 1) (7 17 1) (6 16 1) (6 7 1) (5 15 1) (5 9 1) (15 4 1 :DOWN)
(3 14 1) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (7.2746d0 -5.6d0) (3.6735d0 -3.4995d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (9.429d0 -3.5d0) (6.0622d0 -0.7d0) (4.8497d0 0.0d0)
(1.2124d0 -2.1d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0) (2.4249d0 0.0d0)
(2.4249d0 -2.8d0) (6.0622d0 -4.9d0) (1.2124d0 -0.7d0) (8.6061d0 -4.6326d0)
(6.0622d0 -2.1d0) (3.6373d0 -0.7d0) (7.2746d0 -2.8d0) (4.8497d0 -2.8d0)
(7.2746d0 -4.2d0) (3.6373d0 -2.1d0))
(STRUCTURE-ATOMS C C O O C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 17-α-hydroxysteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(1CMET2-PWY NIL (
(OCELOT-GFP::PARENTS |Folate-Biosynthesis|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(POLYMERIZATION-LINKS
(FORMYL-THF-GLU-N FORMYLTHFGLUSYNTH-RXN FORMYLTHFGLUSYNTH-RXN))
(PRIMARIES (1.5.1.20-RXN (METHYLENE-THF) NIL)
(FORMYLTHFGLUSYNTH-RXN (FORMYL-THF-GLU-N) (FORMYL-THF-GLU-N))
(DIHYDROFOLATESYNTH-RXN (|7,8-dihydropteroate|) NIL)
(FORMATETHFLIG-RXN (FORMATE THF) NIL))
(HYPOTHETICAL-REACTIONS FORMATETHFLIG-RXN)
(REACTION-LIST DIHYDROFOLATESYNTH-RXN THYMIDYLATESYN-RXN HOMOCYSMETB12-RXN
1.5.1.20-RXN GCVMULTI-RXN METHYLENETHFDEHYDROG-NADP-RXN GLYOHMETRANS-RXN
DIHYDROFOLATEREDUCT-RXN FORMYLTHFDEFORMYL-RXN METHENYLTHFCYCLOHYDRO-RXN
FORMATETHFLIG-RXN FORMYLTHFGLUSYNTH-RXN)
(PREDECESSORS (DIHYDROFOLATEREDUCT-RXN DIHYDROFOLATESYNTH-RXN)
(DIHYDROFOLATEREDUCT-RXN THYMIDYLATESYN-RXN)
(GCVMULTI-RXN DIHYDROFOLATEREDUCT-RXN)
(GCVMULTI-RXN HOMOCYSMETB12-RXN)
(GLYOHMETRANS-RXN DIHYDROFOLATEREDUCT-RXN)
(GLYOHMETRANS-RXN HOMOCYSMETB12-RXN)
(THYMIDYLATESYN-RXN GLYOHMETRANS-RXN)
(THYMIDYLATESYN-RXN GCVMULTI-RXN) (1.5.1.20-RXN GCVMULTI-RXN)
(1.5.1.20-RXN GLYOHMETRANS-RXN)
(HOMOCYSMETB12-RXN 1.5.1.20-RXN)
(METHYLENETHFDEHYDROG-NADP-RXN GCVMULTI-RXN)
(METHYLENETHFDEHYDROG-NADP-RXN GLYOHMETRANS-RXN)
(METHENYLTHFCYCLOHYDRO-RXN METHYLENETHFDEHYDROG-NADP-RXN)
(FORMYLTHFDEFORMYL-RXN METHENYLTHFCYCLOHYDRO-RXN)
(FORMYLTHFGLUSYNTH-RXN METHENYLTHFCYCLOHYDRO-RXN)
(FORMYLTHFGLUSYNTH-RXN FORMATETHFLIG-RXN)
(FORMATETHFLIG-RXN FORMYLTHFDEFORMYL-RXN)
(FORMYLTHFDEFORMYL-RXN FORMATETHFLIG-RXN))
(COMMON-NAME "formylTHF biosynthesis I")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/1Cmet/1cmet2pwy.template")
(:CREATION-DATE 3016800295)
(:CREATOR |mriley|) )
((POLYMERIZATION-LINKS
(FORMYL-THF-GLU-N FORMYLTHFGLUSYNTH-RXN FORMYLTHFGLUSYNTH-RXN)
PRODUCT-NAME-SLOT N+1-NAME)))
(1PFRUCTPHOSN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 1PFRUCTPHOSPHN-ENZRXN)
(SYNONYMS "FRUCTOSE 1-PHOSPHATE KINASE")
(RIGHT ADP FRUCTOSE-16-DIPHOSPHATE)
(LEFT ATP FRU1P)
(CITATIONS "[70027910]" "[febslet13-127-71]")
(EC-NUMBER "2.7.1.56")
(COMMENT "E.coli grows readily on fructose as a sole source of carbon.
It was long assumed that the manner in which this sugar is utilized is
analogous to that by which glucose enters the main metabolic pathways
of the cells; this would imply the occurrence of an initial enzymatic
phosphorylation by ATP of fructose to fructose-6-phosphate and ADP,
followed by a second phosphorylation to fructose-1,6-bisphosphate.
Enzymes catalyzing both these reactions have been demonstrated to be
present in E.coli. However, studies in several labs have cast doubt
on this view and have suggested that fructose is initially
phosphorylated to fructose-1-phosphate with concomitant conversion of
PEP to pyruvate. Fructose-1-phosphate is then further phosphorylated to
fructose-1,6-diphosphate through the agency of an ATP-linked
fructose-1-phosphate-kinase. |CITS: [Febslet13-127-71]|
This reaction is part of a pathway for fructose metabolism
in E.coli: fructose = fructose-1-p = fructose-16p. The first reaction,
catalyzed by a phosphotransferase system,involves a
phosphoenolpyruvate-dependent phosphorylation of D-fructose at C-1.
The second reaction is an ATP dependent phosphorylation of
D-fructose-1-phosphate at C-6. The enzyme involved in the latter
is 1-phosphofructokinase. |CITS:[70027910]|")
(COMMON-NAME "1-phosphofructokinase phosphorylation")
(:CREATION-DATE 2945288005)
(:CREATOR |mriley|) )
NIL)
(1PFRUCTPHOSPHN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT)
(INHIBITORS-UNKMECH FRUCTOSE-16-DIPHOSPHATE CPD-5541)
(COFACTORS MG+2)
(SYNONYMS "phosphofructokinase" "fructose-1-phosphate kinase")
(COMMON-NAME "1-phosphofructokinase")
(REACTION 1PFRUCTPHOSN-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[femsletbusch29-231-85]")
(INHIBITORS-COMPETITIVE ADP)
(COMMENT "The enzyme is highly specific for fructose-1-phosphate. ATP
and GTP are the best phosphoryl donors, whereas UTP and CTP only
showed a weak effect. The enzyme is reversibly
inhibited by fructose-1,6-diphosphate and ADP, and irreversibly by
phenylmethanesulfonyl fluoride. |CITS: [femsletbusch29-231-85]|")
(ENZYME 1-PFK)
(:CREATION-DATE 2945288005)
(:CREATOR |mriley|) )
NIL)
(1TRANSKETO-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(IN-PATHWAY NONOXIPENT-PWY DRIBOPMET-PWY)
(ENZYMATIC-REACTION ENZRXN0-1882 TRANSKETOI-ENZRXN)
(RIGHT D-SEDOHEPTULOSE-7-P GAP)
(LEFT RIBOSE-5P XYLULOSE-5-PHOSPHATE)
(EC-NUMBER "2.2.1.1")
(COMMENT "This reaction is involved in the pentose phosphate pathway.")
(:CREATION-DATE 2974477015)
(:CREATOR |mriley|) )
NIL)
(|2,3-dihydrodipicolinate| NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C03340" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3075053323)
(GIBBS-0 -125.9d0)
(COMMON-NAME "L-2,3-dihydrodipicolinate")
(APPEARS-IN-RIGHT-SIDE-OF DIHYDROPICRED-RXN DIHYDRODIPICSYN-RXN)
(MOLECULAR-WEIGHT 169.137d0)
(CHEMICAL-FORMULA (C 7) (H 7) (N 1) (O 4))
(DISPLAY-COORDS-2D (-1.0d0 -0.44079d0) (0.99671d0 -0.44079d0)
(0.0d0 -0.61842d0) (-0.33224d0 -0.04605d0) (0.32895d0 -0.42763d0)
(-0.33224d0 -0.42763d0) (-0.66118d0 -1.0d0) (0.0d0 0.14474d0)
(-0.66118d0 -0.61842d0) (0.32895d0 -0.04605d0) (0.65789d0 -1.0d0)
(0.65789d0 -0.61842d0))
(STRUCTURE-BONDS (12 5 1) (11 12 1) (10 5 1) (9 6 1) (8 4 2) (8 10 1) (7 9 1)
(6 3 2) (5 3 1) (4 6 1) (2 12 2) (1 9 2))
(STRUCTURE-ATOMS O O N C C C O C C C O C)
(SYNONYMS "2,3-dihydrodipicolinate" "dihydrodipicolinate"
"2,3-di-H-dipicolinate") )
((GIBBS-0 -125.9d0 CITATIONS "GibbsGroups97")))
(|2,3-diketo-l-gulonate| NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "2,3-Dioxo-L-gulonate")
(DBLINKS (CAS "583-08-4" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C05409" NIL |kr| 3346617701 NIL NIL)
(PUBCHEM "18" NIL |keseler| 3342473594 NIL NIL)
(LIGAND-CPD "C04575" NIL |keseler| 3342473594 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF RXN0-703)
(:CREATOR |arnaud|)
(:CREATION-DATE 3249247380)
(GIBBS-0 -251.2d0)
(MOLECULAR-WEIGHT 192.125d0)
(CHEMICAL-FORMULA (C 6) (H 8) (O 7))
(DISPLAY-COORDS-2D (-0.56857d0 -1.0d0) (-1.0d0 0.40524d0)
(-0.56857d0 0.99692d0) (-0.56857d0 -0.24807d0) (-0.14638d0 0.07858d0)
(-0.56857d0 -0.57781d0) (-0.56857d0 0.07858d0) (-0.14638d0 -0.57781d0)
(-0.56857d0 0.66718d0) (-0.56857d0 0.40524d0) (-0.15562d0 0.99692d0)
(-0.15562d0 0.66718d0) (-0.14638d0 -0.24807d0))
(STRUCTURE-BONDS (13 4 2) (12 9 1) (11 3 1) (10 7 1) (9 10 1) (8 6 1) (7 4 1)
(6 4 1) (5 7 2) (3 9 1) (2 10 1) (1 6 2))
(STRUCTURE-ATOMS O O C C O C C O C C O O O)
(COMMON-NAME "2,3-diketo-L-gulonate") )
((GIBBS-0 -251.2d0 CITATIONS "GibbsGroups97")))
(2-3-DIHYDROXYBENZOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00196" NIL |kr| 3346617699 NIL NIL) (CAS "303-38-8"))
(:CREATION-DATE 3078153246)
(SYNONYMS "2,3-Dihydroxybenzoic acid")
(AROMATIC-RINGS (2 3 4 5 6 1))
(DISPLAY-COORDS-2D (-0.3292d0 -0.8583d0) (-0.3292d0 -1.6167d0)
(0.3204d0 -2.0d0) (0.9782d0 -1.6167d0) (0.9782d0 -0.8583d0)
(0.3204d0 -0.4833d0) (0.3183d0 0.2667d0) (1.6267d0 -0.4815d0)
(1.6285d0 -1.9904d0) (0.9668d0 0.6435d0) (-0.3323d0 0.6399d0))
(CHEMICAL-FORMULA (C 7) (H 6) (O 4))
(MOLECULAR-WEIGHT 154.122d0)
(STRUCTURE-BONDS (7 11 2) (7 10 1) (4 9 1) (5 8 1) (6 7 1) (6 5 :AROMATIC)
(5 4 :AROMATIC) (4 3 :AROMATIC) (3 2 :AROMATIC) (2 1 :AROMATIC)
(1 6 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C C O O O O)
(APPEARS-IN-RIGHT-SIDE-OF DHBDEHYD-RXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2943 DHBAMPLIG-RXN ENTMULTI-RXN)
(COMMON-NAME "2,3-dihydroxybenzoate") )
NIL)
(2-3-DIHYDROXYPHENYL-PROPIONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04044" NIL |kr| 3346617699 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(AROMATIC-RINGS (7 8 9 10 11 6))
(DISPLAY-COORDS-2D (1.2917d0 3.05d0) (1.9412d0 2.675d0) (2.5907d0 3.05d0)
(2.5907d0 3.8d0) (3.2402d0 2.675d0) (0.6421d0 2.675d0) (0.6414d0 1.9238d0)
(-0.0054d0 1.5447d0) (-0.6556d0 1.9251d0) (-0.6548d0 2.6763d0)
(-0.0039d0 3.0471d0) (-0.002d0 3.7971d0) (-1.303d0 3.0536d0))
(CHEMICAL-FORMULA (C 9) (H 10) (O 4))
(MOLECULAR-WEIGHT 182.176d0)
(STRUCTURE-BONDS (10 13 1) (11 12 1) (1 6 1) (11 10 :AROMATIC)
(10 9 :AROMATIC) (9 8 :AROMATIC) (8 7 :AROMATIC) (7 6 :AROMATIC)
(6 11 :AROMATIC) (3 5 2) (3 4 1) (2 3 1) (1 2 1))
(STRUCTURE-ATOMS C C C O O C C C C C C O O)
(APPEARS-IN-RIGHT-SIDE-OF MHPHYDROXY-RXN PHENPRODIOLDEHYDROG-RXN)
(APPEARS-IN-LEFT-SIDE-OF 1.13.11.16-RXN)
(COMMON-NAME "3-(2,3-dihydroxyphenyl)propionate")
(SYNONYMS "3-(2,3-dihydroxyphenyl)propionic acid" "2,3-DHP"
"3-(2,3-Dihydroxyphenyl)propanoate") )
NIL)
(2-5-PHOSPHORIBOSYL-3-DEPHOSPHO-COA NIL (
(OCELOT-GFP::PARENTS |All-Coas|)
(PROSTHETIC-GROUPS-OF CITLY-ENZRXN)
(DISPLAY-COORDS-2D (12.0528d0 -0.0949d0) (11.3791d0 1.4114d0)
(2.7778d0 3.3602d0) (5.4689d0 3.7727d0) (15.3119d0 0.7014d0)
(14.5588d0 0.3644d0) (17.4017d0 0.0706d0) (18.1547d0 0.4075d0)
(6.6986d0 0.7622d0) (3.3361d0 -1.187d0) (10.9628d0 0.3214d0)
(4.2068d0 4.1852d0) (3.4923d0 4.5977d0) (4.2068d0 3.3602d0)
(6.0303d0 1.2459d0) (3.2484d0 -0.3666d0) (5.2461d0 0.9896d0)
(2.5332d0 0.0446d0) (2.7033d0 0.8519d0) (4.76d0 1.6562d0)
(5.2438d0 2.3245d0) (3.5237d0 0.9396d0) (12.4691d0 0.9951d0)
(15.9802d0 0.2176d0) (13.1374d0 0.5114d0) (11.716d0 0.6583d0)
(3.4923d0 5.4227d0) (2.7778d0 4.1852d0) (3.4923d0 2.9477d0)
(4.9875d0 4.4366d0) (16.7333d0 0.5544d0) (13.8905d0 0.8482d0)
(4.9875d0 3.1087d0) (4.9925d0 0.2045d0) (1.7801d0 -0.2922d0)
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(13.0525d0 -0.3093d0) (7.6362d0 -0.053d0) (3.3576d0 -2.4293d0)
(9.2045d0 1.2215d0) (6.0289d0 2.0709d0) (3.8606d0 0.1865d0)
(7.4517d0 1.099d0) (4.0903d0 -1.5213d0) (10.2945d0 0.8051d0)
(3.935d0 1.6548d0) (8.7883d0 0.1314d0) (4.2656d0 -3.162d0) (8.12d0 0.6152d0)
(4.178d0 -2.3416d0) (9.5414d0 0.4683d0) (18.823d0 -0.0763d0))
(AROMATIC-RINGS (12 13 28 3 29 14))
(CHEMICAL-FORMULA (C 26) (H 44) (N 7) (O 20) (P 3) (S 1))
(MOLECULAR-WEIGHT 899.65d0)
(STRUCTURE-BONDS (53 55 1) (52 56 1) (52 54 1) (50 56 1) (49 55 1) (48 54 1)
(45 56 2) (44 55 2) (43 54 2) (40 56 1) (39 55 1) (38 54 1) (25 42 2)
(25 32 1) (24 41 2) (24 31 1) (23 37 1) (23 26 1) (23 25 1) (22 51 1 :UP)
(22 47 1) (21 46 1) (21 33 1 :UP) (20 51 1 :DOWN) (20 21 1) (19 36 1 :DOWN)
(19 22 1) (18 35 1 :DOWN) (18 19 1) (17 34 1 :DOWN) (17 20 1) (16 47 1)
(16 18 1) (15 46 1) (15 17 1) (14 33 1) (14 29 :AROMATIC) (28 13 :AROMATIC)
(13 27 1) (12 30 1) (12 14 :AROMATIC) (13 12 :AROMATIC) (11 50 1) (11 26 1)
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(6 32 1) (5 24 1) (5 6 1) (4 33 1) (4 30 2) (29 3 :AROMATIC)
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(STRUCTURE-ATOMS C C C C C C C C C C C C C C C C C C C C C C C C C C N N N N
N N N O O O O O O O O O O O O O O O O O O O O P P P S)
(SYNONYMS "2-5-phosphoribosyl-3-dephospho-CoA")
(COMMON-NAME "2'-(5\"-phosphoribosyl)-3'-dephospho-CoA")
(:CREATOR |krieger|)
(:CREATION-DATE 3234112448) )
NIL)
(2-5-TRIPHOSPHORIBOSYL-3-DEPHOSPHO- NIL (
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(APPEARS-IN-LEFT-SIDE-OF 2.7.7.61-RXN RXN0-263)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-309)
(:CREATOR |paley|)
(:CREATION-DATE 3313949585)
(COMMON-NAME "2'-(5''-triphosphoribosyl)-3'-dephospho-CoA")
(STRUCTURE-ATOMS H C N N C H C C O O C O C P O O O N C C C C O O O C C H O O
C C H C C C C S O O O C P P H N N O O O P O O N C P O O O O C O C H C C C N
O O C)
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(7.4154d0 -2.6646d0) (4.4691d0 -1.6884d0) (2.6318d0 -1.6884d0)
(-5.9422d0 -5.1308d0) (-4.237d0 -5.6277d0) (5.5445d0 -1.6884d0)
(0.4305d0 -4.2042d0) (-0.9434d0 -8.4084d0) (-0.8442d0 -6.0414d0)
(-5.214d0 -5.6277d0) (-7.1337d0 -4.2706d0) (-4.237d0 -6.4383d0)
(3.5425d0 -1.6884d0) (0.0992d0 -3.4424d0) (6.5543d0 -1.6884d0)
(0.3809d0 -7.465d0) (-6.5543d0 -5.4949d0) (-2.6983d0 -5.6277d0)
(-2.6983d0 -6.4383d0) (0.5297d0 -2.5822d0) (5.5445d0 -2.6646d0)
(1.3907d0 -2.5822d0) (0.116d0 -2.6646d0) (-1.9037d0 -5.6277d0)
(0.9106d0 -6.7864d0) (1.738d0 -3.1943d0) (-8.4084d0 -3.0287d0)
(-0.2817d0 -6.4383d0) (0.4305d0 -4.7011d0) (-6.2071d0 -2.6486d0)
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(32 66 :AROMATIC) (65 4 1) (63 18 1) (62 71 1) (61 17 1) (61 13 1) (57 56 2)
(56 62 1) (55 42 1) (54 63 2) (53 14 1) (52 21 1) (52 61 1) (51 10 1)
(51 23 2) (51 40 1) (50 43 2) (49 22 1) (48 43 1) (66 47 :AROMATIC)
(46 37 1) (45 67 1) (44 59 2) (44 15 1) (44 53 1) (43 25 1) (42 48 1)
(41 51 1) (40 44 1) (38 27 1) (3 37 :AROMATIC) (36 31 1) (35 41 1) (34 28 1)
(34 13 1) (34 60 1) (33 5 1) (32 54 1) (37 32 :AROMATIC) (31 65 1) (29 56 1)
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(ATOM-CHARGES (20 -1) (19 -1) (18 -1) (17 -1) (16 -1) (15 -1))
(CHEMICAL-FORMULA (C 26) (H 44) (N 7) (O 26) (P 5) (S 1))
(MOLECULAR-WEIGHT 1057.594d0)
(AROMATIC-RINGS (32 37 3 11 47 66)) )
NIL)
(2-ACETO-2-HYDROXY-BUTYRATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF ACETOOHBUTREDUCTOISOM-RXN)
(DBLINKS (LIGAND-CPD "C06006" NIL |keseler| 3342801886 NIL NIL)
(PUBCHEM "21" NIL |keseler| 3342801886 NIL NIL) (CAS "3142-65-2"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -148.6d0)
(COMMON-NAME "2-aceto-2-hydroxy-butyrate")
(APPEARS-IN-RIGHT-SIDE-OF ACETOOHBUTSYN-RXN)
(MOLECULAR-WEIGHT 146.143d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 4))
(DISPLAY-COORDS-2D (-0.49477d0 0.41115d0) (-0.00348d0 -1.0d0)
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(SYNONYMS "α-aceto-α-hydroxybutyrate") )
((GIBBS-0 -148.6d0 CITATIONS "GibbsGroups97")))
(2-ACETO-LACTATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (PUBCHEM "440878" NIL |keseler| 3342802103 NIL NIL)
(LIGAND-CPD "C06010" NIL |keseler| 3342802103 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -150.3d0)
(APPEARS-IN-RIGHT-SIDE-OF ACETOLACTREDUCTOISOM-RXN ACETOLACTSYN-RXN)
(MOLECULAR-WEIGHT 132.116d0)
(CHEMICAL-FORMULA (C 5) (H 8) (O 4))
(DISPLAY-COORDS-2D (0.0d0 -1.3338d0) (1.9549d0 0.0d0) (1.2036d0 -3.3957d0)
(3.826d0 -3.2753d0) (5.145d0 -1.9933d0) (3.6363d0 -0.5191d0)
(1.2036d0 -2.0154d0) (3.7498d0 -1.8774d0) (2.4743d0 -1.3001d0))
(STRUCTURE-BONDS (8 9 1) (7 9 1) (9 6 1 :UP) (5 8 1) (4 8 2) (3 7 2)
(9 2 1 :DOWN) (1 7 1))
(STRUCTURE-ATOMS C C O O O O C C C)
(SYNONYMS "(S)-2-hydroxy-2-methyl-3-oxobutanoate" "α-acetolactate")
(COMMON-NAME "2-acetolactate") )
((GIBBS-0 -150.3d0 CITATIONS "GibbsGroups97")))
(2-ACYL-GPE T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (1.65d0 -1.0083d0) (2.2995d0 -0.6333d0)
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(1.0005d0 0.1167d0) (2.2995d0 0.1167d0) (2.9502d0 0.4895d0)
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(3.0437d0 -1.3792d0) (3.0442d0 -2.8792d0) (4.1708d0 -2.7787d0)
(4.9208d0 -2.7787d0) (5.2958d0 -3.4282d0))
(CHEMICAL-FORMULA (C 6) (H 13) (N 1) (O 7) (R 1) (P 1))
(STRUCTURE-BONDS (15 16 1) (14 15 1) (11 14 1) (10 13 2) (10 12 1) (10 11 1)
(5 10 1) (2 7 1) (7 9 2) (7 8 1) (3 6 1) (4 5 1) (1 4 1) (1 3 1) (1 2 1))
(STRUCTURE-ATOMS C O C C O O C R O P O O O C C N)
(APPEARS-IN-LEFT-SIDE-OF ACYLGPEACYLTRANS-RXN)
(:CREATOR |kr|)
(SYNONYMS "2-acyl-GPE"
"O-(2-acyl-sn-glycero-3-phospho)-ethanolamine")
(COMMON-NAME "a 2-acyl-sn-glycero-3-phosphoethanolamine") )
NIL)
(|2-Acylglycero-Phosphocholines| T (
(OCELOT-GFP::PARENTS |Lysolecithins|)
(APPEARS-IN-RIGHT-SIDE-OF PHOSPHOLIPASE-A1-RXN)
(COMMON-NAME "a 2-acyl-sn-glycero-3-phosphocholine")
(APPEARS-IN-LEFT-SIDE-OF LYSOPHOSPHOLIPASE-RXN)
(DISPLAY-COORDS-2D (2.4676d0 -3.2926d0) (4.1176d0 -3.2926d0)
(-1.6843d0 -1.8764d0) (1.2166d0 -2.5779d0) (-2.1102d0 -2.5779d0)
(0.3916d0 -3.4165d0) (-0.8593d0 -1.8764d0) (3.2926d0 -3.2926d0)
(-2.9075d0 -1.1481d0) (-0.4329d0 -2.5779d0) (0.3916d0 -1.7529d0)
(-2.0829d0 -1.1481d0) (0.3916d0 -2.5779d0) (-2.9352d0 -2.5779d0)
(2.0416d0 -2.5779d0) (3.2926d0 -2.4676d0) (-3.3339d0 -1.8355d0)
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(CHEMICAL-FORMULA (C 9) (H 20) (N 1) (O 7) (R1 1) (P 1))
(ATOM-CHARGES (8 1))
(SYNONYMS "a L-1-lysolecithin" "a 1-lysophosphatidylcholine"
"a 1-lysolecithin" "a β-lysophosphatidylcholine"
"a 2-acylglycerophosphocholine")
(STRUCTURE-BONDS (19 8 1) (18 14 2) (17 14 1) (16 8 1) (15 4 1) (15 1 1)
(12 3 1) (12 9 1) (11 13 1) (10 13 1) (10 7 1) (7 3 1) (6 13 2) (5 3 1)
(5 14 1) (4 13 1) (2 8 1) (1 8 1))
(STRUCTURE-ATOMS C C C O O O C N O O O C P C C C R1 O C)
(SCHEMA? T)
(NAMES "L-2-lysolecithin" "2-acylglycerophosphocholine"
"2-Lysophosphatidylcholine" "2-Lysolecithin")
(:CREATOR |kr|)
(:CREATION-DATE 3267207960) )
NIL)
(|2-Alpha-Mannosyl-Heteroglycans| T (
(OCELOT-GFP::PARENTS |Heteroglycans|)
(COMMON-NAME "2-(α-D-mannosyl)-heteroglycan")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(2-AMINOMALONATE-SEMIALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (2.306d0 0.0d0) (4.612d0 -1.2503d0) (1.1854d0 -3.6397d0)
(0.0d0 -1.491d0) (3.5098d0 -2.1117d0) (1.1854d0 -2.2413d0)
(2.306d0 -1.3986d0))
(CHEMICAL-FORMULA (C 3) (H 5) (N 1) (O 3))
(DBLINKS (LIGAND-CPD "C11822" NIL |sreddy| 3296924273 NIL NIL))
(MOLECULAR-WEIGHT 103.077d0)
(STRUCTURE-BONDS (6 7 1) (5 7 1) (4 6 1) (3 6 2) (2 5 2) (7 1 1 :DOWN))
(STRUCTURE-ATOMS N O O O C C C)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2201)
(COMMON-NAME "2-aminomalonate-semialdehyde")
(:CREATOR |arnaud|)
(:CREATION-DATE 3286057042) )
NIL)
(|2-Arylethylamines| T (
(OCELOT-GFP::PARENTS |Arylalkylamines|)
(COMMON-NAME "a 2-arylethylamine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(2-C-METHYL-D-ERYTHRITOL-4-PHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C11434" NIL |kr| 3346617700 NIL NIL))
(DISPLAY-COORDS-2D (0.67666674d0 -0.120000005d0) (0.03666675d0 -0.73333335d0)
(0.67666674d0 -0.45333332d0) (-0.38666666d0 -0.45333332d0)
(-0.7166667d0 -0.73333335d0) (0.67666674d0 -0.73333335d0)
(0.99666667d0 -0.45333332d0) (-1.0d0 -0.120000005d0)
(-0.38666666d0 -0.120000005d0) (-0.49333334d0 -1.0d0) (-0.9533333d0 -1.0d0)
(-1.0d0 -0.45333332d0) (0.35333335d0 -0.45333332d0))
(CHEMICAL-FORMULA (C 5) (H 13) (O 7) (P 1))
(MOLECULAR-WEIGHT 216.127d0)
(STRUCTURE-BONDS (13 3 1) (12 5 1) (8 12 1) (5 11 1) (5 10 1) (5 4 1) (4 2 1)
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(STRUCTURE-ATOMS O C P C C O O O O O C C O)
(SYNONYMS "MEP")
(APPEARS-IN-LEFT-SIDE-OF 2.7.7.60-RXN DXPREDISOM-RXN)
(COMMON-NAME "2-C-methyl-D-erythritol-4-phosphate")
(:CREATION-DATE 3123241160)
(:CREATOR |ptoole|) )
NIL)
(2-CARBOXYMUCONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2943)
(MOLECULAR-WEIGHT 186.121d0)
(CHEMICAL-FORMULA (C 7) (H 6) (O 6))
(STRUCTURE-BONDS (12 13 1) (11 13 1) (9 13 2) (8 10 1) (7 9 1) (7 8 2)
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(DISPLAY-COORDS-2D (1.2124d0 -3.4999d0) (4.8497d0 -4.2d0) (7.2746d0 0.0d0)
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(2.4248d0 -1.3999d0) (4.8497d0 -1.4d0) (1.2124d0 -2.0999d0)
(6.0621d0 -3.5d0) (7.2746d0 -1.4d0) (6.0621d0 -2.1d0))
(STRUCTURE-ATOMS O O O O O O C C C C C C C)
(COMMON-NAME "2-carboxymuconate")
(:CREATOR |keseler|)
(:CREATION-DATE 3309020471) )
NIL)
(2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04411" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -198.2d0)
(APPEARS-IN-RIGHT-SIDE-OF 3-ISOPROPYLMALISOM-RXN)
(APPEARS-IN-LEFT-SIDE-OF 3-ISOPROPYLMALDEHYDROG-RXN)
(MOLECULAR-WEIGHT 176.169d0)
(CHEMICAL-FORMULA (C 7) (H 12) (O 5))
(DISPLAY-COORDS-2D (0.13667d0 0.44d0) (0.99667d0 -0.54d0)
(-0.20333d0 -0.31333d0) (0.60333d0 0.14d0) (0.60333d0 -0.31333d0)
(-0.20333d0 0.13667d0) (0.19667d0 -1.0d0) (-0.61d0 -0.54667d0)
(0.19667d0 -0.54667d0) (-1.0d0 -0.32d0) (-0.61d0 -1.0d0)
(-0.55667d0 0.42333d0))
(STRUCTURE-BONDS (12 6 2) (11 8 1) (10 8 1) (9 3 1) (8 3 1) (7 9 1) (6 3 1)
(5 9 1) (4 5 2) (2 5 1) (1 6 1))
(STRUCTURE-ATOMS O O C O C C O C C C C O)
(COMMON-NAME "3-isopropylmalate")
(SYNONYMS "2-D-threo-hydroxy-3-carboxy-isocaproate"
"3-carboxy-2-hydroxy-4-methylpentanoate" "β-isopropylmalate") )
((GIBBS-0 -198.2d0 CITATIONS "GibbsGroups97")))
(2-DEHYDRO-3-DEOXY-D-GALACTONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C01216" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -222.3d0)
(APPEARS-IN-RIGHT-SIDE-OF GALACTONDEHYDRAT-RXN)
(APPEARS-IN-LEFT-SIDE-OF DEHYDDEOXGALACTKIN-RXN)
(MOLECULAR-WEIGHT 178.141d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 6))
(DISPLAY-COORDS-2D (-0.6849d0 0.68053d0) (-1.0d0 -0.22101d0)
(-0.6849d0 0.99562d0) (-0.6849d0 0.05908d0) (-1.0d0 0.05908d0)
(-0.36543d0 0.3698d0) (-0.6849d0 -0.22101d0) (-0.43982d0 -1.0d0)
(-0.36543d0 -0.22101d0) (-0.36543d0 -0.50547d0) (-0.6849d0 -0.50547d0)
(-0.6849d0 0.3698d0) (-0.6849d0 -0.78556d0) (-0.9256d0 -1.0d0)
(-1.0d0 0.3698d0) (-0.36543d0 0.05908d0))
(STRUCTURE-BONDS (14 13 2) (13 11 1) (12 1 1) (12 6 1) (12 15 1) (11 7 1)
(10 11 2) (8 13 1) (7 4 1) (7 9 1) (7 2 1) (5 4 1) (4 12 1) (4 16 1) (1 3 1))
(STRUCTURE-ATOMS C H O C O O C O H O C C C O H H)
(SYNONYMS "2-keto-3-deoxy-D-galactonate")
(COMMON-NAME "2-dehydro-3-deoxy-D-galactonate")
(:CREATOR |rahman|) )
((GIBBS-0 -222.3d0 CITATIONS "GibbsGroups97")))
(2-DEHYDRO-3-DEOXY-D-GLUCONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00204" NIL |kr| 3346617699 NIL NIL) (CAS "17510-99-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -222.3d0)
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-113 MANNONDEHYDRAT-RXN ALTRODEHYDRAT-RXN)
(APPEARS-IN-LEFT-SIDE-OF TRANS-RXN-113 DEOXYGLUCONOKIN-RXN)
(MOLECULAR-WEIGHT 178.141d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 6))
(DISPLAY-COORDS-2D (-0.68333d0 -0.22d0) (-0.36667d0 -0.50667d0)
(-1.0d0 -0.22d0) (-1.0d0 0.06d0) (-0.92d0 -1.0d0) (-1.0d0 0.37333d0)
(-0.68333d0 -0.50667d0) (-0.68333d0 0.06d0) (-0.68333d0 -0.78333d0)
(-0.68333d0 0.99667d0) (-0.36667d0 0.06d0) (-0.36667d0 0.37333d0)
(-0.68333d0 0.37333d0) (-0.36667d0 -0.22d0) (-0.45333d0 -1.0d0)
(-0.68333d0 0.68d0))
(STRUCTURE-BONDS (16 10 1) (15 9 1) (13 16 1) (13 12 1) (13 6 1) (9 7 1)
(8 13 1) (8 11 1) (7 1 1) (5 9 2) (4 8 1) (2 7 2) (1 8 1) (1 14 1) (1 3 1))
(STRUCTURE-ATOMS C O H H O H C C C O O O C H O C)
(COMMON-NAME "2-dehydro-3-deoxy-D-gluconate")
(:CREATOR |rahman|)
(SYNONYMS "2-keto-3-deoxy-D-gluconate" "3-deoxy-2-oxo-D-gluconate"
"2-keto-3-deoxygluconate") )
((GIBBS-0 -222.3d0 CITATIONS "GibbsGroups97")))
(2-DEHYDROPANTOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00966" NIL |kr| 3346617701 NIL NIL))
(HISTORY |kr-3290870141|)
(GIBBS-0 -147.4d0)
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (-1.3124d0 2.5625d0) (-0.5624d0 2.5625d0)
(-1.3124d0 1.8125d0) (-0.6618d0 1.4397d0) (-1.9633d0 1.4396d0)
(-1.3124d0 3.3125d0) (-1.3124d0 4.0583d0) (-0.5624d0 3.3125d0)
(-2.0624d0 3.3167d0) (-0.6629d0 4.4333d0))
(CHEMICAL-FORMULA (C 6) (H 10) (O 4))
(MOLECULAR-WEIGHT 146.143d0)
(STRUCTURE-BONDS (7 10 1) (6 9 1) (6 8 1) (6 7 1) (1 6 1) (1 3 1) (3 5 2)
(3 4 1) (1 2 2))
(STRUCTURE-ATOMS C O C O O C C C C O)
(APPEARS-IN-RIGHT-SIDE-OF 2-DEHYDROPANTOATE-REDUCT-RXN
3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN)
(SYNONYMS "ketopantoate" "2-keto-pantoate")
(COMMON-NAME "2-dehydropantoate") )
((GIBBS-0 -147.4d0 CITATIONS "GibbsGroups97")))
(2-DEHYDROPANTOATE-REDUCT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-NONCOMPETITIVE L-PANTOATE)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(INHIBITORS-COMPETITIVE NADP)
(REACTION 2-DEHYDROPANTOATE-REDUCT-RXN)
(REACTION-DIRECTION REVERSIBLE)
(COMMENT "2-Dehydropantoate reductase catalyzes the NADPH-dependent
reduction of ketopantoate to pantoate. The enzyme does not require
added divalent metal ions. The reaction follows an ordered kinetic
mechanism. The reductase is a B-specific enzyme. In both E.
coli and S. typhimurium the reaction can also be carried out by the
ilvC enzyme, acetohydroxy acid isomeroreductase. |CITS: [ColiSalII]
[83082612] [98389700] [20202057]|")
(ENZYME 2-DEHYDROPANTOATE-REDUCT-MONOMER)
(SYNONYMS "ketopantoate reductase" "2-dehydropantoate 2-reductase"
"(R)-pantoate:NADP+ 2-oxidoreductase" "α-ketopantoate reductase")
(COMMON-NAME "2-dehydropantoate reductase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto2/2pan2.template")
(:CREATION-DATE 3027196316)
(:CREATOR |mriley|) )
((INHIBITORS-COMPETITIVE NADP COMMENT
"NADP+ is competitive with respect to
NADPH but noncompetitive with respect to ketopantoate.
")
(INHIBITORS-NONCOMPETITIVE L-PANTOATE COMMENT
"Pantoate was noncompetitive with respect to both
ketopantoate and NADPH. ")
(INHIBITORS-NONCOMPETITIVE L-PANTOATE CITATIONS "20202057")
(INHIBITORS-COMPETITIVE NADP CITATIONS "20202057")))
(2-DEHYDROPANTOATE-REDUCT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P0A9J4" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02558" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(UNIPROT "P0A9J4" NIL |pkarp| 3338704369 NIL NIL)
(REFSEQ "NP_414959" NIL NIL NIL NIL NIL) (PDB "1KS9"))
(MOLECULAR-WEIGHT-SEQ 33.870719999999956d0)
(GENE G6239)
(CATALYZES 2-DEHYDROPANTOATE-REDUCT-ENZRXN)
(COMMENT "In both E. coli and S. typhimurium, the reaction
can also be carried out by the IlvC enzyme, acetohydroxy acid
isomeroreductase. |CITS: [83082612] [98389700]|")
(SYNONYMS "B0425" "PanE" "ketopantoate reductase"
"2-dehydropantoate 2-reductase" "(R)-pantoate:NADP+ 2-oxidoreductase" "ApbA")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/pan2.template")
(:CREATION-DATE 3000590607)
(:CREATOR |mriley|) )
NIL)
(2-DEHYDROPANTOATE-REDUCT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 2-DEHYDROPANTOATE-REDUCT-ENZRXN)
(IN-PATHWAY PANTO-PWY)
(RIGHT 2-DEHYDROPANTOATE NADPH)
(LEFT L-PANTOATE NADP)
(EC-NUMBER "1.1.1.169")
(COMMENT "This is the second reaction in pantothenate biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/pan2.template")
(:CREATION-DATE 3000590607)
(:CREATOR |mriley|) )
NIL)
(2-DEHYDROPANTOYL-LACTONE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(APPEARS-IN-RIGHT-SIDE-OF DEHYDROPANTLACRED-RXN)
(DISPLAY-COORDS-2D (4.9541d0 5.8625d0) (4.9541d0 6.6125d0) (6.249d0 6.6125d0)
(6.249d0 5.8625d0) (5.5995d0 5.4834d0) (6.8994d0 5.489d0)
(6.8086d0 7.1928d0) (4.7572d0 7.3761d0) (4.2333d0 6.8196d0))
(CHEMICAL-FORMULA (C 6) (H 8) (O 3))
(MOLECULAR-WEIGHT 128.127d0)
(STRUCTURE-BONDS (2 9 1) (2 8 1) (3 7 2) (4 6 2) (2 3 1) (5 1 1) (4 5 1)
(3 4 1) (1 2 1))
(STRUCTURE-ATOMS C C C C O O O C C)
(SYNONYMS "2-dehydropantolactone" "2-dehydropantoyl lactone")
(COMMON-NAME "2-oxopantoyl lactone") )
NIL)
(|2-Dehydropyranoses| T (
(OCELOT-GFP::PARENTS |Pyranoses|)
(COMMON-NAME "a 2-dehydropyranose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(2-DEOXY-D-GLUCOSE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF ALDOSE1EPIM-ENZRXN)
(CHEMICAL-FORMULA (C 6) (H 12) (O 5))
(MOLECULAR-WEIGHT 164.158d0)
(DBLINKS (NCI "15193") (CAS "154-17-6"))
(STRUCTURE-BONDS (10 11 1) (9 10 1) (7 11 1) (7 8 1) (6 9 1) (6 8 1)
(11 5 1 :UP) (10 4 1 :DOWN) (9 3 1 :UP) (8 2 1 :DOWN) (1 5 1))
(STRUCTURE-ATOMS O O O O C C O C C C C)
(DISPLAY-COORDS-2D (0.0d0 -3.8938d0) (5.9406d0 -4.2238d0) (3.5864d0 0.0d0)
(1.15d0 -1.327d0) (1.2867d0 -4.4456d0) (4.7429d0 -2.0989d0)
(3.5305d0 -4.1989d0) (4.7429d0 -3.4989d0) (3.5305d0 -1.3989d0)
(2.318d0 -2.0989d0) (2.318d0 -3.4989d0))
(COMMON-NAME "2-deoxy-D-glucose")
(:CREATOR |arnaud|)
(:CREATION-DATE 3252349014) )
NIL)
(2-DEOXYRIBOSE NIL (
(OCELOT-GFP::PARENTS |Pentoses|)
(:CREATOR |keseler|)
(:CREATION-DATE 3342874388)
(SYNONYMS "2'-deoxyribose" "2-deoxyribose" "2-deoxy-D-ribose")
(COMMON-NAME "deoxyribose")
(STRUCTURE-ATOMS C O H O O C C H H O C H H C)
(STRUCTURE-BONDS (14 7 1) (13 7 1) (12 14 1) (11 14 1) (11 4 1) (10 14 1)
(9 11 1) (8 7 1) (6 4 1) (6 7 1) (5 6 1) (3 6 1) (2 1 1) (1 11 1))
(DISPLAY-COORDS-2D (-0.46755d0 0.25458d0) (-1.0d0 0.25458d0)
(0.99667d0 0.19468d0) (0.26456d0 0.29118d0) (0.99667d0 -0.44426d0)
(0.99667d0 -0.12479d0) (0.71381d0 -0.68053d0) (0.71381d0 -0.36106d0)
(-0.46755d0 -0.44426d0) (-0.18802d0 -1.0d0) (-0.46755d0 -0.12479d0)
(-0.18802d0 -0.36106d0) (0.71381d0 -1.0d0) (-0.18802d0 -0.68053d0))
(CHEMICAL-FORMULA (C 5) (H 10) (O 4))
(MOLECULAR-WEIGHT 134.132d0)
(GIBBS-0 -140.0d0)
(DBLINKS (LIGAND-CPD "C01801" NIL |kaipa| 3311532624 NIL NIL)
(CAS "533-67-5")) )
((GIBBS-0 -140.0d0 CITATIONS "GibbsGroups97")))
(2-HYDROXY-2-METHYLPROPANENITRILE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |shearer|)
(:CREATION-DATE 3356361196)
(COMMON-NAME "acetone cyanohydrin")
(DISPLAY-COORDS-2D (2.866d0 -0.067d0) (3.7321d0 0.433d0) (2.0d0 -0.567d0)
(3.366d0 -0.933d0) (2.366d0 0.799d0) (4.5981d0 0.933d0))
(STRUCTURE-ATOMS C C C C O N)
(STRUCTURE-BONDS (1 2 1) (1 3 1) (1 4 1) (1 5 1) (2 6 3))
(DBLINKS (NCI "131093") (CAS "75-86-5"))
(CHEMICAL-FORMULA (C 4) (H 7) (N 1) (O 1))
(MOLECULAR-WEIGHT 85.105d0)
(SYNONYMS "2-hydroxy-2-methylpropanenitrile" "2-hydroxyisobutyronitrile") )
NIL)
(|2-Hydroxy-carboxylates| T (
(OCELOT-GFP::PARENTS |Hydroxy-carboxylates|)
(COMMON-NAME "a 2-hydroxy carboxylate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|2-hydroxyacyl-glutathiones| T (
(OCELOT-GFP::PARENTS |Hydroxyacyl-glutathiones|)
(COMMON-NAME "S-(2-hydroxyacyl)glutathione")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(2-HYDROXYDEOXYADENOSINE-5-TRIPHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Purine-Related| |Base-Derivatives|)
(DISPLAY-COORDS-2D (13.7801d0 -8.5476d0) (13.7801d0 -6.8641d0)
(11.267d0 -7.3821d0) (12.0966d0 -6.8641d0) (14.6089d0 -7.3821d0)
(12.0181d0 0.0d0) (1.3986d0 -4.7137d0) (6.7346d0 -4.7137d0)
(4.1439d0 -4.7137d0) (9.5652d0 -3.9946d0) (12.0966d0 -8.5476d0)
(1.3986d0 -7.5116d0) (0.0d0 -6.1131d0) (6.7346d0 -7.5116d0)
(4.1439d0 -7.5116d0) (15.6707d0 -3.4187d0) (9.9462d0 -6.1131d0)
(15.6707d0 -2.0202d0) (10.8527d0 -2.072d0) (12.0181d0 -4.1439d0)
(8.0814d0 -6.1131d0) (12.8736d0 -5.6469d0) (2.7712d0 -6.1131d0)
(5.4397d0 -6.1131d0) (12.0181d0 -1.3986d0) (10.8527d0 -3.4446d0)
(13.2621d0 -2.0202d0) (13.2621d0 -3.4446d0) (14.6089d0 -4.0921d0)
(13.7801d0 -7.6929d0) (11.267d0 -6.5533d0) (12.0966d0 -7.6929d0)
(14.6089d0 -6.5533d0) (1.3986d0 -6.1131d0) (6.7346d0 -6.1131d0)
(4.1439d0 -6.1131d0))
(AROMATIC-RINGS (20 26 19 25 27 28) (16 18 27 28 29))
(CHEMICAL-FORMULA (C 10) (H 16) (N 5) (O 13) (P 3))
(MOLECULAR-WEIGHT 507.183d0)
(STRUCTURE-BONDS (31 32 1) (30 33 1) (30 32 1) (29 33 1) (29 28 :AROMATIC)
(28 27 :AROMATIC) (27 25 :AROMATIC) (24 36 1) (24 35 1) (23 36 1) (23 34 1)
(22 33 1) (22 31 1) (21 35 1) (20 28 :AROMATIC) (26 20 :AROMATIC)
(19 26 :AROMATIC) (25 19 :AROMATIC) (27 18 :AROMATIC) (17 31 1) (17 21 1)
(16 29 :AROMATIC) (18 16 :AROMATIC) (15 36 1) (14 35 1) (13 34 1) (12 34 1)
(11 32 1) (10 26 1) (9 36 2) (8 35 2) (7 34 2) (6 25 1) (5 33 1) (4 32 1)
(3 31 1) (2 30 1) (1 30 1))
(STRUCTURE-ATOMS H H H H H N O O O O O O O O O C C N N N O O O O C C C C N C
C C C P P P)
(CITATIONS "11676470" "7642627")
(COMMON-NAME "2-hydroxydeoxyadenosine 5'-triphosphate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3280154629) )
NIL)
(2-HYDROXYGLUTARIC_ACID NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF HYDGLUTSYN-RXN)
(INHIBITORS-COMPETITIVE-OF KETOGLUTREDUCT-ENZRXN)
(DBLINKS (CAS "2889-31-8"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -201.0d0)
(SYNONYMS "2-hydroxyglutaric acid" "α-hydroxyglutarate"
"α-hydroxy-glutarate" "2-hydroxyglutarate")
(MOLECULAR-WEIGHT 148.115d0)
(CHEMICAL-FORMULA (C 5) (H 8) (O 5))
(DISPLAY-COORDS-2D (0.33333337d0 -0.618677d0) (0.997406d0 -0.616083d0)
(-1.0d0 -0.616083d0) (0.6679636d0 -0.42412454d0)
(-0.0012969971d0 -0.42412454d0) (-0.67055774d0 -0.040207505d0)
(-0.67055774d0 -0.42412454d0) (0.33333337d0 -1.0d0)
(-0.33852142d0 -0.618677d0) (0.6679636d0 -0.040207505d0))
(STRUCTURE-BONDS (10 4 2) (9 5 1) (8 1 1) (7 9 1) (6 7 2) (5 1 1) (3 7 1)
(2 4 1) (1 4 1))
(STRUCTURE-ATOMS C O O C C O C O C O)
(COMMON-NAME "2-hydroxyglutarate") )
((GIBBS-0 -201.0d0 CITATIONS "GibbsGroups97")))
(2-HYDROXYMALONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF MALIC-NADP-ENZRXN)
(MOLECULAR-WEIGHT 118.046d0)
(CHEMICAL-FORMULA (C 3) (H 2) (O 5))
(ATOM-CHARGES (5 -1) (4 -1))
(STRUCTURE-BONDS (7 8 1) (6 8 1) (5 7 1) (4 6 1) (3 8 1) (2 7 2) (1 6 2))
(DISPLAY-COORDS-2D (0.0d0 -4.2d0) (2.4248d0 0.0d0) (0.0d0 -1.4d0)
(2.4249d0 -4.2d0) (3.6373d0 -2.1d0) (1.2124d0 -3.5d0) (2.4248d0 -1.4d0)
(1.2124d0 -2.1d0))
(STRUCTURE-ATOMS O O O O O C C C)
(SYNONYMS "tartronate")
(COMMON-NAME "2-hydroxymalonate")
(:CREATOR |keseler|)
(:CREATION-DATE 3307713050) )
NIL)
(2-ISOPROPYLMALATESYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 2-ISOPROPYLMALATESYN-ENZRXN)
(COMPONENTS 2-ISOPROPYLMALATESYN-MONOMER)
(:CREATION-DATE 2969204124)
(:CREATOR |mriley|) )
((COMPONENTS 2-ISOPROPYLMALATESYN-MONOMER COEFFICIENT 4)))
(2-ISOPROPYLMALATESYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "mercuric salts" EDTA 2K-4CH3-PENTANOATE)
(INHIBITORS-NONCOMPETITIVE LEU)
(PHYSIOLOGICALLY-RELEVANT LEU)
(INHIBITORS-COMPETITIVE LEU)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(COFACTORS K+)
(SYNONYMS "α-isopropylmalate synthase" "α-IPM synthetase"
"α-IPM synthase"
"3-carboxy-3-hydroxy-4-methylpentanoate 3-methyl-2-oxobutanoate-lyase (CoA-acetylating)")
(COMMON-NAME "2-isopropylmalate synthase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 2-ISOPROPYLMALATESYN-RXN)
(COFACTOR-BINDING-COMMENT "Requires K+")
(COMMENT "There appears to be very little information on the
properties of this enzyme in E. coli. Most of this work was done on
S. typhimurium.")
(ENZYME 2-ISOPROPYLMALATESYN-CPLX)
(:CREATION-DATE 2969204124)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "mercuric salts" COMMENT
"This information comes from work done on S. typhimurium.")
(INHIBITORS-UNKMECH "mercuric salts" CITATIONS "[69177456]" "[72125362]")
(INHIBITORS-UNKMECH EDTA COMMENT
"This information comes from work done on S. typhimurium.")
(INHIBITORS-UNKMECH EDTA CITATIONS "[69177456]" "[72125362]")
(INHIBITORS-UNKMECH 2K-4CH3-PENTANOATE COMMENT
"This information comes from work done on S. typhimurium.")
(INHIBITORS-UNKMECH 2K-4CH3-PENTANOATE CITATIONS "[69177456]" "[72125362]")
(INHIBITORS-NONCOMPETITIVE LEU COMMENT "Noncompetitive with respect to
alpha-ketoisovalerate and competitive with respect to acetyl coA.
Leucine disaggregates the 4-subunit enzyme.")
(INHIBITORS-COMPETITIVE LEU COMMENT "Noncompetitive with respect to
alpha-ketoisovalerate and competitive with respect to acetyl coA.
Leucine disaggregates the 4-subunit enzyme.")
(COFACTOR-BINDING-COMMENT "Requires K+" CITATIONS "[NomenclatureBook]")))
(2-ISOPROPYLMALATESYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0074" "LeuA")
(COMMON-NAME "LeuA")
(DBLINKS (MODBASE "P09151" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00682" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414616" NIL NIL NIL NIL NIL) (UNIPROT "P09151"))
(COMPONENT-OF 2-ISOPROPYLMALATESYN-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 57.29782999999981d0)
(GENE EG11226)
(:CREATION-DATE 2969204124)
(:CREATOR |mriley|) )
NIL)
(2-ISOPROPYLMALATESYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY LEUSYN-PWY)
(ENZYMATIC-REACTION 2-ISOPROPYLMALATESYN-ENZRXN)
(RIGHT 3-CARBOXY-3-HYDROXY-ISOCAPROATE CO-A)
(LEFT 2-KETO-ISOVALERATE ACETYL-COA WATER)
(EC-NUMBER "2.3.3.13")
(COMMENT "This is the first step in the biosynthesis of leucine,
beyond a fork with the valine pathway.")
(:CREATION-DATE 2969204124)
(:CREATOR |mriley|) )
NIL)
(2-KETO-3-DEOXY-6-P-GLUCONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04442" NIL |kr| 3346617701 NIL NIL) (CAS "27244-54-8"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -222.5d0)
(COMMON-NAME "2-keto-3-deoxy-6-phospho-gluconate")
(APPEARS-IN-RIGHT-SIDE-OF DEOXYGLUCONOKIN-RXN PGLUCONDEHYDRAT-RXN)
(APPEARS-IN-LEFT-SIDE-OF KDPGALDOL-RXN)
(MOLECULAR-WEIGHT 258.121d0)
(CHEMICAL-FORMULA (C 6) (H 11) (O 9) (P 1))
(DISPLAY-COORDS-2D (-0.76d0 0.52d0) (-0.51667d0 0.04333d0)
(-0.76d0 0.04333d0) (-1.0d0 -0.19333d0) (-0.51667d0 0.75667d0)
(-0.76d0 -0.19333d0) (-0.51667d0 -0.62333d0) (-0.76d0 0.28d0)
(-0.76d0 0.99667d0) (-0.76d0 -0.40667d0) (-0.76d0 -0.83667d0)
(-1.0d0 0.75667d0) (-1.0d0 -0.40667d0) (-0.58667d0 -1.0d0)
(-1.0d0 0.04333d0) (-0.76d0 0.75667d0) (-0.51667d0 -0.40667d0)
(-0.94333d0 -1.0d0) (-0.76d0 -0.62333d0) (-0.51667d0 -0.19333d0))
(STRUCTURE-BONDS (19 10 1) (18 11 2) (16 12 1) (16 5 1) (16 9 2) (14 11 1)
(11 19 1) (10 13 1) (10 17 1) (10 6 1) (8 1 1) (7 19 2) (6 20 1) (6 3 1)
(4 6 1) (3 15 1) (3 2 1) (3 8 1) (1 16 1))
(STRUCTURE-ATOMS O O C O O C O C O C C O H O H P H O C H)
(SYNONYMS "2-dehydro-3-deoxy-D-gluconate-6-phosphate"
"2-dehydro-3-deoxy-6-phospho-D-gluconate"
"6-phospho-2-dehydro-3-deoxy-D-gluconate"
"2-keto-3-deoxy-6-phosphogluconate" "2-keto-3-deoxy-6-P-gluconate"
"6-p-2-k-3-deo-gluconate" "6-phospho-2-keto-3-deoxygluconate"
"6-phospho-2-dehydro-3-deoxygluconate" "2-keto-3-deoxygluconate-6-P") )
((GIBBS-0 -222.5d0 CITATIONS "GibbsGroups97")))
(2-KETO-3-DEOXY-D-GLUCARATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |kaipa|)
(:CREATION-DATE 3346525588)
(SYNONYMS "2-dehydro-3-deoxy-D-glucarate" "2-keto-3-deoxy-glucarate")
(COMMON-NAME "2-keto-3-deoxy-D-glucarate")
(STRUCTURE-ATOMS O O O C C C C O O C O O C)
(STRUCTURE-BONDS (13 4 1) (12 6 1) (11 5 1) (10 13 1) (9 6 2) (8 4 1)
(7 10 1) (6 4 1) (5 7 1) (3 13 1) (2 7 2) (1 5 2))
(DISPLAY-COORDS-2D (-0.87013d0 0.99675d0) (-0.51948d0 0.37338d0)
(-0.51623d0 -0.1039d0) (-0.86688d0 -0.37662d0) (-0.87013d0 0.6461d0)
(-0.86688d0 -0.64935d0) (-0.87013d0 0.37338d0) (-0.51623d0 -0.37662d0)
(-0.86688d0 -1.0d0) (-1.0d0 0.14286d0) (-0.51948d0 0.6461d0)
(-0.51623d0 -0.64935d0) (-0.86688d0 -0.1039d0))
(CHEMICAL-FORMULA (C 6) (H 8) (O 7))
(MOLECULAR-WEIGHT 192.125d0)
(GIBBS-0 -266.7d0) )
((GIBBS-0 -266.7d0 CITATIONS "GibbsGroups97")))
(2-KETO-3-METHYL-VALERATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00671" NIL |kr| 3346617699 NIL NIL) (CAS "1460-34-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -110.1d0)
(APPEARS-IN-RIGHT-SIDE-OF BRANCHED-CHAINAMINOTRANSFERILEU-RXN
DIHYDROXYMETVALDEHYDRAT-RXN)
(SYNONYMS "(3S)-3-Methyl-2-oxopentanoate" "α-keto-methylvalerate"
"2-oxo-3-methylvalerate" "(S)-2-oxo-3-methylpentanoate"
"(S)-3-methyl-2-oxopentanoate" "2-oxo-3-methylpentanoate"
"3-methyl-2-oxopentanoate" "α-keto-β-methyl-valerate")
(COMMON-NAME "2-keto-3-methyl-valerate")
(STRUCTURE-ATOMS C C C C C O O O C)
(STRUCTURE-BONDS (3 9 1 :UP) (4 8 2) (5 7 2) (5 6 1) (4 5 1) (3 4 1) (2 3 1)
(1 2 1))
(DISPLAY-COORDS-2D (0.15d0 1.7917d0) (0.7995d0 1.4167d0) (1.449d0 1.7917d0)
(2.0986d0 1.4167d0) (2.7481d0 1.7917d0) (2.7481d0 2.5417d0)
(3.3976d0 1.4167d0) (2.0986d0 0.6667d0) (1.449d0 2.5417d0))
(CHEMICAL-FORMULA (C 6) (H 10) (O 3))
(MOLECULAR-WEIGHT 130.143d0) )
((GIBBS-0 -110.1d0 CITATIONS "GibbsGroups97")))
(2-KETO-ISOVALERATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00141" NIL |kr| 3346617699 NIL NIL) (CAS "759-05-7"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -111.8d0)
(APPEARS-IN-LEFT-SIDE-OF 2-ISOPROPYLMALATESYN-RXN
3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN)
(APPEARS-IN-RIGHT-SIDE-OF BRANCHED-CHAINAMINOTRANSFERVAL-RXN
DIHYDROXYISOVALDEHYDRAT-RXN VALINE-PYRUVATE-AMINOTRANSFER-RXN)
(COMMON-NAME "2-keto-isovalerate")
(SYNONYMS "2-oxo-3-methylbutanoate" "3-methyl-2-oxobutanoate"
"α-keto-isovaleric acid" "α-ketoisopentanoic acid"
"α-keto-isovalerate" "α-oxoisovalerate" "α-ketovaline"
"2-oxoisovalerate" "2-ketovaline" "α-keto-valine" "2-oxoisopentanoate"
"2-keto-3-methylbutyric acid")
(STRUCTURE-ATOMS O C C O C C C O)
(STRUCTURE-BONDS (7 8 2) (5 6 1) (3 4 2) (5 2 1) (7 1 1) (5 3 1) (7 3 1))
(DISPLAY-COORDS-2D (0.7373d0 -1.2473d0) (-0.7521d0 -1.2473d0)
(-0.0272d0 0.079d0) (-0.0272d0 0.904d0) (-0.7521d0 -0.4223d0)
(-1.4666d0 -0.0098d0) (0.7373d0 -0.4223d0) (1.4517d0 -0.0098d0))
(CHEMICAL-FORMULA (C 5) (H 8) (O 3))
(MOLECULAR-WEIGHT 116.116d0) )
((GIBBS-0 -111.8d0 CITATIONS "GibbsGroups97")))
(2-KETOGLUTARATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(ACTIVATORS-UNKMECH-OF GSDEADENYLATION-ENZRXN ICITDEHDEPHOSPH-ENZRXN)
(ACTIVATORS-ALLOSTERIC-OF URITRANS-ENZRXN)
(INHIBITORS-UNKMECH-OF ISOCITLYASE-ENZRXN LCYSDESULF-ENZRXN
ICITDEHKINASE-ENZRXN SUCCINYLDIAMINOPIMTRANS-ENZRXN GSADENYLATION-ENZRXN)
(INHIBITORS-COMPETITIVE-OF KETOGLUTREDUCT-ENZRXN CITSYN-ENZRXN)
(DBLINKS (LIGAND-CPD "C00026" NIL |kr| 3346617701 NIL NIL) (CAS "328-50-7"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -191.4d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1863 ISOCITDEH-RXN GLUTDEHYD-RXN
GLUTAMATESYN-RXN RFFTRANS-RXN TRANS-RXN-23 PSERTRANSAMPYR-RXN
HISTAMINOTRANS-RXN PHEAMINOTRANS-RXN TYRAMINOTRANS-RXN)
(APPEARS-IN-LEFT-SIDE-OF BRANCHED-CHAINAMINOTRANSFERILEU-RXN
BRANCHED-CHAINAMINOTRANSFERVAL-RXN BRANCHED-CHAINAMINOTRANSFERLEU-RXN
ALANINE-AMINOTRANSFERASE-RXN KETOGLUTREDUCT-RXN RXN0-1144 RXN0-985 RXN0-986
RXN0-984 PYRDAMPTRANS-RXN PSERTRANSAM-RXN ACETYLORNTRANSAM-RXN RXN0-299
SUCCORNTRANSAM-RXN TRANS-RXN-23 PUTTRANSAM-RXN DIAMTRANSAM-RXN
2-OXOGLUT-DECARBOX-RXN ASPAMINOTRANS-RXN SUCCINYLDIAMINOPIMTRANS-RXN
GABATRANSAM-RXN 2OXOGLUTARATEDEH-RXN)
(MOLECULAR-WEIGHT 146.099d0)
(CHEMICAL-FORMULA (C 5) (H 6) (O 5))
(DISPLAY-COORDS-2D (-0.33887d0 -0.61794d0) (0.99668d0 -0.61462d0)
(0.66777d0 -0.42193d0) (0.33223d0 -1.0d0) (0.66777d0 -0.03987d0)
(0.33223d0 -0.61794d0) (-1.0d0 -0.61462d0) (-0.00332d0 -0.42193d0)
(-0.6711d0 -0.42193d0) (-0.6711d0 -0.03987d0))
(STRUCTURE-BONDS (10 9 2) (9 1 1) (8 6 1) (7 9 1) (6 3 1) (5 3 2) (4 6 2)
(2 3 1) (1 8 1))
(STRUCTURE-ATOMS C O C O O C O C C O)
(COMMON-NAME "α-ketoglutarate")
(SYNONYMS "ketoglutarate" "α-ketoglutarate" "2-oxoglutaric acid"
"α-ketoglutaric acid" "α-oxoglutarate" "2-oxoglutarate"
"2-ketoglutaric acid" "2-ketoglutarate" "2-oxopentanedionic acid"
"2-oxopentanedionate") )
((GIBBS-0 -191.4d0 CITATIONS "GibbsGroups97")))
(2-MERCAPTOETHANOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF BETAGALACTOSID-ENZRXN GLUCUROISOM-ENZRXN
GALACTUROISOM-ENZRXN METHYLENETHFDEHYDROG-NADP-ENZRXN THREODEHYD-ENZRXN)
(ACTIVATORS-UNKMECH-OF METHYLGLYREDUCT-ENZRXN MANNONOXIDOREDUCT-ENZRXN
THYMIDYLATESYN-ENZRXN MENF-ENZRXN GALACTOKIN-ENZRXN ALPHAGALACTOSID-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979755)
(COMMON-NAME "2-mercaptoethanol")
(STRUCTURE-ATOMS O S C C)
(DISPLAY-COORDS-2D (3.6373d0 0.0d0) (0.0d0 -0.7d0) (2.4248d0 -0.7d0)
(1.2124d0 0.0d0))
(STRUCTURE-BONDS (3 4 1) (2 4 1) (1 3 1))
(CHEMICAL-FORMULA (C 2) (H 6) (O 1) (S 1))
(MOLECULAR-WEIGHT 78.129d0)
(SYNONYMS "β-mercaptoethanol") )
NIL)
(2-METHYLCITRATE-DEHYDRATASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(CITATIONS "[11782506]")
(COMMENT
"The prpD gene encodes 2-methylcitrate dehydratase activity |CITS: [11782506]| and also encodes the minor aconitase activity, aconitase C |CITS: [11782506]|, which constitutes 5% or less of cellular activity and is observed in an acnA acnB double mutant |CITS: [9202458]|.")
(ENZYMATIC-REACTION ENZRXN0-1501)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY0-42)
(:CREATOR |ptoole|)
(:CREATION-DATE 3170595263)
(EC-NUMBER "4.2.1.79")
(COMMON-NAME "2-METHYLCITRATE-DEHYDRATASE")
(RIGHT WATER CPD-1136)
(LEFT CPD-622) )
NIL)
(2-METHYLCITRATE-SYNTHASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-245)
(IN-PATHWAY PWY0-42)
(:CREATOR |ptoole|)
(:CREATION-DATE 3170595234)
(EC-NUMBER "2.3.3.5")
(COMMON-NAME "2-METHYLCITRATE-SYNTHASE")
(RIGHT CPD-622 CO-A)
(LEFT OXALACETIC_ACID WATER PROPIONYL-COA) )
NIL)
(2-METHYLTHIO-N-6-ISOPENTYL-ADENOSINE-37- NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-5063)
(COMMON-NAME "2-methylthio-N-6-isopentyl adenosine-37 tRNA")
(:CREATOR |shearer|)
(:CREATION-DATE 3348433915) )
NIL)
(2-O-ALPHA-MANNOSYL-D-GLYCERATE NIL (
(OCELOT-GFP::PARENTS |Glycerates|)
(SYNONYMS "2(α-D-Mannosyl)-D-glycerate")
(DBLINKS (LIGAND-CPD "C11544" NIL |keseler| 3341781246 NIL NIL))
(DISPLAY-COORDS-2D (4.8497d0 -7.7d0) (8.487d0 -5.6d0) (0.0d0 -3.5d0)
(3.6373d0 -5.6d0) (1.2124d0 -1.4d0) (3.6373d0 0.0d0) (6.0622d0 -1.4d0)
(7.2746d0 -6.3d0) (1.2124d0 -4.2d0) (6.0622d0 -4.2d0) (3.6373d0 -4.2d0)
(4.8497d0 -6.3d0) (6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (2.4249d0 -2.1d0)
(3.6373d0 -1.4d0) (4.8497d0 -2.1d0) (4.8497d0 -3.5d0))
(CHEMICAL-FORMULA (C 9) (H 16) (O 9))
(CITATIONS "14645248")
(MOLECULAR-WEIGHT 268.22d0)
(STRUCTURE-BONDS (17 18 1) (16 17 1) (15 16 1) (14 15 1) (12 13 1) (11 18 1)
(11 14 1) (18 10 1 :DOWN) (10 13 1) (14 9 1 :UP) (8 13 1) (17 7 1 :UP)
(16 6 1 :UP) (15 5 1 :DOWN) (4 12 1) (3 9 1) (2 8 1) (1 12 2))
(STRUCTURE-ATOMS O O O O O O O C C O O C C C C C C C)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2522)
(COMMON-NAME "2-O-α-mannosyl-D-glycerate")
(:CREATOR |cvtran|)
(:CREATION-DATE 3289752479) )
NIL)
(|2-o-methyladenosine-rRNAs| T (
(OCELOT-GFP::PARENTS |rRNAs|)
(COMMON-NAME "2'-O-methyladenosine-containing rRNA")
(:CREATOR |paley|)
(:CREATION-DATE 3341087491) )
NIL)
(2-OCTAPRENYL-6-HYDROXYPHENOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C05811" NIL |kr| 3346617700 NIL NIL))
(:CREATION-DATE 3115390701)
(APPEARS-IN-RIGHT-SIDE-OF 2-OCTAPRENYLPHENOL-HYDROX-RXN)
(AROMATIC-RINGS (22 20 21 46 47 48))
(DISPLAY-COORDS-2D (36.7476d0 -2.6232d0) (35.365d0 -0.649d0)
(31.4249d0 -4.4898d0) (27.5327d0 -0.6986d0) (23.5926d0 -4.4898d0)
(19.6525d0 -0.6986d0) (15.7125d0 -4.5394d0) (11.7724d0 -0.7483d0)
(7.8305d0 -4.5394d0) (0.0d0 -3.0428d0) (2.5942d0 -4.5394d0)
(34.067d0 -3.2929d0) (30.1269d0 -2.2449d0) (26.2365d0 -3.2929d0)
(22.2964d0 -2.2449d0) (18.3563d0 -3.2929d0) (14.4145d0 -2.2449d0)
(10.4744d0 -3.2929d0) (6.5343d0 -2.2449d0) (2.6439d0 0.0d0)
(1.2962d0 -0.7483d0) (3.9401d0 -0.7483d0) (33.3701d0 -2.2449d0)
(29.5294d0 -3.2929d0) (25.6886d0 -2.2449d0) (21.7467d0 -3.2929d0)
(17.7073d0 -2.2449d0) (13.7176d0 -3.2929d0) (9.8768d0 -2.2449d0)
(5.2381d0 -3.2929d0) (32.4215d0 -2.2449d0) (28.3307d0 -3.2432d0)
(24.4402d0 -2.2449d0) (20.5498d0 -3.2432d0) (16.6594d0 -2.2449d0)
(12.7689d0 -3.2929d0) (8.8288d0 -2.2449d0) (35.4147d0 -2.1952d0)
(31.4746d0 -3.2929d0) (27.5327d0 -2.2449d0) (23.5926d0 -3.2929d0)
(19.6525d0 -2.2449d0) (15.7125d0 -3.2929d0) (11.7724d0 -2.2449d0)
(7.8802d0 -3.2929d0) (1.2962d0 -2.2945d0) (2.5942d0 -3.0428d0)
(3.9401d0 -2.2945d0))
(CHEMICAL-FORMULA (C 46) (H 70) (O 2))
(MOLECULAR-WEIGHT 655.058d0)
(STRUCTURE-BONDS (48 47 :AROMATIC) (47 46 :AROMATIC) (37 45 1) (36 44 1)
(35 43 1) (34 42 1) (33 41 1) (32 40 1) (31 39 1) (30 48 1) (29 37 1)
(28 36 1) (27 35 1) (26 34 1) (25 33 1) (24 32 1) (23 31 1)
(22 48 :AROMATIC) (46 21 :AROMATIC) (20 22 :AROMATIC) (21 20 :AROMATIC)
(19 45 2) (19 30 1) (18 44 2) (18 29 1) (17 43 2) (17 28 1) (16 42 2)
(16 27 1) (15 41 2) (15 26 1) (14 40 2) (14 25 1) (13 39 2) (13 24 1)
(12 38 2) (12 23 1) (11 47 1) (10 46 1) (9 45 1) (8 44 1) (7 43 1) (6 42 1)
(5 41 1) (4 40 1) (3 39 1) (2 38 1) (1 38 1))
(STRUCTURE-ATOMS C C C C C C C C C O O C C C C C C C C C C C C C C C C C C C
C C C C C C C C C C C C C C C C C C)
(APPEARS-IN-LEFT-SIDE-OF 2-OCTAPRENYL-6-OHPHENOL-METHY-RXN)
(COMMON-NAME "2-octaprenyl-6-hydroxyphenol") )
NIL)
(2-OCTAPRENYL-6-METHOXYPHENOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C05812" NIL |kr| 3346617699 NIL NIL))
(AROMATIC-RINGS (22 20 21 48 47 49))
(:CREATION-DATE 3115390701)
(APPEARS-IN-LEFT-SIDE-OF 2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN)
(DISPLAY-COORDS-2D (0.0d0 -4.3928d0) (36.4013d0 -2.4381d0)
(35.0373d0 -0.6421d0) (31.1392d0 -4.3928d0) (27.3393d0 -0.6912d0)
(23.4395d0 -4.3928d0) (19.6396d0 -0.6912d0) (15.7415d0 -4.4419d0)
(11.9417d0 -0.7403d0) (8.0927d0 -4.4419d0) (2.963d0 -4.3613d0)
(33.7549d0 -3.3069d0) (29.855d0 -2.221d0) (26.0552d0 -3.3069d0)
(22.2062d0 -2.221d0) (18.3572d0 -3.3069d0) (14.5082d0 -2.221d0)
(10.6593d0 -3.3069d0) (6.8103d0 -2.221d0) (2.9613d0 0.0d0)
(4.2437d0 -0.7403d0) (1.6771d0 -0.7403d0) (33.1128d0 -2.221d0)
(29.1638d0 -3.3069d0) (25.3657d0 -2.221d0) (21.7132d0 -3.3069d0)
(17.9625d0 -2.221d0) (14.0153d0 -3.3069d0) (10.2645d0 -2.221d0)
(5.5261d0 -3.3069d0) (32.1251d0 -2.0736d0) (28.1779d0 -3.3069d0)
(24.4272d0 -2.0736d0) (20.5291d0 -3.3069d0) (16.6801d0 -2.221d0)
(12.9293d0 -3.3069d0) (8.9821d0 -2.221d0) (0.3456d0 -2.9613d0)
(35.0373d0 -2.1227d0) (31.1392d0 -3.3069d0) (27.3393d0 -2.1718d0)
(23.4904d0 -3.3069d0) (19.6396d0 -2.221d0) (15.7906d0 -3.3069d0)
(11.9417d0 -2.221d0) (8.0927d0 -3.3069d0) (2.9613d0 -2.9613d0)
(4.2437d0 -2.2701d0) (1.6771d0 -2.221d0))
(CHEMICAL-FORMULA (C 47) (H 72) (O 2))
(MOLECULAR-WEIGHT 669.085d0)
(STRUCTURE-BONDS (49 47 :AROMATIC) (47 48 :AROMATIC) (38 49 1) (37 46 1)
(36 45 1) (35 44 1) (34 43 1) (33 42 1) (32 41 1) (31 40 1) (30 48 1)
(29 37 1) (28 36 1) (27 35 1) (26 34 1) (25 33 1) (24 32 1) (23 31 1)
(22 49 :AROMATIC) (48 21 :AROMATIC) (20 22 :AROMATIC) (21 20 :AROMATIC)
(19 46 2) (19 30 1) (18 45 2) (18 29 1) (17 44 2) (17 28 1) (16 43 2)
(16 27 1) (15 42 2) (15 26 1) (14 41 2) (14 25 1) (13 40 2) (13 24 1)
(12 39 2) (12 23 1) (11 47 1) (10 46 1) (9 45 1) (8 44 1) (7 43 1) (6 42 1)
(5 41 1) (4 40 1) (3 39 1) (2 39 1) (1 38 1))
(STRUCTURE-ATOMS C C C C C C C C C C O C C C C C C C C C C C C C C C C C C C
C C C C C C C O C C C C C C C C C C C)
(APPEARS-IN-RIGHT-SIDE-OF 2-OCTAPRENYL-6-OHPHENOL-METHY-RXN)
(COMMON-NAME "2-octaprenyl-6-methoxyphenol") )
NIL)
(2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.14.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 2-OCTPRNL-6-MTHXPHENOL-HYDROX-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT WATER OCTAPRENYL-METHOXY-BENZOQUINONE)
(LEFT 2-OCTAPRENYL-6-METHOXYPHENOL OXYGEN-MOLECULE)
(EC-NUMBER "1.14.3.-")
(COMMENT "This is the sixth step in ubiquinone biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiH.template")
(:CREATION-DATE 3000651950)
(:CREATOR |mriley|) )
NIL)
(2-OCTAPRENYL-6-OHPHENOL-METHY-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(:CREATION-DATE 3095450002)
(COMMENT
"The biosynthesis of ubiquinone requires two O-methylation reactions. Recent
studies have shown that the ubiG gene product catalyzes both of them.
|CITS: [96312895]|")
(ENZYME DHHB-METHYLTRANSFER-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION 2-OCTAPRENYL-6-OHPHENOL-METHY-RXN)
(COMMON-NAME "2-octaprenyl-6-hydroxyphenol methylase") )
NIL)
(2-OCTAPRENYL-6-OHPHENOL-METHY-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION 2-OCTAPRENYL-6-OHPHENOL-METHY-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT 2-OCTAPRENYL-6-METHOXYPHENOL ADENOSYL-HOMO-CYS)
(LEFT 2-OCTAPRENYL-6-HYDROXYPHENOL S-ADENOSYLMETHIONINE)
(COMMENT "This is the fifth step in ubiquinone
biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/step5.template")
(:CREATION-DATE 3000648782)
(:CREATOR |mriley|) )
NIL)
(2-OCTAPRENYL-METHOXY-BENZOQ-METH-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT
"The ubiE gene product, a C-methyltransferase, catalyzes reactions in both
ubiquinone (Q) and menaquinone (MK) biosynthesis. Q biosynthesis and MK
biosynthesis diverge after the formation of chorismate and the pathways proceed
independently except for the C methylation step. In Q biosynthesis the ubiE
encoded enzyme catalyzes the conversion of 2-octaprenyl-6-methoxy-1,4-benzoquinone
to 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone.
|CITS: [97197541] [98004566]|")
(REACTION 2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubisyn2/ubiE2.template")
(ENZYME 2-OCTAPRENYL-METHOXY-BENZOQ-METH-MONOMER)
(:CREATION-DATE 3035210287)
(COMMON-NAME "2-octaprenyl-6-methoxy-1,4-benzoquinone methylase")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(2-OCTAPRENYL-METHOXY-BENZOQ-METH-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3833" "YigO" "UbiE")
(DBLINKS (MODBASE "P0A887" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A887" NIL |pkarp| 3354911363)
(PFAM "PF01209" IN-FAMILY |pkarp| 3346700421 NIL NIL)
(REFSEQ "NP_418277" NIL NIL NIL NIL NIL))
(MOLECULAR-WEIGHT-SEQ 28.07316899999997d0)
(CATALYZES ADOMET-DMK-METHYLTRANSFER-ENZRXN
2-OCTAPRENYL-METHOXY-BENZOQ-METH-ENZRXN)
(GENE EG11473)
(COMMENT "UbiE mutants have been characterized. |CITS: [71136273] [93074269]|
Regulation has been described |CITS: [10960098]|. The ubiE, yigP, and ubiB genes form an operon |CITS: [10960098]|.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiE.template")
(:CREATION-DATE 3000651699)
(:CREATOR |mriley|) )
NIL)
(2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION 2-OCTAPRENYL-METHOXY-BENZOQ-METH-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT OCTAPRENYL-METHYL-METHOXY-BENZQ ADENOSYL-HOMO-CYS)
(LEFT OCTAPRENYL-METHOXY-BENZOQUINONE S-ADENOSYLMETHIONINE)
(COMMENT "This is the seventh step in ubiquinone biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiE.template")
(:CREATION-DATE 3000651699)
(:CREATOR |mriley|) )
NIL)
(2-OCTAPRENYLPHENOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C05810" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3115390701)
(APPEARS-IN-LEFT-SIDE-OF 2-OCTAPRENYLPHENOL-HYDROX-RXN)
(AROMATIC-RINGS (22 20 19 21 46 47))
(DISPLAY-COORDS-2D (35.8095d0 -3.3023d0) (34.7779d0 -0.687d0)
(30.8038d0 -4.5617d0) (26.7827d0 -0.687d0) (22.7598d0 -4.6105d0)
(18.7369d0 -0.7359d0) (14.7157d0 -4.6105d0) (10.6928d0 -0.7359d0)
(6.6717d0 -4.6594d0) (1.3235d0 -4.6594d0) (33.4526d0 -3.2364d0)
(29.4314d0 -2.3053d0) (25.4086d0 -3.2364d0) (21.4362d0 -2.3053d0)
(17.4133d0 -3.2364d0) (13.3905d0 -2.3053d0) (9.3693d0 -3.2364d0)
(5.3464d0 -2.3053d0) (0.0d0 -0.7847d0) (1.3235d0 0.0d0) (0.0d0 -2.3053d0)
(2.6488d0 -0.7847d0) (33.0602d0 -2.3053d0) (28.8421d0 -3.2364d0)
(24.8697d0 -2.3053d0) (20.8468d0 -3.2364d0) (16.8745d0 -2.3053d0)
(12.8028d0 -3.2364d0) (8.8287d0 -2.3053d0) (3.9723d0 -3.2364d0)
(31.8344d0 -2.1571d0) (27.665d0 -3.2364d0) (23.7415d0 -2.1571d0)
(19.5216d0 -3.2364d0) (15.6957d0 -2.3053d0) (11.6746d0 -3.2364d0)
(7.6517d0 -2.3053d0) (34.8267d0 -2.3053d0) (30.8038d0 -3.2364d0)
(26.7827d0 -2.3053d0) (22.7598d0 -3.2364d0) (18.7369d0 -2.3053d0)
(14.7157d0 -3.2364d0) (10.6928d0 -2.3053d0) (6.6717d0 -3.2364d0)
(1.3235d0 -3.09d0) (2.6488d0 -2.3541d0))
(CHEMICAL-FORMULA (C 46) (H 70) (O 1))
(MOLECULAR-WEIGHT 639.058d0)
(STRUCTURE-BONDS (47 46 :AROMATIC) (37 45 1) (36 44 1) (35 43 1) (34 42 1)
(33 41 1) (32 40 1) (31 39 1) (30 47 1) (29 37 1) (28 36 1) (27 35 1)
(26 34 1) (25 33 1) (24 32 1) (23 31 1) (22 47 :AROMATIC) (46 21 :AROMATIC)
(20 22 :AROMATIC) (21 19 :AROMATIC) (19 20 :AROMATIC) (18 45 2) (18 30 1)
(17 44 2) (17 29 1) (16 43 2) (16 28 1) (15 42 2) (15 27 1) (14 41 2)
(14 26 1) (13 40 2) (13 25 1) (12 39 2) (12 24 1) (11 38 2) (11 23 1)
(10 46 1) (9 45 1) (8 44 1) (7 43 1) (6 42 1) (5 41 1) (4 40 1) (3 39 1)
(2 38 1) (1 38 1))
(STRUCTURE-ATOMS C C C C C C C C C O C C C C C C C C C C C C C C C C C C C C
C C C C C C C C C C C C C C C C C)
(APPEARS-IN-RIGHT-SIDE-OF 3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN)
(COMMON-NAME "2-octaprenylphenol") )
NIL)
(2-OCTAPRENYLPHENOL-HYDROX-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "10960098:EV-EXP-IMP:3336323363:keseler")
(COMMENT
"2-Octaprenylphenol hydroxylase is believed to catalyze the first hydroxylation step in the ubiquinone biosynthesis
pathway. |CITS: [ColiSalII]|")
(REACTION 2-OCTAPRENYLPHENOL-HYDROX-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubisyn2/ubiB2.template")
(ENZYME 2-OCTAPRENYLPHENOL-HYDROX-MONOMER)
(:CREATION-DATE 3035210286)
(COMMON-NAME "2-octaprenylphenol hydroxylase")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(2-OCTAPRENYLPHENOL-HYDROX-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"ubiB mutants contains no detectable ubiquinone |CITS: [9422602]| and accumulate octaprenylphenol
|CITS: [4897112][10960098]|.")
(SYNONYMS "B3835" "YigQ" "YigS" "AarF" "YigR" "UbiB")
(MOLECULAR-WEIGHT-SEQ 63.202654999999694d0)
(GENE EG11476)
(DBLINKS (MODBASE "P0A6A0" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03109" IN-FAMILY |pkarp| 3346700421 NIL NIL)
(UNIPROT "P0A6A0" NIL |keseler| 3336319055 NIL NIL)
(REFSEQ "NP_418279" NIL NIL NIL NIL NIL))
(CATALYZES 2-OCTAPRENYLPHENOL-HYDROX-ENZRXN)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiB.template")
(:CREATION-DATE 3000648815)
(:CREATOR |mriley|) )
NIL)
(2-OCTAPRENYLPHENOL-HYDROX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION 2-OCTAPRENYLPHENOL-HYDROX-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT 2-OCTAPRENYL-6-HYDROXYPHENOL)
(LEFT 2-OCTAPRENYLPHENOL OXYGEN-MOLECULE)
(COMMENT "This is the fourth step in ubiquinone biosynthesis.
The pathway is still under investigation, therefore
not all of the steps have been thoroughly characterized.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiB.template")
(:CREATION-DATE 3000648815)
(:CREATOR |mriley|) )
((RIGHT 2-OCTAPRENYL-6-HYDROXYPHENOL COEFFICIENT 2)
(LEFT 2-OCTAPRENYLPHENOL COEFFICIENT 2)))
(2-OCTPRNL-6-MTHXPHENOL-HYDROX-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "2-octaprenyl-6-methoxyphenol hydroxylase is one of the
aerobic hydroxylases in the ubiquinone biosynthesis pathway. It is
thought that the enzyme contains a flavin adenine dinucleotide.
|CITS: [93054351]| There has not been much work done on this enzyme.")
(REACTION 2-OCTAPRENYL-6-METHOXYPHENOL-HYDROX-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubisyn2/ubiH2.template")
(ENZYME OCTAPRENYL-METHOXYPHENOL-OH-MONOMER)
(:CREATION-DATE 3035210287)
(COMMON-NAME "2-octaprenyl-6-methoxyphenol hydroxylase")
(SYNONYMS "2-octaprenyl-6-methoxyphenol monooxygenase")
(REACTION-DIRECTION REVERSIBLE) )
((PROSTHETIC-GROUPS :FACET COMMENT "The enzyme is believed to be a FAD
flavoprotein. |CITS: [93054351] [SwissProt]|")))
(|2-Oxo-Acids| T (
(OCELOT-GFP::PARENTS |All-Carboxy-Acids|)
(DISPLAY-COORDS-2D (0.22000003d0 0.93999994d0) (0.9799999d0 0.19999993d0)
(0.22000003d0 0.22000003d0) (-0.26d0 -0.3d0) (-1.0d0 0.19999993d0)
(-0.26d0 -1.0d0))
(CHEMICAL-FORMULA (C 2) (H 1) (O 3) (R 1))
(STRUCTURE-BONDS (5 4 1) (4 6 2) (4 3 1) (3 2 2) (3 1 1))
(STRUCTURE-ATOMS O O C C R O)
(APPEARS-IN-RIGHT-SIDE-OF DAADEHYDROG-RXN)
(SYNONYMS "2-oxo acid")
(COMMENT
"This compound class stands for generic and unspecified 2-oxo acids.")
(COMMON-NAME "a 2-oxo acid")
(:CREATOR |kr|)
(:CREATION-DATE 3264456078) )
NIL)
(|2-Oxo-carboxylates| T (
(OCELOT-GFP::PARENTS |Carboxylates|)
(COMMON-NAME "a 2-oxo carboxylate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(2-OXOBUTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ACETOLACTSYNI-ENZRXN)
(ACTIVATORS-UNKMECH-OF DLACTDEHYDROGNAD-ENZRXN)
(INHIBITORS-COMPETITIVE-OF PYRUVATEDEH-ENZRXN)
(DBLINKS (LIGAND-CPD "C00109" NIL |kr| 3346617701 NIL NIL) (CAS "600-18-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -113.2d0)
(SYSTEMATIC-NAME "2-oxobutanoic acid")
(APPEARS-IN-RIGHT-SIDE-OF HOMOSERDEAM-RXN THREDEHYD-RXN CYSTAGLY-RXN)
(APPEARS-IN-LEFT-SIDE-OF KETOBUTFORMLY-RXN METBALT-RXN ACETOOHBUTSYN-RXN)
(MOLECULAR-WEIGHT 102.09d0)
(CHEMICAL-FORMULA (C 4) (H 6) (O 3))
(DISPLAY-COORDS-2D (-0.01113d0 0.22099d0) (-0.59936d0 -0.53259d0)
(0.55803d0 -1.0d0) (-0.01113d0 -0.24642d0) (0.99682d0 -0.37043d0)
(0.55803d0 -0.53259d0) (-1.0d0 -0.29412d0))
(STRUCTURE-BONDS (7 2 1) (6 3 2) (6 5 1) (4 1 2) (4 6 1) (2 4 1))
(STRUCTURE-ATOMS O C O C O C C)
(COMMON-NAME "2-oxobutanoate")
(SYNONYMS "2-oxobutyrate" "2-ketobutyrate" "2-oxobutyric acid"
"α-oxobutyric acid" "α-ketobutyrate" "α-ketobutyric acid"
"2-oxo-butyrate" "2-keto-butyrate" "2-ketobutyric acid")
(:CREATOR |madden|) )
((GIBBS-0 -113.2d0 CITATIONS "GibbsGroups97")))
(|2-Oxobutanoate-Degradation| T (
(OCELOT-GFP::PARENTS CARBOXYLATES-DEG)
(COMMON-NAME "2 oxobutanoate degradation")
(COMMENT "This class holds pathways for the degradation of 2-oxobutanoate.")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3355681269) )
NIL)
(2-OXOGLUT-DECARBOX-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE)
(COMMENT "The menD gene codes for a bifunctional protein. Both
activities catalyze reactions in the menaquinone biosynthetic pathway.
2-Oxoglutarate decarboxylase carries out the first reaction,
decarboxylation of α-ketoglutarate which yields a succinic
semialdehyde-thiamine PPi anion. |CITS: [93094143]|")
(REACTION 2-OXOGLUT-DECARBOX-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/mensyn2/menD2.template")
(ENZYME MEND-MONOMER)
(:CREATION-DATE 3030979245)
(COMMON-NAME "2-oxoglutarate decarboxylase")
(SYNONYMS "α-ketoglutarate decarboxylase" "KDC"
"2-oxoglutarate carboxy-lyase")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(2-OXOGLUT-DECARBOX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION 2-OXOGLUT-DECARBOX-ENZRXN)
(IN-PATHWAY MENAQUINONESYN-PWY)
(RIGHT CARBON-DIOXIDE SUCCINATE-SEMIALDEHYDE-THIAMINE-PPI)
(LEFT 2-KETOGLUTARATE THIAMINE-PYROPHOSPHATE)
(EC-NUMBER "4.1.1.71")
(COMMENT "This is the first reaction in menaquinone biosynthesis.
Menaquinone is an isoprenoid compound related to Vitamin K2 and
functions in electron transport.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/menaq/menD.template")
(:CREATION-DATE 3000590201)
(:CREATOR |mriley|) )
NIL)
(2-OXOPENT-4-ENOATE-HYDRATASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(CITATIONS "[8063106]")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY PWY-5162)
(COMMENT-INTERNAL
"kr98-09-16: merged info from the MHPDHYDROL-RXN frame, which had the EC 4.2.-.-")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/phenylprodeg/mhpD.template")
(ENZYMATIC-REACTION MHPDHYDROL-ENZRXN)
(:CREATOR |mriley|)
(EC-NUMBER "4.2.1.80")
(COMMON-NAME "2-OXOPENT-4-ENOATE-HYDRATASE")
(COMMENT "This is the sixth reaction in the branched meta-cleavage
degradation pathway of 3-phenylpropionate and
3-(3-hydroxyphenyl)propionate.
Also acts, more slowly, on cis-2-oxohex-4-enoate, but not on the trans-isomer.
This is the sixth reaction in the branched meta-cleavage
degradation pathway of 3-phenylpropionate and
3-(3-hydroxyphenyl)propionate.")
(RIGHT 4-HYDROXY-2-KETOVALERATE)
(LEFT OXOPENTENOATE WATER)
(SYNONYMS "OEH" "2-KETO-4-PENTENOATE HYDRATASE") )
NIL)
(2-PG NIL (
(OCELOT-GFP::PARENTS |Glycerates|)
(INHIBITORS-COMPETITIVE-OF DAHPSYNPHE-ENZRXN)
(HISTORY |kr-3290870141|)
(DBLINKS (LIGAND-CPD "C00631" NIL |kr| 3346617700 NIL NIL) (CAS "2553-59-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -157.5d0)
(APPEARS-IN-RIGHT-SIDE-OF GKI-RXN 3PGAREARR-RXN)
(APPEARS-IN-LEFT-SIDE-OF 2PGADEHYDRAT-RXN)
(MOLECULAR-WEIGHT 186.058d0)
(CHEMICAL-FORMULA (C 3) (H 7) (O 7) (P 1))
(DISPLAY-COORDS-2D (4.1501d0 -5.5675d0) (2.0788d0 0.0d0) (0.0d0 -5.5675d0)
(4.1501d0 -3.1713d0) (0.7051d0 -1.5107d0) (3.4653d0 -1.502d0)
(0.6917d0 -4.3693d0) (2.076d0 -2.9894d0) (3.4585d0 -4.3693d0)
(2.0751d0 -4.3693d0) (2.105d0 -1.4909d0))
(STRUCTURE-BONDS (9 10 1) (8 11 1) (10 8 1 :UP) (7 10 1) (6 11 1) (5 11 1)
(4 9 1) (3 7 1) (2 11 2) (1 9 2))
(STRUCTURE-ATOMS O O O O O O C O C C P)
(COMMON-NAME "2-phosphoglycerate")
(SYNONYMS "phosphoglycerate" "2-phosphoglyceric acid" "2-pg" "2-P-glycerate"
"glycerate 2-phosphate" "2-phospho-D-glycerate" "2-P-D-glycerate"
"D-Glycerate 2-phosphate") )
((GIBBS-0 -157.5d0 CITATIONS "GibbsGroups97")))
(2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET NIL (
(OCELOT-GFP::PARENTS CDP-SUGARS |Sugar-Phosphate|)
(SYNONYMS "CDP-ME-2P" "CDP-methyl-D-erylthritol 2-phosphate"
"4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate"
"4-diphosphocytidyl-2-C-methylerythritol 2-phosphate")
(APPEARS-IN-RIGHT-SIDE-OF 2.7.1.148-RXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-302)
(:CREATOR |keseler|)
(:CREATION-DATE 3335542228)
(COMMON-NAME "2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol")
(STRUCTURE-ATOMS C N O O O O O O O O O O O O C C C C C N O O O O O C C C C C
C C N C P P P)
(DISPLAY-COORDS-2D (0.2717d0 -4.5655d0) (20.1894d0 -3.5644d0)
(16.4134d0 -0.2366d0) (2.2082d0 -7.3757d0) (6.1586d0 -4.0314d0)
(8.9599d0 -4.0369d0) (0.0246d0 -1.5173d0) (2.2466d0 -1.2954d0)
(11.6554d0 -0.6157d0) (14.6384d0 0.0d0) (3.6075d0 -5.995d0)
(0.8078d0 -5.9926d0) (6.1322d0 -1.2316d0) (8.971d0 -1.2372d0)
(18.0991d0 -4.0834d0) (16.7077d0 -3.9289d0) (0.0d0 -2.9171d0)
(3.5529d0 -3.3979d0) (11.3192d0 -3.6429d0) (18.3668d0 -1.6734d0)
(4.7458d0 -2.6651d0) (10.3454d0 -2.6371d0) (13.8115d0 -3.527d0)
(2.2064d0 -4.5757d0) (7.5454d0 -2.6362d0) (18.9287d0 -2.9557d0)
(16.9753d0 -1.5189d0) (2.3439d0 -2.692d0) (12.6904d0 -1.5586d0)
(14.0615d0 -1.2756d0) (12.5359d0 -2.9501d0) (14.7543d0 -2.4921d0)
(16.1458d0 -2.6466d0) (1.2444d0 -3.5586d0) (2.2077d0 -5.9757d0)
(6.1454d0 -2.6315d0) (8.9454d0 -2.637d0))
(STRUCTURE-BONDS (32 33 1 :UP) (30 32 1) (29 31 1) (29 30 1) (28 34 1)
(33 27 :AROMATIC) (25 37 1) (25 36 1) (24 35 1) (34 24 1 :DOWN) (23 32 1)
(23 31 1) (22 37 1) (21 36 1) (27 20 :AROMATIC) (20 26 :AROMATIC)
(19 31 1 :UP) (19 22 1) (18 28 1) (18 21 1) (17 34 1) (16 33 :AROMATIC)
(26 15 :AROMATIC) (15 16 :AROMATIC) (14 37 1) (13 36 1) (12 35 1) (11 35 1)
(30 10 1 :DOWN) (29 9 1 :DOWN) (28 8 1 :UP) (7 17 1) (6 37 2) (5 36 2)
(4 35 2) (3 27 2) (2 26 1) (34 1 1 :UP))
(CHEMICAL-FORMULA (C 14) (H 26) (N 3) (O 17) (P 3))
(MOLECULAR-WEIGHT 601.291d0)
(AROMATIC-RINGS (16 15 26 20 27 33)) )
NIL)
(|2-Prime-Ribonucleoside-Monophosphates| T (
(OCELOT-GFP::PARENTS |Nucleotides|)
(DISPLAY-COORDS-2D (5.6679d0 0.0d0) (0.0d0 -5.6523d0) (1.2323d0 -1.3862d0)
(5.6707d0 -2.7999d0) (7.078d0 -1.4076d0) (5.2193d0 -4.2829d0)
(0.2911d0 -4.2829d0) (2.7552d0 -4.6732d0) (4.2781d0 -1.3862d0)
(2.0552d0 -2.5188d0) (3.8878d0 -3.8503d0) (1.6226d0 -3.8503d0)
(3.4552d0 -2.5188d0) (5.678d0 -1.4d0))
(CHEMICAL-FORMULA (C 5) (H 10) (O 7) (R 1) (P 1))
(DBLINKS (LIGAND-CPD "C03418" NIL |sreddy| 3299616868 NIL NIL))
(STRUCTURE-BONDS (11 13 1) (10 13 1) (10 12 1) (9 14 1) (13 9 1 :DOWN)
(8 12 1) (8 11 1) (12 7 1 :UP) (11 6 1 :UP) (5 14 1) (4 14 1) (10 3 1 :DOWN)
(2 7 1) (1 14 2))
(STRUCTURE-ATOMS O O O O O R C O O C C C C P)
(SYNONYMS "nucleoside-2'-phosphate" "nucleoside 2'-phosphate"
"a 2'-ribonucleotide")
(COMMON-NAME "a nucleoside 2'-phosphate")
(:CREATOR |kr|)
(:CREATION-DATE 3330208854) )
NIL)
(2-PROTOCATECHUOYLPHLOROGLUCINOLCARBOXYLA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF QUERCETIN-23-DIOXYGENASE-RXN)
(SYNONYMS "2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate")
(COMMON-NAME "2-protocatechuoylphloroglucinolcarboxylate")
(:CREATOR |keseler|)
(:CREATION-DATE 3344362386) )
NIL)
(2-THIOURIDINE NIL (
(OCELOT-GFP::PARENTS |Pyrimidine-Related| |Base-Derivatives|)
(MOLECULAR-WEIGHT 260.264d0)
(DISPLAY-COORDS-2D (3.3893d0 -7.8308d0) (5.4767d0 -9.2665d0)
(0.0d0 -2.6211d0) (2.3375d0 0.0d0) (4.1575d0 0.0d0) (3.2556d0 -5.5263d0)
(6.495d0 -7.3295d0) (6.495d0 -6.1775d0) (1.1688d0 -3.3392d0)
(3.2389d0 -3.4395d0) (5.4767d0 -7.9139d0) (4.4578d0 -6.1775d0)
(2.3375d0 -1.3693d0) (4.1575d0 -1.3693d0) (2.0367d0 -2.6546d0)
(4.4578d0 -2.6049d0) (4.4578d0 -7.3295d0) (5.4767d0 -5.5765d0))
(AROMATIC-RINGS (11 7 8 18 12 17))
(CHEMICAL-FORMULA (C 9) (H 12) (N 2) (O 5) (S 1))
(STRUCTURE-BONDS (16 18 1 :UP) (14 16 1) (13 15 1) (13 14 1)
(12 18 :AROMATIC) (17 12 :AROMATIC) (11 17 :AROMATIC) (10 16 1) (10 15 1)
(15 9 1 :UP) (18 8 :AROMATIC) (7 11 :AROMATIC) (8 7 :AROMATIC) (6 12 2)
(14 5 1 :DOWN) (13 4 1 :DOWN) (3 9 1) (2 11 2) (1 17 1))
(STRUCTURE-ATOMS H O O O O S C C C O C C C C C C N N)
(COMMENT-INTERNAL
"To the person who is editing the structure-- see PMID=12549933 for a drawing!")
(CITATIONS "12549933")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2023)
(SYNONYMS "s2U")
(COMMON-NAME "2-thiouridine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3281299609) )
NIL)
(|2-trans-4-cis-dienoyl-CoAs| T (
(OCELOT-GFP::PARENTS |All-Coas|)
(SUPERATOMS COA-GROUP)
(AROMATIC-RINGS (45 46 47 48 44) (48 49 50 51 52 47))
(CHEMICAL-FORMULA (C 26) (H 39) (N 7) (O 17) (R1 1) (P 3) (S 1))
(STRUCTURE-BONDS (55 1 1) (54 55 1) (2 3 2) (1 2 1) (3 4 1) (4 5 2) (5 6 1)
(1 7 2) (54 8 1) (8 9 1) (9 10 1) (10 11 2) (10 12 1) (12 13 1) (13 14 1)
(14 15 1) (15 16 2) (15 17 1) (17 18 1) (17 19 1) (19 20 1) (19 21 1)
(19 22 1) (22 23 1) (23 24 1) (24 25 1) (24 26 2) (24 27 1) (27 28 1)
(28 29 1) (28 30 2) (28 31 1) (31 32 1) (32 33 1) (33 34 1) (33 38 1)
(34 35 1) (35 36 1) (35 44 1) (36 37 1) (36 38 1) (38 39 1) (39 40 1)
(40 41 1) (40 42 1) (40 43 2) (45 44 :AROMATIC) (44 48 :AROMATIC)
(46 45 :AROMATIC) (47 46 :AROMATIC) (48 47 :AROMATIC) (47 52 :AROMATIC)
(49 48 :AROMATIC) (50 49 :AROMATIC) (51 50 :AROMATIC) (52 51 :AROMATIC)
(52 53 1))
(DISPLAY-COORDS-2D (-3.393d0 -0.6779d0) (-2.8887d0 -0.1717d0)
(-2.2367d0 -0.3654d0) (-1.5223d0 0.0471d0) (-0.6828d0 0.0721d0)
(-0.0832d0 -0.5959d0) (-2.8712d0 -1.4091d0) (-5.9957d0 -0.9125d0)
(-5.9957d0 -1.7375d0) (-6.7102d0 -2.15d0) (-7.4247d0 -1.7375d0)
(-6.7102d0 -2.975d0) (-7.4247d0 -3.3875d0) (-7.4247d0 -4.2125d0)
(-8.1391d0 -4.625d0) (-8.8536d0 -4.2125d0) (-8.1391d0 -5.45d0)
(-7.4247d0 -5.8625d0) (-8.8536d0 -5.8625d0) (-8.4411d0 -6.577d0)
(-9.2661d0 -5.148d0) (-9.5681d0 -6.275d0) (-9.5681d0 -7.1d0)
(-10.2825d0 -7.5125d0) (-9.87d0 -8.227d0) (-10.695d0 -6.798d0)
(-10.997d0 -7.925d0) (-11.7115d0 -7.5125d0) (-12.124d0 -8.227d0)
(-11.299d0 -6.798d0) (-12.426d0 -7.1d0) (-12.426d0 -6.275d0)
(-13.1404d0 -5.8625d0) (-13.8941d0 -6.1981d0) (-14.4461d0 -5.585d0)
(-14.0336d0 -4.8705d0) (-14.3692d0 -4.1168d0) (-13.2267d0 -5.042d0)
(-12.6136d0 -4.49d0) (-12.7851d0 -3.683d0) (-11.9781d0 -3.5115d0)
(-13.5921d0 -3.8545d0) (-12.9566d0 -2.876d0) (-15.0746d0 -6.1194d0)
(-15.0116d0 -6.942d0) (-15.7745d0 -7.2561d0) (-16.309d0 -6.6276d0)
(-15.8764d0 -5.9251d0) (-16.2685d0 -5.1992d0) (-17.0932d0 -5.1759d0)
(-17.5257d0 -5.8784d0) (-17.1336d0 -6.6043d0) (-17.5662d0 -7.3068d0)
(-5.2813d0 -0.5d0) (-4.4032d0 -0.9619d0))
(STRUCTURE-ATOMS C C C C C R1 O C N C O C C N C O C O C C C C O P O O O P O O
O C C O C C O C O P O O O N C N C C N C N C N C S)
(COMMON-NAME "a 2-trans-4-cis-dienoyl-CoA")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
((SUPERATOMS COA-GROUP REPLACES-ATOM 55)
(SUPERATOMS COA-GROUP CONNECTED-TO 1)))
(2.1.1.34-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.1.1 |tRNA-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-2961)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3285357429)
(COMMON-NAME "tRNA (guanosine-2'-O-)-methyltransferase")
(EC-NUMBER "2.1.1.34")
(RIGHT ADENOSYL-HOMO-CYS |tRNA-Containing-2-O-Methylguanosine|)
(LEFT S-ADENOSYLMETHIONINE |Some-tRNA|) )
NIL)
(2.1.1.63-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.1.1 |DNA-Reactions|
|Protein-Modification-Reactions|)
(LEFT |Protein-L-cysteine| |DNA-6-O-Methyl-Guanines|)
(RIGHT |Protein-S-methyl-L-cysteine| |DNA-Guanines|)
(EC-NUMBER "2.1.1.63")
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-1604 ENZRXN0-1603)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(COMMON-NAME "METHYLATED-DNA--PROTEIN-CYSTEINE-S-METHYLTRANSFERASE")
(COMMENT
"THIS ENZYME IS INVOLVED IN THE REPAIR OF ALKYLATED DNA IN E. COLI AND THE ENZYME ACTS ONLY ON THE ALKYLATED DNA AS AN ADAPTIVE RESPONSE TO ALKYLATING AGENTS (CF. EC 3.2.2.20 AND EC 3.2.2.21).")
(SYNONYMS "6-O-METHYLGUANINE-DNA METHYLTRANSFERASE"
"O-6-METHYLGUANINE-DNA-ALKYLTRANSFERASE") )
NIL)
(2.1.1.72-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.1.1 |DNA-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-1625)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "2.1.1.72")
(COMMON-NAME "SITE-SPECIFIC-DNA-METHYLTRANSFERASE-(ADENINE-SPECIFIC)")
(COMMENT
"THIS IS A LARGE GROUP OF ENZYMES, THE MAJORITY OF WHICH, WITH ENZYMES OF SIMILAR SITE SPECIFICITY LISTED AS EC 3.1.21.3, 4 AND 5, FORM SO-CALLED RESTRICTION-MODIFICATION SYSTEMS."
"SEE THE REBASE DATABASE (FROM RICH ROBERTS) FOR A COMPLETE LIST OF THESE ENZYMES.")
(RIGHT |DNA-6-Methyl-Amino-Purines| ADENOSYL-HOMO-CYS)
(LEFT |DNA-Adenines| S-ADENOSYLMETHIONINE)
(SYNONYMS "N-6 ADENINE-SPECIFIC DNA METHYLASE" "MODIFICATION METHYLASE"
"RESTRICTION-MODIFICATION SYSTEM") )
NIL)
(2.1.1.77-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.1.1)
(ENZYMATIC-REACTION ENZRXN0-1582)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "2.1.1.77")
(COMMON-NAME "PROTEIN-L-ISOASPARTATE(D-ASPARTATE)-O-METHYLTRANSFERASE")
(COMMENT
"D-ASPARTATE (BUT NOT L-ASPARTATE) RESIDUES IN PROTEINS CAN ALSO ACT AS ACCEPTORS.")
(RIGHT ADENOSYL-HOMO-CYS PROTEIN-L-BETA-ISOSPARTATE-METHYL-ESTERS)
(LEFT S-ADENOSYLMETHIONINE PROTEIN-L-BETA-ISOASPARTATES)
(SYNONYMS "PROTEIN L-ISOASPARTYL METHYLTRANSFERASE"
"PROTEIN D-ASPARTATE METHYLTRANSFERASE"
"PROTEIN β-ASPARTATE O-METHYLTRANSFERASE") )
NIL)
(2.1.1.79-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.1.1)
(IN-PATHWAY PWY0-541)
(CITATIONS "[380648]")
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(ENZYMATIC-REACTION CFA-ENZRXN)
(EC-NUMBER "2.1.1.79")
(COMMON-NAME "CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID-SYNTHASE")
(COMMENT
"ADDS A METHYLENE GROUP ACROSS THE 9,10 POSITION OF A δ(9)- OLEFINIC ACYL CHAIN IN PHOSPHATIDYLETHANOLAMINE OR, MORE SLOWLY, PHOSPHATIDYLGLYCEROL OR PHOSPHATIDYLINOSITOL FORMING A CYCLOPROPANE DERIVATIVE (CF. EC 2.1.1.16).")
(RIGHT |Phospholipid-Cyclopropane-Fatty-Acids| ADENOSYL-HOMO-CYS)
(LEFT |Phospholipid-Olefinic-Fatty-Acids| S-ADENOSYLMETHIONINE)
(SYNONYMS "CYCLOPROPANE SYNTHETASE"
"UNSATURATED-PHOSPHOLIPID METHYLTRANSFERASE") )
NIL)
(2.3.1.118-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN-21)
(:CREATOR |ptoole|)
(:CREATION-DATE 3183305693)
(EC-NUMBER "2.3.1.118")
(COMMON-NAME "N-HYDROXYARYLAMINE-O-ACETYLTRANSFERASE")
(RIGHT |N-Acetoxy-Arylamines| CO-A)
(LEFT |N-Hydroxy-Arylamines| ACETYL-COA)
(SYNONYMS "ARYLHYDROXAMATE N,O-ACETYLTRANSFERASE"
"ARYLAMINE N-ACETYLTRANSFERASE") )
NIL)
(2.3.1.128-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-1622 ENZRXN0-1621)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "2.3.1.128")
(COMMON-NAME "RIBOSOMAL-PROTEIN-ALANINE-N-ACETYLTRANSFERASE")
(COMMENT
"A GROUPS OF ENZYMES IN E.COLI WHICH ACETYLATE THE N-TERMINAL ALANINE RESIDUES OF SPECIFIC RIBOSOMAL PROTEINS (CF. EC 2.3.1.88).")
(RIGHT |Ribosomal-Protein-N-Acetyl-L-Alanines| CO-A)
(LEFT |Ribosomal-Protein-L-Alanines| ACETYL-COA) )
NIL)
(2.3.1.157-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(EC-NUMBER "2.3.1.157")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION GLUCOSAMINE1PACETYL-ENZRXN)
(IN-PATHWAY UDPNAGSYN-PWY GLCMANNANAUT-PWY)
(RIGHT N-ACETYL-D-GLUCOSAMINE-1-P CO-A)
(LEFT GLUCOSAMINE-1P ACETYL-COA)
(COMMENT "This is the third reaction in hexosamine biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/wallsyn/post2.template")
(:CREATION-DATE 3023037779)
(:CREATOR |mriley|) )
NIL)
(2.4.1.58-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.4.1)
(ENZYMATIC-REACTION ENZRXN0-6167)
(:CREATOR |keseler|)
(:CREATION-DATE 3347819402)
(LEFT |Lipopolysaccharides| UDP-GLUCOSE)
(RIGHT "D-GLUCOSYL-LIPOPOLYSACCHARIDE" UDP)
(EC-NUMBER "2.4.1.58")
(COMMON-NAME "Lipopolysaccharide glucosyltransferase I")
(OFFICIAL-EC? T) )
NIL)
(2.5.1.19-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ARO-PWY)
(ENZYMATIC-REACTION 3-P-SHIK-1-CARBOXYVINYLXFERASE-ENZRXN)
(RIGHT 3-ENOLPYRUVYL-SHIKIMATE-5P |Pi|)
(LEFT SHIKIMATE-5P PHOSPHO-ENOL-PYRUVATE)
(EC-NUMBER "2.5.1.19")
(COMMENT "This is the sixth step in the shikimate pathway")
(SYNONYMS "5-enolpyruvylshikimate-3-phosphate synthase" "EPSP synthase"
"3-enol-pyruvoylshikimate-5-phosphate synthase")
(:CREATION-DATE 2955043943)
(:CREATOR |mriley|) )
NIL)
(2.7.1.121-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-3981)
(:CREATOR |caspi|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3307473346)
(COMMON-NAME "Phosphoenolpyruvate--glycerone phosphotransferase")
(EC-NUMBER "2.7.1.121")
(RIGHT DIHYDROXY-ACETONE-PHOSPHATE PYRUVATE)
(LEFT DIHYDROXYACETONE PHOSPHO-ENOL-PYRUVATE) )
NIL)
(2.7.1.148-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(IN-PATHWAY NONMEVIPP-PWY)
(ENZYMATIC-REACTION ENZRXN0-273)
(:CREATOR |keseler|)
(:CREATION-DATE 3335543820)
(COMMON-NAME "4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase")
(SYNONYMS "4-diphosphocytidyl-2-C-methyl-D-erythritol kinase" "CDP-ME kinase"
"CMK")
(LEFT 4-CYTIDINE-5-DIPHOSPHO-2-C ATP)
(RIGHT 2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET ADP)
(EC-NUMBER "2.7.1.148")
(OFFICIAL-EC? T)
(BALANCE-STATE :BALANCED) )
NIL)
(2.7.7.1-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.7)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(ENZYMATIC-REACTION ENZRXN0-279)
(EC-NUMBER "2.7.7.1")
(COMMON-NAME "NICOTINAMIDE-NUCLEOTIDE-ADENYLYLTRANSFERASE")
(COMMENT "NICOTINATE NUCLEOTIDE CAN ALSO ACT AS ACCEPTOR."
"SEE ALSO EC 2.7.7.18.")
(RIGHT NAD PPI)
(LEFT NICOTINAMIDE_NUCLEOTIDE ATP)
(SYNONYMS "NAD(+) PYROPHOSPHORYLASE") )
NIL)
(2.7.7.60-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.7)
(OFFICIAL-EC? NIL)
(IN-PATHWAY NONMEVIPP-PWY)
(ENZYMATIC-REACTION ENZRXN0-272)
(:CREATOR |keseler|)
(:CREATION-DATE 3335538399)
(COMMON-NAME "2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase")
(SYNONYMS "MEP cytidylyltransferase" "MCT"
"4-diphosphocytidyl-2C-methyl-D-erythritol synthase")
(LEFT 2-C-METHYL-D-ERYTHRITOL-4-PHOSPHATE CTP)
(RIGHT 4-CYTIDINE-5-DIPHOSPHO-2-C PPI)
(EC-NUMBER "2.7.7.60")
(BALANCE-STATE :BALANCED) )
NIL)
(2.7.7.61-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions| EC-2.7.7)
(IN-PATHWAY P2-PWY)
(ENZYMATIC-REACTION ENZRXN0-4141)
(OFFICIAL-EC? T)
(EC-NUMBER "2.7.7.61")
(RIGHT HOLO-CITRATE-LYASE PPI)
(LEFT 2-5-TRIPHOSPHORIBOSYL-3-DEPHOSPHO- APO-CITRATE-LYASE)
(SYNONYMS "2'-(5''-phosphoribosyl)-3'-dephospho-CoA transferase"
"2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate")
(COMMON-NAME "Holo-citrate lyase synthase")
(:CREATOR |caspi|)
(:CREATION-DATE 3309809178) )
NIL)
(2.7.7.8-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.7.7 |RNA-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-5441)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "2.7.7.8")
(COMMON-NAME "POLYRIBONUCLEOTIDE-NUCLEOTIDYLTRANSFERASE")
(COMMENT "ADP, IDP, GDP, UDP AND CDP CAN ACT AS DONORS.")
(RIGHT RNA |Nucleoside-Diphosphates|)
(LEFT RNA |Pi|)
(SYNONYMS "POLYNUCLEOTIDE PHOSPHORYLASE") )
((RIGHT RNA NAME-SLOT N-NAME) (LEFT RNA NAME-SLOT N+1-NAME)))
(2.7.8.2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.8)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2772)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3284158283)
(SYNONYMS "Cholinephosphotransferase"
"1-alkyl-2-acetylglycerol cholinephosphotransferase"
"Alkylacylglycerol cholinephosphotransferase"
"Phosphorylcholine--glyceride transferase")
(COMMON-NAME "Diacylglycerol cholinephosphotransferase")
(EC-NUMBER "2.7.8.2")
(RIGHT PHOSPHATIDYLCHOLINE CMP)
(LEFT DIACYLGLYCEROL CDP-CHOLINE) )
NIL)
(2.7.9.3-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.7.9 |Small-Molecule-Reactions|)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY PWY0-901)
(ENZYMATIC-REACTION ENZRXN0-253)
(OFFICIAL-EC? T)
(SYNONYMS "Selenium donor protein" "Selenophosphate synthase"
"Selenophosphate synthetase")
(COMMON-NAME "Selenide,water dikinase")
(:CREATION-DATE 3051657441)
(:CREATOR |kr|)
(EC-NUMBER "2.7.9.3")
(RIGHT |Pi| SEPO3 AMP)
(LEFT WATER CPD-678 ATP) )
NIL)
(2.8.1.6-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.8.1)
(OFFICIAL-EC? T)
(SYNONYMS "BIOTIN SYNTHASE" "bioB")
(COMMON-NAME "BIOTIN-SYNTHETASE")
(ENZYMATIC-REACTION BIOTIN-SYN-ENZRXN)
(IN-PATHWAY BIOTIN-SYNTHESIS-PWY)
(RIGHT BIOTIN CH33ADO MET)
(LEFT DETHIOBIOTIN S-ADENOSYLMETHIONINE CPD-249)
(EC-NUMBER "2.8.1.6")
(COMMENT "The fourth and final step in the biosynthesis of biotin.
")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin/bioB.template")
(:CREATION-DATE 3000588742)
(:CREATOR |mriley|) )
((RIGHT MET COEFFICIENT 2) (RIGHT CH33ADO COEFFICIENT 2)
(LEFT S-ADENOSYLMETHIONINE COEFFICIENT 2)))
(2.9.1.1-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.9.1 |tRNA-Reactions|)
(IN-PATHWAY PWY0-901)
(ENZYMATIC-REACTION ENZRXN0-1701)
(OFFICIAL-EC? T)
(SYNONYMS "Cysteinyl-tRNA(Sec)-selenium transferase"
"Cysteinyl-tRNA(Sel)-selenium transferase"
"L-selenocysteinyl-tRNA(Sec) synthase"
"L-selenocysteinyl-tRNA(Sel) synthase" "Selenocysteine synthase")
(COMMON-NAME "L-seryl-tRNA(Sec) selenium transferase")
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3051657440)
(:CREATOR |kr|)
(EC-NUMBER "2.9.1.1")
(RIGHT |Pi| WATER |Charged-SEC-tRNAs|)
(LEFT SEPO3 |L-seryl-SEC-tRNAs|) )
NIL)
(|21-Hydroxysteroids| T (
(OCELOT-GFP::PARENTS |Hydroxysteroids|)
(CHEMICAL-FORMULA (C 21) (H 35) (O 1) (R 1))
(STRUCTURE-BONDS (21 22 1) (20 23 1) (19 23 1) (18 21 1) (18 20 1) (17 22 1)
(16 19 1) (15 23 1) (14 22 1) (13 21 1) (13 15 1) (12 20 1) (11 19 1)
(11 12 1) (10 18 1) (9 17 1) (9 10 1) (8 17 1) (7 14 1) (6 8 1) (6 7 1)
(5 16 1) (4 16 1) (3 5 1) (2 23 1) (1 22 1))
(DISPLAY-COORDS-2D (2.4249d0 -3.5d0) (6.0622d0 -5.6d0) (7.3221d0 -8.336d0)
(9.1957d0 -6.2552d0) (6.8895d0 -7.0045d0) (0.0d0 -0.7d0) (0.0d0 -2.1d0)
(1.2124d0 0.0d0) (3.6373d0 0.0d0) (4.8497d0 -0.7d0) (8.2166d0 -3.5d0)
(7.3937d0 -2.3674d0) (3.6373d0 -4.2d0) (1.2124d0 -2.8d0) (4.8497d0 -4.9d0)
(7.8263d0 -5.9641d0) (2.4249d0 -0.7d0) (4.8497d0 -2.1d0)
(7.3937d0 -4.6326d0) (6.0622d0 -2.8d0) (3.6373d0 -2.8d0) (2.4249d0 -2.1d0)
(6.0622d0 -4.2d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 21-hydroxysteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(|23,24-Dihydrocucurbitacins| T (
(OCELOT-GFP::PARENTS |Triterpenes|)
(COMMON-NAME "a 23,24-dihydrocucurbitacin")
(:CREATOR |paley|)
(:CREATION-DATE 3324143238) )
NIL)
(|23-Didehydropyranoses| T (
(OCELOT-GFP::PARENTS |Pyranoses|)
(COMMON-NAME "a 2,3-didehydropyranose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(23-DIHYDROXYBENZOYLSERINE-MULTIMERS NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (8.487d0 -4.2d0) (4.8497d0 -0.7d0) (8.487d0 0.0d0)
(9.6995d0 -2.1d0) (0.0d0 -2.1d0) (2.4249d0 -0.7d0) (2.4249d0 -4.9d0)
(1.2124d0 -4.2d0) (3.6373d0 -4.2d0) (7.2746d0 -0.7d0) (6.0622d0 -2.8d0)
(8.487d0 -2.8d0) (4.8497d0 -2.1d0) (1.2124d0 -2.8d0) (2.4249d0 -2.1d0)
(3.6373d0 -2.8d0) (7.2746d0 -2.1d0))
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1661)
(AROMATIC-RINGS (9 7 8 14 15 16))
(CHEMICAL-FORMULA (C 10) (H 11) (N 1) (O 6))
(MOLECULAR-WEIGHT 241.2d0)
(STRUCTURE-BONDS (16 15 :AROMATIC) (15 14 :AROMATIC) (13 16 1) (12 17 1)
(17 11 1 :DOWN) (11 13 1) (10 17 1) (9 16 :AROMATIC) (14 8 :AROMATIC)
(7 9 :AROMATIC) (8 7 :AROMATIC) (6 15 1) (5 14 1) (4 12 1) (3 10 1) (2 13 2)
(1 12 2))
(STRUCTURE-ATOMS O O O O O O C C C C N C C C C C C)
(SYNONYMS "N-(2,3-dihydroxybenzoyl)-L-serine"
"2-(2,3-dihydroxybenzoyl)amino-3-hydroxy-propanoic acid")
(COMMON-NAME "2,3-dihydroxybenzoylserine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3275232387) )
NIL)
(23-DIMERCAPTOPROPAN-1-OL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(ACTIVATORS-UNKMECH-OF DIAMINOPIMDECARB-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979849)
(COMMON-NAME "2,3-dimercaptopropan-1-ol") )
NIL)
(23-PENTANEDIONE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF THREODEHYD-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979816)
(COMMON-NAME "2,3-pentane-dione") )
NIL)
(|23S-rRNA-5-Methyl-Uridines| T (
(OCELOT-GFP::PARENTS |23S-rRNAs|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-981)
(COMMON-NAME "5-methyluridine-modified 23S ribosomal RNA")
(SYNONYMS "a 23S-rRNA 5-methyluridine" "23S-rRNA 5-methyluridine"
"5-methyluridine-modified 23S ribosomal RNA")
(COMMENT
"This compound class stands for generic and unspecified 23S-rRNA 5-methyluridines.")
(:CREATOR |kr|)
(:CREATION-DATE 3266271850) )
NIL)
(|23S-rRNA-Methyl-G2251s| T (
(OCELOT-GFP::PARENTS |23S-rRNAs|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1361)
(SYNONYMS "23S-rRNA methyl G2251"
"23S ribosomal RNA methylated at position G2251")
(COMMENT
"This compound class stands for generic and unspecified 23S-rRNAs with the guanine at position 2251 methylated.")
(:CREATOR |kr|)
(:CREATION-DATE 3266271874) )
NIL)
(|23S-rRNAs| T (
(OCELOT-GFP::PARENTS |rRNAs|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-981 RXN0-1361)
(SYNONYMS "23S ribosomal RNA")
(:CREATOR |kr|)
(:CREATION-DATE 3266259246) )
NIL)
(246-TRINITROBENZENE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF CHORISMATEMUT2-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979846)
(COMMON-NAME "246-trinitrobenzene")
(STRUCTURE-ATOMS O O O O O O C C C C C C N N N)
(DISPLAY-COORDS-2D (0.0d0 -4.2d0) (1.2124d0 -6.3d0) (4.8497d0 0.0d0)
(2.4249d0 0.0d0) (6.0622d0 -6.3d0) (7.2746d0 -4.2d0) (2.4249d0 -2.8d0)
(3.6373d0 -4.9d0) (4.8497d0 -2.8d0) (2.4249d0 -4.2d0) (3.6373d0 -2.1d0)
(4.8497d0 -4.2d0) (1.2124d0 -4.9d0) (3.6373d0 -0.7d0) (6.0622d0 -4.9d0))
(STRUCTURE-BONDS (12 15 1) (11 14 1) (10 13 1) (12 9 :AROMATIC)
(9 11 :AROMATIC) (8 12 :AROMATIC) (10 8 :AROMATIC) (11 7 :AROMATIC)
(7 10 :AROMATIC) (6 15 2) (5 15 2) (4 14 2) (3 14 2) (2 13 2) (1 13 2))
(CHEMICAL-FORMULA (C 6) (H 3) (N 3) (O 6))
(MOLECULAR-WEIGHT 213.106d0)
(AROMATIC-RINGS (7 11 9 12 8 10)) )
NIL)
(25-DIDEHYDRO-D-GLUCONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF 1.1.1.274-RXN YIAE1-RXN)
(:CREATOR |keseler|)
(:CREATION-DATE 3332776401)
(COMMON-NAME "2,5-didehydro-D-gluconate")
(SYNONYMS "2,5-diketo-D-gluconate" "2,5-diketogluconic acid"
"2-dehydro-L-idonate")
(DBLINKS (LIGAND-CPD "C02780" NIL |kr| 3346617699 NIL NIL)
(PUBCHEM "102287" NIL |hopkinso| 3317071514 NIL NIL))
(STRUCTURE-ATOMS C C C O C O C O C O O O O)
(DISPLAY-COORDS-2D (4.2365d0 0.2063d0) (4.9509d0 -0.2063d0)
(3.522d0 -0.2063d0) (4.2365d0 1.0313d0) (5.6655d0 0.2063d0)
(4.9509d0 -1.0313d0) (2.8075d0 0.2063d0) (3.522d0 -1.0313d0)
(6.3799d0 -0.2063d0) (5.6655d0 1.0313d0) (2.093d0 -0.2063d0)
(2.8075d0 1.0313d0) (7.0944d0 0.2063d0))
(STRUCTURE-BONDS (9 13 1) (7 12 2) (7 11 1) (5 10 2) (5 9 1) (3 8 2) (3 7 1)
(2 6 1 :DOWN) (2 5 1) (1 4 1 :DOWN) (1 3 1) (1 2 1))
(COMMENT-INTERNAL "This structure was imported from PubChem on Feb-15-2005")
(CHEMICAL-FORMULA (C 6) (H 8) (O 7))
(MOLECULAR-WEIGHT 192.125d0) )
NIL)
(2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C11453" NIL |kr| 3346617700 NIL NIL))
(DISPLAY-COORDS-2D (0.0d0 -3.5627d0) (6.711d0 -2.9577d0) (2.8344d0 -4.123d0)
(0.0d0 0.0d0) (2.0727d0 0.0d0) (6.4643d0 -1.4567d0) (3.9099d0 -4.0111d0)
(0.0d0 -1.1764d0) (3.2041d0 -1.9383d0) (4.3021d0 -1.1764d0)
(1.9494d0 -3.4733d0) (4.7838d0 -3.4844d0) (2.0727d0 -1.1764d0)
(0.885d0 -2.4536d0) (5.7699d0 -2.4536d0) (3.2491d0 -2.9577d0))
(CHEMICAL-FORMULA (C 5) (H 12) (O 9) (P 2))
(MOLECULAR-WEIGHT 278.092d0)
(STRUCTURE-BONDS (13 14 1) (12 16 1) (12 15 1) (11 16 1) (14 11 1 :DOWN)
(10 15 1) (9 13 1) (9 10 1) (8 14 1) (7 16 1) (6 15 1) (13 5 1 :UP) (4 8 1)
(3 16 2) (2 15 2) (14 1 1 :UP))
(STRUCTURE-ATOMS C O O O O O O C C O O O C C P P)
(SYNONYMS "ME-2,4cPP")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-882 RXN0-302)
(COMMON-NAME "2-C-methyl-D-erythritol-2,4-cyclodiphosphate")
(:CREATOR |ptoole|)
(:CREATION-DATE 3165665656) )
NIL)
(|2Comp-Pathways| T (
(OCELOT-GFP::PARENTS |Pathways|)
(SCHEMA? T)
(COMMON-NAME "Signal transduction pathways") )
NIL)
(|2Comp-Reactions| T (
(OCELOT-GFP::PARENTS |Reactions|)
(COMMENT "Delete this class during/after 10.5 release.")
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(2K-4CH3-PENTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF 2-ISOPROPYLMALATESYN-ENZRXN)
(APPEARS-IN-RIGHT-SIDE-OF RXN-7800 BRANCHED-CHAINAMINOTRANSFERLEU-RXN)
(DBLINKS (LIGAND-CPD "C00233" NIL |kr| 3346617700 NIL NIL) (CAS "816-66-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -110.1d0)
(COMMON-NAME "2-ketoisocaproate")
(MOLECULAR-WEIGHT 130.143d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 3))
(DISPLAY-COORDS-2D (-0.59511d0 -1.0d0) (-1.0d0 -0.35428d0)
(0.58464d0 -0.32984d0) (0.99651d0 -0.51483d0) (-0.26003d0 -0.32984d0)
(0.17976d0 -0.53578d0) (-0.59511d0 -0.54974d0) (0.58464d0 0.12042d0)
(0.17976d0 -0.98604d0))
(STRUCTURE-BONDS (9 6 2) (8 3 2) (7 5 1) (6 3 1) (5 6 1) (4 3 1) (2 7 1)
(1 7 1))
(STRUCTURE-ATOMS C C C O C C C O O)
(SYSTEMATIC-NAME "4-methyl-2-oxopentanoic acid")
(SYNONYMS "2-keto-4-methyl-pentanoate" "2-oxoisocaproate"
"4-methyl-2-oxopentanoate" "2-oxo-4-methylpentanoate"
"α-ketoisocaproate" "α-oxoisocaproate") )
((GIBBS-0 -110.1d0 CITATIONS "GibbsGroups97")))
(2K-ADIPATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |krieger|)
(DBLINKS (CAS "3184-35-8"))
(:CREATION-DATE 3287421572)
(GIBBS-0 -189.7d0)
(COMMON-NAME "α-ketoadipate")
(MOLECULAR-WEIGHT 160.126d0)
(CHEMICAL-FORMULA (C 6) (H 8) (O 5))
(DISPLAY-COORDS-2D (0.1505d0 -0.63545d0) (0.42475d0 -0.46488d0)
(-0.42809d0 -0.69231d0) (0.99666d0 -0.41472d0) (-0.73913d0 -0.5786d0)
(-0.15719d0 -0.52174d0) (-0.7893d0 -0.27425d0) (0.73579d0 -0.57525d0)
(-0.42809d0 -1.0d0) (0.77926d0 -0.8796d0) (-1.0d0 -0.74247d0))
(STRUCTURE-BONDS (11 5 1) (10 8 1) (8 2 1) (7 5 2) (6 3 1) (4 8 2) (3 5 1)
(3 9 2) (2 1 1) (1 6 1))
(STRUCTURE-ATOMS C C C O C C O C O O O)
(SYNONYMS "2-ketoadipate" "2-oxoadipate" "2-keto-adipate"
"2-oxohexanedionic acid") )
NIL)
(2OXOGLUTARATEDEH-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3083514383)
(CATALYZES 2OXOGLUTARATEDEH-ENZRXN)
(CITATIONS "[89076356]" "[83234434]" "[90233608]")
(COMPONENTS |E1(O)| |E2(O)| E3-CPLX)
(COMMENT "One of the most complicated enzyme systems known.
A complex composed of multiple copies of 3 enzymes- E1, E2 and E3.
The E3 component is shared with the pyruvate dehydrogenase and glycine cleavage
multi-enzyme complexes. E1
and E2 differ slightly for 2oxoglutarate and pyruvate complexes,
designated (o) and (p) to distinguish them.
Substrate is channeled through the catalytic reactions by attachment
in thioester linkage to lipoyl groups via so-called 'swinging arm',
carrying substrate molecules to successive active sites.")
(:CREATOR |mriley|) )
((COMPONENTS |E1(O)| COEFFICIENT 1) (COMPONENTS |E2(O)| COEFFICIENT 1)
(COMPONENTS E3-CPLX COEFFICIENT 1)))
(2OXOGLUTARATEDEH-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3108927635)
(PROSTHETIC-GROUPS FAD THIAMINE-PYROPHOSPHATE)
(COFACTORS MG+2)
(SYNONYMS "α ketoglutarate dehydrogenase complex")
(COMMON-NAME "2-oxoglutarate dehydrogenase complex")
(REACTION 2OXOGLUTARATEDEH-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[89076356]" "[83234434]" "[90233608]"
"[ReedAccChemRes7-40(74) ]")
(COMMENT "Similar in enzyme composition and complex reactions to
pyruvate dehydrogenase reactions.
SUBREACTIONS:
E1(o) + TPP = E1(o).TPP
E1(o).TPP + succinate = E1(o).hydroxycarboxypropylTPP + CO(2)
E1(o).hydroxycarboxypropylTPP + E2(o).lipoate(S2) = E1(o).TPP + E2(o).lipoate(SH)(S-succinyl)
E2(o).lipoate(SH)(S-succinyl) + CoA = E2(o).lip(SH)2 + succinylCoA E3 + FAD = E3.FAD
E3.FAD + E2(o).lip(SH)2 = E3.FADH(2) + E2(o).lip(S)2
E3.FADH(2) + NAD(+) = E3.FAD + NADH + H(+)")
(ENZYME 2OXOGLUTARATEDEH-CPLX)
(:CREATOR |mriley|) )
NIL)
(2OXOGLUTARATEDEH-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3053895482)
(IN-PATHWAY TCA)
(ENZYMATIC-REACTION 2OXOGLUTARATEDEH-ENZRXN)
(RIGHT SUC-COA CARBON-DIOXIDE NADH)
(LEFT 2-KETOGLUTARATE CO-A NAD)
(DELTAG0 -7.2d0)
(SYNONYMS "2-oxoglutarate dehydrogenation"
"α-ketoglutarate oxidative decarboxylation")
(:CREATOR |mriley|) )
((DELTAG0 -7.2d0 CITATIONS "[stryer88]")))
(2PGADEHYDRAT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PH-OPT 8.1d0)
(INHIBITORS-UNKMECH F-)
(COFACTORS MG+2)
(SYNONYMS "phosphopyruvate hydratase" "2-phosphoglycerate dehydratase"
"2,3-diphospho-D-glycerate" "2-phospho-D glycerate phosphotransferase"
"2-phospho-D-glycerate hydrolyase")
(COMMON-NAME "enolase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 2PGADEHYDRAT-RXN)
(CITATIONS "72060411" ":EV-EXP:3277835750:pkarp")
(COFACTOR-BINDING-COMMENT "Magnesium is required for catalysis and
stabilizing the dimer. There is an absolute dependence on divalent
cations for activity.|CITS:[72060411]|")
(ENZYME ENOLASE-CPLX)
(:CREATION-DATE 2945288050)
(:CREATOR |mriley|) )
((PH-OPT 8.1d0 CITATIONS "72060411") (COFACTORS MG+2 CITATIONS "72060411")
(INHIBITORS-UNKMECH F- CITATIONS "72060411")))
(2PGADEHYDRAT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLYCOLYSIS ANARESP1-PWY GLUCONEO-PWY)
(ENZYMATIC-REACTION 2PGADEHYDRAT-ENZRXN)
(SYNONYMS "ENOLASE" "2-PHOSPHOGLYCERATE DEHYDRATASE")
(RIGHT PHOSPHO-ENOL-PYRUVATE WATER)
(LEFT 2-PG)
(DELTAG0 0.4d0)
(EC-NUMBER "4.2.1.11")
(COMMON-NAME "2-phosphoglycerate dehydration")
(:CREATION-DATE 2945288050)
(:CREATOR |mriley|) )
NIL)
(2PHENDEG-PWY NIL (
(OCELOT-GFP::PARENTS AMINE-DEG AROMATIC-COMPOUNDS-DEGRADATION)
(PATHWAY-LINKS (PHENYLACETATE PWY0-321))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3077535747)
(REACTION-LIST PHENDEHYD-RXN AMINEPHEN-RXN)
(PREDECESSORS (PHENDEHYD-RXN AMINEPHEN-RXN))
(NET-REACTION-EQUATION
"phenylethylamine + O2 + 2 H2O + NAD+ = phenylacetate + NH3 + H2O2 + NADH")
(COMMENT
"Through a two-step process, E. coli is able to use 2-phenylethylamine as a sole
carbon and energy source.")
(COMMON-NAME "phenylethylamine degradation") )
NIL)
(2R-HYDROPEROXY-FATTY-ACIDS T (
(OCELOT-GFP::PARENTS |Fatty-Acids|)
(COMMENT
"This class of compounds, found as intermediates of fatty acid alpha-oxidation, is chemically unstable. The compounds are quickly turned over to alpha-oxidation products.|CITS: [10455113]|")
(CHEMICAL-FORMULA (C 2) (H 3) (O 4) (R 1))
(DISPLAY-COORDS-2D (1.4341d0 -4.6638d0) (3.7685d0 0.0d0) (0.0d0 -2.1164d0)
(3.8774d0 -2.9562d0) (2.5658d0 -0.7166d0) (1.4341d0 -2.9562d0)
(2.585d0 -2.1164d0))
(STRUCTURE-BONDS (6 7 1) (5 7 1) (4 7 1) (3 6 1) (2 5 1) (1 6 2))
(STRUCTURE-ATOMS O O O R O C C)
(COMMON-NAME "a 2(R)-hydroperoxy fatty acid")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|2R-hydroxy-carboxylates| T (
(OCELOT-GFP::PARENTS |2-Hydroxy-carboxylates|)
(COMMON-NAME "a (2R)-hydroxy-carboxylate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(2R-HYDROXY-FATTY-ACIDS T (
(OCELOT-GFP::PARENTS |Fatty-Acids|)
(CHEMICAL-FORMULA (C 2) (H 3) (O 3) (R 1))
(DISPLAY-COORDS-2D (-0.26213592d0 -0.12135923d0) (0.33009708d0 0.6796117d0)
(-1.0d0 0.31067967d0) (-0.26213592d0 -1.0d0) (0.9951457d0 -0.12135923d0)
(0.33009708d0 0.31067967d0))
(STRUCTURE-BONDS (6 2 1) (6 5 1) (4 1 2) (3 1 1) (1 6 1))
(STRUCTURE-ATOMS C O O O R C)
(COMMON-NAME "a 2(R)-hydroxy fatty acid")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(2TRANSKETO-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.2.1)
(EC-NUMBER "2.2.1.1")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY NONOXIPENT-PWY)
(ENZYMATIC-REACTION ENZRXN0-1881 TRANSKETOI-ENZRXN)
(RIGHT FRUCTOSE-6P GAP)
(LEFT ERYTHROSE-4P XYLULOSE-5-PHOSPHATE)
(:CREATION-DATE 2974477015)
(:CREATOR |mriley|) )
NIL)
(3-5-ADP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(HISTORY |kr-3290870141|)
(APPEARS-IN-RIGHT-SIDE-OF ENTDB-RXN ENTD-RXN)
(:CREATION-DATE 3111868695)
(:CREATOR |kr|)
(COMMON-NAME "3',5'-ADP")
(AROMATIC-RINGS (5 8 7 10 6) (2 3 6 5 4 1))
(MOLECULAR-WEIGHT 427.203d0)
(CHEMICAL-FORMULA (C 10) (H 15) (N 5) (O 10) (P 2))
(STRUCTURE-BONDS (18 27 1) (22 24 1) (24 26 2) (24 25 1) (23 24 1)
(15 22 1 :DOWN) (14 21 1 :DOWN) (18 20 2) (18 19 1) (12 18 1) (13 10 1 :UP)
(17 12 1) (16 17 1 :UP) (13 14 1) (15 14 1) (11 13 1) (16 15 1) (16 11 1)
(4 9 1) (6 10 :AROMATIC) (8 5 :AROMATIC) (7 8 :AROMATIC) (10 7 :AROMATIC)
(5 6 :AROMATIC) (4 5 :AROMATIC) (6 3 :AROMATIC) (3 2 :AROMATIC)
(2 1 :AROMATIC) (1 4 :AROMATIC))
(DISPLAY-COORDS-2D (2.1291d0 -0.2667d0) (2.1291d0 0.4916d0)
(2.7787d0 0.875d0) (2.7787d0 -0.6417d0) (3.4365d0 -0.2667d0)
(3.4365d0 0.4916d0) (4.7492d0 -0.2667d0) (4.0928d0 -0.6482d0)
(2.7766d0 -1.3917d0) (4.7476d0 0.4916d0) (3.8163d0 1.3461d0)
(1.4779d0 2.0478d0) (4.4365d0 1.7946d0) (4.2094d0 2.4992d0)
(3.4439d0 2.4992d0) (3.2058d0 1.7836d0) (2.5035d0 1.5628d0)
(0.2813d0 2.0614d0) (0.2866d0 1.3032d0) (-0.4729d0 2.0485d0)
(4.6509d0 3.1055d0) (3.0595d0 3.0367d0) (2.3196d0 2.3185d0)
(2.2615d0 3.0316d0) (1.5284d0 3.05d0) (2.2558d0 3.7858d0) (0.275d0 2.8833d0))
(STRUCTURE-ATOMS N C N C C C C N N N O O C C C C C P O O O O O P O O O) )
NIL)
(|3-Acyl-pyruvates| T (
(OCELOT-GFP::PARENTS |Carbohydrates|)
(CHEMICAL-FORMULA (C 4) (H 3) (O 4) (R1 1))
(STRUCTURE-BONDS (7 9 1) (6 9 1) (6 8 1) (5 8 1) (4 7 1) (3 9 2) (2 8 2)
(1 7 2))
(DISPLAY-COORDS-2D (3.5724d0 -1.2375d0) (0.7145d0 -2.0625d0)
(2.1435d0 -2.0625d0) (2.8579d0 0.0d0) (0.0d0 -0.825d0) (1.4289d0 -0.825d0)
(2.8579d0 -0.825d0) (0.7145d0 -1.2375d0) (2.1435d0 -1.2375d0))
(STRUCTURE-ATOMS O O O O R1 C C C C)
(COMMON-NAME "a 3-acylpyruvate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|3-Acylglycero-Phosphocholines| T (
(OCELOT-GFP::PARENTS |Lysolecithins|)
(DISPLAY-COORDS-2D (6.3584d0 -0.825d0) (7.1834d0 -1.65d0) (6.3584d0 -2.475d0)
(1.1667d0 -3.8834d0) (3.0584d0 -2.475d0) (0.5834d0 0.0d0)
(3.0584d0 -0.825d0) (0.0d0 -3.8834d0) (0.5834d0 -0.825d0) (4.7084d0 -1.65d0)
(1.4084d0 -1.65d0) (5.5334d0 -1.65d0) (3.8834d0 -1.65d0) (2.2334d0 -1.65d0)
(0.5834d0 -2.475d0) (0.5834d0 -3.3d0) (0.5834d0 -1.65d0) (6.3584d0 -1.65d0)
(3.0584d0 -1.65d0))
(COMMON-NAME "a 3-lysophosphatidylcholine")
(CHEMICAL-FORMULA (C 9) (H 20) (N 1) (O 7) (R1 1) (P 1))
(ATOM-CHARGES (18 1))
(SYNONYMS "a 3-lysolecithin" "a L-3-lysolecithin")
(STRUCTURE-BONDS (15 17 1) (15 16 1) (14 19 1) (13 19 1) (12 18 1) (11 17 1)
(11 14 1) (10 13 1) (10 12 1) (9 17 1) (8 16 1) (7 19 1) (6 9 1) (5 19 2)
(4 16 2) (3 18 1) (2 18 1) (1 18 1))
(STRUCTURE-ATOMS C C C O O O O R1 C C C C O O O C C N P)
(SCHEMA? T)
(NAMES "L-3-lysolecithin" "3-lysolecithin")
(:CREATOR |kr|)
(:CREATION-DATE 3267207961) )
NIL)
(|3-Alpha-Mannosyl-Heteroglycans| T (
(OCELOT-GFP::PARENTS |Heteroglycans|)
(COMMON-NAME "3-(alpha-D-mannosyl)-heteroglycan")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(3-AMINO-12-PROPANEDIOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "3-amino-1,2-propanediol")
(:CREATOR |keseler|)
(:CREATION-DATE 3339858587) )
NIL)
(|3-Beta-Hydroxysterol-Esters| T (
(OCELOT-GFP::PARENTS |Steryl-Esters|)
(CHEMICAL-FORMULA (C 19) (H 30) (O 1) (R1 2))
(STRUCTURE-BONDS (18 20 1) (17 19 1) (16 18 1) (16 17 1) (15 20 1) (14 19 1)
(12 15 1) (12 13 1) (11 19 1) (10 20 1) (9 18 1) (9 11 1) (8 17 1) (7 16 1)
(6 13 1) (6 10 1) (5 15 1) (5 7 1) (4 14 1) (4 8 1) (3 14 1) (13 21 1 :UP)
(2 20 1) (1 19 1) (21 22 1))
(DISPLAY-COORDS-2D (4.2868d0 -3.3001d0) (2.1433d0 -2.0626d0)
(5.3262d0 -3.5146d0) (5.5562d0 -2.0625d0) (2.8577d0 0.0d0)
(0.7144d0 -1.2376d0) (3.5722d0 -0.4125d0) (5.0713d0 -1.3951d0)
(2.8577d0 -2.4751d0) (1.4289d0 -1.6501d0) (3.5722d0 -2.8876d0)
(1.4289d0 0.0d0) (0.7144d0 -0.4125d0) (5.0713d0 -2.73d0)
(2.1433d0 -0.4125d0) (3.5722d0 -1.2376d0) (4.2868d0 -1.6501d0)
(2.8577d0 -1.6501d0) (4.2868d0 -2.4751d0) (2.1433d0 -1.2376d0) (0.0d0 0.0d0)
(-0.7145d0 -0.4125d0))
(STRUCTURE-ATOMS C C R1 C C C C C C C C C C C C C C C C C O R1)
(COMMON-NAME "a 3-β-hydroxysterol ester")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(|3-Beta-Hydroxysterols| T (
(OCELOT-GFP::PARENTS |Sterols|)
(CHEMICAL-FORMULA (C 19) (H 31) (O 1) (R1 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(13 16 1) (13 14 1) (12 20 1) (11 21 1) (10 19 1) (10 12 1) (9 18 1)
(8 17 1) (7 14 1) (7 11 1) (6 16 1) (6 8 1) (5 15 1) (5 9 1) (4 15 1)
(14 3 1 :UP) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (7.2745d0 -5.6001d0) (3.6372d0 -3.5001d0) (0.0d0 0.0d0)
(9.0384d0 -5.9641d0) (9.4287d0 -3.5d0) (4.8495d0 0.0d0) (1.2123d0 -2.1001d0)
(6.062d0 -0.7d0) (8.6059d0 -2.3674d0) (4.8495d0 -4.2001d0)
(2.4248d0 -2.8001d0) (6.062d0 -4.9001d0) (2.4248d0 0.0d0) (1.2123d0 -0.7d0)
(8.6059d0 -4.6327d0) (3.6372d0 -0.7d0) (6.062d0 -2.1001d0)
(7.2745d0 -2.8001d0) (4.8495d0 -2.8001d0) (7.2745d0 -4.2001d0)
(3.6372d0 -2.1001d0))
(STRUCTURE-ATOMS C C O R1 C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-β-hydroxysterol")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(3-BROMOPYRUVATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF PYRUVATEDEH-ENZRXN)
(INHIBITORS-UNKMECH-OF 4OH2OXOGLUTARALDOL-ENZRXN ENZRXN0-1521
GMP-SYN-GLUT-ENZRXN DIHYDRODIPICSYN-ENZRXN
3-P-SHIK-1-CARBOXYVINYLXFERASE-ENZRXN PYRUVATEDECARB-ENZRXN)
(DISPLAY-COORDS-2D (4.1128d0 0.0d0) (1.3145d0 -0.0977d0) (4.1974d0 -2.4233d0)
(0.0d0 -2.57d0) (1.3991d0 -2.5211d0) (3.4556d0 -1.2361d0)
(2.0564d0 -1.285d0))
(CHEMICAL-FORMULA (C 3) (H 3) (O 3) (BR 1))
(MOLECULAR-WEIGHT 166.959d0)
(STRUCTURE-BONDS (6 7 1) (5 7 1) (4 5 1) (3 6 1) (2 7 2) (1 6 2))
(STRUCTURE-ATOMS O O O BR C C C)
(SYNONYMS "bromopyruvate" "3-bromopyruvic acid" "bromopyruvic acid"
"3-bromo-2-oxopropanoic acid")
(COMMON-NAME "3-bromopyruvate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3263219137) )
NIL)
(3-CARBOXY-3-HYDROXY-ISOCAPROATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF 2-ISOPROPYLMALATESYN-RXN)
(DBLINKS (LIGAND-CPD "C02504" NIL |kr| 3346617700 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -198.2d0)
(APPEARS-IN-LEFT-SIDE-OF 3-ISOPROPYLMALISOM-RXN)
(MOLECULAR-WEIGHT 176.169d0)
(CHEMICAL-FORMULA (C 7) (H 12) (O 5))
(DISPLAY-COORDS-2D (-0.19934d0 -0.77265d0) (0.11038d0 0.46952d0)
(-0.19934d0 -0.31466d0) (0.59802d0 0.14333d0) (0.59802d0 -0.31466d0)
(0.19934d0 -0.54201d0) (0.99671d0 -0.54201d0) (-0.60132d0 -0.54201d0)
(-0.19934d0 0.13015d0) (-0.60132d0 -1.0d0) (-1.0d0 -0.31137d0)
(-0.55519d0 0.4168d0))
(STRUCTURE-BONDS (12 9 2) (11 8 1) (10 8 1) (9 3 1) (8 3 1) (7 5 1) (6 3 1)
(5 6 1) (4 5 2) (2 9 1) (1 3 1))
(STRUCTURE-ATOMS O O C O C C O C C C C O)
(COMMON-NAME "2-isopropylmalate")
(SYNONYMS "3-hydroxy-4-methyl-3-carboxypentanoate"
"3-carboxy-3-hydroxy-4-methylpentanoate" "3-carboxy-3-hydroxy-isocaproate"
"α-isopropylmalate" "(2S)-2-isopropylmalate") )
((GIBBS-0 -198.2d0 CITATIONS "GibbsGroups97")))
(3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P31057" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02548" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414676" NIL NIL NIL NIL NIL)
(UNIPROT "P31057" NIL NIL |ouzounis| 3027899498))
(COMPONENT-OF 3-METHYL-2-OXOBUT-OHCH3XFER-CPLX)
(PI 5.37d0)
(MOLECULAR-WEIGHT-SEQ 28.237402999999983d0)
(GENE EG11675)
(SYNONYMS "B0134" "PanB" "α-ketoisovalerate hydroxymethyltransferase"
"dehydropantoate hydroxymethyltransferase"
"ketopantoate hydroxymethyltransferase"
"5,10-methylenetetrahydrofolate:3-methyl-2-oxobutanoate hydroxymethyltransferase")
(COMMON-NAME "3-methyl-2-oxobutanoate hydroxymethyltransferase monomer")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/panB.template")
(:CREATION-DATE 3000590637)
(:CREATOR |mriley|) )
NIL)
(3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.1.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 3-METHYL-2-OXOBUT-OHCH3XFER-ENZRXN)
(IN-PATHWAY PANTO-PWY)
(RIGHT 2-DEHYDROPANTOATE THF)
(LEFT WATER 2-KETO-ISOVALERATE METHYLENE-THF)
(EC-NUMBER "2.1.2.11")
(COMMENT "This is the first reaction of the pantothenate biosynthesis
pathway.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/panB.template")
(:CREATION-DATE 3000590637)
(:CREATOR |mriley|) )
NIL)
(3-CHLORO-D-ALANINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (2.6732d0 1.6118d0) (2.681d0 0.7583d0) (3.3996d0 0.5115d0)
(3.3996d0 -0.2368d0) (2.0504d0 0.3324d0) (4.01d0 0.9473d0)
(2.0115d0 -0.3699d0))
(CHEMICAL-FORMULA (C 3) (H 6) (N 1) (O 2) (CL 1))
(MOLECULAR-WEIGHT 123.539d0)
(STRUCTURE-BONDS (5 7 1) (3 6 1) (2 5 1) (3 4 2) (2 3 1) (2 1 1 :DOWN))
(STRUCTURE-ATOMS N C C O C O CL)
(APPEARS-IN-LEFT-SIDE-OF ALADEHYDCHLORO-RXN)
(COMMON-NAME "3-chloro-D-alanine") )
NIL)
(3-DEHYDRO-SHIKIMATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (CAS "10457-99-5" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C02637" NIL |kr| 3346617701 NIL NIL) (CAS "2922-42-1"))
(:CREATION-DATE 3056125303)
(SYNONYMS "3-dehydroshikimic acid" "5-dehydroshikimic acid"
"5-dehydroshikimate")
(COMMENT-INTERNAL
"kr98-07-30: inverted the 5 hydroxyl to point to the other side, so that it is now the same as Ligand cpd C02637 and the Boehringer chart.")
(MOLECULAR-WEIGHT 172.137d0)
(CHEMICAL-FORMULA (C 7) (H 8) (O 5))
(DISPLAY-COORDS-2D (-1.0d0 -0.047619045d0) (0.012987018d0 -1.0d0)
(0.012987018d0 -0.7431457d0) (-0.65945166d0 -1.0d0) (-1.0d0 -0.5526695d0)
(0.012987018d0 0.41125536d0) (-0.65945166d0 -0.49206352d0)
(-0.65367967d0 0.4430014d0) (-1.0d0 -0.30158728d0)
(0.3708514d0 -0.30158728d0) (0.99711394d0 0.047619104d0)
(0.012987018d0 -0.49206352d0) (0.93650794d0 -0.6969697d0)
(0.012987018d0 0.16305912d0) (-0.65945166d0 0.16305912d0)
(-0.65945166d0 -0.7431457d0) (0.76911974d0 -0.30158728d0))
(STRUCTURE-BONDS (17 10 1) (16 3 1) (15 9 1) (15 14 1) (14 10 2) (13 17 1)
(12 3 1) (11 17 2) (10 3 1) (9 16 1) (8 15 2) (7 16 1) (6 14 1) (5 9 1)
(4 16 1) (2 3 1) (1 9 1))
(STRUCTURE-ATOMS H H C H O H O O C C O H O C C C C)
(APPEARS-IN-RIGHT-SIDE-OF SHIKIMATE-5-DEHYDROGENASE-RXN
3-DEHYDROQUINATE-DEHYDRATASE-RXN)
(GIBBS-0 -167.5d0)
(:CREATOR |pkarp|)
(COMMON-NAME "3-dehydro-shikimate") )
NIL)
(|3-Dehydropyranoses| T (
(OCELOT-GFP::PARENTS |Pyranoses|)
(COMMON-NAME "a 3-dehydropyranose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(|3-Dehydropyranosides| T (
(OCELOT-GFP::PARENTS |Pyranosides|)
(COMMON-NAME "a 3-dehydropyranoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(3-DEHYDROQUINATE-DEHYDRATASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(SYNONYMS "3-dehydroquinase" "DHQ dehydratase")
(COMMON-NAME "3-dehydroquinate dehydratase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-DEHYDROQUINATE-DEHYDRATASE-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[87099996]" "[81261964]")
(COMMENT "The enzyme is mechanistically and structurally very similar
to the biosynthetic 3-dehydroquinase component of the arom
multifunctional enzyme of N. crassa. It is known that the mechanism of
the reaction catalyzed by the enzyme involves a covalent interaction
between the substrate 3-dehydroquinate and a lysine residue, but the
precise location of this lysine residue and the histidine residue, also
implicated in the active site, remains to be established
|CITS:[87099996]| The first step of the 3-dehydroquinase reaction
involves the formation of an imine intermediate between the keto group
of 3-dehydroquinate and the e-amino group of a lysine at the active
site of the enzyme. In addition to the lysine side chain involved in
imine formation, the enzyme also requires a basic group for proton
abstraction. The pH activity studies, demonstrate that both
the coli and N. crassa 3-dehydroquinases require groups with pKa
values near to 6, in a deprotonated from, for maximal activity.
Experiments with diethylpyrocarbonate provide evidence that for both
enzymes this group is the imidazole side chain of a histidine residue.
|CITS:[87156536]| The reaction exhibits cis stereochemistry in
both directions.")
(ENZYME AROD-CPLX)
(:CREATION-DATE 2955044017)
(:CREATOR |mriley|) )
NIL)
(3-DEHYDROQUINATE-DEHYDRATASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ARO-PWY)
(ENZYMATIC-REACTION 3-DEHYDROQUINATE-DEHYDRATASE-ENZRXN)
(RIGHT WATER 3-DEHYDRO-SHIKIMATE)
(LEFT DEHYDROQUINATE)
(EC-NUMBER "4.2.1.10")
(COMMENT "This is the third step in the shikimate pathway")
(:CREATION-DATE 2955044017)
(:CREATOR |mriley|) )
NIL)
(3-DEHYDROQUINATE-SYNTHASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "2-OXYGEN SUBSTITUTED QUINATES" NAD
"DAHP-2-O-METHYL GLYCOSIDE")
(INHIBITORS-COMPETITIVE "3-deoxy-D-arabino-heptulosonic acid 7-phosphonate"
"beta-(2,6-anhydro-3-deoxy-D-arabino-heptulopyranosid)onate 7-phosphate"
"alpha-(2,6-anhydro-3-deoxy-D-arabino-heptulopyranosid)onate 7-phosphonate"
"alpha-(2,6-anhydro-3-deoxy-D-arabino-heptulopyranosid)onate 7-phosphate")
(COFACTORS CO+2)
(PROSTHETIC-GROUPS NAD)
(SYNONYMS "dehydroquinate synthase" "DHQ synthase")
(COMMON-NAME "3-dehydroquinate synthase")
(REACTION 3-DEHYDROQUINATE-SYNTHASE-RXN)
(CITATIONS ":EV-EXP:3277835749:pkarp" "[78218223]" "[78130088]" "[85023340]"
"[77065807]" "[86192828]")
(COMMENT "Dehydroquinate synthase catalyzes the cyclization of
3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) to
dehydroquinate. In the course of this conversion the synthase
apparently catalyzes an oxidation, a β-elimination, an
intramolecular aldol condensation, and a reduction
|CITS:[78218223],[85023340]| A
common feature of the DHQ synthase activities of N. crassa and coli is
a catalytic requirement for NAD+. The enzyme was shown to require
catalytic amounts of NAD and Co2+. |CITS:[78218223]|
In the formation of DHQ, a methyl group is
never formed at C-7, and the cyclization step involves an interaction
between the enol formed in phosphate elimination and the carbonyl at
C-2 in an aldolase-type reaction. Kinetic isotope effects were observed
at C-5, supporting a mechanism involving oxidation at C-5 by NAD. The
finding that all the tritium of labeled DAHP is conserved in DHQ
establishes that hydride transfer involved in the subsequent reduction
of C-5 uses the same hydrogen atom as was taken from DAHP. NADH is
enzyme bound and reduces the keto group at C-5 with the regeneration of
NAD.|CITS: [ColiSalII]|")
(ENZYME AROB-MONOMER)
(:CREATION-DATE 2955043970)
(:CREATOR |mriley|) )
((INHIBITORS-COMPETITIVE :FACET CITATIONS "[JAmChemSoc111-1861]"
"[HandEnzInh]")))
(3-DEHYDROQUINATE-SYNTHASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 3-DEHYDROQUINATE-SYNTHASE-ENZRXN)
(IN-PATHWAY ARO-PWY)
(RIGHT |Pi| DEHYDROQUINATE)
(LEFT 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-P)
(EC-NUMBER "4.2.3.4")
(COMMENT "The hydrogen atoms on C-7 of the substrate are retained on
C-2 of the product . This is the second step in the shikimate pathway")
(:CREATION-DATE 2955043970)
(:CREATOR |mriley|) )
NIL)
(3-DEOXY-D-ARABINO-HEPTULOSONATE-7-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF DAHPSYN-RXN)
(DBLINKS (LIGAND-CPD "C04691" NIL |kr| 3346617700 NIL NIL) (CAS "2627-73-8"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -259.3d0)
(APPEARS-IN-LEFT-SIDE-OF 3-DEHYDROQUINATE-SYNTHASE-RXN)
(MOLECULAR-WEIGHT 288.147d0)
(CHEMICAL-FORMULA (C 7) (H 13) (O 10) (P 1))
(DISPLAY-COORDS-2D (-0.50331d0 0.5d0) (-0.74834d0 -0.25497d0)
(-0.01656d0 -0.75497d0) (-0.74834d0 0.99669d0) (-0.50662d0 -0.75497d0)
(-0.26159d0 -0.75497d0) (-0.74834d0 0.24834d0) (-0.50993d0 -0.25497d0)
(-0.26159d0 -1.0d0) (-1.0d0 -0.00331d0) (-0.74834d0 0.75166d0)
(-0.74834d0 -0.00331d0) (-0.74834d0 0.5d0) (-0.74834d0 -0.50662d0)
(-0.26159d0 -0.50993d0) (-0.50993d0 -0.50662d0) (-0.50331d0 0.75166d0)
(-0.74834d0 -0.75497d0))
(STRUCTURE-BONDS (18 5 1) (17 11 1) (16 14 1) (15 6 2) (14 18 1) (13 7 1)
(12 2 1) (11 13 1) (10 12 1) (9 6 1) (8 2 1) (7 12 1) (5 6 1) (4 11 2)
(3 6 1) (2 14 1) (1 13 2))
(STRUCTURE-ATOMS O C O O O P C O O O C C C C O O O C)
(COMMON-NAME "3-deoxy-D-arabino-heptulosonate-7-phosphate")
(SYNONYMS "3-deoxy-D-arabino-heptulosonate-7-P"
"3-deoxy-arabino-heptulosonate 7-phosphate"
"3-deoxy-arabino-heptulosonate-7-P"
"2-dehydro-3-deoxy-D-arabino-heptonate 7-phosphate"
"3-deoxy-D-arabino-hept-2-ulosonate-7-phosphate"
"3-deoxy-arabino-heptulonate 7-phosphate") )
((GIBBS-0 -259.3d0 CITATIONS "GibbsGroups97")))
(|3-Deoxyoctulosonyl-Lipopolysaccharides| T (
(OCELOT-GFP::PARENTS |Lipopolysaccharides|)
(COMMON-NAME "a 3-deoxyoctulosonyl-lipopolysaccharide")
(:CREATOR |paley|)
(:CREATION-DATE 3330790567) )
NIL)
(3-ENOLPYRUVYL-SHIKIMATE-5P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF 3-P-SHIK-1-CARBOXYVINYLXFERASE-ENZRXN)
(DBLINKS (LIGAND-CPD "C01269" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -210.9d0)
(APPEARS-IN-LEFT-SIDE-OF CHORISMATE-SYNTHASE-RXN)
(APPEARS-IN-RIGHT-SIDE-OF 2.5.1.19-RXN)
(MOLECULAR-WEIGHT 324.18d0)
(CHEMICAL-FORMULA (C 10) (H 13) (O 10) (P 1))
(DISPLAY-COORDS-2D (-1.0d0 -0.81188d0) (0.16832d0 -0.9637d0)
(-0.39934d0 -0.16832d0) (-0.39934d0 -0.49175d0) (-0.39934d0 0.27393d0)
(0.16172d0 0.26073d0) (-0.14191d0 -0.08581d0) (0.16832d0 -0.45215d0)
(-0.39934d0 0.033d0) (-0.68977d0 -0.35644d0) (0.16832d0 0.033d0)
(0.46535d0 -0.35644d0) (0.80858d0 -0.35644d0) (0.9967d0 -0.06931d0)
(-0.0264d0 -0.28383d0) (-0.69967d0 -0.80858d0) (-0.68977d0 -0.08581d0)
(-0.68977d0 -0.61386d0) (-0.19802d0 -0.22442d0) (-0.83498d0 -0.71287d0)
(0.16832d0 -0.73597d0) (-0.39934d0 -0.73597d0) (-0.39934d0 -0.9637d0)
(-0.69637d0 -1.0d0) (-0.26403d0 -0.36634d0) (-0.83828d0 -0.51485d0)
(0.93069d0 -0.66667d0))
(STRUCTURE-BONDS (27 13 1) (26 20 2) (25 19 1) (24 16 2) (23 22 1) (21 22 1)
(20 16 1) (19 3 1) (18 10 1) (17 10 1) (16 4 1) (15 19 1) (14 13 2)
(13 12 1) (12 21 1) (12 11 2) (11 9 1) (10 9 1) (10 22 1) (8 21 1) (7 19 2)
(6 11 1) (5 9 1) (4 22 1) (3 9 1) (2 21 1) (1 20 1))
(STRUCTURE-ATOMS O H O O H H O H C C C C C O O C H O P C C C H C O O O)
(COMMON-NAME "5-enolpyruvyl-shikimate-3-phosphate")
(SYNONYMS "EPSP" "3-enolpyruvyl-shikimate-5-phosphate"
"3-enolpyruvyl-shikimate-5-P" "5-O-(1-carboxyvinyl)-3-phosphoshikimate") )
((GIBBS-0 -210.9d0 CITATIONS "GibbsGroups97")))
(3-H-3-M-GLUTARYL-COA-REDUCTASES T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMON-NAME "a 3-hydroxy-3-methylglutaryl-CoA reductase")
(:CREATOR |paley|)
(:CREATION-DATE 3347159102) )
NIL)
(3-H-3-M-GLUTARYL-COA-REDUCTASES-P T (
(OCELOT-GFP::PARENTS 3-H-3-M-GLUTARYL-COA-REDUCTASES)
(COMMON-NAME "a 3-hydroxy-3-methylglutaryl-CoA reductase-phosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3347159102) )
NIL)
(|3-Hydroxy-Flavonoids| T (
(OCELOT-GFP::PARENTS |Flavonoids|)
(COMMON-NAME "a 3'-hydroxy-flavonoid")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(3-HYDROXY-ISOBUTYRATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(HISTORY |kr-3290870141|)
(:CREATOR |arnaud|)
(DBLINKS (CAS "2068-83-9"))
(:CREATION-DATE 3286057177)
(GIBBS-0 -120.1d0)
(MOLECULAR-WEIGHT 104.105d0)
(CHEMICAL-FORMULA (C 4) (H 8) (O 3))
(DISPLAY-COORDS-2D (0.48029d0 0.03584d0) (-1.0d0 0.4086d0)
(0.99642d0 0.36559d0) (-0.07527d0 0.3871d0) (-0.07527d0 1.0d0)
(0.48029d0 -0.57706d0) (-0.50538d0 0.04301d0))
(STRUCTURE-BONDS (7 4 1) (6 1 2) (5 4 1) (4 1 1) (3 1 1) (2 7 1))
(STRUCTURE-ATOMS C O O C C O C)
(COMMON-NAME "3-hydroxy-isobutyrate")
(SYSTEMATIC-NAME "propanoic acid, 3-hydroxy-2-methyl-")
(SYNONYMS "3-Hydroxy-2-methylpropanoate" "3-Hydroxyisobutyric acid"
"3-OH-iso-but" "3-OH-isobutyrate") )
NIL)
(3-HYDROXYACYL-COA T (
(OCELOT-GFP::PARENTS |All-Coas|)
(SUPERATOMS COA-GROUP)
(CHEMICAL-FORMULA (C 24) (H 39) (N 7) (O 18) (R 1) (P 3) (S 1))
(DISPLAY-COORDS-2D (-0.17500001d0 -0.409375d0) (0.44375002d0 -0.24687499d0)
(0.265625d0 -0.825d0) (0.6593751d0 -0.25937498d0) (-0.5625d0 -0.828125d0)
(0.59375d0 -0.34375d0) (-0.36562496d0 -0.24687499d0) (-1.0d0 -0.759375d0)
(0.84375d0 -0.25937498d0) (-0.875d0 -0.099999964d0) (-0.5125d0 -0.340625d0)
(0.59375d0 -0.25d0) (0.74687505d0 -0.16249996d0) (-0.878125d0 -0.834375d0)
(0.55625d0 -0.571875d0) (0.8937501d0 0.30624998d0) (-1.0d0 -0.340625d0)
(0.12812507d0 -0.08125001d0) (0.12812507d0 -0.24687499d0)
(0.009374976d0 -0.834375d0) (0.759375d0 0.24687505d0)
(0.759375d0 0.103124976d0) (0.99687505d0 0.16562498d0)
(0.6281251d0 0.31875002d0) (-0.634375d0 -0.43124998d0)
(0.90312505d0 -0.34375d0) (0.38437498d0 -0.74375d0)
(0.13750005d0 -0.74375d0) (-0.6875d0 -0.59375d0) (0.84375d0 -0.359375d0)
(-0.17500001d0 -0.08125001d0) (0.90312505d0 -0.25d0)
(0.6593751d0 -0.56875d0) (-0.76875d0 -0.509375d0) (-0.875d0 -0.265625d0)
(0.90312505d0 0.021875024d0) (-0.034375012d0 -0.24687499d0)
(0.75625d0 -0.56875d0) (-0.12812501d0 -0.734375d0)
(0.12812507d0 -0.409375d0) (-0.634375d0 -0.265625d0)
(0.5031251d0 0.09687507d0) (-0.17500001d0 -0.24687499d0)
(-0.39999998d0 -0.74375d0) (-0.634375d0 -0.099999964d0)
(-0.6875d0 -0.759375d0) (0.6593751d0 -0.66875d0) (0.6281251d0 0.484375d0)
(0.6437501d0 0.015625d0) (0.6593751d0 -0.46875d0) (0.009374976d0 -1.0d0)
(0.28750002d0 -0.24687499d0) (0.265625d0 -1.0d0) (0.84375d0 -0.45937496d0)
(-0.25937498d0 -0.828125d0) (0.6593751d0 -0.359375d0)
(-0.76875d0 -0.340625d0) (0.5031251d0 0.24062502d0))
(AROMATIC-RINGS (22 21 16 23 36) (49 42 58 24 21 22))
(STRUCTURE-BONDS (58 42 :AROMATIC) (57 41 1) (56 30 1) (56 50 1) (55 44 1)
(54 30 1) (52 2 1) (51 20 2) (49 22 :AROMATIC) (48 24 1) (47 33 1) (46 14 1)
(45 41 1) (44 5 1) (43 37 1) (42 49 :AROMATIC) (41 11 1) (40 19 1) (39 55 1)
(38 33 1) (37 19 1) (36 23 :AROMATIC) (35 57 1) (34 57 1) (33 50 1)
(32 30 1) (32 36 1) (31 43 2) (29 46 2) (28 20 1) (27 3 1) (26 32 1)
(25 41 1) (24 58 :AROMATIC) (23 16 :AROMATIC) (22 36 :AROMATIC)
(21 24 :AROMATIC) (21 22 :AROMATIC) (20 39 1) (19 52 1) (18 19 2) (17 35 1)
(16 21 :AROMATIC) (15 33 2) (14 8 1) (13 32 1) (12 56 1) (12 13 1) (11 7 1)
(10 35 2) (9 30 1) (8 17 1) (7 43 1) (6 12 1) (5 46 1) (4 56 1) (3 53 1)
(3 28 1) (2 12 1) (1 43 1))
(STRUCTURE-ATOMS O C C H N H O C H O C C O C O N N O P C C C C C C H R C O C
O C P O C N O O S O C C P C C C O N N O O O O O C C C N)
(COMMON-NAME "a 3-hydroxyacyl-CoA")
(:CREATOR |paley|)
(:CREATION-DATE 3347159102) )
((SUPERATOMS COA-GROUP REPLACES-ATOM 39)
(SUPERATOMS COA-GROUP CONNECTED-TO 20)))
(3-HYDROXYADIPYL-COA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(AROMATIC-RINGS (56 41 48 36 58 57) (37 60 58 57 29))
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2043)
(DISPLAY-COORDS-2D (4.6259d0 -1.469d0) (-4.4907d0 -0.5741d0)
(-3.1231d0 -1.4352d0) (-0.5569d0 -1.3d0) (4.2884d0 -2.6166d0)
(2.2454d0 -3.731d0) (1.1482d0 -1.3d0) (1.5194d0 -3.2417d0)
(-0.0166d0 -4.4907d0) (4.6259d0 -1.9755d0) (3.2417d0 -1.587d0)
(-0.5569d0 -0.4389d0) (3.2417d0 -5.2d0) (-3.782d0 -0.9963d0)
(-3.1231d0 0.2699d0) (2.9037d0 -0.4389d0) (2.9037d0 -1.9755d0)
(-1.587d0 -3.2583d0) (1.1482d0 -0.4389d0) (-2.4648d0 -0.9963d0)
(-0.5569d0 0.4222d0) (2.3806d0 -4.3389d0) (0.2366d0 -0.4389d0)
(-1.0301d0 -4.5417d0) (2.0259d0 -0.4389d0) (4.1028d0 -4.3389d0)
(3.7482d0 -0.9792d0) (-1.6375d0 -0.4389d0) (4.6259d0 0.0676d0)
(-4.4907d0 0.2699d0) (-3.1231d0 -0.5741d0) (-5.2d0 -0.9963d0)
(-2.6676d0 -3.3093d0) (-4.018d0 -2.4648d0) (1.0301d0 -3.5963d0)
(3.1065d0 1.7222d0) (5.1834d0 0.8778d0) (-3.782d0 -1.8569d0)
(-1.0301d0 -3.6806d0) (-2.0935d0 -3.6468d0) (2.3806d0 0.4389d0)
(0.4727d0 -3.3093d0) (3.2417d0 -4.3389d0) (-5.2d0 -3.2079d0)
(1.5194d0 -2.3806d0) (1.1482d0 0.4222d0) (-0.5231d0 -3.3093d0)
(2.3806d0 1.2834d0) (4.2884d0 -1.587d0) (3.2417d0 -3.3093d0)
(3.2417d0 -2.1102d0) (-3.3259d0 -3.6468d0) (3.1065d0 2.5834d0)
(-0.0166d0 -3.6301d0) (-4.5755d0 -3.6806d0) (3.1907d0 0.0166d0)
(3.8496d0 0.4727d0) (3.8496d0 1.3d0) (-4.018d0 -3.3259d0)
(4.5921d0 1.6375d0) (2.9037d0 -1.469d0) (4.2884d0 -2.1102d0))
(CHEMICAL-FORMULA (C 27) (H 44) (N 7) (O 20) (P 3) (S 1))
(MOLECULAR-WEIGHT 911.661d0)
(SUPERATOMS COA-GROUP)
(STRUCTURE-BONDS (1 62 1) (1 29 1) (2 14 1) (3 31 1) (4 12 1) (5 62 1)
(6 8 1) (7 19 1) (8 35 1) (9 54 1) (10 1 1) (11 51 1) (12 23 1) (13 43 1)
(14 31 1) (15 31 1) (16 61 1) (17 61 1) (18 40 1) (19 25 1) (20 28 1)
(21 12 2) (22 43 2) (23 19 1) (24 39 2) (25 16 1) (26 43 1) (27 1 1)
(28 12 1) (29 57 :AROMATIC) (30 2 2) (31 20 1) (32 2 1) (33 52 1) (34 59 2)
(35 42 1) (36 48 :AROMATIC) (37 29 :AROMATIC) (38 14 1) (39 18 1) (40 33 1)
(41 56 :AROMATIC) (42 54 1) (43 50 1) (44 32 1) (45 8 2) (46 19 2) (47 39 1)
(48 41 :AROMATIC) (49 62 1) (51 62 1) (51 50 1) (52 59 1) (53 36 1)
(54 47 1) (55 44 1) (56 57 :AROMATIC) (57 58 :AROMATIC) (58 36 :AROMATIC)
(58 60 :AROMATIC) (59 55 1) (60 37 :AROMATIC) (61 51 1) (61 27 1))
(STRUCTURE-ATOMS C C C O O O O C O H H P O C C C H S P C O O O O O O O O N O
C N C O C C C O C C C C P C O O C N H O C N N C C N C C C N C C)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2044)
(CITATIONS "12846838")
(COMMON-NAME "3-hydroxyadipyl-CoA")
(:CREATOR |arnaud|)
(:CREATION-DATE 3282428848) )
((SUPERATOMS COA-GROUP REPLACES-ATOM 18)
(SUPERATOMS COA-GROUP CONNECTED-TO 39)))
(3-HYDROXYDECANOYL-ACP-DEHYDR-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "3-decynoyl-N-acetylcysteamine")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-HYDROXYDECANOYL-ACP-DEHYDR-RXN)
(COMMENT "The enzyme is required for the synthesis of unsaturated
fatty acids. |CITS: [94066913]| β-hydroxydecanoyl thioester
dehydrase is responsible for shunting into unsaturated products an
intermediate in the biosynthetic pathway for saturated fatty acids.
The dehydrase can catalyze two reactions: (1) the dehydration of
(R)-3-hydroxydecanoyl-ACP to E-2-decenoyl-ACP, a reaction that also
occurs in the biosynthesis of saturated fatty acids and (2) the
interconversion of E-2-decenoyl-ACP and Z-3-decenoyl-ACP. |CITS:
[90202993]| The enzyme has been crystallized and is specific for chain
length of C(10). Other
β-hydroxyacyl-ACP dehydrases exist in E. coli, they are used in
synthesis of saturated fatty acids.")
(ENZYME FABA-CPLX)
(SYNONYMS "3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase"
"β-hydroxydecanoyl thioester dehydrase"
"3-hydroxydecanoyl-ACP dehydrase"
"β-hydroxydecanoyl thiol ester dehydrase"
"(3R)-3-hydroxydecanoyl-ACP hydro-lyase")
(COMMON-NAME "β-hydroxydecanoyl-ACP dehydrase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabA.template")
(:CREATION-DATE 3001089021)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "3-decynoyl-N-acetylcysteamine" COMMENT "mechanism-based
or `suicide' enzyme inactivation |CITS: [90202993]|")))
(3-HYDROXYDECANOYL-ACP-DEHYDR-RXN NIL (
(OCELOT-GFP::PARENTS EC-4.2.1 |Protein-Modification-Reactions|)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION FABZ-ENZRXN 3-HYDROXYDECANOYL-ACP-DEHYDR-ENZRXN)
(IN-PATHWAY FASYN-ELONG-PWY)
(RIGHT TRANS-D2-ENOYL-ACP WATER)
(LEFT OH-ACYL-ACP)
(EC-NUMBER "4.2.1.60")
(COMMENT "A key step in the anaerobic pathway of unsaturated fatty
acid synthesis.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabA.template")
(:CREATION-DATE 3001089021)
(:CREATOR |mriley|) )
NIL)
(3-HYDROXYPHENYL-PROPIONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER0-1441)
(:CREATION-DATE 3115390701)
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-61)
(AROMATIC-RINGS (8 9 10 1 11 7))
(DISPLAY-COORDS-2D (-0.7171717d0 -0.5064935d0) (0.13997114d0 -0.6709957d0)
(0.4256854d0 -0.5064935d0) (0.7113997d0 -0.6709957d0) (0.7113997d0 -1.0d0)
(0.99711394d0 -0.5064935d0) (-0.14574313d0 -0.5064935d0)
(-0.14574313d0 -0.17748916d0) (-0.43145746d0 -0.01010102d0)
(-0.7171717d0 -0.17748916d0) (-0.4285714d0 -0.6709957d0)
(-1.0d0 -0.67388165d0))
(CHEMICAL-FORMULA (C 9) (H 10) (O 3))
(MOLECULAR-WEIGHT 166.176d0)
(STRUCTURE-BONDS (11 1 :AROMATIC) (10 9 :AROMATIC) (9 8 :AROMATIC)
(8 7 :AROMATIC) (7 11 :AROMATIC) (4 5 1) (4 6 2) (3 4 1) (2 3 1) (2 7 1)
(1 10 :AROMATIC) (1 12 1))
(STRUCTURE-ATOMS C C C C O O C C C C C O)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2841 MHPHYDROXY-RXN TRANS-RXN-61)
(COMMON-NAME "3-(3-hydroxyphenyl)propionate")
(SYNONYMS "3-(3-hydroxyphenyl)propionic acid" "m-hydroxyphenylpropionic acid"
"m-hydroxyphenylpropionate" "MHP" "3HPP") )
NIL)
(3-HYDROXYPHENYLACETYL-COA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "3-hydroxyphenylacetyl-CoA")
(:CREATOR |keseler|)
(:CREATION-DATE 3348522562) )
NIL)
(3-ISOPROPYLMALDEHYDROG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 3-ISOPROPYLMALDEHYDROG-ENZRXN)
(COMPONENTS 3-ISOPROPYLMALDEHYDROG-MONOMER)
(COMMENT "Work done on S. typhimurium has shown it to be a dimer.
|CITS: [69184144]|")
(:CREATION-DATE 2969204127)
(:CREATOR |mriley|) )
((COMPONENTS 3-ISOPROPYLMALDEHYDROG-MONOMER COEFFICIENT 2)))
(3-ISOPROPYLMALDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH P-HYDROXYMERCURIBENZOATE N-ETHYLMALEIMIDE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "β-IPM dehydrogenase" "IMDH"
"3-carboxy-2-hydroxy-4-methylpentanoate: NAD+ oxidoreductase")
(COMMON-NAME "3-isopropylmalate dehydrogenase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-ISOPROPYLMALDEHYDROG-RXN)
(COMMENT "There is not much information available for this enzyme in
E. coli K-12. Enzyme has been purified in Salmonella. |CITS:
[69184144]|")
(ENZYME 3-ISOPROPYLMALDEHYDROG-CPLX)
(:CREATION-DATE 2969204127)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH P-HYDROXYMERCURIBENZOATE COMMENT
"This information refers to work done on S. typhimurium")
(INHIBITORS-UNKMECH P-HYDROXYMERCURIBENZOATE CITATIONS "[69184144]")
(INHIBITORS-UNKMECH N-ETHYLMALEIMIDE COMMENT
"This information refers to work done on S. typhimurium")
(INHIBITORS-UNKMECH N-ETHYLMALEIMIDE CITATIONS "[69184144]")))
(3-ISOPROPYLMALDEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0073" "LeuB")
(DBLINKS (MODBASE "P30125" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00180" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414615" NIL NIL NIL NIL NIL)
(UNIPROT "P30125" NIL NIL |ouzounis| 3027899498))
(COMMON-NAME "LeuB")
(COMPONENT-OF 3-ISOPROPYLMALDEHYDROG-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 39.51696799999989d0)
(GENE EG11577)
(:CREATION-DATE 2969204127)
(:CREATOR |mriley|) )
NIL)
(3-ISOPROPYLMALDEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(IN-PATHWAY LEUSYN-PWY)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 3-ISOPROPYLMALDEHYDROG-ENZRXN)
(RIGHT CPD-7100 NADH PROTON)
(LEFT 2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE NAD)
(EC-NUMBER "1.1.1.85")
(COMMENT "This is the third step in leucine biosynthesis after the
fork from valine synthesis. It is an oxidative decarboxylation.")
(:CREATION-DATE 2969204127)
(:CREATOR |mriley|) )
NIL)
(3-ISOPROPYLMALISOM-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 3-ISOPROPYLMALISOM-ENZRXN)
(COMPONENTS LEUC-MONOMER LEUD-MONOMER)
(COMMENT "The complex consists of two different subunits: LEUC and
LEUD. |CITS: [SwissProt]|")
(:CREATION-DATE 2969204130)
(:CREATOR |mriley|) )
((COMPONENTS LEUD-MONOMER COEFFICIENT 1)
(COMPONENTS LEUC-MONOMER COEFFICIENT 1)))
(3-ISOPROPYLMALISOM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "3-isopropylmalate dehydratase" "α-isopropylmalate isomerase"
"α-IPM isomerase" "IPMI" "3-isopropylmalate isomerase"
"3-carboxy-3-hydroxy-isocaproate isomerase")
(COMMON-NAME "isopropylmalate isomerase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-ISOPROPYLMALISOM-RXN)
(COMMENT "There is little information in E. coli, more in Salmonella.
|CITS: [82030557] [FriedMGG199,486] [ColiSalII]|")
(ENZYME 3-ISOPROPYLMALISOM-CPLX)
(:CREATION-DATE 2969204130)
(:CREATOR |mriley|) )
NIL)
(3-ISOPROPYLMALISOM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY LEUSYN-PWY)
(ENZYMATIC-REACTION 3-ISOPROPYLMALISOM-ENZRXN)
(RIGHT 2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE)
(LEFT 3-CARBOXY-3-HYDROXY-ISOCAPROATE)
(EC-NUMBER "4.2.1.33")
(COMMENT "This is the second step in leucine biosynthesis after the
fork with valine synthesis. The reaction involves hydration to give
an intermediate dimethylcitraconate and dehydration of the
intermediate, to give an isomer of the original substrate, which
effects interconversion of two isomers.")
(:CREATION-DATE 2969204130)
(:CREATOR |mriley|) )
NIL)
(3-KETO-ADIPYL-COA NIL (
(OCELOT-GFP::PARENTS 3-KETOACYL-COA)
(APPEARS-IN-RIGHT-SIDE-OF RXN-3641 RXN0-2044)
(:CREATION-DATE 3282428966)
(SUPERATOMS COA-GROUP)
(GIBBS-0 -250.3d0)
(:CREATOR |arnaud|)
(COMMON-NAME "β-ketoadipyl-CoA")
(SYNONYMS "β-ketoadipyl-CoA" "3-ketoadipyl-CoA" "3-keto-adipyl-coa"
"3-oxoadipyl-CoA")
(DISPLAY-COORDS-2D (0.6257142857142857d0 -0.6371428571428571d0)
(0.56d0 -0.2828571428571428d0) (0.8914285714285715d0 -0.38d0)
(-0.10857142857142854d0 0.08000000000000007d0)
(-0.7742857142857142d0 -0.4742857142857143d0)
(-0.09999999999999998d0 -0.6371428571428571d0)
(-0.6d0 -0.27714285714285714d0) (-0.6d0 0.05142857142857138d0)
(0.7914285714285714d0 -0.8342857142857143d0)
(0.0914285714285714d0 -0.6371428571428571d0) (-1.0d0 -0.1914285714285714d0)
(0.04571428571428582d0 -0.08571428571428574d0) (0.6257142857142857d0 -1.0d0)
(0.4314285714285715d0 -0.7171428571428571d0) (-0.7742857142857142d0 -0.64d0)
(0.6257142857142857d0 -0.4057142857142857d0)
(-0.4028571428571428d0 -0.7028571428571428d0)
(-0.8657142857142857d0 0.05142857142857138d0)
(-0.4742857142857143d0 -0.1914285714285714d0)
(-0.88d0 -0.7085714285714286d0) (0.29142857142857137d0 -0.46d0)
(0.5971428571428572d0 0.3314285714285714d0)
(0.38857142857142857d0 -0.08571428571428574d0) (0.56d0 -0.38d0)
(0.29142857142857137d0 -0.6257142857142857d0)
(0.8257142857142856d0 -0.4057142857142857d0)
(0.5971428571428572d0 0.4971428571428571d0)
(0.6257142857142857d0 -0.8342857142857143d0)
(-0.5142857142857142d0 -0.6371428571428571d0)
(-0.10857142857142854d0 -0.25142857142857145d0)
(0.74d0 0.0914285714285714d0) (0.46d0 0.24571428571428575d0)
(-0.7285714285714286d0 -0.3571428571428571d0)
(-0.3142857142857143d0 -0.08571428571428574d0)
(0.21999999999999997d0 -0.08571428571428574d0)
(0.6257142857142857d0 -0.3057142857142857d0)
(-0.8657142857142857d0 -0.11142857142857145d0)
(0.6142857142857143d0 0.0028571428571428914d0)
(0.21999999999999997d0 0.08000000000000007d0)
(0.56d0 -0.08571428571428574d0)
(0.21999999999999997d0 -0.25142857142857145d0)
(0.8828571428571428d0 0.3142857142857143d0) (-0.64d0 -0.7028571428571428d0)
(0.46d0 0.08571428571428563d0) (-0.6d0 -0.11142857142857145d0)
(0.46d0 -0.8342857142857143d0)
(-0.10857142857142854d0 -0.08571428571428574d0)
(0.8257142857142856d0 -0.5028571428571429d0) (0.74d0 0.25142857142857133d0)
(0.7228571428571429d0 -0.1885714285714286d0)
(-0.3057142857142857d0 -0.6285714285714286d0)
(-0.0028571428571428914d0 -0.8657142857142857d0)
(0.8914285714285715d0 -0.2828571428571428d0)
(-0.0028571428571428914d0 -0.7d0) (-1.0d0 -0.6171428571428572d0)
(0.19714285714285704d0 -0.6914285714285715d0)
(0.9971428571428572d0 0.1685714285714286d0)
(-0.1971428571428572d0 -0.8742857142857143d0)
(-0.7285714285714286d0 -0.1914285714285714d0)
(0.8257142857142856d0 -0.3057142857142857d0)
(-0.1971428571428572d0 -0.7085714285714286d0)
(0.8914285714285715d0 0.014285714285714235d0))
(STRUCTURE-BONDS (62 31 :AROMATIC) (61 51 1) (60 26 1) (59 45 1) (58 61 2)
(57 62 :AROMATIC) (56 10 1) (55 11 1) (54 6 1) (53 26 1) (53 62 1) (52 54 2)
(51 17 1) (50 53 1) (49 22 :AROMATIC) (49 42 :AROMATIC) (48 26 1) (47 12 1)
(46 28 2) (45 19 1) (44 38 :AROMATIC) (43 15 1) (42 57 :AROMATIC) (41 35 1)
(40 2 1) (39 35 2) (38 31 :AROMATIC) (37 59 1) (36 16 1) (35 23 1) (34 47 1)
(33 59 1) (32 44 :AROMATIC) (31 49 :AROMATIC) (30 47 1) (29 43 1) (28 1 1)
(27 22 1) (25 56 1) (24 2 1) (23 40 1) (22 32 :AROMATIC) (21 25 2) (20 55 1)
(19 34 1) (18 37 2) (17 29 1) (16 26 1) (16 1 1) (15 20 1) (14 25 1)
(13 28 1) (12 35 1) (11 37 1) (10 54 1) (9 28 1) (8 45 1) (7 45 1) (6 61 1)
(5 15 2) (4 47 2) (3 53 1) (2 16 1) (2 50 1))
(STRUCTURE-ATOMS O C H O O C C C O C N O O O C C C O C C O C O H C C N P C O
C N O O P H C N O C O N N C C O P O C O S O C C C C C O C H C N)
(CHEMICAL-FORMULA (C 27) (H 42) (N 7) (O 20) (P 3) (S 1))
(MOLECULAR-WEIGHT 909.645d0)
(AROMATIC-RINGS (57 42 49 31 62) (49 22 32 44 38 31)) )
((SUPERATOMS COA-GROUP CONNECTED-TO 61)
(SUPERATOMS COA-GROUP REPLACES-ATOM 51)))
(3-KETO-L-GULONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00618" NIL |kr| 3346617699 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF RXN0-704)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-707 RXN0-703)
(:CREATOR |arnaud|)
(:CREATION-DATE 3249247381)
(GIBBS-0 -260.8d0)
(MOLECULAR-WEIGHT 194.141d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 7))
(DISPLAY-COORDS-2D (-0.61772853d0 0.39058173d0) (-1.0d0 0.65650964d0)
(-1.0d0 -0.28531855d0) (-0.23545706d0 0.39058173d0)
(-0.61772853d0 0.99445975d0) (-0.61772853d0 0.05817175d0)
(-0.61772853d0 0.65650964d0) (-0.61772853d0 -0.61772853d0)
(-0.61772853d0 -0.27977842d0) (-0.23545706d0 -0.61772853d0)
(-0.61772853d0 -1.0d0) (-0.23545706d0 0.99445975d0)
(-0.23545706d0 0.05817175d0))
(STRUCTURE-BONDS (13 6 2) (12 5 1) (11 8 2) (10 8 1) (9 6 1) (8 9 1) (7 1 1)
(5 7 1) (4 1 1) (3 9 1) (2 7 1) (1 6 1))
(STRUCTURE-ATOMS C O O O C C C C C O O O O)
(SYNONYMS "3-dehydro-L-gulonate")
(COMMON-NAME "3-keto-L-gulonate") )
((GIBBS-0 -260.8d0 CITATIONS "GibbsGroups97")))
(3-KETOACYL-COA T (
(OCELOT-GFP::PARENTS |All-Coas|)
(APPEARS-IN-RIGHT-SIDE-OF KETOACYLCOATHIOL-RXN OHACYL-COA-DEHYDROG-RXN)
(SCHEMA? T)
(SUPERATOMS COA-GROUP)
(CHEMICAL-FORMULA (C 24) (H 37) (N 7) (O 18) (R 1) (P 3) (S 1))
(DISPLAY-COORDS-2D (-3.6356d0 -4.0266d0) (-4.0754d0 -1.8093d0)
(-4.6296d0 -0.5219d0) (0.0487d0 -4.4176d0) (4.7763d0 -1.3203d0)
(-2.1193d0 -3.9286d0) (1.4019d0 -4.3689d0) (-4.646d0 -4.4176d0)
(-3.358d0 -2.2825d0) (-0.6845d0 -3.8799d0) (4.4669d0 -1.9073d0)
(4.0266d0 0.5378d0) (3.945d0 -0.8641d0) (3.1461d0 -1.8258d0)
(-1.3696d0 -4.3853d0) (3.4889d0 -3.5376d0) (-0.1791d0 -1.3044d0)
(0.7338d0 -3.9286d0) (0.6845d0 -1.3044d0) (0.0487d0 -5.2982d0)
(2.657d0 0.5054d0) (-4.0754d0 -2.6899d0) (3.3257d0 1.679d0)
(4.7276d0 1.6138d0) (-5.2982d0 -4.0266d0) (2.657d0 1.2716d0)
(3.4073d0 0.0816d0) (0.6845d0 -2.168d0) (-0.9293d0 -0.4239d0)
(3.4889d0 -1.3696d0) (1.4019d0 -5.2982d0) (-3.358d0 -0.5219d0)
(4.7763d0 0.1139d0) (2.0377d0 -3.9286d0) (0.6845d0 -0.4239d0)
(-2.7063d0 -1.8093d0) (2.3476d0 -1.3044d0) (1.5163d0 -1.3044d0)
(-0.9293d0 -1.3044d0) (2.9506d0 -3.0322d0) (-1.9402d0 -1.3044d0)
(3.4889d0 -1.9073d0) (3.3257d0 2.5596d0) (4.0102d0 -3.0157d0)
(-3.6356d0 -3.1461d0) (4.0266d0 1.3044d0) (3.1461d0 -1.3203d0)
(-2.9834d0 -4.3853d0) (4.4669d0 -2.4292d0) (4.7763d0 -1.8258d0)
(-5.2982d0 -1.8093d0) (4.4669d0 -1.3696d0) (-0.9293d0 -2.168d0)
(3.4889d0 -2.478d0) (-3.358d0 -1.4019d0) (3.4889d0 -3.0157d0)
(-4.6296d0 -1.4019d0) (5.2818d0 0.8806d0))
(AROMATIC-RINGS (12 46 24 58 33) (27 21 26 23 46 12))
(STRUCTURE-BONDS (1 8 1) (2 55 1) (3 57 2) (4 10 1) (5 33 1) (5 11 1)
(6 48 1) (7 18 1) (7 31 2) (8 25 1) (9 55 1) (10 15 1) (46 12 :AROMATIC)
(13 5 1) (14 47 1) (15 6 1) (16 56 1) (17 19 1) (18 4 1) (19 38 1) (20 4 2)
(21 27 :AROMATIC) (22 2 1) (23 26 :AROMATIC) (58 24 :AROMATIC) (25 51 1)
(26 21 :AROMATIC) (27 12 :AROMATIC) (28 19 1) (29 39 2) (30 42 1) (32 55 1)
(12 33 :AROMATIC) (34 7 1) (35 19 2) (36 41 1) (37 47 1) (38 37 1) (39 17 1)
(40 56 2) (41 39 1) (42 54 1) (42 11 1) (43 23 1) (44 56 1) (45 1 2)
(24 46 :AROMATIC) (46 23 :AROMATIC) (47 13 1) (47 42 1) (48 1 1) (49 11 1)
(50 5 1) (51 57 1) (52 11 1) (53 39 1) (55 36 1) (56 54 1) (57 2 1)
(33 58 :AROMATIC))
(STRUCTURE-ATOMS C C O C C C C C C S C C O H C O O C P O C O C N C N N O O H
O C N R O C C O P O O C N O O C C N O H N H O O C P C C)
(COMMON-NAME "a 3-ketoacyl-CoA")
(SYNONYMS "RCOCH2CO-CoA" "3-oxoacyl-CoA" "β-ketoacyl-CoA") )
((SUPERATOMS COA-GROUP CONNECTED-TO 4)
(SUPERATOMS COA-GROUP REPLACES-ATOM 10)))
(3-KETOBUTYRATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00164" NIL |kawakami| 3276028317 NIL NIL)
(CAS "541-50-4"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -113.2d0)
(APPEARS-IN-LEFT-SIDE-OF ACETOACETYL-COA-TRANSFER-RXN)
(MOLECULAR-WEIGHT 102.09d0)
(CHEMICAL-FORMULA (C 4) (H 6) (O 3))
(DISPLAY-COORDS-2D (-0.0066d0 -0.42904d0) (-0.0099d0 0.70297d0)
(-1.0d0 0.12871d0) (-0.33993d0 0.12871d0) (0.9901d0 0.14191d0)
(0.66007d0 -0.42904d0) (0.9967d0 -1.0d0))
(STRUCTURE-BONDS (7 6 2) (6 1 1) (5 6 1) (4 1 1) (3 4 2) (2 4 1))
(STRUCTURE-ATOMS C O O C C C O)
(COMMON-NAME "acetoacetate")
(SYNONYMS "3-ketobutyrate" "3-oxobutanate" "oxobutyrate" "acetoacetic acid"
"3-oxobutyric acid" "3-oxobutanoic acid" "diacetic acid"
"β-ketobutyric acid") )
((GIBBS-0 -113.2d0 CITATIONS "GibbsGroups97")))
(3-MERCAPTO-PYRUVATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00957" NIL |kr| 3346617699 NIL NIL) (CAS "2464-23-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -107.7d0)
(APPEARS-IN-LEFT-SIDE-OF MERCAPYSTRANS-RXN)
(COMMON-NAME "3-mercaptopyruvate")
(MOLECULAR-WEIGHT 120.123d0)
(CHEMICAL-FORMULA (C 3) (H 4) (O 3) (S 1))
(DISPLAY-COORDS-2D (0.54723d0 -0.45277d0) (0.54723d0 -1.0d0)
(0.04235d0 -0.19218d0) (-0.45277d0 -0.49511d0) (0.99674d0 -0.13681d0)
(0.04235d0 0.35505d0) (-1.0d0 -0.49511d0))
(STRUCTURE-BONDS (7 4 1) (6 3 2) (5 1 1) (4 3 1) (3 1 1) (2 1 2))
(STRUCTURE-ATOMS C O C C O O S)
(SYNONYMS "mercaptopyruvate" "3-mercaptopyruvic acid" "β-thiopyruvate"
"β-mercaptopyruvate") )
((GIBBS-0 -107.7d0 CITATIONS "GibbsGroups97")))
(3-METHYL-2-OXOBUT-OHCH3XFER-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 3-METHYL-2-OXOBUT-OHCH3XFER-ENZRXN)
(COMPONENTS 3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto2/panB2.template")
(:CREATION-DATE 3027196316)
(:CREATOR |mriley|) )
((COMPONENTS 3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER CITATIONS "[93209959]")
(COMPONENTS 3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-MONOMER COEFFICIENT 6)))
(3-METHYL-2-OXOBUT-OHCH3XFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CPD-3642 VAL "3-methyl-2-butanone" PYRUVATE ISOVALERATE
L-PANTOATE PANTOTHENATE CO-A THF FORMALDEHYDE)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(COFACTORS MG+2)
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-CH3-2-OXOBUTANOATE-OH-CH3-XFER-RXN)
(COMMENT "3-methyl-2-oxobutanoate hydroxymethyltransferase (KPHMT)
catalyzes the first committed step of the pantothenate biosynthesis
pathway. The product of the reaction, dehydropantoate is an essential
precursor of pantothenate |CITS: [76213236]|.
The enzyme requires the l-isomer of
THF, but it can utilize conjugates containing 1-6 additional
glutamate residues, such as tetrahydropteroylpentaglutamate,
tetrahydropteroyltetraglutamate and tetrahydropteroyltriglutamate.
The specificity for the ketoacid substrate is not as strict,
α-ketobutyrate, α-ketovalerate and
α-keto-β-methylvalerate could all replace 2-oxo-isovalerate as
substrates. |CITS: [76213236]|")
(ENZYME 3-METHYL-2-OXOBUT-OHCH3XFER-CPLX)
(SYNONYMS "α-ketoisovalerate hydroxymethyltransferase"
"dehydropantoate hydroxymethyltransferase"
"ketopantoate hydroxymethyltransferase" "KPHMT"
"5,10-methylenetetrahydrofolate:3-methyl-2-oxobutanoate hydroxymethyltransferase")
(COMMON-NAME "3-methyl-2-oxobutanoate hydroxymethyltransferase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto2/panB2.template")
(:CREATION-DATE 3027196316)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH CPD-3642 COMMENT "inhibited
the forward reaction |CITS: [76213236]|")
(INHIBITORS-UNKMECH VAL COMMENT "inhibited the
forward reaction |CITS: [76213236]|")
(INHIBITORS-UNKMECH "3-methyl-2-butanone" COMMENT "inhibited the forward
reaction |CITS: [76213236]|")
(INHIBITORS-UNKMECH PYRUVATE COMMENT "inhibited the forward reaction |CITS:
[76213236]|")
(INHIBITORS-UNKMECH ISOVALERATE COMMENT
"inhibited the forward reaction |CITS:
[76213236]|")
(INHIBITORS-UNKMECH L-PANTOATE COMMENT "inhibited
both the forward and reverse reactions |CITS: [76213236]|")
(INHIBITORS-UNKMECH PANTOTHENATE COMMENT "inhibited both the forward
and reverse reactions |CITS: [76213236]|")
(INHIBITORS-UNKMECH CO-A COMMENT "inhibited the forward reaction
|CITS: [76213236]|")
(INHIBITORS-UNKMECH THF COMMENT "inhibited the forward reaction
|CITS: [76213236]|")
(INHIBITORS-UNKMECH FORMALDEHYDE COMMENT "inhibited the forward reaction
|CITS: [76213236]|")
(COFACTORS MG+2 COMMENT "Mg++ is required for activity, Mn++, Co++ and
Zn++ are progressively less active. |CITS: [76213236]|")))
(3-METHYL-CROTONYL-COA NIL (
(OCELOT-GFP::PARENTS |All-Coas|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2301)
(:CREATOR |arnaud|)
(:CREATION-DATE 3286577232)
(SYNONYMS "β-methylcrotonoyl-CoA" "3-methylbut-2-enoyl-CoA")
(SUPERATOMS COA-GROUP)
(GIBBS-0 -124.3d0)
(COMMON-NAME "3-methylcrotonyl-CoA")
(STRUCTURE-ATOMS C N C C N O O C O C O N C O C N O C O O O C H C O C N C P O
O C O O S H C C C O O C C N H P C C P C C C C C O C N H)
(STRUCTURE-BONDS (58 3 1) (57 24 1) (56 31 1) (56 3 1) (55 29 1) (54 14 1)
(54 56 1) (53 54 1) (52 26 1) (51 26 1) (50 35 1) (49 33 1) (48 15 1)
(27 47 :AROMATIC) (46 17 1) (45 56 1) (44 10 :AROMATIC) (43 13 1)
(42 5 :AROMATIC) (41 52 1) (40 50 2) (39 4 1) (47 38 :AROMATIC)
(38 44 :AROMATIC) (37 26 1) (36 54 1) (35 39 1) (34 49 1) (33 46 1)
(32 30 1) (30 49 1) (29 31 1) (28 15 1) (26 32 1) (25 46 1)
(38 24 :AROMATIC) (23 1 1) (22 50 1) (21 46 2) (20 49 2) (19 18 2) (18 43 1)
(17 53 1) (16 18 1) (15 22 2) (14 1 1) (13 2 1) (12 42 :AROMATIC)
(24 12 :AROMATIC) (11 29 2) (10 27 :AROMATIC) (9 3 1) (8 52 1) (7 29 1)
(6 8 2) (5 47 :AROMATIC) (4 16 1) (2 8 1) (1 27 1) (1 3 1))
(DISPLAY-COORDS-2D (0.89073d0 -0.26821d0) (-1.0d0 -0.17881d0)
(0.8245d0 -0.39073d0) (-0.3543d0 -0.61258d0) (0.61258d0 0.01656d0)
(-0.86424d0 0.07947d0) (0.72848d0 -1.0d0) (-0.86424d0 -0.09934d0)
(0.8245d0 -0.49669d0) (0.99669d0 0.18212d0) (0.54967d0 -0.82119d0)
(0.45695d0 0.25828d0) (-1.0d0 -0.62914d0) (0.72185d0 -0.1755d0)
(0.36093d0 -0.70199d0) (-0.52649d0 -0.70861d0) (0.39073d0 -0.07285d0)
(-0.71523d0 -0.61589d0) (-0.71523d0 -0.43709d0) (-0.10927d0 0.10596d0)
(0.21854d0 0.10596d0) (0.22848d0 -0.61258d0) (0.89073d0 -0.37417d0)
(0.59603d0 0.34437d0) (0.21854d0 -0.25166d0) (-0.60265d0 -0.09934d0)
(0.89073d0 0.02318d0) (0.36093d0 -0.88079d0) (0.72848d0 -0.82119d0)
(-0.31457d0 -0.07285d0) (0.72848d0 -0.62252d0) (-0.47351d0 -0.17881d0)
(0.04305d0 -0.07285d0) (-0.10927d0 -0.25166d0) (-0.06291d0 -0.60265d0)
(0.55629d0 -0.37417d0) (-0.60265d0 0.07947d0) (0.73841d0 0.2649d0)
(-0.19868d0 -0.70861d0) (0.09272d0 -0.89404d0) (-0.72848d0 -0.35762d0)
(0.45695d0 0.09934d0) (-0.87086d0 -0.71523d0) (0.88079d0 0.32781d0)
(0.62252d0 -0.28477d0) (0.21854d0 -0.07285d0) (0.73841d0 0.10596d0)
(0.50993d0 -0.60265d0) (-0.10927d0 -0.07285d0) (0.09272d0 -0.71523d0)
(-0.60265d0 -0.27815d0) (-0.72848d0 -0.17881d0) (0.55629d0 -0.07285d0)
(0.55629d0 -0.26821d0) (0.90728d0 -0.82119d0) (0.62252d0 -0.39073d0)
(0.59603d0 0.52318d0) (0.8245d0 -0.28477d0))
(CHEMICAL-FORMULA (C 26) (H 42) (N 7) (O 17) (P 3) (S 1))
(MOLECULAR-WEIGHT 849.636d0)
(AROMATIC-RINGS (10 44 38 47 27) (5 42 12 24 38 47)) )
((SUPERATOMS COA-GROUP CONNECTED-TO 50)
(SUPERATOMS COA-GROUP REPLACES-ATOM 35)))
(3-NITROBENZALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "3-nitrobenzaldehyde")
(:CREATOR |keseler|)
(:CREATION-DATE 3332781149) )
NIL)
(3-NITROPROPANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ISOCITLYASE-ENZRXN)
(:CREATOR |pkarp|)
(:CREATION-DATE 3352228467)
(COMMON-NAME "3-nitropropanoate")
(DISPLAY-COORDS-2D (3.7321d0 0.25d0) (4.5981d0 -0.25d0) (2.866d0 -0.25d0)
(5.4641d0 0.25d0) (2.0d0 0.25d0) (2.866d0 -1.25d0) (6.3301d0 -0.25d0)
(5.4641d0 1.25d0))
(STRUCTURE-ATOMS C C C N O O O O)
(STRUCTURE-BONDS (1 2 1) (1 3 1) (2 4 1) (3 5 2) (3 6 1) (4 7 2) (4 8 1))
(ATOM-CHARGES (4 1) (8 -1))
(DBLINKS (NCI "64266") (CAS "504-88-1"))
(CHEMICAL-FORMULA (C 3) (H 5) (N 1) (O 4))
(MOLECULAR-WEIGHT 119.077d0)
(SYNONYMS "3-nitropropionate") )
NIL)
(3-NUCLEOTID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH CO+2)
(INHIBITORS-UNKMECH RNA CPD-7082 EDTA ZN+2 CU+2)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(PHYSIOLOGICALLY-RELEVANT RNA CU+2 ZN+2 CO+2)
(COMMENT "The cpdB gene codes for a bifunctional enzyme which
catalyzes two sequential reactions during ribonucleic acid
degradation. The first enzymatic activity is a 2',3'-cyclic nucleotide
2'-phosphodiesterase in which a 2',3'-cyclic nucleotide is converted
to a 3'-nucleotide. The second activity is a 3'-nucleotidase which
yields a ribonucleotide and phosphate. The enzyme has two kinetically
distinguishable active sites. |CITS: [86139859]|")
(REACTION 3-NUCLEOTID-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/cpdB.template")
(ENZYME CPDB-MONOMER)
(:CREATION-DATE 3041804851)
(COMMON-NAME "3'-nucleotidase")
(SYNONYMS "3'-ribonucleotide phosphohydrolase")
(REACTION-DIRECTION REVERSIBLE) )
((ACTIVATORS-UNKMECH CO+2 CITATIONS "[AnrakuJBC239,3412]")
(INHIBITORS-UNKMECH RNA CITATIONS "[AnrakuJBC239,3412]")
(INHIBITORS-UNKMECH CPD-7082 CITATIONS "[AnrakuJBC239,3412]")
(INHIBITORS-UNKMECH EDTA CITATIONS "[AnrakuJBC239,3412]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[AnrakuJBC239,3412]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[AnrakuJBC239,3412]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme is highly specific for the
3'(2')-isomers of ribonucleoside monophosphates. |CITS:
[AnrakuJBC239,3412]|")))
(3-NUCLEOTID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(COMMENT
"This is the second of two consecutive reactions in the degradation of ribonucleic acids.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/cpdB.template")
(ENZYMATIC-REACTION ENZRXN0-5182 3-NUCLEOTID-ENZRXN)
(EC-NUMBER "3.1.3.6")
(:CREATION-DATE 3041804851)
(LEFT |3-Prime-Ribonucleoside-Monophosphates| WATER)
(RIGHT |Ribonucleosides| |Pi|) )
NIL)
(3-OCTAPRENYL-4-HYDROXYBENZOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C05809" NIL |kr| 3346617698 NIL NIL))
(:CREATION-DATE 3115390701)
(AROMATIC-RINGS (23 49 22 21 48 50))
(DISPLAY-COORDS-2D (29.6517d0 -4.9592d0) (28.5652d0 -2.7639d0)
(25.2701d0 -6.7568d0) (21.9473d0 -2.7639d0) (18.6801d0 -6.7568d0)
(15.3851d0 -2.7639d0) (12.0344d0 -6.7568d0) (8.795d0 -2.8195d0)
(5.4444d0 -6.533d0) (0.1112d0 0.0d0) (2.0938d0 -0.1112d0)
(1.0886d0 -6.533d0) (27.4488d0 -5.4444d0) (24.1537d0 -4.0763d0)
(21.166d0 -5.3054d0) (17.6193d0 -4.0763d0) (14.2687d0 -5.4444d0)
(10.9737d0 -4.0763d0) (7.7064d0 -5.4444d0) (4.3836d0 -4.1319d0)
(0.0d0 -4.0763d0) (0.0d0 -2.8473d0) (2.1786d0 -2.9029d0)
(27.0288d0 -4.0763d0) (23.8465d0 -5.4444d0) (19.9647d0 -5.4444d0)
(17.2564d0 -5.4444d0) (13.7098d0 -4.0763d0) (10.5274d0 -5.4444d0)
(7.288d0 -4.0763d0) (3.2394d0 -5.1927d0) (26.0515d0 -4.0763d0)
(22.8135d0 -5.4444d0) (19.7409d0 -4.0763d0) (16.4751d0 -5.4444d0)
(12.8172d0 -4.0763d0) (9.5222d0 -5.4444d0) (6.1423d0 -4.0763d0)
(28.5652d0 -4.0763d0) (25.2701d0 -5.4444d0) (21.9473d0 -4.0763d0)
(18.6801d0 -5.4444d0) (15.3851d0 -4.0763d0) (12.0344d0 -5.4444d0)
(8.795d0 -4.1319d0) (5.4444d0 -5.1927d0) (1.0886d0 -0.9774d0)
(1.0886d0 -5.1927d0) (1.0886d0 -2.2606d0) (2.1786d0 -4.1319d0))
(CHEMICAL-FORMULA (C 47) (H 70) (O 3))
(MOLECULAR-WEIGHT 683.068d0)
(STRUCTURE-BONDS (50 48 :AROMATIC) (47 49 1) (38 46 1) (37 45 1) (36 44 1)
(35 43 1) (34 42 1) (33 41 1) (32 40 1) (31 50 1) (30 38 1) (29 37 1)
(28 36 1) (27 35 1) (26 34 1) (25 33 1) (24 32 1) (23 50 :AROMATIC)
(49 23 :AROMATIC) (22 49 :AROMATIC) (48 21 :AROMATIC) (21 22 :AROMATIC)
(20 46 2) (20 31 1) (19 45 2) (19 30 1) (18 44 2) (18 29 1) (17 43 2)
(17 28 1) (16 42 2) (16 27 1) (15 41 2) (15 26 1) (14 40 2) (14 25 1)
(13 39 2) (13 24 1) (12 48 1) (11 47 1) (10 47 2) (9 46 1) (8 45 1) (7 44 1)
(6 43 1) (5 42 1) (4 41 1) (3 40 1) (2 39 1) (1 39 1))
(STRUCTURE-ATOMS C C C C C C C C C O O O C C C C C C C C C C C C C C C C C C
C C C C C C C C C C C C C C C C C C C C)
(APPEARS-IN-RIGHT-SIDE-OF 4OHBENZOATE-OCTAPRENYLTRANSFER-RXN)
(APPEARS-IN-LEFT-SIDE-OF 3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN)
(COMMON-NAME "3-octaprenyl-4-hydroxybenzoate") )
NIL)
(3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(EC-NUMBER "4.1.1.-")
(ENZYMATIC-REACTION UBIX-ENZRXN 3-OCTPRNL-4-OHBENZOATE-DECARBOX-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT 2-OCTAPRENYLPHENOL CARBON-DIOXIDE)
(LEFT 3-OCTAPRENYL-4-HYDROXYBENZOATE)
(COMMENT "This is the third step in ubiquinone biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiD.template")
(:CREATION-DATE 3000649050)
(:CREATOR |mriley|) )
NIL)
(3-OCTPRNL-4-OHBENZOATE-DECARBOX-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH METOH DITHIOTHREITOL)
(INHIBITORS-UNKMECH EDTA)
(CITATIONS ":EV-EXP:3277835751:pkarp" "[4615746]" "[782527]")
(COFACTORS MN+2)
(REACTION 3-OCTAPRENYL-4-OHBENZOATE-DECARBOX-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubisyn2/ubiD2.template")
(ENZYME CPLX0-301)
(:CREATION-DATE 3035210287)
(COMMON-NAME "3-octaprenyl-4-hydroxybenzoate decarboxylase")
(SYNONYMS "3-polyprenyl 4-hydroxybenzoate decarboxylase" "PPHB decarboxylase"
"3-octaprenyl-4-hydroxybenzoate carboxy-lyase")
(REACTION-DIRECTION REVERSIBLE) )
((ACTIVATORS-UNKMECH METOH CITATIONS "[76253689]")
(ACTIVATORS-UNKMECH DITHIOTHREITOL CITATIONS "[76253689]")
(INHIBITORS-UNKMECH EDTA COMMENT "The inhibition could be overcome by the
addition of divalent metal ions, of which Mn++ was the most effective.
|CITS: [76253689]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme is highly specific for its
octaprenyl substrate. |CITS: [75109379]|")
(COFACTORS MN+2 COMMENT "A number of other divalent metal ions were
acceptable, but Mn++ was the most effective. |CITS: [76253689]|")))
(3-OHMYRISTOYL-ACP NIL (
(OCELOT-GFP::PARENTS OH-ACYL-ACP)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(CHEMICAL-FORMULA (C 14) (H 27) (O 2) (ACP 1))
(STRUCTURE-BONDS (15 17 1) (1 4 1) (2 15 2) (16 3 1 :DOWN) (4 5 1) (5 6 1)
(6 7 1) (7 8 1) (8 9 1) (9 10 1) (10 11 1) (11 12 1) (12 13 1) (13 16 1)
(14 15 1) (14 16 1))
(DISPLAY-COORDS-2D (10.713d0 -0.0023d0) (0.7115d0 0.0d0) (2.8534d0 -1.2399d0)
(9.9985d0 -0.4148d0) (9.2841d0 -0.0023d0) (8.5695d0 -0.4148d0)
(7.8551d0 -0.0023d0) (7.1404d0 -0.4148d0) (6.426d0 -0.0023d0)
(5.7115d0 -0.4148d0) (4.997d0 -0.0023d0) (4.2825d0 -0.4148d0)
(3.5679d0 -0.0023d0) (2.139d0 -0.0023d0) (1.4244d0 -0.4148d0)
(2.8534d0 -0.4148d0) (1.423d0 -1.2398d0))
(STRUCTURE-ATOMS C O O C C C C C C C C C C C C C ACP)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(:CREATION-DATE 3054508280)
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(SYNONYMS "B1094" "AcpP" "3-hydroxytetradecanoyl-ACP")
(APPEARS-IN-LEFT-SIDE-OF UDPNACETYLGLUCOSAMACYLTRANS-RXN
UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN)
(COMMON-NAME "(R)-3-hydroxymyristoyl-ACP") )
NIL)
(|3-Oxo-5-Alpha-Steroids| T (
(OCELOT-GFP::PARENTS |3-Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (20 22 1) (19 22 1) (18 21 1) (17 19 1) (17 18 1) (16 21 1)
(14 20 1) (14 15 1) (13 21 1) (12 20 1) (11 22 1) (10 19 1) (10 13 1)
(9 17 1) (9 12 1) (8 18 1) (7 16 1) (7 8 1) (6 15 1) (6 11 1) (5 16 1)
(4 15 2) (3 22 1) (2 21 1) (20 1 1 :DOWN))
(DISPLAY-COORDS-2D (3.6373d0 0.0d0) (7.2746d0 -6.3d0) (3.6373d0 -4.2d0)
(0.0d0 -0.7d0) (9.0387d0 -6.6641d0) (1.2124d0 -2.8d0) (9.429d0 -4.2d0)
(8.6061d0 -3.0674d0) (6.0622d0 -1.4d0) (4.8497d0 -4.9d0) (2.4249d0 -3.5d0)
(4.8497d0 -0.7d0) (6.0622d0 -5.6d0) (2.4249d0 -0.7d0) (1.2124d0 -1.4d0)
(8.6061d0 -5.3326d0) (6.0622d0 -2.8d0) (7.2746d0 -3.5d0) (4.8497d0 -3.5d0)
(3.6373d0 -1.4d0) (7.2746d0 -4.9d0) (3.6373d0 -2.8d0))
(STRUCTURE-ATOMS H C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxo-5-α-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(|3-Oxo-5-Beta-Steroids| T (
(OCELOT-GFP::PARENTS |3-Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (20 22 1) (19 22 1) (18 21 1) (17 19 1) (17 18 1) (16 21 1)
(14 20 1) (14 15 1) (13 21 1) (12 20 1) (11 22 1) (10 19 1) (10 13 1)
(9 17 1) (9 12 1) (8 18 1) (7 16 1) (7 8 1) (6 15 1) (6 11 1) (5 16 1)
(4 15 2) (3 22 1) (2 21 1) (20 1 1 :UP))
(DISPLAY-COORDS-2D (3.6373d0 0.0d0) (7.2746d0 -6.3d0) (3.6373d0 -4.2d0)
(0.0d0 -0.7d0) (9.0387d0 -6.6641d0) (1.2124d0 -2.8d0) (9.429d0 -4.2d0)
(8.6061d0 -3.0674d0) (6.0622d0 -1.4d0) (4.8497d0 -4.9d0) (2.4249d0 -3.5d0)
(4.8497d0 -0.7d0) (6.0622d0 -5.6d0) (2.4249d0 -0.7d0) (1.2124d0 -1.4d0)
(8.6061d0 -5.3326d0) (6.0622d0 -2.8d0) (7.2746d0 -3.5d0) (4.8497d0 -3.5d0)
(3.6373d0 -1.4d0) (7.2746d0 -4.9d0) (3.6373d0 -2.8d0))
(STRUCTURE-ATOMS H C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxo-5-β-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(|3-oxo-D5-steroids| T (
(OCELOT-GFP::PARENTS |3-Oxosteroids|)
(DISPLAY-COORDS-2D (3.6373d0 -3.5d0) (7.2746d0 -5.6d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (4.8497d0 0.0d0) (6.0622d0 -0.7d0) (1.2124d0 -2.1d0)
(2.4249d0 0.0d0) (9.429d0 -3.5d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0)
(2.4249d0 -2.8d0) (6.0622d0 -4.9d0) (1.2124d0 -0.7d0) (3.6373d0 -0.7d0)
(8.6061d0 -4.6326d0) (6.0622d0 -2.1d0) (4.8497d0 -2.8d0) (7.2746d0 -2.8d0)
(3.6373d0 -2.1d0) (7.2746d0 -4.2d0))
(CHEMICAL-FORMULA (C 19) (H 27) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(13 21 1) (12 20 1) (11 18 1) (11 13 1) (10 19 1) (9 16 1) (9 10 1) (8 15 1)
(8 14 1) (7 14 1) (7 12 1) (6 17 1) (5 15 2) (5 6 1) (4 16 1) (3 14 2)
(2 21 1) (1 20 1))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxo-δ5-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|3-Oxo-Delta-1-Steroids| T (
(OCELOT-GFP::PARENTS |3-Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 27) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 20 1) (15 21 1)
(13 16 1) (13 14 1) (12 21 1) (11 18 1) (11 12 1) (10 19 1) (9 17 1)
(8 16 1) (8 9 1) (7 15 1) (7 10 1) (6 20 1) (5 14 1) (5 6 2) (4 15 1)
(3 14 2) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (3.6373d0 -3.5d0) (7.2746d0 -5.6d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (1.2124d0 -2.1d0) (2.4249d0 -2.8d0) (9.429d0 -3.5d0)
(4.8497d0 0.0d0) (6.0622d0 -0.7d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0)
(6.0622d0 -4.9d0) (2.4249d0 0.0d0) (1.2124d0 -0.7d0) (8.6061d0 -4.6326d0)
(3.6373d0 -0.7d0) (6.0622d0 -2.1d0) (4.8497d0 -2.8d0) (7.2746d0 -2.8d0)
(3.6373d0 -2.1d0) (7.2746d0 -4.2d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxo-D1-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(|3-Oxo-Delta-4-Steroids| T (
(OCELOT-GFP::PARENTS |3-Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 27) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(13 21 1) (12 20 1) (11 18 1) (11 13 1) (10 19 1) (9 16 1) (9 10 1) (8 17 1)
(7 14 1) (7 12 1) (6 15 1) (6 8 1) (5 15 2) (5 14 1) (4 16 1) (3 14 2)
(2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (3.6373d0 -3.5d0) (7.2746d0 -5.6d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (2.4249d0 0.0d0) (4.8497d0 0.0d0) (1.2124d0 -2.1d0)
(6.0622d0 -0.7d0) (9.429d0 -3.5d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0)
(2.4249d0 -2.8d0) (6.0622d0 -4.9d0) (1.2124d0 -0.7d0) (3.6373d0 -0.7d0)
(8.6061d0 -4.6326d0) (6.0622d0 -2.1d0) (4.8497d0 -2.8d0) (7.2746d0 -2.8d0)
(3.6373d0 -2.1d0) (7.2746d0 -4.2d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxo-δ4-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(3-OXOACYL-ACP-COA-SYNTHIII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin")
(ALTERNATIVE-SUBSTRATES (ACETYL-COA BUTYRYL-COA) (ACETYL-COA PROPIONYL-COA))
(INHIBITORS-OTHER ACYL-ACP)
(PHYSIOLOGICALLY-RELEVANT ACYL-ACP)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(INHIBITORS-COMPETITIVE BUTYRYL-COA ACYL-ACP)
(REACTION 3-OXOACYL-ACP-COA-SYNTHIII-RXN)
(COMMENT "There are three β-ketoacyl-ACP synthases (KAS) in E.
coli. All three are genetically and biochemically distinct. Each of
the three enzymes is capable of initiating fatty acid biosynthesis.
KASIII is coded for by the fabH gene and has recently been shown to
also possess acetyl CoA:ACP transacylase activity. KASIII selectively
catalyzes the formation of acetoacetyl-ACP and specifically uses CoA
thioesters rather than acyl-ACP as the primer. The products tend to
be shorter than the products of KASI and II. It cannot participate
in the terminal elongation steps of fatty acid biosynthesis. KASIII is inhibited
by acyl-ACP, indicating a role in feedback regulation of fatty acid synthesis.
As KASIII catalyzes the first condensation step in fatty acid synthesis, it
is ideally situated in the pathway to control the rate of fatty acid initiation.
|CITS: [96210042] [96147146] [89214213] [92202232] [94066913]|")
(ENZYME CPLX0-252)
(SYNONYMS "3-oxoacyl-ACP synthase III" "KASIII" "acetoacetyl-ACP synthase"
"acyl-[acyl carrier protein]:malonyl-[acyl carrier protein] C-acyltransferase (decarboxylating)"
"β-ketoacyl-acyl carrier protein synthase III")
(COMMON-NAME "β-ketoacyl-ACP synthase III")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabH.template")
(:CREATION-DATE 3001089029)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "thiolactomycin" COMMENT
"Cerulenin and thiolactomycin are antibiotics.")
(INHIBITORS-UNKMECH "thiolactomycin" CITATIONS "[89214213]")
(INHIBITORS-OTHER ACYL-ACP COMMENT
"Acyl-ACP showed a mixed type inhibition with respect to acetyl-CoA.")
(ALTERNATIVE-SUBSTRATES (ACETYL-COA BUTYRYL-COA) CITATIONS "[96210042]")
(ALTERNATIVE-SUBSTRATES (ACETYL-COA PROPIONYL-COA) CITATIONS "[96210042]")
(INHIBITORS-OTHER ACYL-ACP CITATIONS "96210042")
(INHIBITORS-COMPETITIVE ACYL-ACP COMMENT
"Acyl-ACP was competitive with respect to malonyl-ACP. |CITS: [96210042]|")))
(3-OXOACYL-ACP-COA-SYNTHIII-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(EC-NUMBER "2.3.1.-")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY FASYN-INITIAL-PWY)
(ENZYMATIC-REACTION 3-OXOACYL-ACP-COA-SYNTHIII-ENZRXN)
(RIGHT |Acetoacetyl-ACPs| CO-A CARBON-DIOXIDE)
(LEFT ACETYL-COA MALONYL-ACP)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabH.template")
(:CREATION-DATE 3001089029)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-REDUCT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3-OXOACYL-ACP-REDUCT-RXN)
(COMMENT
"β-ketoacyl-ACP reductase exhibits a marked preference for acyl-carrier
protein derivatives over CoA derivatives as substrates. The enzyme shows
activity towards both short and long chain saturated and unsaturated
β-ketoacyl-ACPs. The reductase functions in every cycle of the fatty acid
elongation pathway. Other reductases of this type also exist
in E. coli. |CITS: [94066913] [97066974]|")
(ENZYME 3-OXOACYL-ACP-REDUCT-MONOMER)
(SYNONYMS "β-ketoacyl-ACP reductase"
"(3R)-3-hydroxyacyl-[ACP]:NADP+ oxidoreductase" "3-ketoacyl-ACP reductase"
"3-oxoacyl-[acyl-carrier-protein] reductase"
"3-ketoacyl-acyl carrier protein reductase")
(COMMON-NAME "β-ketoacyl-[acyl-carrier-protein] reductase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabG.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-REDUCT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT-INTERNAL "3/17/06 keseler removed FabD, AccD as synonyms")
(SYNONYMS "B1093" "FabG")
(DBLINKS (MODBASE "P0AEK2" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0AEK2" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00106" IN-FAMILY |pkarp| 3346700328 NIL NIL)
(PDB "1Q7B" NIL |pkarp| 3346695108 NIL NIL)
(UNIPROT "P0AEK2" NIL |pkarp| 3343984414 NIL NIL)
(REFSEQ "NP_415611" NIL NIL NIL NIL NIL) (PDB "1I01"))
(CATALYZES ENZRXN0-2861 3-OXOACYL-ACP-REDUCT-ENZRXN)
(PI 7.38d0)
(MOLECULAR-WEIGHT-SEQ 25.560256999999993d0)
(GENE EG11318)
(COMMENT "Cotranscribed with acpP. |CITS: [92210530]|")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabG.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-REDUCT-RXN NIL (
(OCELOT-GFP::PARENTS EC-1.1.1 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY FASYN-ELONG-PWY)
(ENZYMATIC-REACTION 3-OXOACYL-ACP-REDUCT-ENZRXN)
(RIGHT NADPH B-KETOACYL-ACP)
(LEFT OH-ACYL-ACP NADP)
(EC-NUMBER "1.1.1.100")
(COMMENT "This is the first reduction step in the fatty acid
biosynthesis pathway.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabG.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-SYNTH-BASE-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY FASYN-INITIAL-PWY)
(ENZYMATIC-REACTION 3-OXOACYL-ACP-SYNTHI-BASE-ENZRXN
3-OXOACYL-ACP-SYNTHII-BASE-ENZRXN)
(RIGHT |All-ACPs| |Acetoacetyl-ACPs| CARBON-DIOXIDE)
(LEFT ACETYL-ACP MALONYL-ACP)
(EC-NUMBER "2.3.1.41")
(COMMENT "This reaction is involved in the elongation of fatty acids.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabB.template")
(:CREATION-DATE 3001089023)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-SYNTH-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY FASYN-ELONG-PWY)
(ENZYMATIC-REACTION 3-OXOACYL-ACP-SYNTHII-ENZRXN 3-OXOACYL-ACP-SYNTHI-ENZRXN)
(RIGHT ACP B-KETOACYL-ACP CARBON-DIOXIDE)
(LEFT ACYL-ACP MALONYL-ACP)
(EC-NUMBER "2.3.1.41")
(COMMENT "This reaction is involved in the elongation of fatty acids.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabB.template")
(:CREATION-DATE 3001089023)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-SYNTHI-BASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin" CPD-6901 IODOACETAMIDE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(REACTION 3-OXOACYL-ACP-SYNTH-BASE-RXN)
(COMMENT "There are three β-ketoacyl-ACP synthases (KAS) in E.
coli. All three are genetically and biochemically distinct. Each of
the three enzymes is capable of initiating fatty acid biosynthesis.
KASI is coded for by the fabB gene and differs from the others in that
it alone is required for the elongation of short-chain unsaturated
acyl-ACP. It can catalyze all the condensation reactions of long
chain fatty acid synthesis except the elongation of pamitoleoyl-ACP,
and is also capable of initiating fatty acid synthesis in the absence
of acetyl-ACP primer by the utilization of a side reaction involving
malonyl-ACP decarboxylase. |CITS: [81069887] [89214213] [94066913]|")
(ENZYME FABB-CPLX)
(SYNONYMS "3-oxoacyl-ACP-synthase I"
"3-oxoacyl-[acyl-carrier-protein]-synthase I" "KASI"
"acyl-[acyl carrier protein]:malonyl-[acyl carrier protein] C-acyltransferase (decarboxylating)")
(COMMON-NAME "β-ketoacyl-ACP synthase I")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabB.template")
(:CREATION-DATE 3001089023)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "thiolactomycin" COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH "thiolactomycin" CITATIONS "[89214213]")
(INHIBITORS-UNKMECH CPD-6901 COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH CPD-6901 CITATIONS "[87222428]")
(INHIBITORS-UNKMECH IODOACETAMIDE COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH IODOACETAMIDE CITATIONS "[70042059]")))
(3-OXOACYL-ACP-SYNTHI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin" CPD-6901 IODOACETAMIDE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(ALTERNATIVE-SUBSTRATES
(ACYL-ACP "saturated and unsaturated acyl-ACPs of various lengths"))
(REACTION 3-OXOACYL-ACP-SYNTH-RXN)
(COMMENT "There are three β-ketoacyl-ACP synthases (KAS) in E.
coli. All three are genetically and biochemically distinct. Each of
the three enzymes is capable of initiating fatty acid biosynthesis.
KASI is coded for by the fabB gene and differs from the others in that
it alone is required for the elongation of short-chain unsaturated
acyl-ACP. It can catalyze all the condensation reactions of long
chain fatty acid synthesis except the elongation of pamitoleoyl-ACP,
and is also capable of initiating fatty acid synthesis in the absence
of acetyl-ACP primer by the utilization of a side reaction involving
malonyl-ACP decarboxylase. |CITS: [81069887] [89214213] [94066913]|")
(ENZYME FABB-CPLX)
(SYNONYMS "3-oxoacyl-ACP-synthase I"
"3-oxoacyl-[acyl-carrier-protein]-synthase I" "KASI"
"acyl-[acyl carrier protein]:malonyl-[acyl carrier protein] C-acyltransferase (decarboxylating)")
(COMMON-NAME "β-ketoacyl-ACP synthase I")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabB.template")
(:CREATION-DATE 3001089023)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "thiolactomycin" COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH "thiolactomycin" CITATIONS "[89214213]")
(INHIBITORS-UNKMECH CPD-6901 COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH CPD-6901 CITATIONS "[87222428]")
(INHIBITORS-UNKMECH IODOACETAMIDE COMMENT "cerulenin and
thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH IODOACETAMIDE CITATIONS "[70042059]")))
(3-OXOACYL-ACP-SYNTHII-BASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin" CPD-6901)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(ALTERNATIVE-SUBSTRATES (MALONYL-ACP PALMITOLEOYL-ACP))
(REACTION 3-OXOACYL-ACP-SYNTH-BASE-RXN)
(COMMENT "There are three β-ketoacyl-ACP synthases (KAS) in E.
coli. All three are genetically and biochemically distinct. Each of
the three enzymes is capable of initiating fatty acid biosynthesis.
KASII is coded for by the fabF gene and the enzyme plays a major role
in the thermal regulation of fatty acid composition of the membrane
phospholipids of E. coli. KASII is also needed for the elongation of
palmitoleate to cis-vaccenate, which is essential to temperature
control of fatty acid composition of membrane phospholipids. KASI
does not carry out this reaction. KasII does not synthesize
unsaturated fatty acids. |CITS: [80159932] [81069887] [89214213]|")
(ENZYME 3-OXOACYL-ACP-SYNTHII-CPLX)
(SYNONYMS "3-oxoacyl-ACP synthase II"
"β ketoacyl-acyl carrier protein synthase II")
(COMMON-NAME "β-ketoacyl-ACP synthase II")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabF.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
NIL)
(3-OXOACYL-ACP-SYNTHII-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 3-OXOACYL-ACP-SYNTHII-BASE-ENZRXN 3-OXOACYL-ACP-SYNTHII-ENZRXN)
(COMPONENTS 3-OXOACYL-ACP-SYNTHII-MONOMER)
(SYNONYMS "3-oxoacyl-ACP synthase II" "KASII"
"acyl-[acyl carrier protein]:malonyl-[acyl carrier protein] C-acyltransferase (decarboxylating)"
"β ketoacyl-acyl carrier protein synthase I")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabF.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
((COMPONENTS 3-OXOACYL-ACP-SYNTHII-MONOMER COEFFICIENT 2)))
(3-OXOACYL-ACP-SYNTHII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin" CPD-6901)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(ALTERNATIVE-SUBSTRATES (MALONYL-ACP PALMITOLEOYL-ACP))
(REACTION 3-OXOACYL-ACP-SYNTH-RXN)
(COMMENT "There are three β-ketoacyl-ACP synthases (KAS) in E.
coli. All three are genetically and biochemically distinct. Each of
the three enzymes is capable of initiating fatty acid biosynthesis.
KASII is coded for by the fabF gene and the enzyme plays a major role
in the thermal regulation of fatty acid composition of the membrane
phospholipids of E. coli. KASII is also needed for the elongation of
palmitoleate to cis-vaccenate, which is essential to temperature
control of fatty acid composition of membrane phospholipids. KASI
does not carry out this reaction. KasII does not synthesize
unsaturated fatty acids. |CITS: [80159932] [81069887] [89214213]|")
(ENZYME 3-OXOACYL-ACP-SYNTHII-CPLX)
(SYNONYMS "3-oxoacyl-ACP synthase II")
(COMMON-NAME "β-ketoacyl-ACP synthase II")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabF.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "thiolactomycin" COMMENT
"Cerulenin and thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH "thiolactomycin" CITATIONS "[89214213]")
(INHIBITORS-UNKMECH CPD-6901 COMMENT
"Cerulenin and thiolactomycin are antibiotics")
(INHIBITORS-UNKMECH CPD-6901 CITATIONS "[87222428]")
(ALTERNATIVE-SUBSTRATES (MALONYL-ACP PALMITOLEOYL-ACP) CITATIONS
"[81069887]")))
(3-OXOACYL-ACP-SYNTHII-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1095" "Vtr" "Cvc" "VtrB" "FabJ" "FabF")
(DBLINKS (PFAM "PF00109" IN-FAMILY |pkarp| 3346700328 NIL NIL)
(UNIPROT "P0AAI5" NIL |pkarp| 3343984388 NIL NIL)
(REFSEQ "NP_415613" NIL NIL NIL NIL NIL) (PDB "1KAS"))
(COMMON-NAME "FabF")
(COMPONENT-OF 3-OXOACYL-ACP-SYNTHII-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (FABB-MONOMER NO))
(MOLECULAR-WEIGHT-SEQ 43.04571299999991d0)
(GENE EG12606)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabF.template")
(:CREATION-DATE 3001089027)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-SEQ :FACET COMMENT "The apparent weight of the
enzyme was between 44.000 and 45.000 |CITS: [81069887]|")))
(|3-Oxosteroids| T (
(OCELOT-GFP::PARENTS |Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (15 20 1)
(13 16 1) (13 14 1) (12 20 1) (11 21 1) (10 19 1) (10 12 1) (9 18 1)
(8 17 1) (7 16 1) (7 8 1) (6 15 1) (6 9 1) (5 14 1) (5 11 1) (4 15 1)
(3 14 2) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (7.2746d0 -5.6d0) (3.6373d0 -3.5d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (1.2124d0 -2.1d0) (9.429d0 -3.5d0) (4.8497d0 0.0d0)
(6.0622d0 -0.7d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0) (2.4249d0 -2.8d0)
(6.0622d0 -4.9d0) (2.4249d0 0.0d0) (1.2124d0 -0.7d0) (8.6061d0 -4.6326d0)
(3.6373d0 -0.7d0) (6.0622d0 -2.1d0) (7.2746d0 -2.8d0) (4.8497d0 -2.8d0)
(7.2746d0 -4.2d0) (3.6373d0 -2.1d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3-oxosteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(3-P-HYDROXYPYRUVATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF KETOGLUTREDUCT-ENZRXN)
(DBLINKS (LIGAND-CPD "C03232" NIL |kr| 3346617699 NIL NIL) (CAS "3913-50-6"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -150.6d0)
(COMMON-NAME "3-phospho-hydroxypyruvate")
(APPEARS-IN-RIGHT-SIDE-OF PSERTRANSAM-RXN PGLYCDEHYDROG-RXN)
(MOLECULAR-WEIGHT 184.042d0)
(CHEMICAL-FORMULA (C 3) (H 5) (O 7) (P 1))
(DISPLAY-COORDS-2D (0.7d0 -0.08d0) (-0.65333d0 -1.0d0)
(-0.65333d0 -0.65333d0) (-0.65333d0 -0.30667d0) (-0.01333d0 -0.43333d0)
(0.33667d0 -0.64667d0) (-1.0d0 -0.65333d0) (0.33667d0 -0.3d0)
(0.7d0 -0.42667d0) (0.99667d0 -0.60333d0) (-0.3d0 -0.65333d0))
(STRUCTURE-BONDS (11 3 1) (10 9 1) (9 6 1) (8 6 2) (7 3 1) (6 5 1) (5 11 1)
(4 3 2) (2 3 1) (1 9 2))
(STRUCTURE-ATOMS O O P O C C O O C O O)
(SYNONYMS "3-phosphonooxypyruvate" "3-P-hydroxypyruvate" "3-p-OH-pyr"
"3-phosphohydroxypyruvate" "3-p-OH-pyruvate" "3-p-hydroxy-pyr"
"3-phosphohydroxy-pyr" "phosphohydroxypyruate") )
((GIBBS-0 -150.6d0 CITATIONS "GibbsGroups97")))
(3-P-SERINE NIL (
(OCELOT-GFP::PARENTS |Phosphoserines|)
(INHIBITORS-NONCOMPETITIVE-OF ORNDECARBOX-BIO-ENZRXN)
(DBLINKS (CAS "407-41-0" NIL |kr| 3346617700 NIL NIL)
(LIGAND-CPD "C01005" NIL |kr| 3346617700 NIL NIL)
(CAS "17885-08-4" NIL |kaipa| 3311532843 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -123.9d0)
(COMMON-NAME "3-phospho-serine")
(APPEARS-IN-LEFT-SIDE-OF RXN0-5114 PSERTRANSAM-RXN TRANS-RXN-37)
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-37)
(MOLECULAR-WEIGHT 185.073d0)
(CHEMICAL-FORMULA (C 3) (H 8) (N 1) (O 6) (P 1))
(DISPLAY-COORDS-2D (0.04d0 0.04923d0) (0.51385d0 0.52308d0)
(0.04d0 0.52308d0) (0.04d0 0.99692d0) (-1.0d0 0.52308d0) (-1.0d0 -0.01846d0)
(-0.52615d0 -0.01846d0) (-0.52615d0 -0.52615d0) (-1.0d0 -0.52615d0)
(-1.0d0 -1.0d0) (-0.50769d0 0.52308d0))
(STRUCTURE-BONDS (11 3 1) (10 9 1) (9 6 1) (8 9 2) (7 6 1) (6 5 1) (5 11 1)
(4 3 2) (2 3 1) (1 3 1))
(STRUCTURE-ATOMS O O P O C C N O C O O)
(SYNONYMS "O-phospho-L-serine" "serine phosphate" "phosphorylserine"
"seryl phosphate" "3-P-serine" "serine-3-p" "serine-3-phosphate"
"phosphoserine" "P-serine" "3-phospho-1-serine" "P-ser" "3-phosphoserine") )
((GIBBS-0 -123.9d0 CITATIONS "GibbsGroups97")))
(3-P-SHIK-1-CARBOXYVINYLXFERASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH 3-BROMOPYRUVATE PYRIDOXAL_PHOSPHATE
3-ENOLPYRUVYL-SHIKIMATE-5P)
(SYNONYMS "5-enol-pyruvylshikimate-3-phosphate synthase" "EPSP synthase"
"phosphoenolpyruvate: 3-phosphoshikimate 1-carboxyvinyl transferase")
(COMMON-NAME "3-phosphoshikimate-1-carboxyvinyltransferase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 2.5.1.19-RXN)
(CITATIONS ":EV-EXP:3277835749:pkarp" "[FEBS(84)170-59]" "[83308516]"
"[72063512]" "[86215119]" "[84108861]" "[88087192]")
(INHIBITORS-COMPETITIVE "glyphosate")
(COMMENT "EPSP synthase catalyzes the transfer of the enolpyruvoyl
moiety from phosphoenolpyruvate to the hydroxyl group of carbon 5 of
shikimate 3-phosphate with the elimination of phosphate to produce
5-enolpyruvoyl shikimate 3-phosphate (EPSP). |CITS:[88209530]|
This is an addition-elimination
reaction. It is an ordered reaction in which shikimate 3-phosphate
binds first. It involves the transfer of an enolpyruvyl group unchanged
to the acceptor molecule. The reaction introduces the three carbon
fragment that is destined to become the side chain of phenylalanine and
tyrosine and to be removed again in the synthesis of tryptophan.
|CITS:[ColiSalII]| Two reactive cysteines have been identified.
|CITS:[JBC263-1798-88]| A lysine has been designated a potential
active site residue |CITS:[88087192]| Mechanistic and steriochemical
studies on EPSP synthase suggest that a phospholactyl intermediate is
produced at least transiently during the enzymatic reaction by
addition of a nucleophile to C-2 of P-enolpyruvate on the pathway to
phosphate release. The nucleophie may be the side chain of an active
site amino acid residue based on the exchange of the C-3 hydrogens of
P-enolpyruvate in the presense of the substrate analog
4,5-deoxyshikimate 3-phosphate|CITS:[JBC263-1798-88]|")
(ENZYME AROA-MONOMER)
(:CREATION-DATE 2955043943)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH 3-BROMOPYRUVATE CITATIONS "[91112841]" "[HandEnzInh]")))
(3-PHENYLPROPIONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER0-2081)
(DBLINKS (CAS "2628-17-3" NIL |kr| 3346617699 NIL NIL)
(LIGAND-CPD "C05629" NIL |kr| 3346617699 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3112732531)
(AROMATIC-RINGS (2 3 4 5 6 1))
(DISPLAY-COORDS-2D (1.7243d0 7.5445d0) (1.0225d0 8.7751d0)
(1.7353d0 9.9971d0) (3.1499d0 9.9883d0) (3.8517d0 8.7577d0)
(3.1389d0 7.5358d0) (5.075d0 8.0417d0) (6.3d0 8.75d0) (7.525d0 8.0375d0)
(8.7536d0 8.7421d0) (7.5195d0 6.6204d0))
(CHEMICAL-FORMULA (C 9) (H 10) (O 2))
(MOLECULAR-WEIGHT 150.177d0)
(STRUCTURE-BONDS (9 11 2) (9 10 1) (5 4 :AROMATIC) (4 3 :AROMATIC) (8 9 1)
(3 2 :AROMATIC) (7 8 1) (2 1 :AROMATIC) (5 7 1) (1 6 :AROMATIC)
(6 5 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C C C C O O)
(APPEARS-IN-LEFT-SIDE-OF HCAMULTI-RXN RXN0-4101)
(COMMON-NAME "3-phenylpropionate")
(SYNONYMS "3-phenylpropionic acid" "hydrocinnamic acid" "HCA"
"Phenylpropanoate") )
NIL)
(|3-Phosphopolynucleotides| T (
(OCELOT-GFP::PARENTS |Polynucleotides|)
(COMMON-NAME "a 3'-phosphopolynucleotide")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(|3-Prime-Phosphate-Terminated-RNAs| T (
(OCELOT-GFP::PARENTS RNA)
(APPEARS-IN-LEFT-SIDE-OF |RNA-3'-PHOSPHATE-CYCLASE-RXN|)
(SYNONYMS "a 3'-phosphate-terminated RNA" "3'-phosphate-terminated RNA"
"RNA 3'-terminal-phosphate")
(COMMENT
"This compound class collects RNA species that are terminated by a 3'-phosphate.")
(:CREATOR |kr|)
(:CREATION-DATE 3265477947) )
NIL)
(|3-Prime-Ribonucleoside-Monophosphates| T (
(OCELOT-GFP::PARENTS |Nucleotides|)
(DISPLAY-COORDS-2D (0.0d0 -3.3308d0) (3.0756d0 -2.5238d0)
(0.1715d0 -2.5238d0) (1.6236d0 -2.7538d0) (2.521d0 -0.8169d0)
(1.2111d0 -1.4843d0) (2.291d0 -2.2689d0) (0.9562d0 -2.2689d0)
(2.0361d0 -1.4843d0) (0.7262d0 -0.8169d0) (-0.0988d0 -1.6419d0)
(-0.9238d0 -0.8169d0) (-0.0988d0 -0.8169d0) (-0.0988d0 0.0081d0))
(CHEMICAL-FORMULA (C 5) (H 10) (O 7) (R 1) (P 1))
(STRUCTURE-BONDS (13 14 2) (13 11 1) (13 12 1) (10 13 1) (1 3 1)
(6 10 1 :DOWN) (7 2 1 :UP) (8 3 1 :UP) (4 7 1) (4 8 1) (9 5 1 :DOWN) (6 8 1)
(6 9 1) (7 9 1))
(STRUCTURE-ATOMS O R C O O C C C C O O O P O)
(APPEARS-IN-RIGHT-SIDE-OF CYCPHOSDIESTER-RXN)
(APPEARS-IN-LEFT-SIDE-OF 3-NUCLEOTID-RXN)
(SYNONYMS "nucleoside 3'-phosphate" "a 3'-ribonucleotide")
(COMMON-NAME "a nucleoside 3'-phosphate")
(:CREATOR |kr|)
(:CREATION-DATE 3263063511) )
NIL)
(3-SULFINOALANINE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(HISTORY |kr-3290870141|)
(DBLINKS (LIGAND-CPD "C00606" NIL |kaipa| 3311532637 NIL NIL)
(CAS "1115-65-7"))
(APPEARS-IN-LEFT-SIDE-OF RXN0-279)
(:CREATION-DATE 3169827339)
(SYNONYMS "3-Sulfino-L-alanine" "L-Cysteinesulfinic acid"
"3-sulphino-L-alanine")
(MOLECULAR-WEIGHT 153.153d0)
(CHEMICAL-FORMULA (C 3) (H 7) (N 1) (O 4) (S 1))
(DISPLAY-COORDS-2D (1.151d0 0.1753d0) (1.8407d0 -0.0841d0)
(1.8268d0 -0.8437d0) (2.53d0 -1.0998d0) (2.4566d0 0.3628d0)
(1.2085d0 -1.2683d0) (3.1416d0 0.0572d0) (3.7487d0 0.4977d0)
(3.1236d0 -0.7262d0))
(STRUCTURE-BONDS (7 9 2) (7 8 1) (5 7 1) (3 6 1) (2 5 1) (3 4 2) (2 3 1)
(2 1 1 :DOWN))
(STRUCTURE-ATOMS N C C O C O S O O)
(COMMON-NAME "3-sulfinoalanine")
(:CREATOR |ptoole|) )
NIL)
(3.1.13.1-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.13)
(ENZYMATIC-REACTION ENZRXN0-4921 ENZRXN0-3101)
(OFFICIAL-EC? T)
(SYNONYMS "Ribonuclease II")
(COMMON-NAME "Exoribonuclease II")
(:CREATION-DATE 3286206697)
(:CREATOR |arnaud|)
(EC-NUMBER "3.1.13.1") )
NIL)
(3.1.13.3-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.13)
(COMMENT "from the IUBMB Enzyme Nomenclature web site:
\"Exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates.
Also hydrolyses NAD+ to NMN and AMP. Formerly EC 3.1.4.19.\"")
(ENZYMATIC-REACTION ENZRXN0-2681)
(OFFICIAL-EC? T)
(COMMON-NAME "Oligonucleotidase")
(:CREATION-DATE 3283883588)
(:CREATOR |arnaud|)
(EC-NUMBER "3.1.13.3") )
NIL)
(3.1.21.1-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.21)
(COMMENT "This reaction is the endonucleolytic cleavage of duplex DNA.")
(ENZYMATIC-REACTION ENZRXN0-6154)
(:CREATOR |keseler|)
(:CREATION-DATE 3344972089)
(EC-NUMBER "3.1.21.1")
(COMMON-NAME "Deoxyribonuclease I")
(SYNONYMS "Thymonuclease" "DNase" "Pancreatic DNase")
(OFFICIAL-EC? T) )
NIL)
(3.1.26.3-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.26)
(CITATIONS "1091644")
(COMMENT
"This reaction is the endonucleolytic cleavage of double-stranded RNA to yield a 5'-phosphate and a 3'-hydroxyl.")
(ENZYMATIC-REACTION ENZRXN0-4961)
(:CREATOR |shearer|)
(:CREATION-DATE 3321300060)
(EC-NUMBER "3.1.26.3")
(COMMON-NAME "Ribonuclease III")
(SYNONYMS "RNase D" "RNase O" "RNase III")
(OFFICIAL-EC? T) )
NIL)
(3.1.26.4-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.26)
(CITATIONS "4572736")
(COMMENT
"This reaction is the endonucleolytic cleavage of RNA in an RNA-DNA hybrid to yield a 5'-phosphomonoester.")
(ENZYMATIC-REACTION ENZRXN0-5521 ENZRXN0-5501)
(:CREATOR |shearer|)
(:CREATION-DATE 3329833169)
(EC-NUMBER "3.1.26.4")
(COMMON-NAME "Ribonuclease H")
(SYNONYMS "RNase H" "Endoribonuclease H")
(OFFICIAL-EC? T) )
NIL)
(3.1.26.5-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.26)
(ENZYMATIC-REACTION ENZRXN0-1981)
(OFFICIAL-EC? T)
(SPECIES ECOLI)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3069621160)
(:CREATOR |kr|)
(EC-NUMBER "3.1.26.5")
(COMMENT
"ENDONUCLEOLYTIC CLEAVAGE OF RNA, REMOVING 5'-EXTRA-NUCLEOTIDE FROM TRNA PRECURSOR."
"ESSENTIAL FOR TRNA PROCESSING; GENERATES 5'-TERMINI OF MATURE TRNA MOLECULES."
"SIMILAR ENZYME: RNASE P3.")
(COMMON-NAME "RIBONUCLEASE P") )
NIL)
(3.1.27.6-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.27)
(CITATIONS "SPAHR1961")
(COMMENT
"This reaction is the endonucleolytic cleavage of RNA to yield nucleoside 3'-phosphates and
3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.")
(ENZYMATIC-REACTION ENZRXN0-4901)
(:CREATOR |shearer|)
(:CREATION-DATE 3320430640)
(EC-NUMBER "3.1.27.6")
(COMMON-NAME "Enterobacter ribonuclease")
(OFFICIAL-EC? T) )
NIL)
(3.1.3.16-RXN NIL (
(OCELOT-GFP::PARENTS EC-3.1.3 |Protein-Modification-Reactions|)
(COMMENT
"A group of reactions removing the serine- or threonine-bound phosphate group from a wide
range of phosphoproteins, including enzymes that have been phosphorylated by the action
of a kinase (cf EC 3.1.3.48). In some cases, these reactions can also act on
phenolic phosphates and phosphamides.")
(ENZYMATIC-REACTION ENZRXN0-1631 ENZRXN0-1629)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "3.1.3.16")
(COMMON-NAME "SERINE/THREONINE-SPECIFIC-PROTEIN-PHOSPHATASE")
(RIGHT |Pi| |Protein|)
(LEFT WATER A-PHOSPHOPROTEIN)
(SYNONYMS "PHOSPHOPROTEIN PHOSPHATASE" "PROTEIN PHOSPHATASE-1"
"PROTEIN PHOSPHATASE-2A" "PROTEIN PHOSPHATASE-2B" "PROTEIN PHOSPHATASE-2C") )
NIL)
(3.1.4.14-RXN NIL (
(OCELOT-GFP::PARENTS EC-3.1.4 |Protein-Modification-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-5902)
(:CREATOR |mhance|)
(:CREATION-DATE 3334504316)
(LEFT WATER ACP)
(RIGHT |apo-ACP| PANTETHEINE-P)
(EC-NUMBER "3.1.4.14")
(COMMON-NAME "[Acyl-carrier protein] phosphodiesterase")
(OFFICIAL-EC? T) )
NIL)
(3.1.4.17-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.4)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2422)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3279912720)
(COMMON-NAME "3',5'-cyclic-nucleotide phosphodiesterase")
(EC-NUMBER "3.1.4.17")
(RIGHT NUC-5-PHOSPHATE)
(LEFT WATER |Cyclic-3-5-Ribonucleoside-Monophosphates|) )
NIL)
(3.2.1.21-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(ENZYMATIC-REACTION ENZRXN0-6204)
(:CREATOR |shearer|)
(:CREATION-DATE 3356361196)
(EC-NUMBER "3.2.1.21")
(COMMON-NAME "β-glucosidase")
(SYNONYMS "β-D-glucosidase" "Amygdalase" "Cellobiase" "Gentobiase")
(OFFICIAL-EC? T) )
NIL)
(3.2.1.33-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(COMMENT
"Reaction: Hydrolysis of (1-->6)-a-D-glucosidic branch linkages in glycogen phosphorylase limit dextrin.")
(ENZYMATIC-REACTION ENZRXN0-2142)
(OFFICIAL-EC? T)
(SYNONYMS "Dextrin 6-α-D-glucosidase")
(COMMON-NAME "Amylo-1,6-glucosidase")
(:CREATION-DATE 3275414917)
(:CREATOR |arnaud|)
(EC-NUMBER "3.2.1.33") )
NIL)
(3.2.1.37-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(ENZYMATIC-REACTION ENZRXN0-3321)
(OFFICIAL-EC? T)
(SYNONYMS "Exo-1,4-β-xylosidase" "Xylobiase"
"1,4-β-D-xylan xylohydrolase" "β-xylosidase")
(COMMON-NAME "Xylan 1,4-β-xylosidase")
(:CREATION-DATE 3287765560)
(:CREATOR |arnaud|)
(EC-NUMBER "3.2.1.37") )
NIL)
(3.2.1.52-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-241)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3177262225)
(:CREATOR |ptoole|)
(EC-NUMBER "3.2.1.52")
(SYNONYMS "β-HEXOSAMINIDASE" "HEXOSAMINIDASE"
"N-ACETYL-β-GLUCOSAMINIDASE")
(COMMON-NAME "β-N-ACETYLHEXOSAMINIDASE") )
NIL)
(3.4.11.1-RXN NIL (
(OCELOT-GFP::PARENTS EC-3.4.11 |Protein-Modification-Reactions|)
(RIGHT |Amino-Acid| |Peptides|)
(LEFT |Peptides| WATER)
(CITATIONS "355237" "11157967")
(COMMENT
"This reaction is the hydrolysis of a peptide bond in a dipeptide. Substrates include cysteinylglycine.")
(ENZYMATIC-REACTION ENZRXN0-4441)
(:CREATOR |shearer|)
(:CREATION-DATE 3316815181)
(EC-NUMBER "3.4.11.1")
(COMMON-NAME "Leucyl aminopeptidase")
(SYNONYMS "Peptidase S" "Leucine aminopeptidase" "Cytosol aminopeptidase")
(OFFICIAL-EC? T) )
((RIGHT |Peptides| NAME-SLOT N-1-NAME) (LEFT |Peptides| NAME-SLOT N-NAME)))
(3.4.11.18-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.11)
(ENZYMATIC-REACTION ENZRXN0-3801)
(OFFICIAL-EC? T)
(SYNONYMS "Peptidase M" "Methionine aminopeptidase")
(COMMON-NAME "Methionyl aminopeptidase")
(:CREATION-DATE 3304704318)
(:CREATOR |keseler|)
(EC-NUMBER "3.4.11.18") )
NIL)
(3.4.11.2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.11)
(COMMENT
"This reaction is the hydrolysis of a peptide bond either at the end of a small peptide or
in the middle of a protein. In its exopeptidase activity, this reaction shows a cleavage
preference for basic and small amino acids, in the order arginine > alanine > lysine > glycine |CITS: [14663077]|.
Other substrates include cysteinylglycine |CITS: [11157967]|. Phosphorylation of peptide side chains near the cut site
can prevent hydrolysis of the peptide bond |CITS: [9026356]|.")
(ENZYMATIC-REACTION ENZRXN0-4461)
(:CREATOR |shearer|)
(:CREATION-DATE 3316889125)
(EC-NUMBER "3.4.11.2")
(COMMON-NAME "Membrane alanine aminopeptidase")
(SYNONYMS "Peptidase E" "Membrane aminopeptidase I" "Amino-oligopeptidase"
"Particle-bound aminopeptidase" "Aminopeptidase N" "Aminopeptidase M"
"Microsomal aminopeptidase")
(OFFICIAL-EC? T) )
NIL)
(3.4.11.4-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.11)
(CITATIONS "764862" "356879")
(COMMENT
"This reaction is the hydrolysis of a peptide bond between the most first and second residues in
a tripeptide. It can cleave peptides beginning with leucine, lysine, methionine and phenylalanine,
including x-glycine-glycine, x-glycine-x and x-leucine-glycine. It cannot cleave dipeptides or
tetrapeptides.")
(ENZYMATIC-REACTION ENZRXN0-4421)
(:CREATOR |shearer|)
(:CREATION-DATE 3316790908)
(EC-NUMBER "3.4.11.4")
(COMMON-NAME "Tripeptide aminopeptidase")
(SYNONYMS "Peptidase B" "Imidoendopeptidase" "Lymphopeptidase"
"Aminoexotripeptidase" "Aminotripeptidase" "Tripeptidase")
(OFFICIAL-EC? T) )
NIL)
(3.4.11.9-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.11)
(CITATIONS "2851590" "8185318")
(COMMENT
"This reaction is the hydrolysis of a peptide bond between the amino-terminal
residue of a polypeptide and the following residue, as long as the following
residue is proline. Hydrolysis of dipeptides is slower than hydrolysis of
longer polypeptides. Dipeptides with proline followed by a hydrophobic
residue competitively inhibit this reaction.")
(ENZYMATIC-REACTION ENZRXN0-4481)
(:CREATOR |shearer|)
(:CREATION-DATE 3316966751)
(EC-NUMBER "3.4.11.9")
(COMMON-NAME "Xaa-Pro aminopeptidase")
(SYNONYMS "Aminoacylproline aminopeptidase" "Aminopeptidase P"
"Proline aminopeptidase" "X-Pro aminopeptidase")
(OFFICIAL-EC? T) )
NIL)
(3.4.13.21-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.13)
(COMMENT
"This reaction is the hydrolysis of a peptide bond in a dipeptide where the first amino acid is aspartate.")
(OFFICIAL-EC? YES)
(ENZYMATIC-REACTION ENZRXN0-4841)
(:CREATOR |shearer|)
(:CREATION-DATE 3319478637)
(COMMON-NAME "Dipeptidase E")
(SYNONYMS "Aspartyl dipeptidase" "Peptidase E"
"PepE gene product (Salmonella typhimurium)")
(EC-NUMBER "3.4.13.21") )
NIL)
(3.4.13.3-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.13)
(CITATIONS "7988883" "11157967")
(COMMENT
"This reaction is the hydrolysis of a peptide bond in a dipeptide with an unblocked amino-terminus. Substrates include
cysteinylglycine, among others.")
(ENZYMATIC-REACTION ENZRXN0-4381)
(:CREATOR |shearer|)
(:CREATION-DATE 3316466894)
(EC-NUMBER "3.4.13.3")
(COMMON-NAME "Xaa-His dipeptidase")
(SYNONYMS "Homocarnosinase" "Carnosinase" "Aminoacyl-histidine dipeptidase"
"X-His dipeptidase")
(OFFICIAL-EC? T) )
NIL)
(3.4.13.9-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.13)
(ENZYMATIC-REACTION ENZRXN0-4121)
(OFFICIAL-EC? T)
(SYNONYMS "γ-peptidase" "Peptidase D" "Prolidase" "Imidodipeptidase"
"Proline dipeptidase" "X-Pro dipeptidase")
(COMMON-NAME "Xaa-Pro dipeptidase")
(:CREATION-DATE 3309271340)
(:CREATOR |keseler|)
(EC-NUMBER "3.4.13.9") )
NIL)
(3.4.15.5-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.15)
(CITATIONS "4554640" "216006" "8226676")
(COMMENT
"This reaction is the hydrolysis of a peptide bond in an amino-blocked small peptide.")
(ENZYMATIC-REACTION ENZRXN0-4502)
(:CREATOR |shearer|)
(:CREATION-DATE 3317054663)
(EC-NUMBER "3.4.15.5")
(COMMON-NAME "Peptidyl-dipeptidase Dcp")
(SYNONYMS "Dipeptidyl carboxypeptidase")
(OFFICIAL-EC? T) )
NIL)
(3.4.16.4-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.16)
(ENZYMATIC-REACTION ENZRXN0-4801 ENZRXN0-4781 ENZRXN0-4761)
(:CREATOR |shearer|)
(:CREATION-DATE 3318691258)
(LEFT D-ALA-D-ALA WATER)
(RIGHT D-ALANINE)
(EC-NUMBER "3.4.16.4")
(COMMON-NAME "Serine-type D-Ala-D-Ala carboxypeptidase")
(SYNONYMS "DD-peptidase" "D-alanyl-D-alanine carboxypeptidase")
(OFFICIAL-EC? T)
(BALANCE-STATE :BALANCED) )
((RIGHT D-ALANINE COEFFICIENT 2)))
(3.4.17.14-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.17)
(ENZYMATIC-REACTION ENZRXN0-2641)
(OFFICIAL-EC? T)
(SYNONYMS "D-alanyl-D-alanine hydrolase" "Zn(2+) G peptidase")
(COMMON-NAME "Zinc D-Ala-D-Ala carboxypeptidase")
(:CREATION-DATE 3282586807)
(:CREATOR |arnaud|)
(EC-NUMBER "3.4.17.14") )
NIL)
(3.4.21.102-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.21)
(COMMENT
"This reaction is the hydrolysis of a peptide bond in the carboxy-terminal region of a protein.
The carboxy-terminal residue is an important determinant of cleavage rate, with the highest rates
afforded by alanine, cysteine, serine, threonine and valine. Nonpolar residues at the second and third
position from the carboxy-terminus also allow more rapid proteolysis|CITS: [8576225]|.
Actual hydrolysis occurs most often after alanine, as well as following serine, valine, isoleucine
and leucine|CITS: [1729701][8520476][2681146]|.")
(OFFICIAL-EC? YES)
(ENZYMATIC-REACTION ENZRXN0-4321)
(:CREATOR |shearer|)
(:CREATION-DATE 3315926344)
(COMMON-NAME "C-terminal processing peptidase")
(SYNONYMS "Photosystem II D1 protein processing peptidase" "Protease Re"
"Tail-specific protease" "Tsp protease")
(EC-NUMBER "3.4.21.102") )
NIL)
(3.4.21.53-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.21)
(ENZYMATIC-REACTION ENZRXN0-4263)
(:CREATOR |shearer|)
(:CREATION-DATE 3315666951)
(EC-NUMBER "3.4.21.53")
(COMMON-NAME "Endopeptidase La")
(SYNONYMS "ATP-dependent protease La" "ATP-dependent serine proteinase")
(OFFICIAL-EC? T) )
NIL)
(3.4.21.83-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.21)
(CITATIONS "240839")
(COMMENT
"This reaction is the hydrolysis of a peptide bond following an arginine or lysine.")
(ENZYMATIC-REACTION ENZRXN0-4241)
(:CREATOR |shearer|)
(:CREATION-DATE 3315600318)
(EC-NUMBER "3.4.21.83")
(COMMON-NAME "Oligopeptidase B")
(SYNONYMS "Protease II")
(OFFICIAL-EC? T) )
NIL)
(3.4.21.89-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.21)
(ENZYMATIC-REACTION ENZRXN0-3941)
(OFFICIAL-EC? NIL)
(SYNONYMS "Phage-procoat-leader peptidase" "SPase I"
"Bacterial leader peptidase I")
(COMMON-NAME "Signal peptidase I")
(:CREATION-DATE 3307215163)
(:CREATOR |keseler|)
(EC-NUMBER "3.4.21.89") )
NIL)
(3.4.21.92-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.21)
(CITATIONS "8407953")
(COMMENT
"This reaction is the hydrolysis of a peptide bond by a serine protease activity. Specificity is chiefly defined by an associated
chaperone activity provided by the ATP-dependent chaperones ClpA and ClpX.")
(ENZYMATIC-REACTION ENZRXN0-4564 ENZRXN0-4563 ENZRXN0-4562 ENZRXN0-4561)
(:CREATOR |shearer|)
(:CREATION-DATE 3317562727)
(EC-NUMBER "3.4.21.92")
(COMMON-NAME "Endopeptidase Clp")
(SYNONYMS "Caseinolytic protease" "Protease Ti" "Endopeptidase Ti")
(OFFICIAL-EC? T) )
NIL)
(3.4.23.36-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.23)
(ENZYMATIC-REACTION ENZRXN0-2710)
(OFFICIAL-EC? T)
(SPECIES ECOLI)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3069621149)
(:CREATOR |kr|)
(EC-NUMBER "3.4.23.36")
(COMMENT
"CLEAVAGE OF N-TERMINAL LEADER SEQUENCES FROM MEMBRANE PROLIPOPROTEINS. HYDROLYSES XAA-XBB-XBB-|-CYS, IN WHICH XAA IS HYDROPHOBIC (PREFERABLY LEU), XBB IS OFTEN SER OR ALA, XCC IS OFTEN GLY OR ALA, AND THE CYS IS ALKYLATED ON SULFUR WITH A DIACYLGLYCERYL GROUP."
"INHIBITED BY PEPSTATIN AND THE ANTIBIOTIC GLOBOMYCIN."
"BELONGS TO PEPTIDASE FAMILY A8.")
(SYNONYMS "BACTERIAL LEADER PEPTIDASE I" "SPASE II"
"PREMUREIN-LEADER PEPTIDASE" "PROLIPOPROTEIN-SIGNAL PEPTIDASE"
"LIPOPROTEIN SIGNAL PEPTIDASE")
(COMMON-NAME "SIGNAL PEPTIDASE II") )
NIL)
(3.4.23.43-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.23)
(ENZYMATIC-REACTION ENZRXN0-4641)
(:CREATOR |shearer|)
(:CREATION-DATE 3318194478)
(COMMON-NAME "Prepilin peptidase")
(EC-NUMBER "3.4.23.43") )
NIL)
(3.4.24.55-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.24)
(CITATIONS "374413" "15502359" "7680857")
(COMMENT
"This reaction is hydrolysis of a peptide bond within a small protein or peptide substrate, less than 7 kDa.")
(ENZYMATIC-REACTION ENZRXN0-4341)
(:CREATOR |shearer|)
(:CREATION-DATE 3315946131)
(EC-NUMBER "3.4.24.55")
(COMMON-NAME "Pitrilysin")
(SYNONYMS "Protease Pi" "Protease III")
(OFFICIAL-EC? T) )
NIL)
(3.4.24.70-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.4.24)
(CITATIONS "1336454" "7691339" "3053642")
(COMMENT
"This reaction involves broad-specificity hydrolysis of peptide bonds. In hydrolysis of bonds in signal sequence
peptides, some specificity was seen for cleavage near alanine and glycine.")
(ENZYMATIC-REACTION ENZRXN0-4262)
(:CREATOR |shearer|)
(:CREATION-DATE 3315666398)
(EC-NUMBER "3.4.24.70")
(COMMON-NAME "Oligopeptidase A")
(OFFICIAL-EC? T) )
NIL)
(3.5.1.88-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-3802)
(OFFICIAL-EC? T)
(EC-NUMBER "3.5.1.88")
(RIGHT METHIONYL-PEPTIDE FORMATE)
(LEFT WATER FORMYL-L-METHIONYL-PEPTIDE)
(SYNONYMS "Polypeptide deformylase" "PDF")
(COMMON-NAME "Peptide deformylase")
(:CREATOR |keseler|)
(:CREATION-DATE 3304705487) )
NIL)
(3.6.1.41-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.6.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2061)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "3.6.1.41")
(COMMON-NAME "BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE-(SYMMETRICAL)")
(COMMENT
"ALSO ACTS ON BIS(5'-GUANOSYL) TETRAPHOSPHATE AND BIS(5'-ADENOSYL) PENTAPHOSPHATE, AND, MORE SLOWLY, ON SOME OTHER POLYPHOSPHATES, FORMING A NUCLEOSIDE BIS-PHOSPHATE AS ONE PRODUCT IN ALL CASES (CF. EC 3.6.1.17).")
(RIGHT ADP)
(LEFT WATER ADENOSYL-P4)
(SYNONYMS "DINUCLEOSIDETETRAPHOSPHATASE (SYMMETRICAL)"
"DIADENOSINETETRAPHOSPHATASE (SYMMETRICAL)") )
((RIGHT ADP COEFFICIENT 2)))
(3.6.3.39-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.6.3
|Transport-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-6152)
(:CREATOR |djohnson|)
(:CREATION-DATE 3343409934)
(COMMON-NAME "Lipopolysaccharide-transporting ATPase")
(LEFT |Lipopolysaccharides| WATER ATP)
(RIGHT |Lipopolysaccharides| |Pi| ADP)
(EC-NUMBER "3.6.3.39")
(OFFICIAL-EC? NIL) )
((RIGHT |Lipopolysaccharides| COMPARTMENT OUT)))
(|34-Didehydropyranosides| T (
(OCELOT-GFP::PARENTS |Pyranosides|)
(COMMON-NAME "a 3,4-didehydropyranoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(34-DIHYDROXYPHENYLACETALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |keseler|)
(:CREATION-DATE 3325597595)
(COMMON-NAME "3,4-dihydroxyphenylacetaldehyde")
(SYNONYMS "protocatechuatealdehyde")
(DBLINKS (LIGAND-CPD "C04043" NIL |sreddy| 3298309802 NIL NIL))
(STRUCTURE-ATOMS C O C O C C C C C C O)
(DISPLAY-COORDS-2D (0.0106d0 -0.8889d0) (-2.1286d0 -0.4781d0)
(0.7261d0 -2.1286d0) (-0.7048d0 0.3436d0) (-0.7048d0 -0.4781d0)
(1.3919d0 -1.6399d0) (-1.4132d0 -0.8889d0) (-0.7048d0 -2.1286d0)
(0.0106d0 -1.7178d0) (-1.4132d0 -1.7178d0) (2.1216d0 -2.0224d0))
(STRUCTURE-BONDS (5 1 :AROMATIC) (2 7 1) (3 9 1) (3 6 1) (4 5 1)
(7 5 :AROMATIC) (10 7 :AROMATIC) (9 8 :AROMATIC) (1 9 :AROMATIC)
(8 10 :AROMATIC) (11 6 2))
(CHEMICAL-FORMULA (C 8) (H 8) (O 3))
(MOLECULAR-WEIGHT 152.149d0)
(AROMATIC-RINGS (5 7 10 8 9 1)) )
NIL)
(34-DIHYDROXYPHENYLACETYL-COA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-5065)
(COMMON-NAME "3,4-dihydroxyphenylacetyl-CoA")
(:CREATOR |keseler|)
(:CREATION-DATE 3348522166) )
NIL)
(|3b-hydroxy-D5-steroids| T (
(OCELOT-GFP::PARENTS |Hydroxysteroids|)
(DISPLAY-COORDS-2D (3.6373d0 -3.5d0) (7.2746d0 -5.6d0) (0.0d0 0.0d0)
(9.0387d0 -5.9641d0) (4.8497d0 0.0d0) (6.0622d0 -0.7d0) (9.429d0 -3.5d0)
(1.2124d0 -2.1d0) (8.6061d0 -2.3674d0) (4.8497d0 -4.2d0) (2.4249d0 -2.8d0)
(6.0622d0 -4.9d0) (2.4249d0 0.0d0) (3.6373d0 -0.7d0) (1.2124d0 -0.7d0)
(8.6061d0 -4.6326d0) (6.0622d0 -2.1d0) (4.8497d0 -2.8d0) (7.2746d0 -2.8d0)
(3.6373d0 -2.1d0) (7.2746d0 -4.2d0))
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (19 21 1) (18 20 1) (17 19 1) (17 18 1) (16 21 1) (14 20 1)
(13 15 1) (13 14 1) (12 21 1) (11 20 1) (10 18 1) (10 12 1) (9 19 1)
(8 15 1) (8 11 1) (7 16 1) (7 9 1) (6 17 1) (5 14 2) (5 6 1) (4 16 1)
(15 3 1 :UP) (2 21 1) (1 20 1))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 3β-hydroxy-δ5-steroid")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(3FE-4S NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(PROSTHETIC-GROUPS-OF SUCCINATE-OXN-ENZRXN NITRATREDUCTA-ENZRXN
FUMARATE-REDN-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3355616958)
(COMMON-NAME "Fe3S4 iron-sulfur cluster")
(SYNONYMS "Fe3S4 iron-sulfur cluster"
"Fe3S4 cluster" "Fe3S4 center"
"Fe3S4"
"Fe3S4 iron-sulfur center" "3Fe-4S")
(STRUCTURE-ATOMS FE S S FE S S FE)
(DISPLAY-COORDS-2D (0.4158d0 -1.9798d0) (-0.4092d0 -1.9798d0)
(0.4158d0 -1.1292d0) (-0.4092d0 -1.1292d0) (-0.0313d0 -1.3563d0)
(-0.8437d0 -0.5187d0) (-0.0313d0 -0.5187d0))
(STRUCTURE-BONDS (3 7 1) (4 6 1) (1 5 1) (6 7 1) (5 7 1) (1 3 1) (4 3 1)
(2 4 1) (2 1 1))
(COMMENT
"Iron-sulfur clusters are prosthetic groups of many proteins, which function as intracellular electron carriers
with a low reduction potential.
In addition to their roles in electron transfer reactions, iron-sulfur clusters are also known to participate in
the activation of substrates, the stabilization of radicals and structures, the protection of proteins from enzymes
and the storage of iron and sulfur.
In addition, they act as sensors of iron, dioxygen, the superoxide ion, and possibly nitric oxide, and participate
in gene expression |CITS: [16466637]|.
")
(CHEMICAL-FORMULA (S 4) (FE 3))
(MOLECULAR-WEIGHT 295.781d0) )
NIL)
(3OH-4P-OH-ALPHA-KETOBUTYRATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "2-Oxo-3-hydroxy-4-phosphobutanoate")
(DBLINKS (PUBCHEM "440900" NIL |keseler| 3342798911 NIL NIL)
(LIGAND-CPD "C06054" NIL |keseler| 3342798911 NIL NIL))
(ATOM-CHARGES (7 -1))
(DISPLAY-COORDS-2D (-0.575d0 -0.099999964d0) (0.9958334d0 0.25833344d0)
(-0.575d0 -0.8041667d0) (-0.575d0 0.25833344d0)
(-0.116666615d0 -0.45416665d0) (0.5375d0 -0.1916666d0) (-1.0d0 -1.0d0)
(0.5375d0 0.7166667d0) (-0.16666663d0 -1.0d0) (0.5375d0 0.25833344d0)
(-0.575d0 -0.45416665d0) (0.029166698d0 0.25833344d0)
(-0.116666615d0 -0.099999964d0))
(CHEMICAL-FORMULA (C 4) (H 6) (O 8) (P 1))
(MOLECULAR-WEIGHT 213.06d0)
(STRUCTURE-BONDS (13 1 1) (12 10 1) (11 1 1) (9 3 2) (8 10 1) (7 3 1)
(6 10 2) (5 11 2) (4 12 1) (3 11 1) (2 10 1) (1 4 1))
(STRUCTURE-ATOMS C O C C O O O O O P C O O)
(:CREATION-DATE 3054404381)
(APPEARS-IN-RIGHT-SIDE-OF ERYTHRON4PDEHYDROG-RXN)
(COMMON-NAME "3-hydroxy-4-phospho-hydroxy-α-ketobutyrate")
(APPEARS-IN-LEFT-SIDE-OF PSERTRANSAMPYR-RXN) )
NIL)
(3PGAREARR-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CPD-4584)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "E. coli contains three phosphoglycerate mutases.
Two are 2,3-bisphosphoglyerate-dependent enzymes,
encoded by the gpmA and gpmB genes. The third is a
2,3-bisphosphoglyerate-independent enzyme encoded
by the pgmI gene. |CITS: [99364512]|")
(SYNONYMS "D-phosphoglycerate 2,3-phosphomutase 1" "BPG-dependent PGAM1"
"phosphoglycerate phosphomutase 1" "phosphoglyceromutase 1" "PGAM 1")
(COMMON-NAME "phosphoglycerate mutase 1")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 3PGAREARR-RXN)
(ENZYME PHOSGLYCMUTASE)
(:CREATION-DATE 2945290596)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH CPD-4584 COMMENT
"Vanadate strongly inhibits the enzyme. |CITS: [99364512]| ")))
(3PGAREARR-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.4.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLYCOLYSIS GLUCONEO-PWY)
(ENZYMATIC-REACTION PGMI-ENZRXN PGAM2-ENZRXN 3PGAREARR-ENZRXN)
(SYNONYMS "PHOSPHOGLYCERATE PHOSPHOMUTASE" "PHOSPHOGLYCEROMUTASE" "PGAM")
(RIGHT 2-PG)
(LEFT G3P)
(DELTAG0 1.1d0)
(EC-NUMBER "5.4.2.1")
(:CREATION-DATE 2945290596)
(:CREATOR |mriley|) )
NIL)
(4-AMINO-4-DEOXY-L-ARABINOSE NIL (
(OCELOT-GFP::PARENTS |Modified-Sugars|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2001)
(DISPLAY-COORDS-2D (0.0d0 -4.2d0) (4.8497d0 -1.4d0) (0.0d0 -1.4d0)
(2.4249d0 0.0d0) (2.4249d0 -4.2d0) (3.6373d0 -3.5d0) (1.2124d0 -3.5d0)
(3.6373d0 -2.1d0) (1.2124d0 -2.1d0) (2.4249d0 -1.4d0))
(CHEMICAL-FORMULA (C 5) (H 11) (N 1) (O 4))
(MOLECULAR-WEIGHT 149.146d0)
(STRUCTURE-BONDS (9 10 1) (8 10 1) (7 9 1) (6 8 1) (5 7 1) (5 6 1)
(10 4 1 :DOWN) (9 3 1 :UP) (8 2 1 :DOWN) (7 1 1 :UP))
(STRUCTURE-ATOMS N O O O C O C C C C)
(CITATIONS "11535605" "11535604")
(SYNONYMS "L-Ara4N")
(COMMON-NAME "4-amino-4-deoxy-L-arabinose")
(:CREATOR |arnaud|)
(:CREATION-DATE 3281113143) )
NIL)
(4-AMINO-4-DEOXYCHORISMATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C11355" NIL |kr| 3346617700 NIL NIL) (CAS "97279-79-3"))
(:CREATION-DATE 3119733453)
(MOLECULAR-WEIGHT 225.201d0)
(CHEMICAL-FORMULA (C 10) (H 11) (N 1) (O 5))
(DISPLAY-COORDS-2D (1.3557d0 -2.4043d0) (2.0719d0 -1.1895d0)
(0.0d0 -4.4123d0) (8.787d0 0.0d0) (2.1614d0 -5.538d0) (8.8508d0 -2.3405d0)
(5.7685d0 -0.051d0) (4.2337d0 -0.051d0) (5.7685d0 -2.4171d0)
(3.4404d0 -3.5428d0) (2.1104d0 -3.5428d0) (1.3686d0 -4.4123d0)
(8.1218d0 -1.1895d0) (6.6637d0 -1.1895d0) (3.4404d0 -1.1895d0)
(4.2337d0 -2.4171d0))
(STRUCTURE-BONDS (15 16 1) (13 14 1) (11 12 1) (16 10 1 :DOWN) (10 11 1)
(9 16 1) (9 14 2) (8 15 1) (7 14 1) (7 8 2) (6 13 1) (5 12 1) (4 13 2)
(3 12 2) (2 15 1) (1 11 2))
(STRUCTURE-ATOMS C N O O O O C C C O C C C C C C)
(APPEARS-IN-LEFT-SIDE-OF ADCLY-RXN)
(APPEARS-IN-RIGHT-SIDE-OF PABASYN-RXN)
(COMMENT-INTERNAL
"kr98-11-10: stereochemistry is missing, but could probably be obtained and would be interesting.")
(COMMON-NAME "4-amino-4-deoxychorismate") )
NIL)
(4-AMINO-BUTYRALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Aliphatic-Omega-Amino-Aldehydes|)
(DBLINKS (LIGAND-CPD "C00555" NIL |kr| 3346617701 NIL NIL) (CAS "4390-05-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -32.0d0)
(APPEARS-IN-RIGHT-SIDE-OF PUTTRANSAM-RXN)
(APPEARS-IN-LEFT-SIDE-OF AMINOBUTDEHYDROG-RXN)
(:CREATOR |shevelev|)
(STRUCTURE-ATOMS C C O C N C)
(STRUCTURE-BONDS (6 2 1) (5 4 1) (4 6 1) (3 1 2) (2 1 1))
(DISPLAY-COORDS-2D (0.59736d0 -1.0d0) (0.19802d0 -0.76898d0)
(0.9967d0 -0.76898d0) (-0.60066d0 -0.76898d0) (-1.0d0 -1.0d0)
(-0.20462d0 -1.0d0))
(MOLECULAR-WEIGHT 87.121d0)
(CHEMICAL-FORMULA (C 4) (H 9) (N 1) (O 1))
(COMMON-NAME "4-amino-butyraldehyde")
(SYNONYMS "4-aminobutanal" "γ-aminobutyraldehyde"
"4-aminobutyraldehyde") )
((GIBBS-0 -32.0d0 CITATIONS "GibbsGroups97")))
(4-AMINO-BUTYRATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF PANTOATE-BETA-ALANINE-LIG-ENZRXN)
(CITATIONS "Steward49")
(DBLINKS (LIGAND-CPD "C00334" NIL |kr| 3346617701 NIL NIL) (CAS "56-12-2"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -86.2d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-3942 TRANS-RXN-261 TRANS-RXN-57
AMINOBUTDEHYDROG-RXN GLUTDECARBOX-RXN)
(APPEARS-IN-LEFT-SIDE-OF TRANS-RXN-261 TRANS-RXN-57 GABATRANSAM-RXN)
(MOLECULAR-WEIGHT 103.121d0)
(CHEMICAL-FORMULA (C 4) (H 9) (N 1) (O 2))
(DISPLAY-COORDS-2D (0.59934d0 -0.53974d0) (-0.60265d0 -0.30795d0)
(-1.0d0 -0.53974d0) (0.99669d0 -0.30795d0) (-0.2053d0 -0.53974d0)
(0.59934d0 -1.0d0) (0.19868d0 -0.30795d0))
(STRUCTURE-BONDS (7 1 1) (6 1 1) (5 7 1) (4 1 2) (3 2 1) (2 5 1))
(STRUCTURE-ATOMS C C N O C O C)
(COMMON-NAME "4-aminobutyrate")
(SYSTEMATIC-NAME "butanoic acid, 4-amino-")
(SYNONYMS "GABA" "4-aminobutyric acid" "4-aminobutanoate"
"γ-aminobutyrate" "4-amino-n-butyric acid"
"γ-amino-n-butyric acid") )
((GIBBS-0 -86.2d0 CITATIONS "GibbsGroups97")))
(4-COUMARATE--COA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.2.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2823)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3284239457)
(SYNONYMS "4-coumaryl-CoA synthetase" "4-coumaroyl-CoA synthase")
(COMMON-NAME "4-coumarate--CoA ligase")
(EC-NUMBER "6.2.1.12")
(RIGHT COUMARYL-COA PPI AMP)
(LEFT CO-A COUMARATE ATP) )
NIL)
(4-CYTIDINE-5-DIPHOSPHO-2-C NIL (
(OCELOT-GFP::PARENTS CDP-SUGARS)
(DBLINKS (LIGAND-CPD "C11435" NIL |kr| 3346617701 NIL NIL))
(SYNONYMS "CDP-ME" "CDP-methyl-D-erythritol"
"4-diphosphocytidyl-2C-methyl-D-erythritol"
"4-diphosphocytidyl-2-C-methylerythritol")
(APPEARS-IN-LEFT-SIDE-OF 2.7.1.148-RXN)
(APPEARS-IN-RIGHT-SIDE-OF 2.7.7.60-RXN)
(:CREATOR |keseler|)
(:CREATION-DATE 3335538398)
(COMMON-NAME "4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol")
(STRUCTURE-ATOMS C N O O O O O O O O O O C C C C C N O O O O C C C C C C C N
C P P)
(DISPLAY-COORDS-2D (0.2493d0 -5.8676d0) (19.5638d0 -2.8175d0)
(15.3113d0 0.0d0) (5.8856d0 -4.8164d0) (8.6851d0 -4.8361d0)
(0.0d0 -2.7655d0) (2.1919d0 -2.4655d0) (10.7486d0 -1.4012d0)
(13.5272d0 -0.1537d0) (2.1982d0 -5.8557d0) (5.8834d0 -2.0164d0)
(8.6818d0 -2.0361d0) (17.7906d0 -3.3901d0) (16.3987d0 -3.5408d0)
(0.0d0 -4.1655d0) (3.4837d0 -4.4385d0) (11.0764d0 -4.4293d0)
(17.5296d0 -0.9793d0) (4.4901d0 -3.4653d0) (10.0891d0 -3.4368d0)
(13.4842d0 -3.7761d0) (7.2892d0 -3.4272d0) (18.356d0 -2.1094d0)
(16.1377d0 -1.13d0) (2.2064d0 -3.8654d0) (11.9632d0 -2.0974d0)
(13.2404d0 -1.524d0) (12.1139d0 -3.4893d0) (14.1804d0 -2.5615d0)
(15.5723d0 -2.4108d0) (1.2176d0 -4.8565d0) (5.8892d0 -3.4164d0)
(8.6891d0 -3.4361d0))
(STRUCTURE-BONDS (29 30 1 :UP) (27 29 1) (26 28 1) (26 27 1) (25 31 1)
(30 24 :AROMATIC) (22 33 1) (22 32 1) (21 29 1) (21 28 1) (20 33 1)
(19 32 1) (24 18 :AROMATIC) (18 23 :AROMATIC) (17 28 1 :UP) (17 20 1)
(16 25 1) (16 19 1) (15 31 1) (14 30 :AROMATIC) (23 13 :AROMATIC)
(13 14 :AROMATIC) (12 33 1) (11 32 1) (31 10 1 :DOWN) (27 9 1 :DOWN)
(26 8 1 :DOWN) (25 7 1 :UP) (6 15 1) (5 33 2) (4 32 2) (3 24 2) (2 23 1)
(31 1 1 :UP))
(CHEMICAL-FORMULA (C 14) (H 25) (N 3) (O 14) (P 2))
(MOLECULAR-WEIGHT 521.311d0)
(AROMATIC-RINGS (14 13 23 18 24 30)) )
NIL)
(4-HYDROXY-2-KETOVALERATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF 2-OXOPENT-4-ENOATE-HYDRATASE-RXN)
(HISTORY |kr-3290870141|)
(DBLINKS (CAS "111844-33-8" NIL |kr| 3346617699 NIL NIL)
(LIGAND-CPD "C03589" NIL |kr| 3346617699 NIL NIL)
(LIGAND-CPD "c03589" NIL |kawakami| 3278870285 NIL NIL)
(UM-BBD-CPD "c0101" NIL |kawakami| 3278870285 NIL NIL))
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (0.9292d0 3.5292d0) (1.5787d0 3.1542d0)
(2.2282d0 3.5292d0) (2.8777d0 3.1542d0) (3.5272d0 3.5292d0)
(3.5456d0 4.2832d0) (4.1756d0 3.152d0) (2.8777d0 2.4042d0)
(1.5787d0 2.4042d0))
(CHEMICAL-FORMULA (C 5) (H 8) (O 4))
(MOLECULAR-WEIGHT 132.116d0)
(STRUCTURE-BONDS (2 9 1) (4 8 2) (4 5 1) (5 7 2) (5 6 1) (3 4 1) (2 3 1)
(1 2 1))
(STRUCTURE-ATOMS C C C C C O O O O)
(APPEARS-IN-LEFT-SIDE-OF MHPELY-RXN)
(COMMON-NAME "4-hydroxy-2-ketovalerate")
(SYNONYMS "HKP" "4-hydroxy-2-keto-pentanoic acid"
"4-hydroxy-2-ketovaleric acid" "4-hydroxy-2-oxo-valeric acid"
"4-hydroxy-2-oxo-pentanoic acid" "4-hydroxy-2-oxovaleric acid"
"2-oxo-4-hydroxyvalerate" "4-hydroxy-2-oxo-valerate"
"4-hydroxy-2-oxopentanoate") )
NIL)
(4-HYDROXY-BENZYL-ALCOHOL NIL (
(OCELOT-GFP::PARENTS |Aryl-Alcohol|)
(APPEARS-IN-RIGHT-SIDE-OF THIAZOLSYN2-RXN)
(CHEMICAL-FORMULA (C 7) (H 8) (O 2))
(MOLECULAR-WEIGHT 124.139d0)
(DISPLAY-COORDS-2D (2.866d0 1.75d0) (3.7321d0 2.25d0) (2.866d0 0.75d0)
(2.0d0 0.25d0) (3.7321d0 0.25d0) (2.0d0 -0.75d0) (3.7321d0 -0.75d0)
(2.866d0 -1.25d0) (2.866d0 -2.25d0))
(DBLINKS (NCI "227926") (CAS "623-05-2"))
(STRUCTURE-BONDS (1 2 1) (1 3 1) (3 4 2) (3 5 1) (4 6 1) (5 7 2) (6 8 2)
(8 9 1) (7 8 1))
(STRUCTURE-ATOMS C O C C C C C C O)
(:CREATION-DATE 3198856245)
(COMMON-NAME "4-hydroxybenzyl alcohol") )
NIL)
(|4-hydroxybenzoate| NIL (
(OCELOT-GFP::PARENTS |Aromatics|)
(INHIBITORS-COMPETITIVE-OF CHORPYRLY-ENZRXN)
(DBLINKS (LIGAND-CPD "C00156" NIL |kr| 3346617700 NIL NIL) (CAS "99-96-7"))
(APPEARS-IN-LEFT-SIDE-OF 4OHBENZOATE-OCTAPRENYLTRANSFER-RXN)
(:CREATION-DATE 3075053323)
(GIBBS-0 -90.8d0)
(APPEARS-IN-RIGHT-SIDE-OF CHORPYRLY-RXN)
(:CREATOR |pkarp|)
(SYNONYMS "4-hydroxybenzoate")
(COMMON-NAME "p-hydroxybenzoate")
(STRUCTURE-ATOMS C C C O C C C C O O)
(STRUCTURE-BONDS (2 1 :AROMATIC) (2 6 1) (3 5 :AROMATIC) (5 2 :AROMATIC)
(6 4 2) (6 10 1) (1 7 :AROMATIC) (8 3 :AROMATIC) (7 8 :AROMATIC) (9 8 1))
(DISPLAY-COORDS-2D (0.0721d0 -1.0d0) (0.30408d0 -0.6395d0)
(-0.36677d0 -0.25078d0) (0.95611d0 -0.99373d0) (0.0721d0 -0.25078d0)
(0.72414d0 -0.6395d0) (-0.36677d0 -1.0d0) (-0.57994d0 -0.6395d0)
(-1.0d0 -0.6395d0) (0.99687d0 -0.31348d0))
(CHEMICAL-FORMULA (C 7) (H 6) (O 3))
(MOLECULAR-WEIGHT 138.123d0)
(AROMATIC-RINGS (2 5 3 8 7 1)) )
((GIBBS-0 -90.8d0 CITATIONS "GibbsGroups97")))
(4-HYDROXYPHENYLACETYL-COA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "4-hydroxyphenylacetyl-CoA")
(:CREATOR |keseler|)
(:CREATION-DATE 3348522587) )
NIL)
(|4-Hydroxyproline-Degradation| T (
(OCELOT-GFP::PARENTS |Amino-Acid-Degradation|)
(COMMON-NAME "4-hydroxyproline degradation")
(COMMENT "This class holds pathways for the degradation of 4-hydroxyproline.")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3355681269) )
NIL)
(4-P-PANTOTHENATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF P-PANTOCYSLIG-ENZRXN)
(DBLINKS (LIGAND-CPD "C03492" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3075053323)
(GIBBS-0 -183.8d0)
(APPEARS-IN-RIGHT-SIDE-OF PANTOTHENATE-KIN-RXN)
(APPEARS-IN-LEFT-SIDE-OF P-PANTOCYSLIG-RXN)
(MOLECULAR-WEIGHT 299.217d0)
(CHEMICAL-FORMULA (C 9) (H 18) (N 1) (O 8) (P 1))
(DISPLAY-COORDS-2D (-0.39535d0 -0.79734d0) (0.6412d0 -0.79734d0)
(-1.0d0 -0.701d0) (-0.79734d0 -0.701d0) (-0.57143d0 -0.701d0)
(-0.04983d0 -0.79734d0) (0.12292d0 -0.701d0) (0.12292d0 -0.49834d0)
(-0.79734d0 -0.90365d0) (-0.04983d0 -1.0d0) (-0.79734d0 -0.49834d0)
(-0.21927d0 -0.49834d0) (-0.21927d0 -0.701d0) (0.299d0 -0.79734d0)
(0.81728d0 -0.49834d0) (0.81728d0 -0.701d0) (0.99668d0 -0.79734d0)
(-0.21927d0 -0.90365d0) (0.46512d0 -0.701d0))
(STRUCTURE-BONDS (19 14 1) (18 13 1) (17 16 1) (16 2 1) (15 16 2) (14 7 1)
(13 1 1) (12 13 1) (11 4 2) (10 6 1) (9 4 1) (8 7 2) (7 6 1) (6 13 1)
(5 4 1) (3 4 1) (2 19 1) (1 5 1))
(STRUCTURE-ATOMS C C O P O C C O O O O C C N O C O C C)
(COMMON-NAME "D-4'-phosphopantothenate")
(SYNONYMS "4'-phosphopantothenate" "4'-P-Pantothenate"
"(R)-4'-phosphopantothenate") )
((GIBBS-0 -183.8d0 CITATIONS "GibbsGroups97")))
(|4-Toluenesulfonate-Degradation| T (
(OCELOT-GFP::PARENTS AROMATIC-COMPOUNDS-DEGRADATION)
(COMMON-NAME "4-toluenesulfonate degradation")
(COMMENT
"This class holds pathways for the degradation of 4-Toluenesulfonate.")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(4.2.1.99-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(EC-NUMBER "4.2.1.99")
(BALANCE-STATE :BALANCED)
(CITATIONS "[12473114]")
(ENZYMATIC-REACTION ENZRXN0-1505)
(IN-PATHWAY PWY0-42)
(OFFICIAL-EC? T)
(RIGHT CPD-1136 WATER)
(LEFT CPD-618)
(:CREATOR |ptoole|)
(:CREATION-DATE 3170604749) )
NIL)
(4.2.3.12-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.3)
(ENZYMATIC-REACTION ENZRXN0-6161)
(:CREATOR |shearer|)
(:CREATION-DATE 3346168965)
(COMMON-NAME "6-pyruvoyltetrahydropterin synthase")
(SYNONYMS "6-pyruvoyl tetrahydrobiopterin synthase" "PTPS")
(LEFT DIHYDRONEOPTERIN-P3)
(RIGHT P3I 6-PYRUVOYL-5678-TETRAHYDROPTERIN)
(EC-NUMBER "4.2.3.12")
(OFFICIAL-EC? T)
(BALANCE-STATE :BALANCED) )
NIL)
(4.2.99.18-RXN NIL (
(OCELOT-GFP::PARENTS EC-4.2.99)
(OFFICIAL-EC? YES)
(COMMENT
"In E.coli endonuclease VIII (the nei gene product) functions similarly to DNA glycosylase Nth (the nth gene product)
and also releases damaged T and C residues |CITS:[9171429]|.")
(RIGHT
"C-O-P bond 3' to AP site in DNA is broken. 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate")
(LEFT "C-O-P bond 3' to AP site in DNA intact")
(ENZYMATIC-REACTION ENZRXN0-02002)
(EC-NUMBER "4.2.99.18")
(:CREATOR |mhance|)
(:CREATION-DATE 3294843538) )
NIL)
(4.3.1.15-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2002)
(OFFICIAL-EC? YES)
(:CREATION-DATE 3274216952)
(EC-NUMBER "4.3.1.15")
(RIGHT AMMONIA PYRUVATE)
(LEFT CPD-1782 WATER)
(SYNONYMS "Diaminopropionatase"
"α,β-diaminopropionate ammonia-lyase")
(COMMON-NAME "Diaminopropionate ammonia-lyase")
(:CREATOR |arnaud|) )
((RIGHT AMMONIA COEFFICIENT 2)))
(4.3.1.17-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY SERDEG-PWY)
(COMMENT "This reaction degrades L-serine to pyruvate.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/rodeo1/ecocyc/templates/new/serdeam/sdaA.template")
(ENZYMATIC-REACTION LSERINEDEAM3-ENZRXN LSERINEDEAM2-ENZRXN
LSERINEDEAM1-ENZRXN)
(EC-NUMBER "4.3.1.17")
(:CREATION-DATE 3040393195)
(LEFT SER)
(RIGHT PYRUVATE AMMONIA) )
NIL)
(4.3.99.1-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.99)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY CYANCAT-PWY)
(COMMENT
"This reaction is part of cyanate catabolism. The initial product of the
reaction is carbamate or a related, unstable compound that decomposes
to NH3 and bicarbonate |CITS: [80242541]|.")
(ENZYMATIC-REACTION CYANLY-ENZRXN)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3051657428)
(:CREATOR |kr|)
(EC-NUMBER "4.3.99.1")
(RIGHT CARBAMATE CARBON-DIOXIDE)
(LEFT HCO3 CPD-69)
(SYNONYMS "CYANATE HYDROLASE" "CYANASE") )
NIL)
(4AMINOBUTMETAB-PWY NIL (
(OCELOT-GFP::PARENTS AMINE-DEG)
(SYNONYMS "γ-amino-butyrate shunt" "GABA degradation")
(COMMENT-INTERNAL "rearranged arginine degradation pwys per SP -arnaud")
(IN-PATHWAY ARGDEG-PWY)
(SUPER-PATHWAYS ARGDEG-PWY)
(PATHWAY-LINKS (4-AMINO-BUTYRATE PUTDEG-PWY))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(COMMENT
"E. coli strains K-12 and C have a second succinate semialdehyde dehydrogenase, sad, used in strain C in degradation of 4-hydroxyphenylacetate. Function in strain K-12 is unknown.")
(REACTION-LIST SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN
SUCCSEMIALDDEHYDROG-RXN GABATRANSAM-RXN)
(ENZYME-USE (GLUTDECARBOX-RXN GLUTDECARBOXA-ENZRXN)
(GLUTDECARBOX-RXN GLUTDECARBOXB-ENZRXN))
(PREDECESSORS (GABATRANSAM-RXN) (SUCCSEMIALDDEHYDROG-RXN GABATRANSAM-RXN)
(SUCCINATE-SEMIALDEHYDE-DEHYDROGENASE-RXN GABATRANSAM-RXN))
(COMMON-NAME "4-aminobutyrate degradation I")
(:CREATION-DATE 2974227213)
(:CREATOR |mriley|) )
NIL)
(4OH2OXOGLUTARALDOL-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH 3-BROMOPYRUVATE N-ETHYLMALEIMIDE IODOACETATE
"P-MERCURIPHENYLSULFONATE")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "4-hydroxy-2-oxoglutarate glyoxylate-lyase" "KHG-aldolase"
"2-oxo-4-hydroxyglutarate aldolase" "4-hydroxy-2-oxoglutarate aldolase")
(COMMON-NAME "2-keto-4-hydroxyglutarate aldolase")
(ALTERNATIVE-SUBSTRATES (D-4-HYDROXY-2-KETO-GLUTARATE OXALACETIC_ACID)
(D-4-HYDROXY-2-KETO-GLUTARATE "2-KETO-4-HYDROXYBUTYRATE")
(D-4-HYDROXY-2-KETO-GLUTARATE "2-KETO-4-HYDROXYBUTYRATE" OXALACETIC_ACID))
(REACTION-DIRECTION REVERSIBLE)
(REACTION 4OH2OXOGLUTARALDOL-RXN)
(INHIBITORS-COMPETITIVE PYRUVATE GLYOX D-4-HYDROXY-2-KETO-GLUTARATE OH-PYR
CIT ACETALD GLYOX)
(COMMENT "The gene eda codes for a trimeric multifunctional enzyme. The
enzyme 2-dehydro-3-deoxyphosphogluconate aldolase catalyzes an aldol
cleavage reaction in the Entner-Doudoroff pathway. The enzyme
4-hydroxy-2-oxoglutarate aldolase participates in the regulation of
the intracellular level of glyoxylate. The aldolase can also catalyze
the β-decarboxylation of oxalacetate. |CITS: [88298837] [92104948]
[92325055]| The E. coli KHG aldolase is stereoselective for the L
isomer of 2-keto-4-hydroxyglutarate. |CITS: [92104948]
[NishiharaJBC247,5079]| It is a Schiff-base mechanism (class I type)
aldolase. |CITS: [GradyBch20,2497]|")
(ENZYME KDPGALDOL-4OH2OXOGLUTARALDOL-CPLX)
(:CREATION-DATE 2974476895)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH 3-BROMOPYRUVATE CITATIONS "[HandEnzInh]" "[91056084]")
(INHIBITORS-UNKMECH N-ETHYLMALEIMIDE COMMENT
"partially inhibit enzyme activity |CITS:
[NishiharaJBC247,5079]|")
(INHIBITORS-COMPETITIVE GLYOX CITATIONS "GradyBch202497")
(INHIBITORS-COMPETITIVE D-4-HYDROXY-2-KETO-GLUTARATE COMMENT
"all three bind at the same active
site of the enzyme |CITS: [NishiharaJBC247,5079]|")))
(4OH2OXOGLUTARALDOL-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 4OH2OXOGLUTARALDOL-ENZRXN)
(RIGHT GLYOX PYRUVATE)
(LEFT D-4-HYDROXY-2-KETO-GLUTARATE)
(EC-NUMBER "4.1.3.16")
(COMMENT "Participates in the regulation of the intracellular level of
glyoxylate.")
(:CREATION-DATE 2974476895)
(:CREATOR |mriley|) )
NIL)
(4OHBENZOATE-OCTAPRENYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ALTERNATIVE-SUBSTRATES
(FARNESYLFARNESYLGERANIOL "all-trans-solanesyldiphosphate")
(FARNESYLFARNESYLGERANIOL "all-trans-farnesyldiphosphate")
(FARNESYLFARNESYLGERANIOL GERANYL-PP))
(ACTIVATORS-UNKMECH
"3-[(3-cholamidopropyl)dimethylammonio]-1-propansulfonate")
(INHIBITORS-UNKMECH "Triton X-100" CPD-3563 "sodiumdeoxycholate")
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS MG+2)
(COMMENT "4-Hydroxybenzoate octaprenyltransferase is a key enzyme in
the biosynthesis of ubiquinone. It is responsible for the prenylation
of 4-hydroxybenzoate using a polyprenyldiphosphate as a side chain
precursor. |CITS: [94207029]|")
(REACTION 4OHBENZOATE-OCTAPRENYLTRANSFER-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubisyn2/ubiA2.template")
(ENZYME 4OHBENZOATE-OCTAPRENYLTRANSFER-MONOMER)
(:CREATION-DATE 3035210278)
(COMMON-NAME "4-hydroxybenzoate octaprenyltransferase")
(SYNONYMS "4-HB polyprenyltransferase"
"polyprenyldiphosphate:4-hydroxybenzoate polyprenyltransferase")
(REACTION-DIRECTION REVERSIBLE) )
((ALTERNATIVE-SUBSTRATES
(FARNESYLFARNESYLGERANIOL "all-trans-solanesyldiphosphate") CITATIONS
"[94207029]")
(ALTERNATIVE-SUBSTRATES
(FARNESYLFARNESYLGERANIOL "all-trans-farnesyldiphosphate") CITATIONS
"[94207029]")
(ALTERNATIVE-SUBSTRATES (FARNESYLFARNESYLGERANIOL GERANYL-PP) CITATIONS
"[94207029]")
(ACTIVATORS-UNKMECH
"3-[(3-cholamidopropyl)dimethylammonio]-1-propansulfonate" CITATIONS
"[94207029]")
(INHIBITORS-UNKMECH "Triton X-100" CITATIONS "[94207029]")
(INHIBITORS-UNKMECH CPD-3563 CITATIONS "[94207029]")
(INHIBITORS-UNKMECH "sodiumdeoxycholate" CITATIONS "[94207029]")
(COFACTORS MG+2 COMMENT "Mn++ and Co++ could substitute for Mg++.
|CITS: [94207029]|")))
(4OHBENZOATE-OCTAPRENYLTRANSFER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"The sdgG mutation, which suppresses a conditional mutation in dnaG (DNA primase), has been localized to either the ubiC, ubiA or yjbI gene |CITS: [9093842]|.")
(CATALYZES 4OHBENZOATE-OCTAPRENYLTRANSFER-ENZRXN)
(CITATIONS "[94014977]")
(DBLINKS (PFAM "PF01040" IN-FAMILY |pkarp| 3346700431 NIL NIL)
(UNIPROT "P0AGK1" NIL |pkarp| 3343984428 NIL NIL)
(REFSEQ "NP_418464" NIL NIL NIL NIL NIL))
(PI 9.16d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 32.51169699999994d0)
(GENE EG11370)
(SYNONYMS "B4040" "Cyr" "UbiA" "4-HB polyprenyltransferase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiA.template")
(:CREATION-DATE 3000648804)
(:CREATOR |mriley|) )
((LOCATIONS CCO-PM-BAC-NEG COMMENT "integral membrane protein")))
(4OHBENZOATE-OCTAPRENYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(ENZYMATIC-REACTION 4OHBENZOATE-OCTAPRENYLTRANSFER-ENZRXN)
(IN-PATHWAY UBISYN-PWY)
(RIGHT PPI 3-OCTAPRENYL-4-HYDROXYBENZOATE)
(LEFT OCTAPRENYL-DIPHOSPHATE |4-hydroxybenzoate|)
(EC-NUMBER "2.5.1.-")
(COMMENT "This is the second step in ubiquinone biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/ubiq/ubiA.template")
(:CREATION-DATE 3000648804)
(:CREATOR |mriley|) )
NIL)
(|5'-NUCLEOTID-ENZRXN| NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS-OR-PROSTHETIC-GROUPS ZN+2)
(COMMENT
"The enzyme has two zinc ions at the active site. |CITS: [99260739]|")
(REACTION-DIRECTION REVERSIBLE)
(REACTION |5'-NUCLEOTID-RXN|)
(ENZYME USHA-MONOMER)
(SYNONYMS "5'-ribonucleotide phosphohydrolase")
(COMMON-NAME "5'-nucleotidase")
(:CREATION-DATE 3107192843)
(:CREATOR |jwagg|) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT
"The 5'-nucleotidase will hydrolyze all 5'-ribo- and deoxyribonucleotides showing optimal activity with 5'-AMP.
It will also hydrolyze ATP and bis(p-nitro-phenyl)phosphate, a synthetic chromogenic compound. By contrast, the sugar hydrolase
activity of the same enzyme is specific, hydrolyzing only UDP-glucose. |CITS: [67219103]|")
(COFACTORS-OR-PROSTHETIC-GROUPS ZN+2 COMMENT
"The enzyme has two zinc ions at the active site. |CITS: [99260739]| ")))
(|5'-NUCLEOTID-RXN| NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-6193 ENZRXN0-5241 ENZRXN0-5181
|5'-NUCLEOTID-ENZRXN|)
(RIGHT |Ribonucleosides| |Pi|)
(LEFT |Ribonucleoside-Monophosphates| WATER)
(EC-NUMBER "3.1.3.5")
(COMMENT "This reaction is involved in the hydrolysis of
nucleotides.")
(TEMPLATE-FILE "~ecocyc/templates/new/onlies/ushA.template")
(:CREATION-DATE 3054505284)
(:CREATOR |mriley|) )
NIL)
(|5,10-methenyl-thf| NIL (
(OCELOT-GFP::PARENTS |All-Folates|)
(DBLINKS (LIGAND-CPD "C00445" NIL |kr| 3346617701 NIL NIL) (CAS "7444-29-3"))
(:CREATION-DATE 3075053323)
(GIBBS-0 -117.2d0)
(APPEARS-IN-LEFT-SIDE-OF METHENYLTHFCYCLOHYDRO-RXN)
(APPEARS-IN-RIGHT-SIDE-OF METHYLENETHFDEHYDROG-NADP-RXN)
(COMMON-NAME "5,10-methenyl-THF")
(ATOM-CHARGES (34 1))
(SYNONYMS "n5-n10-CH-THF" "n5-n10-methenyltetrahydrofolate" "CH-THF"
"5,10-methenyltetrahydrofolate" "anhydroleucovorin"
"methenyl-tetrahydrofolate" "methenyl-THF" "methenyl-H4F")
(STRUCTURE-ATOMS H N O O O O O O C C C C C C C C C N N N C C C C C C C C C C
C N N N)
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(5-AMINO-5-DEOXY-D-GALACTOPYRANOSIDE NIL (
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(:CREATOR |paley|)
(:CREATION-DATE 3340979755)
(COMMON-NAME "5-amino-5-deoxy-D-galactopyranoside") )
NIL)
(5-AMINO-LEVULINATE NIL (
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(:CREATION-DATE 3067720847)
(GIBBS-0 -113.4d0)
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(APPEARS-IN-LEFT-SIDE-OF PORPHOBILSYNTH-RXN)
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"5-amino-levulinic acid" "5-amino-4-oxopentanoic acid"
"γ-aminolevulinic acid" "5-aminolevulinic acid" "5-aminolevulinate"
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((GIBBS-0 -113.4d0 CITATIONS "GibbsGroups97")))
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(SYNONYMS "UDP-4-keto-pyranose"
"uridine 5'-β-L-threo-pentapyranosyl-4\"-ulose diphosphate")
(COMMON-NAME "UDP-L-Ara4O")
(:CREATOR |arnaud|)
(:CREATION-DATE 3279484957) )
NIL)
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(COMMON-NAME "5'-chloroformycin")
(:CREATOR |arnaud|)
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NIL)
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(STRUCTURE-ATOMS C N O O C C C C N N N O S C C C C C C C N)
(CITATIONS "782530")
(COMMON-NAME "5'-ethylthioadenosine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3277486826) )
NIL)
(5-FORMYL-THF-GLU-N T (
(OCELOT-GFP::PARENTS |All-Folates|)
(COMMON-NAME "an N5-formyl-tetrahydrofolate")
(:CREATOR |paley|)
(:CREATION-DATE 3330790568) )
NIL)
(5-HYDROXY-CTP NIL (
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(STRUCTURE-ATOMS N O O O O O O O O O O O C C N O O O O C C C C C C C N P P P)
(COMMON-NAME "5-hydroxy-CTP")
(:CREATOR |arnaud|)
(:CREATION-DATE 3280154916) )
NIL)
(5-IODOPENTAPHOSPHONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-IRREVERSIBLE-OF ENZRXN0-3801)
(COMMON-NAME "5-iodopentaphosphonate")
(:CREATOR |keseler|)
(:CREATION-DATE 3347042078) )
NIL)
(5-KETO-4-DEOXY-D-GLUCARATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00679" NIL |kr| 3346617698 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -266.7d0)
(APPEARS-IN-RIGHT-SIDE-OF GLUCARDEHYDRA-RXN GALACTARDEHYDRA-RXN)
(APPEARS-IN-LEFT-SIDE-OF KDGALDOL-RXN)
(COMMON-NAME "5-keto-4-deoxy-D-glucarate")
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(DISPLAY-COORDS-2D (-0.76878613d0 -0.12909442d0)
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(STRUCTURE-ATOMS C O O O O C C C C O O O C)
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(MOLECULAR-WEIGHT 192.125d0) )
((GIBBS-0 -266.7d0 CITATIONS "GibbsGroups97")))
(5-L-GLUTAMYL-L-AMINO-ACID NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
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(:CREATOR |paley|)
(:CREATION-DATE 3330791545)
(COMMON-NAME "(5-L-glutamyl)-L-amino acid")
(SYNONYMS "L-γ-glutamyl-L-amino acid")
(STRUCTURE-ATOMS N O O O O O R C C N C C C C C)
(DISPLAY-COORDS-2D (8.487d0 0.0d0) (9.6996d0 -3.5d0) (1.2124d0 -2.0d-4)
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(CHEMICAL-FORMULA (C 7) (H 11) (N 2) (O 5) (R 1)) )
NIL)
(5-L-GLUTAMYL-PEPTIDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF GAMMA-GLUTAMYLTRANSFERASE-RXN)
(:CREATOR |paley|)
(:CREATION-DATE 3330376203)
(COMMON-NAME "(5-L-glutamyl)-L-peptide")
(STRUCTURE-ATOMS C C C O C C O N N |Protein| O)
(DISPLAY-COORDS-2D (0.42489266d0 -0.5064378d0) (-0.42918456d0 -0.6695279d0)
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NIL)
(5-METHYL-THF NIL (
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(:CREATION-DATE 3073857204)
(GIBBS-0 -135.9d0)
(APPEARS-IN-LEFT-SIDE-OF 1.5.1.20-RXN HOMOCYSMETB12-RXN)
(SYNONYMS "N5-methyltetrahydropteroyl mono-L-glutamate"
"5-methyl-tetrahydrofolate" "5-methyl-5,6,7,8-tetrahydrofolate"
"n5-methyltetrahydrofolate" "N5-methyl-THF" "methyl-THF"
"methyl-tetrahydrofolate" "methyl-H4F")
(COMMON-NAME "5-methyl-THF")
(STRUCTURE-ATOMS H C N O O O O O O C C C C C C C C N N N N C C C C C C C C C
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(CHEMICAL-FORMULA (C 20) (H 25) (N 7) (O 6))
(MOLECULAR-WEIGHT 459.461d0)
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((GIBBS-0 -135.9d0 CITATIONS "GibbsGroups97")))
(5-METHYL-THF-GLU-N T (
(OCELOT-GFP::PARENTS |All-Folates|)
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(AROMATIC-RINGS (11 8 12 13 14 17))
(CHEMICAL-FORMULA (C 8) (H 13) (N 6) (O 1) (R 1))
(STRUCTURE-BONDS (15 16 1) (17 14 :AROMATIC) (13 16 1) (14 13 :AROMATIC)
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(STRUCTURE-ATOMS H C N O R C C N N N C C C C C N N)
(COMMON-NAME "an N5-methyl-tetrahydrofolate") )
NIL)
(5-METHYLAMINOMETHYL-2-SELENOURIDINE NIL (
(OCELOT-GFP::PARENTS |Nucleosides| |Pyrimidine-Related| |Base-Derivatives|)
(DISPLAY-COORDS-2D (-1.0d0 0.45214522d0) (-0.07590759d0 -1.0d0)
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(-0.07590759d0 -0.11551154d0) (-0.07590759d0 0.45214522d0)
(-0.37953794d0 -0.49174917d0) (-0.18811882d0 0.9933994d0)
(-0.3993399d0 0.2343235d0) (0.7887789d0 -0.65016496d0)
(-0.07590759d0 -0.65016496d0) (-0.5379538d0 0.9933994d0)
(0.56435645d0 -0.51155114d0) (0.13531351d0 -0.51155114d0)
(-1.0d0 0.7161716d0) (0.37953794d0 -0.65016496d0))
(CHEMICAL-FORMULA (C 11) (H 17) (N 3) (O 5) (SE 1))
(MOLECULAR-WEIGHT 350.232d0)
(STRUCTURE-BONDS (20 17 1) (18 20 1) (18 5 2) (17 14 1) (15 18 1) (13 10 1)
(11 15 1) (10 9 1) (10 3 1) (9 7 1) (8 1 1) (8 13 1) (7 4 2) (7 11 1)
(6 16 1) (6 8 1) (5 9 1) (3 12 1) (3 6 1) (2 15 2) (1 19 1))
(STRUCTURE-ATOMS C O C SE C C C C N C N O O C C O N C O C)
(CITATIONS "14594807")
(SYNONYMS "mnm(5)se(2)U")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2281)
(COMMON-NAME "5-methylaminomethyl-2-selenouridine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3286554283) )
NIL)
(5-METHYLAMINOMETHYL-2-THIOURIDINE NIL (
(OCELOT-GFP::PARENTS |Nucleosides| |Pyrimidine-Related| |Base-Derivatives|)
(AROMATIC-RINGS (21 20 3 12 9 7))
(DISPLAY-COORDS-2D (-0.10204083d0 0.99489796d0) (-0.040816367d0 0.43367338d0)
(-0.040816367d0 -0.3367347d0) (0.17857146d0 -1.0d0)
(-0.49489796d0 0.99489796d0) (0.57142854d0 -0.67857146d0)
(0.3979591d0 -0.5867347d0) (-0.30102044d0 -0.19387758d0)
(0.3979591d0 -0.3367347d0) (-0.30102044d0 0.25510204d0)
(-0.56122446d0 0.4234693d0) (0.17857146d0 -0.20408165d0)
(-0.27040815d0 -0.6938776d0) (-0.10204083d0 0.6989796d0)
(0.9132652d0 -0.6938776d0) (-0.49489796d0 0.6989796d0) (-1.0d0 0.42857134d0)
(-0.75d0 0.2755102d0) (0.7346939d0 -0.5969388d0)
(-0.040816367d0 -0.5867347d0) (0.17857146d0 -0.7091837d0))
(CHEMICAL-FORMULA (C 11) (H 17) (N 3) (O 5) (S 1))
(MOLECULAR-WEIGHT 303.332d0)
(STRUCTURE-BONDS (21 7 :AROMATIC) (20 21 :AROMATIC) (19 15 1) (18 11 1)
(17 18 1) (16 14 1) (16 11 1) (14 2 1) (13 20 1) (12 3 :AROMATIC) (11 10 1)
(10 2 1) (9 12 :AROMATIC) (8 3 2) (7 6 1) (7 9 :AROMATIC) (6 19 1) (5 16 1)
(4 21 2) (3 20 :AROMATIC) (2 12 1) (1 14 1))
(STRUCTURE-ATOMS O C C O O C C S C O C N H C C C O C N N C)
(CITATIONS "14594807")
(APPEARS-IN-LEFT-SIDE-OF RXN0-2281)
(COMMON-NAME "5-methylaminomethyl-2-thiouridine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3286554276) )
NIL)
(5-METHYLTHIOADENOSINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF SPERMIDINESYN-ENZRXN)
(HISTORY |kr-3290870141|)
(DBLINKS (LIGAND-CPD "C00170" NIL |kr| 3346617701 NIL NIL) (CAS "2457-80-9"))
(:CREATION-DATE 3115390701)
(SYNONYMS "methylthioadenosine" "S-methyl-5'-thioadenosine"
"5'-S-methyl-5'-thioadenosine" "MTA" "S-methyl-adenosine")
(AROMATIC-RINGS (13 14 15 16 17 18) (11 12 13 18 10))
(DISPLAY-COORDS-2D (4.6726d0 4.5918d0) (3.043d0 4.5947d0) (3.8365d0 2.8321d0)
(2.0627d0 3.6426d0) (4.4574d0 3.2781d0) (4.2316d0 3.9832d0)
(3.4742d0 3.9832d0) (3.2291d0 3.2671d0) (2.5169d0 3.0404d0)
(4.8949d0 1.9417d0) (4.8949d0 1.1916d0) (4.2454d0 0.8125d0) (3.6d0 1.1916d0)
(2.9447d0 0.8151d0) (2.2894d0 1.1886d0) (2.2946d0 1.9464d0)
(2.9499d0 2.323d0) (3.6d0 1.9417d0) (2.946d0 0.0651d0) (1.3333d0 3.4458d0))
(CHEMICAL-FORMULA (C 11) (H 15) (N 5) (O 3) (S 1))
(MOLECULAR-WEIGHT 297.331d0)
(STRUCTURE-BONDS (4 20 1) (14 19 1) (18 17 :AROMATIC) (17 16 :AROMATIC)
(16 15 :AROMATIC) (15 14 :AROMATIC) (14 13 :AROMATIC) (13 18 :AROMATIC)
(10 18 :AROMATIC) (13 12 :AROMATIC) (12 11 :AROMATIC) (11 10 :AROMATIC)
(5 10 1 :UP) (6 1 1 :DOWN) (7 2 1 :DOWN) (9 4 1) (8 9 1 :UP) (5 6 1) (7 6 1)
(3 5 1) (8 7 1) (8 3 1))
(STRUCTURE-ATOMS O O O S C C C C C N C N C C N C N C N C)
(APPEARS-IN-RIGHT-SIDE-OF SPERMIDINESYN-RXN)
(COMMON-NAME "5'-methylthioadenosine") )
NIL)
(5-METHYLTHIOFORMYCIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-2245)
(DISPLAY-COORDS-2D (11.9769d0 -2.3926d0) (0.0d0 -3.1502d0) (8.6638d0 0.0d0)
(5.618d0 0.0d0) (2.1189d0 -0.1121d0) (9.605d0 -2.8967d0) (0.9863d0 -0.935d0)
(3.3979d0 -0.6815d0) (4.2442d0 -4.2282d0) (2.8442d0 -4.2282d0)
(7.1409d0 -3.287d0) (10.6454d0 -1.9599d0) (1.1326d0 -2.3273d0)
(4.6768d0 -2.8967d0) (3.5442d0 -2.0738d0) (2.4116d0 -2.8967d0)
(7.8409d0 -1.1326d0) (6.4409d0 -1.1326d0) (8.2736d0 -2.4641d0)
(6.0083d0 -2.4641d0))
(AROMATIC-RINGS (8 5 7 13 16 15))
(CHEMICAL-FORMULA (C 11) (H 15) (N 5) (O 3) (S 1))
(MOLECULAR-WEIGHT 297.331d0)
(STRUCTURE-BONDS (18 20 1) (17 19 1) (17 18 1) (15 16 :AROMATIC)
(14 20 1 :DOWN) (14 15 1) (16 13 :AROMATIC) (11 20 1) (11 19 1) (10 16 1)
(9 14 2) (9 10 1) (8 15 :AROMATIC) (13 7 :AROMATIC) (19 6 1 :DOWN) (6 12 1)
(5 8 :AROMATIC) (7 5 :AROMATIC) (18 4 1 :UP) (17 3 1 :UP) (2 13 1) (1 12 1))
(STRUCTURE-ATOMS C N O O C C N N N N O S C C C C C C C C)
(SYNONYMS "5'-Mtf"
"D-Ribitol, 1-C-(7-amino-1H-pyrazolo(4,3-d)pyrimidin-3-yl)-1,4-anhydro-5-S-methyl-5-thio-, (S)-")
(CITATIONS "3911944")
(COMMON-NAME "5'-methylthioformycin")
(:CREATOR |arnaud|)
(:CREATION-DATE 3277486929) )
NIL)
(5-METHYLTHIOTUBERCIDIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-2245)
(DISPLAY-COORDS-2D (0.0d0 -2.3926d0) (11.9769d0 -3.1502d0) (3.3131d0 0.0d0)
(6.3589d0 0.0d0) (9.858d0 -0.1121d0) (9.1327d0 -4.2282d0)
(7.7327d0 -4.2282d0) (2.3719d0 -2.8967d0) (10.9906d0 -0.935d0)
(8.5791d0 -0.6815d0) (4.836d0 -3.287d0) (1.3315d0 -1.9599d0)
(10.8443d0 -2.3273d0) (9.5653d0 -2.8967d0) (8.4327d0 -2.0738d0)
(4.136d0 -1.1326d0) (5.536d0 -1.1326d0) (3.7034d0 -2.4641d0)
(5.9686d0 -2.4641d0) (7.3001d0 -2.8967d0))
(AROMATIC-RINGS (10 5 9 13 14 15))
(CHEMICAL-FORMULA (C 12) (H 16) (N 4) (O 3) (S 1))
(MOLECULAR-WEIGHT 296.343d0)
(STRUCTURE-BONDS (19 20 1 :UP) (17 19 1) (16 18 1) (16 17 1) (15 20 1)
(15 14 :AROMATIC) (14 13 :AROMATIC) (11 19 1) (11 18 1) (10 15 :AROMATIC)
(13 9 :AROMATIC) (18 8 1 :UP) (8 12 1) (7 20 1) (6 14 1) (6 7 2)
(5 10 :AROMATIC) (9 5 :AROMATIC) (17 4 1 :DOWN) (16 3 1 :DOWN) (2 13 1)
(1 12 1))
(STRUCTURE-ATOMS C N O O C C C C N N O S C C C C C C C N)
(SYNONYMS
"7-(5-S-methyl-5-thio-β-D-ribofuranosyl)-7H-pyrrolo(2,3-d)pyrimidin-4-amine")
(CITATIONS "3911944")
(COMMON-NAME "5'-methylthiotubercidin")
(:CREATOR |arnaud|)
(:CREATION-DATE 3277487097) )
NIL)
(5-N-PROPYLTHIOADENOSINE NIL (
(OCELOT-GFP::PARENTS |Purine-Related|)
(INHIBITORS-COMPETITIVE-OF ENZRXN0-2245)
(DISPLAY-COORDS-2D (0.0d0 -1.3698d0) (5.1413d0 -7.8588d0) (5.3096d0 0.0d0)
(8.1369d0 -0.005d0) (4.0111d0 -4.5947d0) (8.5226d0 -5.9043d0)
(1.3517d0 -1.0051d0) (2.3433d0 -1.9933d0) (4.3968d0 -2.6967d0)
(4.0021d0 -5.9095d0) (5.148d0 -3.9413d0) (7.3957d0 -6.562d0)
(6.6863d0 -3.0581d0) (3.6088d0 -1.6519d0) (5.139d0 -6.5575d0)
(6.2759d0 -5.9043d0) (6.2759d0 -4.6029d0) (6.0577d0 -1.0609d0)
(7.3717d0 -1.0609d0) (5.6324d0 -2.3034d0) (7.7635d0 -2.2843d0)
(8.5226d0 -4.6029d0))
(AROMATIC-RINGS (11 5 10 15 16 17) (6 12 16 17 22))
(CHEMICAL-FORMULA (C 13) (H 19) (N 5) (O 3) (S 1))
(MOLECULAR-WEIGHT 325.385d0)
(STRUCTURE-BONDS (21 22 1 :UP) (19 21 1) (18 20 1) (18 19 1)
(22 17 :AROMATIC) (17 16 :AROMATIC) (16 15 :AROMATIC) (13 21 1) (13 20 1)
(16 12 :AROMATIC) (11 17 :AROMATIC) (15 10 :AROMATIC) (20 9 1 :UP) (9 14 1)
(8 14 1) (7 8 1) (6 22 :AROMATIC) (12 6 :AROMATIC) (5 11 :AROMATIC)
(10 5 :AROMATIC) (19 4 1 :DOWN) (18 3 1 :DOWN) (2 15 1) (1 7 1))
(STRUCTURE-ATOMS C N O O C C C C C N N N O S C C C C C C C N)
(CITATIONS "782530")
(COMMON-NAME "5'-n-propylthioadenosine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3277486858) )
NIL)
(5-P-BETA-D-RIBOSYL-AMINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF GLYRIBONUCSYN-ENZRXN)
(DBLINKS (LIGAND-CPD "C03090" NIL |kr| 3346617700 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -144.2d0)
(APPEARS-IN-LEFT-SIDE-OF PRPPAMIDOTRANS-RXN GLYRIBONUCSYN-RXN)
(MOLECULAR-WEIGHT 229.126d0)
(CHEMICAL-FORMULA (C 5) (H 12) (N 1) (O 7) (P 1))
(DISPLAY-COORDS-2D (0.9971428571428572d0 -0.6628571428571428d0)
(0.10285714285714276d0 -0.24d0) (-1.0d0 -0.24d0)
(0.10285714285714276d0 -0.6628571428571428d0)
(-0.3028571428571428d0 -0.24d0)
(0.9971428571428572d0 -0.24285714285714288d0) (0.8257142857142856d0 -1.0d0)
(0.26857142857142846d0 -0.6171428571428572d0)
(0.9971428571428572d0 -0.4685714285714285d0) (-0.6828571428571428d0 -0.24d0)
(0.26857142857142846d0 -1.0d0) (0.5485714285714285d0 -0.2171428571428572d0)
(-0.6828571428571428d0 -0.56d0)
(-0.6828571428571428d0 0.07714285714285718d0)
(0.8257142857142856d0 -0.8085714285714286d0)
(0.8257142857142856d0 -0.6171428571428572d0)
(0.26857142857142846d0 -0.8085714285714286d0)
(0.10285714285714276d0 -0.4685714285714285d0))
(STRUCTURE-BONDS (18 17 1) (18 12 1) (17 15 1) (16 15 1) (14 10 2) (13 10 1)
(12 9 1) (11 17 1) (10 5 1) (9 15 1) (8 17 1) (7 15 1) (6 9 1) (5 2 1)
(4 18 1) (3 10 1) (2 18 1) (1 9 1))
(STRUCTURE-ATOMS H C O H O N O H C P O O O O C H C C)
(SYNONYMS "5-phospho-β-D-ribosyl-amine" "5-P-β-D-ribosyl-amine"
"PRA" "5-phosphoribosylamine")
(COMMON-NAME "5-phospho-β-D-ribosyl-amine") )
((GIBBS-0 -144.2d0 CITATIONS "GibbsGroups97")))
(5-P-NITROPHENYLTHIOADENOSINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-2245)
(DISPLAY-COORDS-2D (7.9335d0 -7.8588d0) (0.0d0 -1.219d0) (0.2965d0 -3.6256d0)
(8.1018d0 0.0d0) (10.9291d0 -0.005d0) (4.1685d0 -0.7054d0)
(4.465d0 -3.112d0) (2.779d0 -0.8766d0) (3.0755d0 -3.2832d0)
(6.8033d0 -4.5947d0) (11.3148d0 -5.9043d0) (7.189d0 -2.6967d0)
(6.7943d0 -5.9095d0) (7.9402d0 -3.9413d0) (10.1879d0 -6.562d0)
(9.4785d0 -3.0581d0) (6.401d0 -1.6519d0) (7.9312d0 -6.5575d0)
(5.0115d0 -1.8231d0) (2.2325d0 -2.1655d0) (9.0681d0 -5.9043d0)
(9.0681d0 -4.6029d0) (8.8499d0 -1.0609d0) (10.1639d0 -1.0609d0)
(8.4246d0 -2.3034d0) (10.5557d0 -2.2843d0) (0.843d0 -2.3367d0)
(11.3148d0 -4.6029d0))
(AROMATIC-RINGS (6 8 20 9 7 19) (15 11 28 22 21) (13 10 14 22 21 18))
(CHEMICAL-FORMULA (C 16) (H 16) (N 6) (O 5) (S 1))
(MOLECULAR-WEIGHT 404.4d0)
(STRUCTURE-BONDS (26 28 1 :UP) (24 26 1) (23 25 1) (23 24 1)
(22 28 :AROMATIC) (21 22 :AROMATIC) (20 27 1) (18 21 :AROMATIC) (17 19 1)
(16 26 1) (16 25 1) (15 21 :AROMATIC) (22 14 :AROMATIC) (13 18 :AROMATIC)
(25 12 1 :UP) (12 17 1) (28 11 :AROMATIC) (11 15 :AROMATIC)
(14 10 :AROMATIC) (10 13 :AROMATIC) (9 20 :AROMATIC) (20 8 :AROMATIC)
(19 7 :AROMATIC) (7 9 :AROMATIC) (6 19 :AROMATIC) (8 6 :AROMATIC)
(24 5 1 :DOWN) (23 4 1 :DOWN) (3 27 2) (2 27 2) (1 18 1))
(STRUCTURE-ATOMS N O O O O C C C C C C C N N N O S C C C C C C C C C N N)
(CITATIONS "8941345")
(COMMON-NAME "5'-(p-nitrophenyl)thioadenosine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3277487171) )
NIL)
(5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(DBLINKS (PUBCHEM "440313" NIL |keseler| 3342456871 NIL NIL)
(LIGAND-CPD "C04376" NIL |keseler| 3342456871 NIL NIL))
(:CREATION-DATE 3075053323)
(GIBBS-0 -197.4d0)
(APPEARS-IN-RIGHT-SIDE-OF GARTRANSFORMYL2-RXN GART-RXN)
(APPEARS-IN-LEFT-SIDE-OF FGAMSYN-RXN)
(MOLECULAR-WEIGHT 314.188d0)
(CHEMICAL-FORMULA (C 8) (H 15) (N 2) (O 9) (P 1))
(DISPLAY-COORDS-2D (0.5264d0 -0.68d0) (0.1296d0 0.0496d0)
(-0.1872d0 -0.3728d0) (-0.0528d0 -0.6608d0) (-0.0656d0 -0.1552d0)
(0.5264d0 -0.5104d0) (-0.7184d0 -0.3728d0) (-0.1872d0 -0.552d0)
(0.3888d0 -0.8304d0) (-0.4624d0 -0.3728d0) (0.9968d0 0.5584d0)
(-1.0d0 -0.3728d0) (0.5264d0 0.0496d0) (0.3888d0 -0.6608d0)
(0.52d0 0.3184d0) (0.1744d0 -0.3472d0) (0.8464d0 0.3184d0)
(-0.7184d0 -0.0912d0) (-0.0528d0 -0.8304d0) (-0.1872d0 -0.7216d0)
(-0.7184d0 -0.6544d0) (-0.0528d0 -1.0d0) (0.3888d0 -1.0d0)
(0.1296d0 0.3184d0))
(STRUCTURE-BONDS (24 2 1) (23 9 1) (22 19 1) (21 7 1) (20 8 1) (19 9 1)
(18 7 2) (17 15 1) (16 6 1) (15 24 1) (14 9 1) (13 6 1) (12 7 1) (11 17 2)
(10 3 1) (8 19 1) (8 16 1) (7 10 1) (6 9 1) (5 2 2) (4 19 1) (3 8 1)
(2 13 1) (1 6 1))
(STRUCTURE-ATOMS H C C H O C P C C O O O N H N O C O C H O O O C)
(COMMON-NAME "5'-phosphoribosyl-N-formylglycineamide")
(SYNONYMS "N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide"
"5'-P-ribosyl-N-formylglycineamide"
"5'-phosphoribosyl-N-formylglycinamide"
"5'-phosphoribosyl-N-formylglycineamide" "FGAR"
"5-phosphoribosyl-N-formalglycineamide"
"5'-phosphoribosyl-formylglycinamide") )
((GIBBS-0 -197.4d0 CITATIONS "GibbsGroups97")))
(5-PHOSPHO-RIBOSYL-GLYCINEAMIDE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(DBLINKS (LIGAND-CPD "C03838" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -172.5d0)
(COMMON-NAME "5-phospho-ribosyl-glycineamide")
(SYNONYMS "N1-(5-Phospho-D-ribosyl)glycinamide"
"5'-phosphoribosylglycinamide" "5'-phosphoribosylglycineamide"
"5'-p-ribosylglycinamide" "5'-p-ribosylglycineamide" "GAR")
(APPEARS-IN-RIGHT-SIDE-OF GLYRIBONUCSYN-RXN)
(APPEARS-IN-LEFT-SIDE-OF GARTRANSFORMYL2-RXN GART-RXN)
(DISPLAY-COORDS-2D (0.5353846153846153d0 -0.15384615384615385d0)
(0.8092307692307692d0 -0.56d0) (0.476923076923077d0 0.3630769230769231d0)
(0.476923076923077d0 0.7076923076923076d0)
(-0.6307692307692307d0 -0.1815384615384615d0) (-1.0d0 -0.1815384615384615d0)
(0.236923076923077d0 -0.56d0) (0.996923076923077d0 -0.5846153846153845d0)
(0.06461538461538452d0 -0.4184615384615384d0)
(-0.29846153846153844d0 -0.1815384615384615d0) (0.236923076923077d0 -1.0d0)
(-0.6307692307692307d0 -0.5476923076923077d0)
(0.996923076923077d0 -0.3630769230769231d0)
(0.22769230769230764d0 0.09846153846153838d0)
(0.8092307692307692d0 -0.7784615384615384d0)
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(0.06461538461538452d0 -0.64d0) (0.996923076923077d0 0.3630769230769231d0)
(0.8430769230769231d0 0.7076923076923076d0) (0.8092307692307692d0 -1.0d0)
(0.06461538461538452d0 -0.1815384615384615d0)
(0.236923076923077d0 -0.7784615384615384d0))
(STRUCTURE-BONDS (22 15 1) (21 9 1) (20 15 1) (19 4 1) (18 13 1) (17 9 1)
(16 5 2) (14 3 2) (13 15 1) (12 5 1) (11 22 1) (10 21 1) (9 22 1) (9 1 1)
(8 13 1) (7 22 1) (6 5 1) (5 10 1) (4 3 1) (3 18 1) (2 15 1) (1 13 1))
(STRUCTURE-ATOMS O H C C P O H H C O O O C O C O H N N O C C)
(CHEMICAL-FORMULA (C 7) (H 15) (N 2) (O 8) (P 1))
(MOLECULAR-WEIGHT 286.178d0) )
((GIBBS-0 -172.5d0 CITATIONS "GibbsGroups97")))
(|5-Phosphopolynucleotides| T (
(OCELOT-GFP::PARENTS |Polynucleotides|)
(COMMON-NAME "a 5'-phosphopolynucleotide")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF AIRS-ENZRXN)
(DBLINKS (CAS "25635-88-5" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C03373" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3075053323)
(GIBBS-0 -98.7d0)
(COMMON-NAME "5-aminoimidazole ribonucleotide")
(APPEARS-IN-LEFT-SIDE-OF RXN0-742 PYRIMSYN1-RXN)
(APPEARS-IN-RIGHT-SIDE-OF AIRS-RXN)
(SYNONYMS "5-amino-1-(5-phospho-D-ribosyl)imidazole"
"5-aminoimidazole ribotide" "AIR" "1-(5'-phosphoribosyl)-5-aminoimidazole"
"5'-phosphoribosyl-5-aminoimidazole" "phosphoribosylaminoimidazole")
(STRUCTURE-ATOMS N O O O O O C C C N O O C C C C C N P)
(STRUCTURE-BONDS (17 18 1) (15 17 1) (14 16 1) (14 15 1) (13 18 :AROMATIC)
(12 17 1) (12 16 1) (11 19 1) (9 16 1) (9 11 1) (18 8 :AROMATIC)
(8 10 :AROMATIC) (7 13 :AROMATIC) (10 7 :AROMATIC) (6 19 1) (5 19 1)
(4 15 1) (3 14 1) (2 19 2) (1 13 1))
(DISPLAY-COORDS-2D (5.0719d0 -2.3503d0) (1.3747d0 -3.4911d0)
(4.687d0 -7.9446d0) (6.8862d0 -7.9446d0) (0.0d0 -4.9068d0)
(1.3747d0 -6.24d0) (6.3779d0 -0.5224d0) (8.5221d0 -1.2368d0)
(3.9998d0 -4.9068d0) (7.5737d0 0.0d0) (2.6392d0 -4.9068d0)
(5.8278d0 -4.7693d0) (6.3779d0 -1.8416d0) (4.687d0 -7.1201d0)
(6.8862d0 -7.1201d0) (3.9998d0 -5.7591d0) (7.6011d0 -5.5529d0)
(7.6011d0 -2.4877d0) (1.3747d0 -4.9068d0))
(CHEMICAL-FORMULA (C 8) (H 14) (N 3) (O 7) (P 1))
(MOLECULAR-WEIGHT 295.188d0)
(AROMATIC-RINGS (7 10 8 18 13)) )
((GIBBS-0 -98.7d0 CITATIONS "GibbsGroups97")))
(5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(DBLINKS (PUBCHEM "440417" NIL |keseler| 3342800794 NIL NIL)
(LIGAND-CPD "C04640" NIL |keseler| 3342800794 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -154.4d0)
(COMMON-NAME "5-phosphoribosyl-N-formylglycineamidine")
(APPEARS-IN-LEFT-SIDE-OF AIRS-RXN)
(APPEARS-IN-RIGHT-SIDE-OF FGAMSYN-RXN)
(MOLECULAR-WEIGHT 313.203d0)
(CHEMICAL-FORMULA (C 8) (H 16) (N 3) (O 8) (P 1))
(DISPLAY-COORDS-2D (0.48254d0 -0.69206d0) (0.09841d0 0.01587d0)
(-0.20952d0 -0.39365d0) (-0.07937d0 -0.66984d0) (0.88571d0 0.26984d0)
(0.48254d0 -0.52698d0) (-0.72381d0 -0.39365d0) (-0.20952d0 -0.56825d0)
(0.34921d0 -0.83492d0) (-0.47302d0 -0.39365d0) (0.99683d0 0.51111d0)
(-1.0d0 -0.39365d0) (0.48254d0 0.01587d0) (0.34921d0 -0.66984d0)
(0.47619d0 0.26984d0) (0.14286d0 -0.37143d0) (-0.09206d0 -0.18413d0)
(-0.72381d0 -0.11746d0) (-0.07937d0 -0.83492d0) (-0.20952d0 -0.73333d0)
(-0.72381d0 -0.66984d0) (-0.07937d0 -1.0d0) (0.34921d0 -1.0d0)
(0.09841d0 0.26984d0))
(STRUCTURE-BONDS (24 2 1) (23 9 1) (22 19 1) (21 7 1) (20 8 1) (19 9 1)
(18 7 2) (17 2 2) (16 6 1) (15 24 1) (14 9 1) (13 6 1) (12 7 1) (11 5 2)
(10 3 1) (8 19 1) (8 16 1) (7 10 1) (6 9 1) (5 15 1) (4 19 1) (3 8 1)
(2 13 1) (1 6 1))
(STRUCTURE-ATOMS H C C H C C P C C O O O N H N O N O C H O O O C)
(SYNONYMS "2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine"
"5'-phosphoribosyl-N-formyl glycineamidine" "FGAM"
"5-phosphoribosyl-N-formylglycineamidine"
"5'-phosphoribosylformylglycinamidine") )
((GIBBS-0 -154.4d0 CITATIONS "GibbsGroups97")))
(5.1.3.20-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.1.3)
(IN-PATHWAY PWY0-1241)
(ENZYMATIC-REACTION ENZRXN0-5762)
(:CREATOR |keseler|)
(:CREATION-DATE 3333293211)
(COMMON-NAME "ADP-glyceromanno-heptose 6-epimerase")
(SYNONYMS "ADP-L-glycero-D-manno-heptose 6-epimerase")
(LEFT ADP-D-GLYCERO-D-MANNO-HEPTOSE)
(RIGHT ADP-L-GLYCERO-D-MANNO-HEPTOSE)
(EC-NUMBER "5.1.3.20")
(OFFICIAL-EC? T)
(BALANCE-STATE :BALANCED) )
NIL)
(5.3.4.1-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Reactions| EC-5.3.4)
(RIGHT |Proteins-with-correct-disulfides|)
(LEFT |Proteins-with-incorrect-disulfides|)
(OFFICIAL-EC? T)
(COMMENT "This reaction rearranges the disulfide bonds of proteins.")
(ENZYMATIC-REACTION DSBG-ENZRXN DISULISOM-ENZRXN)
(TEMPLATE-FILE "enzyme.asn v.20.0")
(:CREATION-DATE 3069621145)
(:CREATOR |kr|)
(EC-NUMBER "5.3.4.1")
(SYNONYMS "S-S REARRANGASE")
(COMMON-NAME "PROTEIN DISULFIDE ISOMERASE") )
NIL)
(5.99.1.2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.99.1)
(ENZYMATIC-REACTION ENZRXN0-4041 ENZRXN0-3962)
(OFFICIAL-EC? T)
(SYNONYMS "ω-protein" "Nicking-closing enzyme"
"Type I DNA topoisomerase" "Swivelase" "Untwisting enzyme" "Relaxing enzyme"
"DNA topoisomerase I")
(COMMON-NAME "DNA topoisomerase")
(:CREATION-DATE 3307385321)
(:CREATOR |keseler|)
(EC-NUMBER "5.99.1.2") )
NIL)
(5.99.1.3-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.99.1)
(COMMENT
"This reaction is the ATP-dependent breakage, passage and rejoining of double-stranded DNA.")
(ENZYMATIC-REACTION ENZRXN0-6160)
(:CREATOR |shearer|)
(:CREATION-DATE 3346002854)
(EC-NUMBER "5.99.1.3")
(COMMON-NAME "DNA topoisomerase (ATP-hydrolysing)")
(SYNONYMS "Type II DNA topoisomerase" "DNA gyrase" "DNA topoisomerase II")
(OFFICIAL-EC? T) )
NIL)
(55-DITHIO-BIS2-NITROBENZOIC-ACID NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF TRANSENOYLCOARED-ENZRXN GMP-SYN-GLUT-ENZRXN
GABATRANSAM-ENZRXN ENZRXN0-1641 THREODEHYD-ENZRXN 6PGLUCONDEHYDROG-ENZRXN
ASPARTASE-ENZRXN ANGLYC3PDEHYDROG-ENZRXN GLUCOSAMINE1PACETYL-ENZRXN
ENZRXN0-263)
(:CREATOR |paley|)
(:CREATION-DATE 3340979761)
(COMMON-NAME "5,5'-dithio-bis(2-nitrobenzoic acid)")
(STRUCTURE-ATOMS O O O O O O O O C C C C C C S S C C C C C C C C N N)
(DISPLAY-COORDS-2D (9.6995d0 0.0d0) (2.4249d0 -11.2d0) (12.1244d0 -2.8d0)
(10.9119d0 -0.7d0) (0.0d0 -8.4d0) (1.2124d0 -10.5d0) (7.2746d0 0.0d0)
(4.8497d0 -11.2d0) (8.487d0 -4.9d0) (3.6373d0 -6.3d0) (9.6995d0 -4.2d0)
(2.4249d0 -7.0d0) (7.2746d0 -2.8d0) (4.8497d0 -8.4d0) (6.0622d0 -4.9d0)
(6.0622d0 -6.3d0) (8.487d0 -0.7d0) (3.6373d0 -10.5d0) (7.2746d0 -4.2d0)
(4.8497d0 -7.0d0) (8.487d0 -2.1d0) (3.6373d0 -9.1d0) (9.6995d0 -2.8d0)
(2.4249d0 -8.4d0) (10.9119d0 -2.1d0) (1.2124d0 -9.1d0))
(STRUCTURE-BONDS (24 26 1) (23 25 1) (22 24 :AROMATIC) (21 23 :AROMATIC)
(18 22 1) (17 21 1) (16 20 1) (15 19 1) (15 16 1) (14 22 :AROMATIC)
(20 14 :AROMATIC) (13 21 :AROMATIC) (19 13 :AROMATIC) (24 12 :AROMATIC)
(23 11 :AROMATIC) (10 20 :AROMATIC) (12 10 :AROMATIC) (9 19 :AROMATIC)
(11 9 :AROMATIC) (8 18 1) (7 17 1) (6 26 2) (5 26 2) (4 25 2) (3 25 2)
(2 18 2) (1 17 2))
(CHEMICAL-FORMULA (C 14) (H 8) (N 2) (O 8) (S 2))
(MOLECULAR-WEIGHT 396.346d0)
(AROMATIC-RINGS (10 12 24 22 14 20) (13 19 9 11 23 21))
(SYNONYMS "5-(3-carboxy-4-nitro-phenyl)disulfanyl-2-nitro-benzoic acid"
"DTNB") )
NIL)
(5678-TETRAHYDROPTERIDINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF 1.5.1.34-RXN)
(DISPLAY-COORDS-2D (0.4609928d0 -1.0d0) (0.9858155d0 -0.6879433d0)
(0.9858155d0 -0.1914894d0) (0.4609928d0 0.12056732d0) (-0.56028366d0 -1.0d0)
(-1.0d0 -0.6879433d0) (-1.0d0 -0.1914894d0) (-0.56028366d0 0.12056732d0)
(-0.0070922375d0 -0.1914894d0) (-0.0070922375d0 -0.6879433d0))
(CHEMICAL-FORMULA (C 6) (H 8) (N 4))
(MOLECULAR-WEIGHT 136.156d0)
(STRUCTURE-BONDS (10 1 1) (10 9 2) (9 8 1) (8 7 1) (7 6 1) (6 5 1) (5 10 1)
(4 9 1) (3 4 2) (2 3 1) (1 2 2))
(STRUCTURE-ATOMS N C N C N C C N C C)
(SYNONYMS "tetrahydropteridine")
(COMMON-NAME "5,6,7,8-tetrahydropteridine") )
NIL)
(5K-GLUCONATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER0-1301)
(DBLINKS (LIGAND-CPD "C01062" NIL |kr| 3346617699 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF RXN0-2701)
(:CREATION-DATE 3073857204)
(APPEARS-IN-RIGHT-SIDE-OF YIAE1-RXN GLUCONATE-5-DEHYDROGENASE-RXN
IDONDEHYD-RXN)
(GIBBS-0 -260.8d0)
(MOLECULAR-WEIGHT 194.141d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 7))
(DISPLAY-COORDS-2D (-0.14146d0 -0.24228d0) (-1.0d0 0.02439d0)
(-0.13496d0 1.0d0) (-0.57073d0 -0.24228d0) (-0.57073d0 -0.99675d0)
(-0.57073d0 -0.56748d0) (-0.57073d0 0.02439d0) (-0.13496d0 0.34309d0)
(-0.13496d0 0.66829d0) (-0.57073d0 0.34309d0) (-0.57073d0 1.0d0)
(-0.14146d0 -0.56748d0) (-0.57073d0 0.66829d0))
(STRUCTURE-BONDS (13 10 1) (12 6 1) (11 13 1) (10 7 1) (9 13 2) (8 10 1)
(7 4 1) (6 4 1) (5 6 2) (3 11 1) (2 7 1) (1 4 1))
(STRUCTURE-ATOMS O O O C O C C O O C C O C)
(COMMON-NAME "5-ketogluconate")
(SYNONYMS "5-dehydro-D-gluconate" "5-keto-D-gluconate" "5-k-gluconate") )
((GIBBS-0 -260.8d0 CITATIONS "GibbsGroups97")))
(|5S-rRNAs| T (
(OCELOT-GFP::PARENTS |rRNAs|)
(:CREATOR |kr|)
(:CREATION-DATE 3266259220) )
NIL)
(|6-a-D-mannosyl-b-D-mannosyl-R| T (
(OCELOT-GFP::PARENTS |Modified-Proteins|)
(COMMENT
"R represents the remainder of the N-linked oligosaccharide in the glycoprotein acceptor.")
(SYNONYMS "6-(a-D-mannosyl)-b-D-mannosyl-R")
(COMMON-NAME "6-(α-D-mannosyl)-β-D-mannosyl-R")
(CHEMICAL-FORMULA (C 12) (H 21) (O 11) (R1 1) (|Protein| 1))
(STRUCTURE-BONDS (24 25 1) (1 7 1) (14 2 1 :UP) (15 3 1 :DOWN) (16 4 1 :UP)
(17 5 1 :DOWN) (18 6 1 :UP) (24 9 1) (19 7 1 :UP) (8 10 1) (20 8 1 :UP)
(21 9 1 :UP) (22 10 1 :DOWN) (11 19 1) (11 22 1) (12 20 1) (12 21 1)
(23 13 1 :UP) (14 15 1) (14 16 1) (15 19 1) (16 22 1) (17 20 1) (17 23 1)
(18 21 1) (18 23 1))
(DISPLAY-COORDS-2D (0.0d0 -5.526d0) (2.0865d0 -3.537d0) (0.6683d0 -4.3525d0)
(3.521d0 -4.3525d0) (3.8144d0 -4.8413d0) (6.5692d0 -4.1242d0)
(0.6683d0 -5.9988d0) (4.2221d0 -6.4225d0) (6.9769d0 -5.7055d0)
(3.521d0 -5.9988d0) (2.0865d0 -5.9988d0) (5.5911d0 -6.064d0)
(4.972d0 -3.6841d0) (2.0865d0 -4.3525d0) (1.3858d0 -4.7598d0)
(2.804d0 -4.7598d0) (4.5971d0 -5.0531d0) (5.9824d0 -4.6945d0)
(1.3858d0 -5.5911d0) (4.8089d0 -5.8522d0) (6.1783d0 -5.4932d0)
(2.804d0 -5.5911d0) (5.1839d0 -4.4828d0) (7.5473d0 -5.1182d0)
(8.3723d0 -5.1182d0))
(STRUCTURE-ATOMS O O O O O O C C O O O O O C C C C C C C C C C R1 |Protein|)
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(|6-Acetyl-Beta-D-Galactosides| T (
(OCELOT-GFP::PARENTS |Carbohydrate-Derivatives|)
(APPEARS-IN-RIGHT-SIDE-OF GALACTOACETYLTRAN-RXN)
(SYNONYMS "a 6-acetyl-β-D-galactoside" "6-acetyl-β-D-galactoside")
(COMMENT
"This compound class stands for generic and unspecified 6-acetyl-β-D-galactosides.")
(:CREATOR |kr|)
(:CREATION-DATE 3265036284) )
NIL)
(|6-alpha-D--1-4-alpha-D-Glucano--Glucan| T (
(OCELOT-GFP::PARENTS |Glycogens|)
(COMMENT
"Glycogen is a glucose-containing polysaccharide, comprised of approximately 95%
α-1,4 linkages and the remainder α-1,6 branch glucosyl linkages, which occur approximately
every 12 glucose residues.
The average chain length is about 12 to 14 glucose units.")
(DBLINKS (LIGAND-CPD "C00182" NIL |kr| 3346617701 NIL NIL)
(CAS "9005-79-2" NIL |kaipa| 3311445804 NIL NIL))
(N+1-NAME "{6-α-D-(1,4-α-D-glucano)-glucan}n+1")
(N-1-NAME "{6-α-D-(1,4-α-D-glucano)-glucan}n-1")
(SYNONYMS "6-α-D-(1,4-α-D-glucano)-glucan")
(MOLECULAR-WEIGHT 666.583d0)
(CHEMICAL-FORMULA (C 24) (H 42) (O 21))
(STRUCTURE-BONDS (40 35 1) (37 29 1) (18 23 1) (10 8 1) (40 45 1 :DOWN)
(38 44 1) (37 43 1 :DOWN) (35 42 1 :DOWN) (34 41 1) (33 40 1) (29 39 1 :UP)
(28 38 1 :UP) (28 37 1) (27 36 1 :UP) (35 27 1) (26 34 1 :UP) (26 33 1)
(24 32 1) (23 31 1 :DOWN) (22 30 1 :DOWN) (29 22 1) (21 28 1) (27 20 1)
(20 26 1) (18 25 1 :UP) (17 24 1 :UP) (23 17 1) (22 16 1) (16 21 1)
(20 15 1 :DOWN) (13 19 1 :DOWN) (13 18 1) (17 12 1) (16 11 1 :DOWN)
(10 15 1 :DOWN) (8 14 1 :DOWN) (7 13 1) (12 7 1) (6 11 1) (5 10 1)
(4 9 1 :UP) (8 4 1) (7 3 1 :DOWN) (2 6 1 :UP) (2 5 1) (4 1 1) (1 3 1 :DOWN)
(1 2 1))
(DISPLAY-COORDS-2D (-1.2494d0 -3.7161d0) (-0.6932d0 -2.1926d0)
(-2.6682d0 -4.4255d0) (-0.2257d0 -4.8285d0) (0.8625d0 -1.9427d0)
(-1.7009d0 -1.0076d0) (-4.1191d0 -3.9337d0) (1.2414d0 -4.5706d0)
(-0.7094d0 -6.2956d0) (1.8057d0 -3.176d0) (-0.9351d0 0.3144d0)
(-4.6834d0 -2.507d0) (-5.1026d0 -5.1671d0) (2.2087d0 -5.7636d0)
(3.3695d0 -3.3775d0) (-1.9346d0 1.4832d0) (-6.2311d0 -2.3135d0)
(-6.5939d0 -4.9655d0) (-4.5303d0 -6.6019d0) (4.5706d0 -2.4263d0)
(-1.4187d0 2.9261d0) (-3.442d0 1.2011d0) (-7.1823d0 -3.5549d0)
(-6.9082d0 -0.9109d0) (-7.537d0 -6.1908d0) (4.6512d0 -0.8867d0)
(5.8926d0 -3.2244d0) (-2.4183d0 4.095d0) (-4.4416d0 2.3619d0)
(-3.9337d0 -0.266d0) (-8.7058d0 -3.3856d0) (-5.8764d0 0.1854d0)
(6.0296d0 -0.1693d0) (3.4098d0 -0.0161d0) (7.2146d0 -2.5392d0)
(5.8361d0 -4.7721d0) (-3.9337d0 3.8128d0) (-1.7815d0 5.5701d0)
(-5.949d0 2.0475d0) (7.3113d0 -0.9996d0) (3.8854d0 1.459d0)
(8.4882d0 -3.3856d0) (-4.9817d0 4.9817d0) (-2.8697d0 6.6342d0)
(8.6978d0 -0.3063d0))
(STRUCTURE-ATOMS C C O C O C C C O C O O C O O C C C O C O C C C O C C C C O
O O O C C O C C O C O O O O O)
(APPEARS-IN-RIGHT-SIDE-OF GLYCOGEN-BRANCH-RXN)
(COMMON-NAME "a glycogen")
(:CREATION-DATE 3114279020)
(:CREATOR |kr|) )
NIL)
(6-AMINOPENICILLANATE NIL (
(OCELOT-GFP::PARENTS |Beta-Lactams|)
(HISTORY |kr-3290870141|)
(DBLINKS (CAS "551-16-6"))
(:CREATION-DATE 3115390701)
(SYNONYMS "6-Aminopenicillanic acid")
(DISPLAY-COORDS-2D (1.65d0 1.7041d0) (1.65d0 2.45d0) (2.9449d0 2.4542d0)
(2.9449d0 1.7041d0) (2.2954d0 1.325d0) (0.9d0 1.7d0) (0.9d0 2.45d0)
(1.65d0 0.95d0) (0.9d0 0.95d0) (0.15d0 1.7d0) (0.3697d0 2.9803d0)
(3.4744d0 2.9853d0) (3.6328d0 2.0932d0) (2.9417d0 0.95d0)
(3.2791d0 3.7095d0) (4.1991d0 2.7924d0))
(CHEMICAL-FORMULA (C 8) (H 12) (N 2) (O 3) (S 1))
(MOLECULAR-WEIGHT 216.254d0)
(STRUCTURE-BONDS (12 16 2) (12 15 1) (4 14 1) (4 13 1) (3 12 1 :DOWN)
(7 11 2) (6 10 1 :UP) (6 9 1 :DOWN) (1 8 1 :DOWN) (7 2 1) (6 7 1) (1 6 1)
(2 3 1) (5 1 1) (4 5 1) (3 4 1) (1 2 1))
(STRUCTURE-ATOMS C N C C S C C H H N O C C C O O)
(COMMON-NAME "6-aminopenicillanate") )
NIL)
(6-DEOXY-D-GLUCOSE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |kaipa|)
(:CREATION-DATE 3346525587)
(COMMON-NAME "6-deoxy-D-glucose") )
NIL)
(6-DIAZO-5-OXO-L-NORLEUCINE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(INHIBITORS-COMPETITIVE-OF GLUTAMINB-ENZRXN L-GLN-FRUCT-6-P-AMINOTRANS-ENZRXN
GMP-SYN-GLUT-ENZRXN GMP-SYN-NH3-ENZRXN)
(INHIBITORS-IRREVERSIBLE-OF GLUTAMINA-ENZRXN)
(INHIBITORS-UNKMECH-OF PABASYN-ENZRXN)
(DBLINKS (CAS "764-17-0"))
(COMMON-NAME "6-diazo-5-oxo-L-norleucine")
(MOLECULAR-WEIGHT 171.155d0)
(CHEMICAL-FORMULA (C 6) (H 9) (N 3) (O 3))
(DISPLAY-COORDS-2D (-0.25289d0 -0.26612d0) (0.24628d0 -0.56033d0)
(-0.74215d0 -0.56033d0) (0.49091d0 -0.70579d0) (-0.49752d0 -0.70579d0)
(-1.0d0 -0.70248d0) (0.99669d0 -0.70909d0) (-0.25289d0 -0.56033d0)
(0.74215d0 -0.56033d0) (0.49091d0 -1.0d0) (-0.00496d0 -0.70579d0)
(0.74215d0 -0.26612d0))
(STRUCTURE-BONDS (12 9 2) (11 8 1) (10 4 1) (9 4 1) (8 5 1) (7 9 1) (6 3 2)
(5 3 2) (4 2 1) (2 11 1) (1 8 2))
(STRUCTURE-ATOMS O C N C C N O C C N C O)
(SYSTEMATIC-NAME "Norleucine, 6-diazo-5-oxo-")
(SYNONYMS "diazooxonorleucine" "6-diazo-5-oxo-L-norleucine")
(ATOM-CHARGES (6 -1) (3 1)) )
NIL)
(|6-Phospho-b-D-galactosides| T (
(OCELOT-GFP::PARENTS HEXOSE-6-PHOSPHATES)
(COMMON-NAME "a 6-phospho-β-D-galactoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(6-PHOSPHO-BETA-GLUCOSIDASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-765 ENZRXN0-764 ENZRXN0-763 ENZRXN0-762
ENZRXN0-761)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "3.2.1.86")
(COMMON-NAME "6-PHOSPHO-β-GLUCOSIDASE")
(COMMENT
"ALSO HYDROLYSES SEVERAL OTHER PHOSPHO-β-D-GLUCOSIDES, BUT NOT THEIR NON-PHOSPHORYLATED FORMS.")
(RIGHT GLC-6-P GLC)
(LEFT CPD-507 WATER) )
NIL)
(6-PHYT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH CIT)
(INHIBITORS-UNKMECH CPD-4584 CPD-3 |Pi| ZN+2 CU+2)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 6-PHYT-RXN)
(INHIBITORS-COMPETITIVE F- TARTRATE)
(COMMENT "Phytase has just recently been found in E. coli. It is
expressed under anaerobic conditions and in late stationary phase
growth. |CITS: [GreinerBiolChemHoppe-Seyler372,664]| Phytase is
considered to be a special type of acid phosphatase, which is capable
of splitting off phosphate from phytate as well as other diversified
organophosphates. The E. coli phytase is capable of degrading phytate
to free myo-inositol, however the later steps are inhibited by the
released phosphate. |CITS: [93256556]| The appA gene codes for
both phytase and the ph 2.5 acid phosphatase.")
(ENZYME CPLX-722)
(SYNONYMS "phytase" "phytate 6-phosphatase"
"myo-inositol-hexakisphosphate 6-phosphohydrolase")
(COMMON-NAME "6-phytase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/appA.template")
(:CREATION-DATE 3016372603)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH CIT COMMENT "slightly activating |CITS:
[93256556]|")
(INHIBITORS-UNKMECH CPD-4584 COMMENT
"Both Cu++ and Zn++ showed strong inhibitory effects. The E. coli
phytase also shows substrate inhibition. |CITS: [93256556]|")
(INHIBITORS-UNKMECH CPD-3 COMMENT
"Both Cu++ and Zn++ showed strong inhibitory effects. The E. coli
phytase also shows substrate inhibition. |CITS: [93256556]|")
(INHIBITORS-UNKMECH |Pi| COMMENT
"Both Cu++ and Zn++ showed strong inhibitory effects. The E. coli
phytase also shows substrate inhibition. |CITS: [93256556]|")
(INHIBITORS-UNKMECH ZN+2 COMMENT
"Both Cu++ and Zn++ showed strong inhibitory effects. The E. coli
phytase also shows substrate inhibition. |CITS: [93256556]|")
(INHIBITORS-UNKMECH CU+2 COMMENT
"Both Cu++ and Zn++ showed strong inhibitory effects. The E. coli
phytase also shows substrate inhibition. |CITS: [93256556]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme has a high specificity for
phytate, however there is some activity with p-nitrophenyl-phosphate
and fructose-1,6-diphosphate. |CITS:
[GreinerBiolChemHoppe-Seyler372,664] [93256556]|")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[93256556]")))
(6-PHYT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 6-PHYT-ENZRXN)
(RIGHT |Pi| MI-PENTAKISPHOSPHATE)
(LEFT WATER MI-HEXAKISPHOSPHATE)
(EC-NUMBER "3.1.3.26")
(COMMENT "This reaction is part of central intermediary metabolism.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/appA.template")
(:CREATION-DATE 3016372603)
(:CREATOR |mriley|) )
NIL)
(6-PYRUVOYL-5678-TETRAHYDROPTERIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF 4.2.3.12-RXN)
(:CREATOR |shearer|)
(:CREATION-DATE 3346168965)
(COMMON-NAME "6-pyruvoyltetrahydropterin")
(SYNONYMS "6-pyruvoyl-5,6,7,8-tetrahydropterin"
"6-(1,2-Dioxopropyl)-5,6,7,8-tetrahydropterin"
"pyruvoyl-H4-pterin")
(STRUCTURE-ATOMS C N O O O C N N N N C C C C C C C)
(DISPLAY-COORDS-2D (9.6995d0 -1.4d0) (0.0d0 -4.2d0) (8.487d0 -3.5d0)
(7.2746d0 0.0d0) (2.4249d0 0.0d0) (6.0622d0 -3.5d0) (2.4249d0 -4.2d0)
(4.8497d0 -4.2d0) (4.8497d0 -1.4d0) (1.2124d0 -2.1d0) (8.487d0 -2.1d0)
(7.2746d0 -1.4d0) (1.2124d0 -3.5d0) (3.6373d0 -3.5d0) (3.6373d0 -2.1d0)
(2.4249d0 -1.4d0) (6.0622d0 -2.1d0))
(STRUCTURE-BONDS (15 16 :AROMATIC) (14 15 :AROMATIC) (12 17 1) (11 12 1)
(16 10 :AROMATIC) (10 13 :AROMATIC) (9 17 1) (9 15 1) (8 14 1)
(7 14 :AROMATIC) (13 7 :AROMATIC) (6 17 1) (6 8 1) (5 16 2) (4 12 2)
(3 11 2) (2 13 1) (1 11 1))
(CHEMICAL-FORMULA (C 9) (H 11) (N 5) (O 3))
(MOLECULAR-WEIGHT 237.218d0)
(AROMATIC-RINGS (14 7 13 10 16 15)) )
NIL)
(6-SELENO-OCTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-1085)
(DISPLAY-COORDS-2D (9.6995d0 -1.4d0) (1.2124d0 -3.4999d0) (0.0d0 -1.3999d0)
(7.2746d0 0.0d0) (8.487d0 -2.1d0) (3.6373d0 -2.1d0) (4.8497d0 -1.4d0)
(2.4248d0 -1.3999d0) (6.0621d0 -2.1d0) (1.2124d0 -2.0999d0)
(7.2746d0 -1.4d0))
(CHEMICAL-FORMULA (C 8) (H 15) (O 2) (SE 1))
(MOLECULAR-WEIGHT 222.165d0)
(STRUCTURE-BONDS (9 11 1) (8 10 1) (7 9 1) (6 8 1) (6 7 1) (5 11 1) (4 11 1)
(3 10 1) (2 10 2) (1 5 1))
(STRUCTURE-ATOMS C O O SE C C C C C C C)
(COMMON-NAME "6-seleno-octanoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3257714500) )
NIL)
(6-THIO-OCTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (9.6995d0 -1.4d0) (1.2124d0 -3.4999d0) (0.0d0 -1.3999d0)
(7.2746d0 0.0d0) (8.487d0 -2.1d0) (3.6373d0 -2.1d0) (4.8497d0 -1.4d0)
(2.4248d0 -1.3999d0) (6.0621d0 -2.1d0) (1.2124d0 -2.0999d0)
(7.2746d0 -1.4d0))
(CHEMICAL-FORMULA (C 8) (H 16) (O 2) (S 1))
(MOLECULAR-WEIGHT 176.273d0)
(STRUCTURE-BONDS (9 11 1) (8 10 1) (7 9 1) (6 8 1) (6 7 1) (5 11 1) (4 11 1)
(3 10 1) (2 10 2) (1 5 1))
(STRUCTURE-ATOMS C O O S C C C C C C C)
(COMMON-NAME "6-thio-octanoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3257714396) )
NIL)
(67-DIHYDROPTERIDINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF 1.5.1.34-RXN)
(DISPLAY-COORDS-2D (-0.5030303d0 -1.0d0) (0.5030303d0 0.23636365d0)
(0.9878787d0 -0.06666672d0) (0.030303001d0 -0.6484848d0)
(0.9878787d0 -0.6484848d0) (0.030303001d0 -0.06666672d0)
(0.5030303d0 -1.0d0) (-1.0d0 -0.6484848d0) (-0.5030303d0 0.23636365d0)
(-1.0d0 -0.06666672d0))
(CHEMICAL-FORMULA (C 6) (H 6) (N 4))
(MOLECULAR-WEIGHT 134.14d0)
(STRUCTURE-BONDS (10 8 1) (9 10 1) (8 1 1) (7 5 2) (6 9 2) (5 3 1) (4 7 1)
(4 6 1) (3 2 2) (2 6 1) (1 4 2))
(STRUCTURE-ATOMS N C N C C C N C N C)
(SYNONYMS "dihydropteridine")
(COMMON-NAME "6,7-dihydropteridine") )
NIL)
(6P-GLUCOSIDE-GLUCOSE NIL (
(OCELOT-GFP::PARENTS |Oligosaccharide-Phosphate|)
(DISPLAY-COORDS-2D (1.4d0 -3.7478d0) (7.7677d0 -8.4574d0)
(12.6214d0 -6.8547d0) (12.6544d0 -4.1047d0) (5.3679d0 0.0d0)
(2.9568d0 -1.3921d0) (7.7791d0 -1.3921d0) (10.3598d0 -2.6334d0)
(0.0d0 -5.1506d0) (1.4d0 -6.5478d0) (7.7759d0 -7.0653d0) (2.8d0 -3.7427d0)
(2.8d0 -5.1427d0) (10.219d0 -6.873d0) (5.3679d0 -4.1764d0)
(7.7791d0 -4.1764d0) (11.415d0 -6.1602d0) (11.4305d0 -4.7683d0)
(5.3679d0 -1.3921d0) (4.1624d0 -2.0883d0) (6.5736d0 -2.0883d0)
(10.2555d0 -4.0215d0) (4.1624d0 -3.4803d0) (8.9456d0 -6.3104d0)
(6.5736d0 -3.4803d0) (8.9571d0 -4.9183d0) (1.4d0 -5.1478d0))
(CHEMICAL-FORMULA (C 12) (H 23) (O 14) (P 1))
(MOLECULAR-WEIGHT 422.279d0)
(STRUCTURE-BONDS (24 26 1) (22 26 1) (21 25 1) (20 23 1) (19 21 1) (19 20 1)
(18 22 1) (17 18 1) (16 26 1 :DOWN) (25 16 1 :UP) (15 25 1) (15 23 1)
(14 24 1) (14 17 1) (13 27 1) (23 12 1 :UP) (12 13 1) (24 11 1 :UP)
(10 27 1) (9 27 1) (22 8 1 :UP) (21 7 1 :DOWN) (20 6 1 :DOWN) (19 5 1 :UP)
(18 4 1 :DOWN) (17 3 1 :UP) (2 11 1) (1 27 2))
(STRUCTURE-ATOMS O O O O O O O O O O C C O O O O C C C C C C C C C C P)
(DBLINKS (LIGAND-CPD "C04534" NIL |sreddy| 3295881254 NIL NIL))
(COMMON-NAME "6-phospho-β-D-glucosyl-(1,4)-D-glucose") )
NIL)
(6PFK-1-CPX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 6PFRUCTPHOS-ENZRXN)
(CITATIONS "[89342465]" "[89125622]" "[90276415]" "[91255189]")
(COMPONENTS 6PFK-1-MONOMER)
(COMMENT "This enzyme is an isozyme with phosphofructokinase-2. The
nucleotide sequences of the genes are not similar |CITS: [85203917]|. The
tetrameric species is the only one which can bind both substrates and
effectors, and thus have both catalytic and regulatory properties. The
C terminal end of the peptide is required for allosteric
properties.|CITS: [90276415]| Crystal structures have been solved
with and without activators and inhibitors. |CITS: [89342465], [89125622]|")
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
((COMPONENTS 6PFK-1-MONOMER COEFFICIENT 4)))
(6PFK-1-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CATALYZES ENZRXN0-2771)
(SYNONYMS "B3916" "PfkA")
(DBLINKS (MODBASE "P0A796" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A796" NIL |pkarp| 3354911363)
(PFAM "PF00365" IN-FAMILY |pkarp| 3346700425 NIL NIL)
(REFSEQ "NP_418351" NIL NIL NIL NIL NIL) (PDB "2PFK"))
(COMPONENT-OF 6PFK-1-CPX)
(PI 5.32d0)
(MOLECULAR-WEIGHT-SEQ 34.84198699999995d0)
(GENE EG10699)
(COMMON-NAME "6-phosphofructokinase-1 monomer")
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
NIL)
(6PFK-2-CPX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES TAGAKIN-ENZRXN PFRUCTPHOS-ENZRXN)
(CITATIONS "[82027179]" "[85203917]")
(COMPONENTS 6PFK-2-MONOMER)
(COMMENT "This enzyme is an isozyme with phosphofructokinase-1. The
nucleotide sequences of the genes are not similar.|CITS: [85203917]|")
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
((COMPONENTS 6PFK-2-MONOMER CITATIONS "[82027179]")
(COMPONENTS 6PFK-2-MONOMER COEFFICIENT 2)))
(6PFK-2-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1723" "PfkB")
(DBLINKS (MODBASE "P06999" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00294" IN-FAMILY |pkarp| 3346700341 NIL NIL)
(REFSEQ "NP_416237" NIL NIL NIL NIL NIL) (UNIPROT "P06999"))
(COMPONENT-OF 6PFK-2-CPX)
(PI 6.05d0)
(MOLECULAR-WEIGHT-SEQ 32.455950999999985d0)
(GENE EG10700)
(CITATIONS "[84262485]")
(COMMON-NAME "6-phosphofructokinase-2 monomer")
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
NIL)
(6PFRUCTPHOS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH AMP)
(PHYSIOLOGICALLY-RELEVANT PHOSPHO-ENOL-PYRUVATE GDP AMP ADP)
(COFACTORS MG+2)
(SYNONYMS "PFK I" "fructose-6-p-1-kinase"
"fructose-6-phosphate-1-phosphotransferase")
(COMMON-NAME "6-phosphofructokinase-1")
(INHIBITORS-ALLOSTERIC PHOSPHO-ENOL-PYRUVATE)
(REACTION-DIRECTION REVERSIBLE)
(REACTION 6PFRUCTPHOS-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[89342465]" "[89342465]" "[89125622]"
"[91255189]" "[90276415]" "[91355204]" "[90057358]" "[92144584]")
(ACTIVATORS-NONALLOSTERIC FRUCTOSE-6P)
(ACTIVATORS-ALLOSTERIC ADP GDP)
(COFACTOR-BINDING-COMMENT "The binding sites have been identified in the
crystalline structure.|CITS: [89342465], [91255189]|")
(COMMENT "90% of the activity present in the wild type strain is pfk-1.
|CITS: [83294514]|
The enzyme shows cooperative kinetics with the substrate
fructose-6-phosphate but not with the other
substrate ATP. |CITS: [85203917]| The reverse reaction does
not participate in gluconeogenesis: fdp phosphatase mutants
are deficient in gluconeogenesis.|CITS: [78194149]|
Studies on phosphfructokinase-1 include subunit structure
|CITS:[91255189]|, ligand binding |CITS: [91355204]| and pH
dependence |CITS: [91255189]|. The allosteric properties of
phosphofructokinase-1 are due in part to ligand binding and in
part to the kinetics of the reaction. |CITS: [92144584]|")
(ENZYME 6PFK-1-CPX)
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
NIL)
(6PFRUCTPHOS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLYCOLYSIS)
(ENZYMATIC-REACTION 6PFRUCTPHOS-ENZRXN PFRUCTPHOS-ENZRXN)
(RIGHT ADP FRUCTOSE-16-DIPHOSPHATE)
(LEFT FRUCTOSE-6P ATP)
(CITATIONS "[79100775]" "[Stryer88]")
(DELTAG0 -3.4d0)
(EC-NUMBER "2.7.1.11")
(COMMENT "This is a key control step in glycolysis |CITS: [79100775]|")
(SYNONYMS "fructose-6-phosphate phosphorylation")
(:CREATION-DATE 2945290601)
(:CREATOR |mriley|) )
((DELTAG0 -3.4d0 CITATIONS "[Stryer88]")))
(6PGLUCONDEHYDROG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 6PGLUCONDEHYDROG-ENZRXN)
(COMPONENTS 6PGLUCONDEHYDROG-MONOMER)
(:CREATION-DATE 2974476917)
(:CREATOR |mriley|) )
((COMPONENTS 6PGLUCONDEHYDROG-MONOMER CITATIONS "[VeroneseBiochem15,4026]")
(COMPONENTS 6PGLUCONDEHYDROG-MONOMER COEFFICIENT 2)))
(6PGLUCONDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH MG+2)
(INHIBITORS-UNKMECH "HEAVY METALS" RIBULOSE-5P CO-A FRUCTOSE-16-DIPHOSPHATE
55-DITHIO-BIS2-NITROBENZOIC-ACID CPD-29)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(SYNONYMS "phosphogluconate dehydrogenase"
"phosphogluconic acid dehydrogenase" "6-phosphogluconic dehydrogenase"
"6-phosphogluconic carboxylase" "6PGD" "P-gluconate dehydrogenase"
"6-phospho-D-gluconate:NADP+ 2-oxidoreductase (decarboxylating)")
(COMMON-NAME "6-phosphogluconate dehydrogenase (decarboxylating)")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 6PGLUCONDEHYDROG-RXN)
(INHIBITORS-COMPETITIVE NADP ATP)
(COFACTOR-BINDING-COMMENT "The enzyme shows a high degree of
specificity for NADP. |CITS: [VeroneseBiochem15,4026]|")
(ENZYME 6PGLUCONDEHYDROG-CPLX)
(:CREATION-DATE 2974476917)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH MG+2 COMMENT "activates at low concentrations, inhibits
at high, 6-PGD has no absolute requirement for Mg++ |CITS:
[WestwoodMicrobios9,143]|")
(INHIBITORS-UNKMECH "HEAVY METALS" CITATIONS "WestwoodMicrobios9143")
(INHIBITORS-UNKMECH FRUCTOSE-16-DIPHOSPHATE COMMENT
"mixed type inhibition with respect to both substrate and coenzyme
|CITS: [WestwoodMicrobios9,143]|")
(INHIBITORS-COMPETITIVE NADP COMMENT "competitive in the presence
and non-competitive in the absence of 2-mercaptoethanol with respect
to NADP+, a mixed type inhibition is observed in both cases with
respect to 6-phosphogluconate")
(INHIBITORS-COMPETITIVE ATP COMMENT "competitive for both
substrate and coenzyme")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[WestwoodMicrobios9,143]")))
(6PGLUCONDEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"A null mutation in the gnd gene encoding 6-phosphogluconate dehydrogenase does not affect the growth rate
significantly. However, cellular metabolism and metabolic flux is changed |CITS: [14661115][12670695]|.
Expression of 6-phosphogluconate dehydrogenase is growth rate regulated. Regulation is both
at transcriptional |CITS: [8282686]| and posttranscriptional (translation initiation) |CITS: [7592434]| levels.
The enzyme is a homodimer |CITS: [786365]|.")
(SYNONYMS "B2029" "Gnd")
(COMMON-NAME "Gnd")
(DBLINKS (MODBASE "P00350" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03446" IN-FAMILY |pkarp| 3346700349 NIL NIL)
(REFSEQ "NP_416533" NIL NIL NIL NIL NIL)
(SWISSMODEL "P00350" NIL |pkarp| 3064870651) (UNIPROT "P00350"))
(COMPONENT-OF 6PGLUCONDEHYDROG-CPLX)
(PI 5.3d0)
(MOLECULAR-WEIGHT-SEQ 51.48124699999977d0)
(GENE EG10411)
(:CREATION-DATE 2974476917)
(:CREATOR |mriley|) )
NIL)
(6PGLUCONDEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY OXIDATIVEPENT-PWY GLUCONSUPER-PWY)
(ENZYMATIC-REACTION 6PGLUCONDEHYDROG-ENZRXN)
(RIGHT RIBULOSE-5P CARBON-DIOXIDE |NAD(P)H|)
(LEFT CPD-2961 |NAD(P)|)
(EC-NUMBER "1.1.1.44")
(COMMENT
"While the official EC reaction includes NADP+ rather than NAD(P)+,
the comments state that some preparations reduce NAD+ as well as NADP+,
making NAD(P)+ a more accurate depiction.")
(:CREATION-DATE 2974476917)
(:CREATOR |mriley|) )
NIL)
(6PGLUCONOLACT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "15576773:EV-EXP-IDA-PURIFIED-PROTEIN:3314044114:keseler"
"15766779:EV-EXP-IDA-PART-PURIFIED-PROTEIN:3334680781:keseler")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(COMMON-NAME "6-phosphogluconolactonase")
(REACTION 6PGLUCONOLACT-RXN)
(COMMENT
"This reaction can also proceed spontaneously, so the physiological role of the enzyme is not understood.
|CITS:[4902810]|")
(ENZYME 6PGLUCONOLACT-MONOMER)
(:CREATION-DATE 2974476924)
(:CREATOR |mriley|) )
NIL)
(6PGLUCONOLACT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 36.307594999999964d0)
(DBLINKS (MODBASE "P52697" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P52697" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P52697" NIL |keseler| 3314044114 NIL NIL))
(SPECIES ECOLI)
(CITATIONS "4552019")
(SYNONYMS "B0767" "Pgl" "YbhE")
(CATALYZES 6PGLUCONOLACT-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(GENE G6397)
(COMMENT
"A pgl mutant strain has the Blu- phenotype, which is diagnostic for 6-phosphogluconolactonase
mutants |CITS: [15576773]|. The phenotype of a pgl deletion strain can be complemented by expression of the
pgl gene from Pseudomonas putida, although there is no detectable similarity between the two genes
|CITS: [15766779]|.")
(:CREATION-DATE 2974476924)
(:CREATOR |mriley|) )
NIL)
(6PGLUCONOLACT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY OXIDATIVEPENT-PWY GLYCOLYSIS/E-D)
(ENZYMATIC-REACTION 6PGLUCONOLACT-ENZRXN)
(RIGHT CPD-2961)
(LEFT D-6-P-GLUCONO-DELTA-LACTONE WATER)
(EC-NUMBER "3.1.1.31")
(COMMENT "This is the second step in the pentose phosphate pathway.")
(:CREATION-DATE 2974476924)
(:CREATOR |mriley|) )
NIL)
(6R-6-FLUORO-EPSP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF CHORISMATE-SYNTHASE-ENZRXN)
(DISPLAY-COORDS-2D (0.0d0 -2.1d0) (10.3995d0 -0.8876d0) (7.2746d0 -6.3d0)
(2.4249d0 -3.5d0) (10.9296d0 -2.7684d0) (1.2124d0 0.0d0) (4.8497d0 -6.3d0)
(6.0622d0 0.0d0) (8.9995d0 -3.3124d0) (3.6373d0 -4.2d0) (7.2746d0 -3.5d0)
(3.6373d0 -1.4d0) (8.487d0 -1.4d0) (1.2124d0 -1.4d0) (6.0622d0 -5.6d0)
(2.4249d0 -2.1d0) (6.0622d0 -4.2d0) (6.0622d0 -1.4d0) (4.8497d0 -3.5d0)
(7.2746d0 -2.1d0) (4.8497d0 -2.1d0) (9.6995d0 -2.1d0))
(CHEMICAL-FORMULA (C 11) (H 14) (O 9) (F 1) (P 1))
(MOLECULAR-WEIGHT 340.198d0)
(STRUCTURE-BONDS (21 19 1 :DOWN) (21 18 1 :DOWN) (20 18 1 :DOWN)
(19 17 1 :UP) (15 17 1) (14 16 1) (13 22 1) (20 13 1 :UP) (21 12 1 :UP)
(12 16 1) (20 11 1 :UP) (11 17 2) (19 10 1 :UP) (9 22 1) (18 8 1 :UP)
(7 15 1) (6 14 1) (5 22 2) (4 16 2) (3 15 2) (2 22 1) (1 14 2))
(STRUCTURE-ATOMS C C O O O O O O O F C O O C C C C C C C C P)
(CITATIONS "10956653")
(SYNONYMS "(6R)-6-fluoro-5-enolpyruvylshikimate 3-phosphate")
(COMMON-NAME "(6R)-6-fluoro-EPSP")
(:CREATOR |arnaud|)
(:CREATION-DATE 3273519912) )
NIL)
(6S-6-FLUORO-EPSP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF CHORISMATE-SYNTHASE-ENZRXN)
(DISPLAY-COORDS-2D (0.0d0 -2.1d0) (10.3995d0 -0.8876d0) (7.2746d0 -6.3d0)
(2.4249d0 -3.5d0) (10.9296d0 -2.7684d0) (1.2124d0 0.0d0) (4.8497d0 -6.3d0)
(6.0622d0 0.0d0) (8.9995d0 -3.3124d0) (3.6373d0 -4.2d0) (7.2746d0 -3.5d0)
(3.6373d0 -1.4d0) (8.487d0 -1.4d0) (1.2124d0 -1.4d0) (6.0622d0 -5.6d0)
(2.4249d0 -2.1d0) (6.0622d0 -4.2d0) (6.0622d0 -1.4d0) (4.8497d0 -3.5d0)
(7.2746d0 -2.1d0) (4.8497d0 -2.1d0) (9.6995d0 -2.1d0))
(CHEMICAL-FORMULA (C 11) (H 14) (O 9) (F 1) (P 1))
(MOLECULAR-WEIGHT 340.198d0)
(STRUCTURE-BONDS (21 19 1 :DOWN) (21 18 1 :DOWN) (20 18 1 :DOWN)
(19 17 1 :UP) (15 17 1) (14 16 1) (13 22 1) (20 13 1 :UP) (21 12 1 :UP)
(12 16 1) (20 11 1 :UP) (11 17 2) (19 10 1 :DOWN) (9 22 1) (18 8 1 :UP)
(7 15 1) (6 14 1) (5 22 2) (4 16 2) (3 15 2) (2 22 1) (1 14 2))
(STRUCTURE-ATOMS C C O O O O O O O F C O O C C C C C C C C P)
(CITATIONS "7559411")
(SYNONYMS "(6S)-6-fluoro-5-enolpyruvylshikimate-3-phosphate")
(COMMON-NAME "(6S)-6-fluoro-EPSP")
(:CREATOR |arnaud|)
(:CREATION-DATE 3273520438) )
NIL)
(6S-RNA NIL (
(OCELOT-GFP::PARENTS |Misc-RNAs|)
(COMMENT
"The 6S RNA is involved in stationary phase regulation of transcription by the sigma70-holoenzyme
|CITS: [10892648]|. The 6S RNA binds to both sigma70 and the beta/beta' subunits of core RNA polymerase and
enables stable association between sigma70 and the core RNA polymerase |CITS: [10892648]|. During stationary
phase, 6S RNA represses expression from a subset of sigma70-dependent promoters containing an extended -10
promoter element |CITS: [10892648][15357303][15262935]|. 6S RNA also has an effect on the transcription of several
sigmaS-dependent promoters |CITS: [15262935]|.
The 6S RNA is not required for growth and is not essential for export of proteins |CITS: [2579059]|, but cells lacking
6S RNA show a stationary phase survival defect and are less competitive during growth |CITS: [15262935]|.
The RNA secondary structure has been discussed |CITS: [2438656]|.
The 6S RNA has been detected in a ribonucleoprotein particle |CITS: [342486]|.
Regulation has been described |CITS: [6183252], [2579060], [10892648]|. The 6S RNA is expressed at stationary
phase |CITS: [10892648]|. Overexpression of Spot 42 RNA increases the abundance of 6S RNA |CITS: [6183252]|.
Reviews: |CITS: [10068996], [12732300]|.")
(CITATIONS "4929322" "4570237" "1098044" "6231216")
(SYNONYMS "SsrS" "B2911" "Ssr")
(COMMON-NAME "6S RNA")
(GENE EG30099)
(:CREATOR |arnaud|)
(:CREATION-DATE 3270488766) )
NIL)
(|7,8-dihydropteroate| NIL (
(OCELOT-GFP::PARENTS |All-Folates|)
(INHIBITORS-UNKMECH-OF FOLYLPOLYGLUTAMATESYNTH-ENZRXN)
(INHIBITORS-COMPETITIVE-OF H2PTEROATESYNTH-ENZRXN)
(DBLINKS (LIGAND-CPD "C00921" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3075053323)
(GIBBS-0 -27.2d0)
(APPEARS-IN-RIGHT-SIDE-OF H2PTEROATESYNTH-RXN)
(APPEARS-IN-LEFT-SIDE-OF DIHYDROFOLATESYNTH-RXN)
(SYNONYMS "dihydropterate" "H2Pte" "dihydropteroate")
(COMMON-NAME "7,8-dihydropteroate")
(STRUCTURE-ATOMS H N O O O C C C C C C N N N N C C C C C C C C N)
(STRUCTURE-BONDS (24 23 :AROMATIC) (23 22 :AROMATIC) (22 21 :AROMATIC)
(18 24 :AROMATIC) (16 20 1) (15 21 1) (14 19 1) (21 13 :AROMATIC)
(13 18 :AROMATIC) (12 22 1) (12 17 2) (11 17 1) (11 15 1) (10 17 1)
(10 14 1) (9 20 :AROMATIC) (20 8 :AROMATIC) (19 7 :AROMATIC) (7 9 :AROMATIC)
(6 19 :AROMATIC) (8 6 :AROMATIC) (5 16 1) (4 23 2) (3 16 2) (2 18 1)
(1 24 1))
(DISPLAY-COORDS-2D (0.0d0 -3.0156d0) (0.1631d0 0.0d0) (14.8058d0 -4.6201d0)
(2.4449d0 -4.3694d0) (14.8167d0 -2.1952d0) (10.5511d0 -2.1851d0)
(10.5511d0 -4.6362d0) (11.9834d0 -2.1851d0) (11.9834d0 -4.6362d0)
(7.2021d0 -3.3982d0) (6.1341d0 -0.8987d0) (4.9202d0 -2.9855d0)
(2.4449d0 -0.2184d0) (8.561d0 -3.3982d0) (4.9202d0 -0.2184d0)
(14.1113d0 -3.4045d0) (6.1341d0 -2.306d0) (1.2069d0 -0.8987d0)
(9.8475d0 -3.3982d0) (12.7113d0 -3.3982d0) (3.6822d0 -0.8987d0)
(3.6822d0 -2.306d0) (2.4449d0 -2.9855d0) (1.2069d0 -2.306d0))
(CHEMICAL-FORMULA (C 14) (H 14) (N 6) (O 3))
(MOLECULAR-WEIGHT 314.303d0)
(AROMATIC-RINGS (6 8 20 9 7 19) (18 13 21 22 23 24)) )
((GIBBS-0 -27.2d0 CITATIONS "GibbsGroups97")))
(7-ALPHA-HYDROXYSTEROID-DEH-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 7-ALPHA-HYDROXYSTEROID-DEH-ENZRXN)
(COMPONENTS 7-ALPHA-HYDROXYSTEROID-DEH-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/hdhA.template")
(:CREATION-DATE 3016372634)
(:CREATOR |mriley|) )
((COMPONENTS 7-ALPHA-HYDROXYSTEROID-DEH-MONOMER COEFFICIENT 4)))
(7-ALPHA-HYDROXYSTEROID-DEH-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "some heavy-metal ions" DIETHYLPYROCARBONATE
N-BROMOSUCCINIMIDE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION 7-ALPHA-HYDROXYSTEROID-DEH-RXN)
(COMMENT "7-α-hydroxysteroid dehydrogenase catalyzes the
dehydroxylation of cholic and chenodeoxycholic acids, major human bile
acids, yielding deoxycholic and lithocholic acids respectively. The
enzyme belongs to the short-chain nonmetalloenzyme-alcohol
dehydrogenase protein family. The enzyme shows activity with several
substrates having a hydroxyl group at position 7 of the steroid
skeleton. NAD+ is required for enzyme activity. |CITS: [91177803]|")
(ENZYME 7-ALPHA-HYDROXYSTEROID-DEH-CPLX)
(SYNONYMS "7-α-hydroxysteroid:NAD+ 7-oxidoreductase")
(COMMON-NAME "7-α-hydroxysteroid dehydrogenase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/hdhA.template")
(:CREATION-DATE 3016372634)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "some heavy-metal ions" COMMENT
"for example, CoCl2, FeCl3 and CuCl2")
(INHIBITORS-UNKMECH "some heavy-metal ions" CITATIONS "[91177803]")
(INHIBITORS-UNKMECH DIETHYLPYROCARBONATE CITATIONS "[91177803]")
(INHIBITORS-UNKMECH N-BROMOSUCCINIMIDE CITATIONS "[91177803]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme is active toward several
substrates which contain a hydroxyl group at postion 7 of the steroid
skeleton. The highest affinity was observed on taurochenodeoxycholic
acid. The enzyme was inert toward some steroids lacking a
7-alpha-hydroxy group. |CITS: [91177803]|")))
(7-ALPHA-HYDROXYSTEROID-DEH-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1619" "Hsd" "HsdH" "HdhA")
(COMMON-NAME "HdhA")
(DBLINKS (MODBASE "P0AET8" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0AET8" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00106" IN-FAMILY |pkarp| 3346700339 NIL NIL)
(UNIPROT "P0AET8" NIL |pkarp| 3343984415 NIL NIL)
(REFSEQ "NP_416136" NIL NIL NIL NIL NIL) (PDB "1FMC") (PDB "1AHI")
(PDB "1AHH"))
(COMPONENT-OF 7-ALPHA-HYDROXYSTEROID-DEH-CPLX)
(PI 5.47d0)
(MOLECULAR-WEIGHT-SEQ 26.77855999999998d0)
(GENE EG10425)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/hdhA.template")
(:CREATION-DATE 3016372634)
(:CREATOR |mriley|) )
NIL)
(7-ALPHA-HYDROXYSTEROID-DEH-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION 7-ALPHA-HYDROXYSTEROID-DEH-ENZRXN)
(RIGHT NADH CHOLANATE2)
(LEFT NAD CHOLATE)
(EC-NUMBER "1.1.1.159")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/hdhA.template")
(:CREATION-DATE 3016372634)
(:CREATOR |mriley|) )
NIL)
(7-AMINOMETHYL-7-DEAZAGUANINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-1321)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-4022)
(AROMATIC-RINGS (8 11 13 9 6 5))
(DISPLAY-COORDS-2D (0.7149221d0 0.74610245d0) (0.99554574d0 -0.006681502d0)
(0.8975502d0 -1.0d0) (-0.15812916d0 -0.9688196d0)
(-0.15812916d0 -0.48775053d0) (0.25612473d0 -0.25167036d0)
(-1.0d0 0.47438753d0) (-0.58129174d0 -0.25167036d0)
(0.25612473d0 0.2338531d0) (0.7149221d0 0.38530076d0)
(-0.58129174d0 0.22494435d0) (0.6837417d0 -0.46993315d0)
(-0.15812916d0 0.47438753d0) (0.6837417d0 -0.76837415d0)
(-1.0d0 -0.5634744d0))
(CHEMICAL-FORMULA (C 7) (H 9) (N 5) (O 1))
(MOLECULAR-WEIGHT 179.181d0)
(STRUCTURE-BONDS (14 12 1) (14 3 1) (13 11 2) (12 2 2) (11 8 1) (10 2 1)
(10 1 1) (9 13 1) (9 10 1) (8 5 1) (8 15 1) (7 11 1) (6 9 2) (6 12 1)
(5 6 1) (4 5 2))
(STRUCTURE-ATOMS H C N O C C N N C N C C N C H)
(SYNONYMS "preQ1")
(COMMON-NAME "7-aminomethyl-7-deazaguanine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3264878893) )
NIL)
(|7-Beta-Hydroxysteroids| T (
(OCELOT-GFP::PARENTS |Hydroxysteroids|)
(CHEMICAL-FORMULA (C 19) (H 31) (O 1) (R 1))
(STRUCTURE-BONDS (18 21 1) (18 19 1) (17 20 1) (17 19 1) (16 21 1) (15 20 1)
(14 19 1) (13 16 1) (13 14 1) (12 20 1) (11 21 1) (10 18 1) (10 12 1)
(9 17 1) (8 15 1) (8 9 1) (7 16 1) (6 11 1) (5 7 1) (5 6 1) (4 15 1)
(14 3 1 :UP) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (6.0622d0 0.0d0)
(7.8263d0 -5.9641d0) (0.0d0 -0.7d0) (0.0d0 -2.1d0) (1.2124d0 0.0d0)
(8.2166d0 -3.5d0) (7.3937d0 -2.3674d0) (3.6373d0 -4.2d0) (1.2124d0 -2.8d0)
(4.8497d0 -4.9d0) (3.6373d0 0.0d0) (4.8497d0 -0.7d0) (7.3937d0 -4.6326d0)
(2.4249d0 -0.7d0) (6.0622d0 -2.8d0) (3.6373d0 -2.8d0) (4.8497d0 -2.1d0)
(6.0622d0 -4.2d0) (2.4249d0 -2.1d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 7-β-hydroxysteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(7-CYANO-7-DEAZAGUANINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(AROMATIC-RINGS (5 7 12 13 10) (11 8 9 6 12 13))
(MOLECULAR-WEIGHT 175.149d0)
(CHEMICAL-FORMULA (C 7) (H 5) (N 5) (O 1))
(STRUCTURE-BONDS (13 12 :AROMATIC) (11 13 :AROMATIC) (10 13 :AROMATIC)
(8 11 :AROMATIC) (9 8 :AROMATIC) (12 7 :AROMATIC) (12 6 :AROMATIC)
(6 9 :AROMATIC) (5 10 :AROMATIC) (7 5 :AROMATIC) (4 10 1) (3 11 2) (2 9 1)
(1 4 3))
(DISPLAY-COORDS-2D (6.7708d0 -4.1552d0) (0.0d0 0.0d0) (2.4249d0 -4.2d0)
(5.4014d0 -3.8641d0) (5.7917d0 -1.4d0) (2.4249d0 0.0d0) (4.9688d0 -0.2674d0)
(1.2124d0 -2.1d0) (1.2124d0 -0.7d0) (4.9688d0 -2.5326d0) (2.4249d0 -2.8d0)
(3.6373d0 -0.7d0) (3.6373d0 -2.1d0))
(STRUCTURE-ATOMS N N O C C N N N C C C C C)
(SYNONYMS "preQ0")
(APPEARS-IN-LEFT-SIDE-OF RXN0-4022)
(COMMON-NAME "7-cyano-7-deazaguanine")
(:CREATOR |keseler|)
(:CREATION-DATE 3326662876) )
NIL)
(|7-hydroxyisoflavones| T (
(OCELOT-GFP::PARENTS |Isoflavones|)
(COMMON-NAME "a 7-hydroxyisoflavone")
(:CREATOR |paley|)
(:CREATION-DATE 3330790567) )
NIL)
(|7-methoxyisoflavones| T (
(OCELOT-GFP::PARENTS |Isoflavones|)
(COMMON-NAME "a 7-methoxyisoflavone")
(:CREATOR |paley|)
(:CREATION-DATE 3330790567) )
NIL)
(|7-Oxosteroids| T (
(OCELOT-GFP::PARENTS |Oxosteroids|)
(CHEMICAL-FORMULA (C 19) (H 29) (O 1) (R 1))
(STRUCTURE-BONDS (18 21 1) (18 19 1) (17 20 1) (17 19 1) (16 21 1) (15 20 1)
(14 19 1) (13 16 1) (13 14 1) (12 20 1) (11 21 1) (10 18 1) (10 12 1)
(9 17 1) (8 15 1) (8 9 1) (7 16 1) (6 11 1) (5 7 1) (5 6 1) (4 15 1)
(3 14 2) (2 21 1) (1 20 1))
(DISPLAY-COORDS-2D (6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (6.0622d0 0.0d0)
(7.8263d0 -5.9641d0) (0.0d0 -0.7d0) (0.0d0 -2.1d0) (1.2124d0 0.0d0)
(8.2166d0 -3.5d0) (7.3937d0 -2.3674d0) (3.6373d0 -4.2d0) (1.2124d0 -2.8d0)
(4.8497d0 -4.9d0) (3.6373d0 0.0d0) (4.8497d0 -0.7d0) (7.3937d0 -4.6326d0)
(2.4249d0 -0.7d0) (6.0622d0 -2.8d0) (3.6373d0 -2.8d0) (4.8497d0 -2.1d0)
(6.0622d0 -4.2d0) (2.4249d0 -2.1d0))
(STRUCTURE-ATOMS C C O R C C C C C C C C C C C C C C C C C)
(COMMON-NAME "a 7-oxosteroid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790566) )
NIL)
(7KAPSYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3131189897)
(CATALYZES 7KAPSYN-ENZRXN)
(CITATIONS "[99033055]")
(COMPONENTS 7KAPSYN-MONOMER) )
((COMPONENTS 7KAPSYN-MONOMER COEFFICIENT 2)))
(7KAPSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CYS)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(COMMENT
"8-Amino-7-oxononanoate synthase catalyzes the first committed step in
biotin biosynthesis, the decarboxylative condensation of L-alanine and
6-carboxyhexanoyl-CoA. |CITS: [99033055]|")
(REACTION 7KAPSYN-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin2/bioF2.template")
(ENZYME 7KAPSYN-CPLX)
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(ALTERNATIVE-SUBSTRATES (L-ALPHA-ALANINE SER))
(:CREATION-DATE 3033846057)
(COMMON-NAME "8-amino-7-oxononanoate synthase")
(SYNONYMS "AONS" "7-keto-8-amino-pelargonic acid synthetase"
"7-KAP synthetase"
"6-carboxyhexanoyl-CoA:L-alanine C-carboxyhexanoyltransferase (decarboxylating)")
(REACTION-DIRECTION REVERSIBLE) )
((INHIBITORS-UNKMECH CYS CITATIONS "[69017437]" "[74169143]")
(ALTERNATIVE-SUBSTRATES (L-ALPHA-ALANINE SER) COMMENT "Serine can
replace alanine to some extent. |CITS: [69017437] [74169143]|")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE COMMENT "absolute
requirement |CITS: [69017437] [74169143]|")))
(7KAPSYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMPONENT-OF 7KAPSYN-CPLX)
(COMMON-NAME "BioF")
(DBLINKS (MODBASE "P12998" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00155" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(REFSEQ "NP_415297" NIL NIL NIL NIL NIL) (UNIPROT "P12998"))
(PI 7.08d0)
(MOLECULAR-WEIGHT-SEQ 41.594215999999896d0)
(GENE EG10121)
(SYNONYMS "B0776" "BioF" "7-keto-8-amino-pelargonic acid synthetase"
"7-KAP synthetase"
"6-carboxyhexanoyl-CoA:L-alanine C-carboxyhexanoyltransferase (decarboxylating)")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin/bioF.template")
(:CREATION-DATE 3000588761)
(:CREATOR |mriley|) )
NIL)
(7KAPSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(SYNONYMS "7-KAP SYNTHETASE" "7-KETO-8-AMINO-PELAGONIC ACID SYNTHETASE")
(COMMON-NAME "8-AMINO-7-OXONONANOATE-SYNTHASE")
(ENZYMATIC-REACTION 7KAPSYN-ENZRXN)
(IN-PATHWAY BIOTIN-SYNTHESIS-PWY)
(RIGHT CARBON-DIOXIDE CO-A 8-AMINO-7-OXONONANOATE)
(LEFT L-ALPHA-ALANINE CPD-558)
(EC-NUMBER "2.3.1.47")
(COMMENT "The first reaction in the biosynthesis of biotin.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin/bioF.template")
(:CREATION-DATE 3000588761)
(:CREATOR |mriley|) )
NIL)
(8-AMINO-7-OXONONANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C01092" NIL |kr| 3346617701 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(SYNONYMS "7-keto-8-aminopelargonate" "KAPA" "7-KAP")
(DISPLAY-COORDS-2D (1.95d0 5.3d0) (2.5995d0 4.925d0) (3.249d0 5.3d0)
(2.5995d0 4.175d0) (1.3005d0 4.925d0) (1.95d0 6.05d0) (3.8986d0 4.925d0)
(4.5481d0 5.3d0) (5.1976d0 4.925d0) (5.8471d0 5.3d0) (6.4966d0 4.925d0)
(7.1448d0 5.3021d0) (6.4942d0 4.1749d0))
(CHEMICAL-FORMULA (C 9) (H 17) (N 1) (O 3))
(MOLECULAR-WEIGHT 187.238d0)
(STRUCTURE-BONDS (10 11 1) (11 13 2) (11 12 1) (9 10 1) (8 9 1) (7 8 1)
(3 7 1) (1 6 1) (1 5 1) (2 4 2) (2 3 1) (1 2 1))
(STRUCTURE-ATOMS C C C O N C C C C C C O O)
(APPEARS-IN-RIGHT-SIDE-OF 7KAPSYN-RXN)
(APPEARS-IN-LEFT-SIDE-OF DAPASYN-RXN)
(COMMON-NAME "8-amino-7-oxononanoate") )
NIL)
(8-HYDROXYDEOXYGUANOSINE-5-TRIPHOSPHAT NIL (
(OCELOT-GFP::PARENTS |Purine-Related| |Base-Derivatives|)
(DISPLAY-COORDS-2D (7.9423d0 -1.4457d0) (12.4109d0 -7.7353d0)
(12.4109d0 -9.4629d0) (9.4064d0 -8.0921d0) (10.1766d0 -7.7353d0)
(13.1239d0 -8.0921d0) (7.7353d0 -3.9994d0) (10.0826d0 0.0d0)
(1.4083d0 -4.8819d0) (6.7594d0 -4.9194d0) (4.1683d0 -4.8819d0)
(14.2706d0 -1.3563d0) (10.1766d0 -9.4629d0) (1.4083d0 -7.6794d0)
(0.0d0 -6.3277d0) (6.7594d0 -7.7353d0) (4.1683d0 -7.6794d0)
(9.4064d0 -6.3277d0) (10.0826d0 -4.0934d0) (12.2229d0 -1.5206d0)
(8.1677d0 -6.3277d0) (11.2464d0 -6.1397d0) (2.6476d0 -6.3277d0)
(5.4261d0 -6.3277d0) (8.9747d0 -3.3232d0) (13.1239d0 -2.1594d0)
(10.0826d0 -1.3892d0) (11.209d0 -2.0838d0) (11.209d0 -3.3232d0)
(8.9747d0 -2.0838d0) (13.1239d0 -3.3232d0) (12.4109d0 -8.5804d0)
(9.4064d0 -7.2477d0) (10.1766d0 -8.5804d0) (13.1239d0 -7.2477d0)
(1.4083d0 -6.3277d0) (6.7594d0 -6.3277d0) (4.1683d0 -6.3277d0))
(AROMATIC-RINGS (20 26 31 29 28) (25 19 29 28 27 30))
(CHEMICAL-FORMULA (C 10) (H 16) (N 5) (O 14) (P 3))
(MOLECULAR-WEIGHT 523.183d0)
(STRUCTURE-BONDS (33 34 1) (32 35 1) (32 34 1) (31 35 1) (29 31 :AROMATIC)
(28 29 :AROMATIC) (30 27 :AROMATIC) (27 28 :AROMATIC) (31 26 :AROMATIC)
(25 30 :AROMATIC) (24 38 1) (24 37 1) (23 38 1) (23 36 1) (22 35 1)
(22 33 1) (21 37 1) (20 28 :AROMATIC) (26 20 :AROMATIC) (29 19 :AROMATIC)
(19 25 :AROMATIC) (18 33 1) (18 21 1) (17 38 1) (16 37 1) (15 36 1)
(14 36 1) (13 34 1) (12 26 1) (11 38 2) (10 37 2) (9 36 2) (8 27 2) (7 25 1)
(6 35 1) (5 34 1) (4 33 1) (3 32 1) (2 32 1) (1 30 1))
(STRUCTURE-ATOMS H H H H H H N O O O O O O O O O O C N N O O O O C C C C C N
N C C C C P P P)
(CITATIONS "11676470" "12867278")
(COMMON-NAME "8-hydroxydeoxyguanosine 5'-triphosphate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3280154704) )
NIL)
(8-HYDROXYQUINOLINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF GLYCDEH-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979763)
(COMMON-NAME "8-hydroxyquinoline") )
NIL)
(8-SELENO-OCTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-1085)
(DISPLAY-COORDS-2D (1.2124d0 -2.1d0) (0.0d0 0.0d0) (10.9119d0 -0.7001d0)
(9.6995d0 -1.0d-4) (8.487d0 -0.7001d0) (7.2746d0 -1.0d-4)
(6.0621d0 -0.7001d0) (4.8497d0 0.0d0) (3.6373d0 -0.7d0) (2.4248d0 0.0d0)
(1.2124d0 -0.7d0))
(CHEMICAL-FORMULA (C 8) (H 15) (O 2) (SE 1))
(MOLECULAR-WEIGHT 222.165d0)
(STRUCTURE-BONDS (10 11 1) (9 10 1) (8 9 1) (7 8 1) (6 7 1) (5 6 1) (4 5 1)
(3 4 1) (2 11 1) (1 11 2))
(STRUCTURE-ATOMS O O SE C C C C C C C C)
(COMMON-NAME "8-seleno-octanoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3257714473) )
NIL)
(8-THIO-OCTANOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-1085)
(DISPLAY-COORDS-2D (1.2124d0 -2.1d0) (0.0d0 0.0d0) (10.9119d0 -0.7001d0)
(9.6995d0 -1.0d-4) (8.487d0 -0.7001d0) (7.2746d0 -1.0d-4)
(6.0621d0 -0.7001d0) (4.8497d0 0.0d0) (3.6373d0 -0.7d0) (2.4248d0 0.0d0)
(1.2124d0 -0.7d0))
(CHEMICAL-FORMULA (C 8) (H 16) (O 2) (S 1))
(MOLECULAR-WEIGHT 176.273d0)
(STRUCTURE-BONDS (10 11 1) (9 10 1) (8 9 1) (7 8 1) (6 7 1) (5 6 1) (4 5 1)
(3 4 1) (2 11 1) (1 11 2))
(STRUCTURE-ATOMS O O S C C C C C C C C)
(COMMON-NAME "8-thio-octanoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3257714763) )
NIL)
(|9-apo-Carotenones| T (
(OCELOT-GFP::PARENTS |carotenoids|)
(COMMON-NAME "a 9-apo-carotenone")
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(|9-cis-Epoxycarotenoids| T (
(OCELOT-GFP::PARENTS |Xanthophylls|)
(COMMON-NAME "a 9-cis-epoxycarotenoid")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|a fatty acid| T (
(OCELOT-GFP::PARENTS |Fatty-Acids| |Holder-Class|)
(DISPLAY-COORDS-2D (0.99462366d0 -0.123655915d0) (0.32795703d0 0.3118279d0)
(-0.26344085d0 -0.123655915d0) (-1.0d0 0.3118279d0) (-0.26344085d0 -1.0d0))
(CHEMICAL-FORMULA (C 2) (H 3) (O 2) (R 1))
(N-1-NAME "a fatty acidn-1")
(STRUCTURE-BONDS (5 3 2) (4 3 1) (3 2 1) (2 1 1))
(STRUCTURE-ATOMS R C C O O)
(COMMENT
"The various synonyms reflect some of the variations of names that can occur in the ENZYME db. It is not clear to what degree minor nuances should be distinguished between. A more formalized classification system of broadness of substrate specificity would definitely be useful.")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1802 ACECOATRANS-RXN THIOESTER-RXN)
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF RXN0-1802 ACYLCOASYN-RXN ACYLACPSYNTH-RXN)
(SYNONYMS "free fatty acid" "a fatty acid anion")
(:CREATION-DATE 3052158301)
(:CREATOR |kr|)
(COMMON-NAME "a fatty acid") )
NIL)
(|a fatty aldehyde| T (
(OCELOT-GFP::PARENTS |an aldehyde|)
(DISPLAY-COORDS-2D (0.0d0 -0.529d0) (0.8875d0 -2.5848d0) (3.1709d0 -0.2668d0)
(1.7966d0 0.0d0) (0.8783d0 -1.0568d0))
(CHEMICAL-FORMULA (C 2) (H 3) (O 1) (R 1))
(N-1-NAME "a fatty aldehyden-1")
(STRUCTURE-BONDS (4 5 1) (3 4 1) (2 5 2) (1 5 1))
(STRUCTURE-ATOMS H O R C C)
(COMMON-NAME "a fatty aldehyde")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104639) )
NIL)
(|a glycerophosphodiester| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF GLYCPDIESTER-RXN)
(SYNONYMS "glycerophosphodiester" "glycerol-3-P-OR")
(:CREATION-DATE 3052248724)
(:CREATOR |kr|)
(COMMON-NAME "a glycerophosphodiester") )
NIL)
(|a primary alcohol| T (
(OCELOT-GFP::PARENTS |Alcohols| |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (-1.0d0 -1.0d0) (0.9787233d0 -1.0d0))
(CHEMICAL-FORMULA (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(STRUCTURE-ATOMS R O)
(SYNONYMS "1-Alcohol")
(COMMON-NAME "a primary alcohol") )
NIL)
(|a quinone| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF NQOR-RXN L-LACTDEHYDROGFMN-RXN
|NADH-DEHYDROGENASE-(QUINONE)-RXN| RXN0-271 QOR-RXN)
(SYNONYMS "quinone")
(:CREATION-DATE 3053278207)
(:CREATOR |kr|)
(COMMON-NAME "a quinone") )
NIL)
(|a reduced quinone| T (
(OCELOT-GFP::PARENTS |a quinone|)
(SYNONYMS "a reduced quinone" "quinol")
(APPEARS-IN-RIGHT-SIDE-OF L-LACTDEHYDROGFMN-RXN
|NADH-DEHYDROGENASE-(QUINONE)-RXN| RXN0-271 NQOR-RXN)
(SCHEMA? T)
(:CREATION-DATE 3106947331)
(:CREATOR |kr|)
(COMMON-NAME "a hydroquinone") )
NIL)
(|a secondary alcohol| T (
(OCELOT-GFP::PARENTS |Alcohols| |Unclassified-Compounds|)
(COMMON-NAME "a secondary alcohol")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104638) )
NIL)
(|a semiquinone| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SCHEMA? T)
(APPEARS-IN-RIGHT-SIDE-OF QOR-RXN)
(SYNONYMS "semiquinone")
(:CREATION-DATE 3053278209)
(:CREATOR |kr|)
(COMMON-NAME "a semiquinone") )
NIL)
(A-2-HYDROXYCARBONYL-COMPOUND NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |keseler|)
(:CREATION-DATE 3313787367)
(COMMON-NAME "a 2-hydroxycarbonyl compound")
(STRUCTURE-ATOMS H O O R C C)
(DISPLAY-COORDS-2D (3.6373d0 -2.1d0) (2.4249d0 0.0d0) (1.2124d0 -3.5d0)
(0.0d0 -1.4d0) (2.4248d0 -1.4d0) (1.2124d0 -2.1d0))
(STRUCTURE-BONDS (5 6 1) (4 6 1) (3 6 1) (2 5 2) (1 5 1))
(CHEMICAL-FORMULA (C 2) (H 3) (O 2) (R 1)) )
NIL)
(A-FATTY-ALCOHOL T (
(OCELOT-GFP::PARENTS |Alcohols| |Unclassified-Compounds|)
(COMMON-NAME "a fatty alcohol")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(A-GLYCEROL-ESTER NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1842)
(COMMON-NAME "a glycerol ester")
(:CREATOR |keseler|)
(:CREATION-DATE 3342298277) )
NIL)
(A-L-GLYCOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATOR |keseler|)
(:CREATION-DATE 3313787367)
(COMMON-NAME "a L-glycol")
(STRUCTURE-ATOMS O O R C C)
(DISPLAY-COORDS-2D (0.0d0 -1.4d0) (2.4249d0 0.0d0) (3.6373d0 -2.1d0)
(1.2124d0 -2.1d0) (2.4248d0 -1.4d0))
(STRUCTURE-BONDS (4 5 1) (3 5 1) (5 2 1 :UP) (1 4 1))
(CHEMICAL-FORMULA (C 2) (H 5) (O 2) (R 1)) )
NIL)
(|a-long-chain-alcohol| T (
(OCELOT-GFP::PARENTS |Alcohols| |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (0.7177d0 -1.1886d0) (0.0d0 0.0d0) (0.7145d0 -0.4125d0))
(CHEMICAL-FORMULA (C 1) (H 3) (O 1) (R 1))
(STRUCTURE-BONDS (2 3 1) (1 3 1))
(STRUCTURE-ATOMS O R C)
(COMMON-NAME "a long-chain alcohol")
(:CREATOR |pkarp|)
(:CREATION-DATE 3244404126) )
NIL)
(A-PHOSPHOPROTEIN NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(APPEARS-IN-LEFT-SIDE-OF 3.1.3.16-RXN)
(:CREATOR |paley|)
(:CREATION-DATE 3314379758)
(COMMON-NAME "a phosphoprotein")
(UNMODIFIED-FORM |Protein|) )
NIL)
(AAS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2836" "Aas")
(LOCATIONS CCO-PM-BAC-NEG)
(DBLINKS (MODBASE "P31119" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF01553" IN-FAMILY |pkarp| 3346700376 NIL NIL)
(REFSEQ "NP_417313" NIL NIL NIL NIL NIL)
(UNIPROT "P31119" NIL |pkarp| 3064869797))
(CATALYZES ENZRXN0-5321 ACYLGPEACYLTRANS-ENZRXN ACYLACPSYNTH-ENZRXN)
(PI 9.37d0)
(MOLECULAR-WEIGHT-SEQ 80.69988899999971d0)
(GENE EG11679)
(COMMENT "The protein contains bound ACP. |CITS: [91310656][89214178]|
Based on sequence similarity, Aas has been predicted to be a hydroxycinnamate-CoA ligase |CITS: [12952533]|.")
(TEMPLATE-FILE "~ecocyc/templates/new/aas/aas.template")
(:CREATION-DATE 3047852706)
(:CREATOR |mriley|) )
NIL)
(ABBREV-NAME NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |kr|)
(:CREATION-DATE 3339519669)
(:DOMAIN |Organizations| |Databases|)
(:VALUE-TYPE :STRING)
(:DOCUMENTATION
"This is the version of the database name that is used in links.
Additionally, it is used for the short form of the name of an organization.") )
NIL)
(ABC-10-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CPLX0-1944)
(:CREATION-DATE 3059864719)
(COMMENT
"FepBCDG are components of a ferric enterobactin transport complex that is a member of the ATP-binding
cassette (ABC) family of transporters. E. coli and several other species of Enterobacteriaceae
secrete the catecholate siderophore enterobactin. The enterobactin siderophore is a small organic
molecule with a high affinity for Fe 3+. FepA has been shown |CITS:[21424666]|, to be
involved in transport of ferric enterobactin across the outer membrane into the periplasm in a TonB-
dependent process which requires the transduction of energy derived from the cytoplasmic membrane
across the periplasm to FepA. Deletion studies |CITS: [92157868]| indicate that fepD and
fepG are essential for transport and sequence analysis indicates that these two proteins are highly
homologous with other integral membrane proteins involved in iron-chelating ABC uptake systems. Based
on sequence similarity, FepC is the ATP-binding component and provides the energy required for transport
across the inner membrane. FepB is not coded in the same operon but has been shown to bind ferric
enterobactin and probably functions as the periplasmic binding protein of the ferric enterobactin ABC
transporter |CITS: [96004464]|.")
(CATALYZES ABC-10-ENZRXN)
(COMMON-NAME "ferric enterobactin ABC transporter")
(COMPONENTS FEPC-MONOMER FEPD-MONOMER FEPG-MONOMER FEPB-MONOMER) )
((COMPONENTS FEPB-MONOMER COEFFICIENT 1)
(COMPONENTS FEPG-MONOMER COEFFICIENT 1)
(COMPONENTS FEPD-MONOMER COEFFICIENT 1)
(COMPONENTS FEPC-MONOMER COEFFICIENT 2)))
(ABC-10-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "21424666:EV-COMP-HINF-FN-FROM-SEQ:3279558457:mhance"
"92157868:EV-EXP-IMP-REACTION-BLOCKED:3277471733:ipaulsen"
"96004464:EV-EXP-IGI:3277471733:ipaulsen")
(:CREATION-DATE 3059948758)
(ENZYME ABC-10-CPLX)
(REACTION ABC-10-RXN) )
NIL)
(ABC-10-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| FERRIC-ENTEROBACTIN-COMPLEX)
(LEFT ATP FERRIC-ENTEROBACTIN-COMPLEX WATER)
(ENZYMATIC-REACTION ABC-10-ENZRXN) )
((LEFT FERRIC-ENTEROBACTIN-COMPLEX COMPARTMENT CCO-PERI-BAC)))
(ABC-11-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CPLX0-1981)
(:CREATION-DATE 3059864719)
(COMMENT
"The FhuBCD ATP-dependent iron (III) hydroxamate transporter is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. FhuBCD catalyzes transport of iron (III)-hydroxamate
compounds across the inner membrane into the cytoplasm of E. coli. Hydroxamates, or siderophores,
are used to increase the solubility of iron (III), which is normally insoluble at pH 7 |CITS: [88038363]|.
Based on sequence similarity, FhuB is the transmembrane component |CITS: [98086115]|, FhuC is the
ATP-binding subunit |CITS: [87279948]|, and FhuD is the periplasmic siderophore-binding component of
the ABC transporter |CITS: [98273640]|. A mutant with overproduced periplasmic FhuD protein was shown
to bind to radioactively labeled iron (III) ferrichrome |CITS: [91307893]|. Resistance of FhuD to protease K
in the presence of ferrichrome, aerobactin, and coprogen also indicated binding of these substrates to
FhuD |CITS: [91307893]|. In E. coli, hydroxamate transport across the outer membrane (via FhuA
and the TonB-ExbB-ExbD complex), coupled with the FhuBCD-mediated hydroxamate transport across
the cytoplasmic membrane completes the uptake of iron (III) hydroxamates into the cell. fhuA-fhuB
mutants exhibited completely abolished growth promotion by natural hydroxamates |CITS: [20048384]|.")
(CATALYZES ABC-11-ENZRXN)
(COMMON-NAME "iron (III) hydroxamate ABC transporter")
(COMPONENTS FHUC-MONOMER FHUB-MONOMER FHUD-MONOMER) )
((COMPONENTS FHUD-MONOMER COEFFICIENT 1)
(COMPONENTS FHUB-MONOMER COEFFICIENT 2)
(COMPONENTS FHUC-MONOMER COEFFICIENT 2)))
(ABC-11-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279562301:mhance"
"91307893:EV-EXP-IMP-REACTION-ENHANCED:3277472453:ipaulsen"
"20048384:EV-EXP-IMP-REACTION-BLOCKED:3279974425:mhance")
(:CREATION-DATE 3059948758)
(ENZYME ABC-11-CPLX)
(REACTION ABC-11-RXN) )
NIL)
(ABC-11-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| |Ferric-Hydroxamate-Complexes|)
(LEFT ATP |Ferric-Hydroxamate-Complexes| WATER)
(ENZYMATIC-REACTION ABC-11-ENZRXN) )
((LEFT |Ferric-Hydroxamate-Complexes| COMPARTMENT CCO-PERI-BAC)))
(ABC-12-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(COMMENT
"The GlnHPQ high-affinity glutamine transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, GlnH is the periplasmic
glutamine-binding protein, GlnQ is the ATP-binding component, and GlnP is the membrane component
of the ABC transporter. Mutation of glnP results in the impaired ability to transport glutamine as well
as the inability to utilized glutamine as a sole source of carbon |CITS: [82007680] [87115160]|. Expression
of the cloned glnHPQ genes on a plasmid vector restored the glnH, glnP, and
glnQ mutants' abilities to transport glutamine and utilize glutamine as a sole carbon source
|CITS: [87115160]|.")
(CATALYZES ABC-12-ENZRXN)
(COMMON-NAME "glutamine ABC transporter")
(COMPONENTS GLNQ-MONOMER GLNP-MONOMER GLNH-MONOMER) )
((COMPONENTS GLNH-MONOMER COEFFICIENT 1)
(COMPONENTS GLNP-MONOMER COEFFICIENT 2)
(COMPONENTS GLNQ-MONOMER COEFFICIENT 2)))
(ABC-12-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279561854:mhance"
"82007680:EV-EXP-IMP-REACTION-BLOCKED:3279561854:mhance"
"87115160:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279561854:mhance")
(:CREATION-DATE 3059948758)
(ENZYME ABC-12-CPLX)
(REACTION ABC-12-RXN) )
NIL)
(ABC-12-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| GLN)
(LEFT ATP GLN WATER)
(ENZYMATIC-REACTION ABC-12-ENZRXN) )
((LEFT GLN COMPARTMENT CCO-PERI-BAC)))
(ABC-13-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"The GltIJKL glutamate transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS:[98254124]|. Sequence similarity with known ABC transporter components suggests that GltJK are
integral membrane components and GltL is the ABC protein. GltI (also known as YbeJ) is the presumed
periplasmic binding protein.")
(CATALYZES ABC-13-ENZRXN)
(COMMON-NAME "glutamate ABC transporter")
(COMPONENTS GLTL-MONOMER GLTJ-MONOMER GLTK-MONOMER) )
((COMPONENTS GLTK-MONOMER COEFFICIENT 1)
(COMPONENTS GLTJ-MONOMER COEFFICIENT 1)
(COMPONENTS GLTL-MONOMER COEFFICIENT 2)))
(ABC-13-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "98254124:EV-COMP-HINF-FN-FROM-SEQ:3279561634:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-13-CPLX)
(REACTION ABC-13-RXN) )
NIL)
(ABC-13-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| GLT)
(LEFT ATP GLT WATER)
(ENZYMATIC-REACTION ABC-13-ENZRXN) )
((LEFT GLT COMPARTMENT CCO-PERI-BAC)))
(ABC-14-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"HisPMQJ is an ATP-dependent histidine transport system that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, HisJ is the
periplasmic histidine-binding protein, HisQ and HisM are the integral membrane components, and HisP is
the ATP-binding component of the ABC transport complex |CITS: [98188231]|. Although the transport
properties of the His complex in E. coli have not yet been characterized, extensive investigations on
the orthologous proteins in Salmonella typhimurium have been reported. The His complex of
Salmonella typhimurium was purified and reconstituted into ATP-encapsulated proteoliposomes,
and histidine transport activity was observed |CITS: [97150838]|. His-mediated transport activity is
completely dependent on the presence of all four protein components and on the internal ATP concentration,
with apparent Km of 8 mM for ATP |CITS: [97150838] [89386658]|. The transport activity is
also affected by pH, temperature, and salt concentration |CITS: [97150838]|. Transport is irreversible and
accumulation reaches a plateau at which point transport ceases |CITS: [97150838]|. The transport complex is
inhibited by ADP and by high concentrations of internal histidine |CITS: [97150838]|.")
(CATALYZES ABC-14-ENZRXN)
(COMMON-NAME "histidine ABC transporter")
(COMPONENTS HISP-MONOMER HISM-MONOMER HISQ-MONOMER HISJ-MONOMER) )
((COMPONENTS HISJ-MONOMER COEFFICIENT 1)
(COMPONENTS HISQ-MONOMER COEFFICIENT 1)
(COMPONENTS HISM-MONOMER COEFFICIENT 1)
(COMPONENTS HISP-MONOMER COEFFICIENT 2)))
(ABC-14-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279562172:mhance"
"97150838:EV-EXP-IMP-REACTION-BLOCKED:3279975527:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-14-CPLX)
(REACTION ABC-14-RXN) )
NIL)
(ABC-14-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| HIS)
(LEFT ATP HIS WATER)
(ENZYMATIC-REACTION ABC-14-ENZRXN) )
((LEFT HIS COMPARTMENT CCO-PERI-BAC)))
(ABC-15-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in E. coli.
They have shared membrane and ATP-binding components but have distinctive periplasmic binding proteins.
Due to the different periplasmic binding components, the two complexes differ in their binding specificity:
LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for leucine, isoleucine,
and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity analysis, LivJ and LivK
are the two periplasmic animo acid-binding proteins, LivH and LivM are the membrane components, and
LivG and LivF are the ATP-binding component of the ABC transport complexes |CITS: [90307651]|.
Deletions each of the liv genes resulted in the inability to transport leucine |CITS: [90307651]|. In
addition, a deletion strain that does not express any of the liv genes was unable to carry out high-
affinity transport of leucine unless one of the binding protein genes and all of the membrane complex genes
were provided on a plasmid |CITS: [90307651]|. In a separate experiment, liv gene mutants were
found to be resistant to a toxic analog of leucine, azaleucine, due to its inability in branched-chain amino
acid transport |CITS: [85288998]|. This system has also been shown |CITS:[14702302]| to serve as a third (along
with the AroP and PheP systems) complex for transport of phenylanine across the inner membrane.")
(CATALYZES ABC-15A-ENZRXN ABC-15B-ENZRXN ABC-15-ENZRXN)
(COMMON-NAME "branched chain amino acids ABC transporter")
(COMPONENTS LIVF-MONOMER LIVG-MONOMER LIVH-MONOMER LIVM-MONOMER LIVJ-MONOMER) )
((COMPONENTS LIVF-MONOMER COEFFICIENT 1)
(COMPONENTS LIVJ-MONOMER COEFFICIENT 1)
(COMPONENTS LIVM-MONOMER COEFFICIENT 1)
(COMPONENTS LIVH-MONOMER COEFFICIENT 1)
(COMPONENTS LIVG-MONOMER COEFFICIENT 1)))
(ABC-15-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059948342)
(ENZYME ABC-15-CPLX)
(REACTION ABC-15-RXN) )
NIL)
(ABC-15-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| ILE)
(LEFT ATP ILE WATER)
(ENZYMATIC-REACTION ABC-15-ENZRXN) )
((LEFT ILE COMPARTMENT CCO-PERI-BAC)))
(ABC-15A-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "90307651:EV-EXP-IMP-REACTION-BLOCKED:3278870708:mhance"
"20053876:EV-COMP-HINF-FN-FROM-SEQ:3279554818:mhance")
(:CREATION-DATE 3059950155)
(REACTION ABC-35-RXN)
(ENZYME ABC-15-CPLX) )
NIL)
(ABC-15B-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059950155)
(REACTION ABC-36-RXN)
(ENZYME ABC-15-CPLX) )
NIL)
(ABC-15D-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "20053876:EV-COMP-AINF-FN-FROM-SEQ:3278870245:mhance"
"90307651:EV-EXP-IMP-REACTION-BLOCKED:3278870245:mhance"
"90307651:EV-COMP-HINF-FN-FROM-SEQ:3279975306:mhance")
(REACTION ABC-35-RXN)
(ENZYME ABC-304-CPLX)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3202755029) )
NIL)
(ABC-16-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CPLX0-2101)
(:CREATION-DATE 3059948342)
(COMMENT
"MalKFGE is a maltose transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, MalE is the periplasmic maltose-binding
protein, MalF and MalG are the integral membrane components, and MalK is the ATP-binding component
of the ABC transporter. A 10-fold increase in the level of maltose transport activity was observed in
membrane vesicles when the membrane associated components of the transport system (MalF, MalG, and
MalK) were overproduced |CITS: [90170921]|. Maltose transport activity abolished in proteoliposomes
prepared from a strain with a deletion of the mal genes |CITS: [90170921]|. The purified MalKFGE
complex exhibits transport-associated ATPase activity, and mutations in the malK gene resulted in
loss of transport activity without affecting protein stability |CITS: [94043174]|.")
(CATALYZES ABC-16-ENZRXN)
(COMMON-NAME "maltose ABC transporter")
(COMPONENTS MALK-MONOMER MALF-MONOMER MALG-MONOMER MALE-MONOMER) )
((COMPONENTS MALE-MONOMER COEFFICIENT 1)
(COMPONENTS MALG-MONOMER COEFFICIENT 1)
(COMPONENTS MALF-MONOMER COEFFICIENT 1)
(COMPONENTS MALK-MONOMER COEFFICIENT 2)))
(ABC-16-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279975757:mhance"
"90170921:EV-EXP-IGI:3276356350:ipaulsen"
"90170921:EV-EXP-IMP-REACTION-BLOCKED:3276356350:ipaulsen"
"94043174:EV-EXP-IDA-PURIFIED-PROTEIN:3276356350:ipaulsen")
(:CREATION-DATE 3059948342)
(ENZYME ABC-16-CPLX)
(REACTION ABC-16-RXN) )
NIL)
(ABC-16-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13 EC-3.6.3)
(EC-NUMBER "3.6.3.19")
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| MALTOSE)
(LEFT ATP MALTOSE WATER)
(ENZYMATIC-REACTION ABC-16-ENZRXN) )
((LEFT MALTOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-18-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"MglABC is a beta-methylgalactoside transport system that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, mglB encodes the galactose-binding component,
mglC encodes the integral membrane component, and mglA encodes the ATP-binding component of the ABC
transporter. Insertional mutations in each gene indicate that all three components are necessary for beta-methylgalactoside
transport function |CITS: [83082637]|. Complementation experiments show that mlg genes cloned into a plasmid
vector are able to complement the transport functions of the mglA, mglB, and mglC mutants
|CITS: [82239395]|. MglB, but not MglA or MglC, was found to also serve as the galactose chemoreceptor in E. coli
|CITS: [83082637]|. mglB mutants eliminate the chemotactic function in E. coli; however, mglA and
MglC mutants exhibit normal galactose taxis but defective galactoside uptake activities |CITS: [87286407] [83082637]|.")
(CATALYZES ABC-18-ENZRXN)
(COMMON-NAME "galactose ABC transporter")
(COMPONENTS MGLA-MONOMER MGLC-MONOMER MGLB-MONOMER) )
((COMPONENTS MGLB-MONOMER COEFFICIENT 1)
(COMPONENTS MGLC-MONOMER COEFFICIENT 2)
(COMPONENTS MGLA-MONOMER COEFFICIENT 2)))
(ABC-18-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279561123:mhance"
"83082637:EV-EXP-IMP-REACTION-BLOCKED:3278077039:ipaulsen"
"82239395:EV-EXP-IGI-FUNC-COMPLEMENTATION:3278077039:ipaulsen")
(:CREATION-DATE 3059948342)
(ENZYME ABC-18-CPLX)
(REACTION ABC-18-RXN) )
NIL)
(ABC-18-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| GALACTOSE)
(LEFT ATP GALACTOSE WATER)
(ENZYMATIC-REACTION ABC-18-ENZRXN) )
((LEFT GALACTOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-19-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"ModCBA is a high-affinity molybdate transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, modA encodes the
periplasmic binding component, modB encodes the integral membrane component, and modC
encodes the ATP-binding component of the ABC transporter. Complementation of a mod mutant with
the cloned mod genes restored molybdate uptake activities |CITS: [96151473]|. In a mod
mutant, molybdate is not transported by the ModCBA system but by the sulfate transport system or by a
nonspecific anion transporter |CITS: [98004559]|. Transcription of mod genes is regulated by
molybdate and a repressor protein, ModE |CITS: [98004559]|.")
(CATALYZES ABC-19-ENZRXN)
(COMMON-NAME "molybdate ABC transporter")
(COMPONENTS MODC-MONOMER MODB-MONOMER MODA-MONOMER) )
((COMPONENTS MODA-MONOMER COEFFICIENT 1)
(COMPONENTS MODB-MONOMER COEFFICIENT 2)
(COMPONENTS MODC-MONOMER COEFFICIENT 2)))
(ABC-19-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279976608:mhance"
"96151473:EV-EXP-IGI-FUNC-COMPLEMENTATION:3276623693:ipaulsen"
"98004559:EV-EXP-IMP-REACTION-BLOCKED:3279976608:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-19-CPLX)
(REACTION ABC-19-RXN) )
NIL)
(ABC-19-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| CPD-3)
(LEFT ATP CPD-3 WATER)
(ENZYMATIC-REACTION ABC-19-ENZRXN) )
((LEFT CPD-3 COMPARTMENT CCO-PERI-BAC)))
(ABC-2-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(COMMENT
"The AraFGH arabinose transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily.
Expression of all three components was necessary to complement high-affinity arabinose transport in an
araFGH knockout strain |CITS: [89255061]| Membrane vesicle studies have shown that there are
two main arabinose uptake systems in E. coli: the low affinity proton-driven AraE transporter and a
high affinity ATP-driven system utilizing AraF as a binding protein |CITS:[82205973]|. The AraF binding
protein has been purified, crystallized and its high resolution structure shown to bind arabinose
|CITS:[78070158]|. Based on sequence similarity, AraH is the membrane component and AraG is the
ATP-binding component of this ABC transporter |CITS: [88062740]|.")
(CATALYZES ABC-2-ENZRXN)
(COMMON-NAME "arabinose ABC transporter")
(COMPONENTS ARAG-MONOMER ARAH-MONOMER ARAF-MONOMER) )
((COMPONENTS ARAF-MONOMER COEFFICIENT 1)
(COMPONENTS ARAH-MONOMER COEFFICIENT 2)
(COMPONENTS ARAG-MONOMER COEFFICIENT 2)))
(ABC-2-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "89255061:EV-EXP-IMP-REACTION-BLOCKED:3276278340:ipaulsen"
"89255061:EV-EXP-IGI-FUNC-COMPLEMENTATION:3276278340:ipaulsen"
"78070158:EV-COMP-HINF-FN-FROM-SEQ:3279551500:mhance"
"78070158:EV-EXP-IDA-PURIFIED-PROTEIN:3276278340:ipaulsen")
(:CREATION-DATE 3059948758)
(REACTION ABC-2-RXN)
(ENZYME ABC-2-CPLX) )
NIL)
(ABC-2-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(COMMON-NAME "Transport of α-L-arabinose")
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION ABC-2-ENZRXN)
(RIGHT ARABINOSE |Pi| ADP)
(LEFT WATER ARABINOSE ATP)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3225030096) )
((LEFT ARABINOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-20-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"The NikABCDE ATP-dependent nickel (II) uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. The Nik system exhibits significant sequence similarity to
the components of other ABC transporters for dipeptides or oligopeptides |CITS: [95020649]|. Based on
sequence similarity, NikA is the periplasmic binding protein, NikB and NikC are the membrane components,
and NikD and NikE are the ATP-binding components of the ABC transporter. The nickel-binding
properties of the protein have been studied by monitoring the quenching of intrinsic protein fluorescence
|CITS: [95172074]|. NikA binds one atom of nickel per molecule of protein with a Kd of less
than 0.1 μM. The transporter's high specificity for nickel ion has also been demonstrated by
high-performance immobilized-metal-ion affinity chromatography |CITS:[95172074]|. The structure of NikA
has been determined to a resolution of 1.8 angstroms showing that it binds FeEDTA(H2O)
with very high affinity. It also binds the nickel ion associated with a metallophore which is at least similar
to EDTA |CITS:[16011372]|. Insertional mutation in the nik operon severely reduces nickel transport
ability |CITS:[95020649]|. Nickel is an important cofactor in a variety of enzymatic reactions in prokaryotes
|CITS:[20112624]|. However, nickel at high intracellular concentrations is toxic because it can catalyze the
formation of reactive forms of oxygen that can damage cellular constituents |CITS: [20112624]|. Because of
the toxicity of nickel, the synthesis of the Nik system is tightly controlled by nickel concentration. At high
nickel concentrations (0.3 mM) synthesis of Nik is completely repressed by the protein NikR
|CITS:[20112624]|. Expression of NikABCDE corresponds to expression of NiFe hydrogenases for which
nickel is a cofactor. Mutation and LacZ fusion experiments show that nitrate, via the activity of the NarLX
two-component system, represses expression of nikABCDE considerably. NikABCDE is
upregulated by FNR under anaerobic conditions |CITS:[16159764]|.
")
(CATALYZES ABC-20-ENZRXN)
(COMMON-NAME "nickel ABC transporter")
(COMPONENTS NIKD-MONOMER NIKE-MONOMER NIKB-MONOMER NIKC-MONOMER NIKA-MONOMER) )
((COMPONENTS NIKA-MONOMER COEFFICIENT 1)
(COMPONENTS NIKC-MONOMER COEFFICIENT 1)
(COMPONENTS NIKB-MONOMER COEFFICIENT 1)
(COMPONENTS NIKE-MONOMER COEFFICIENT 1)
(COMPONENTS NIKD-MONOMER COEFFICIENT 1)))
(ABC-20-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "95020649:EV-COMP-HINF-FN-FROM-SEQ:3279984540:mhance"
"95020649:EV-EXP-IMP-REACTION-BLOCKED:3279984540:mhance"
"95172074:EV-EXP-IDA-UNPURIFIED-PROTEIN:3279984540:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-20-CPLX)
(REACTION ABC-20-RXN) )
NIL)
(ABC-20-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13 EC-3.6.3)
(:CREATOR |jchen|)
(EC-NUMBER "3.6.3.24")
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342 3201867802)
(RIGHT NI+2 ADP |Pi|)
(LEFT NI+2 ATP WATER)
(ENZYMATIC-REACTION ABC-20-ENZRXN TRANS-ENZRXN-250) )
((LEFT NI+2 COMPARTMENT CCO-PERI-BAC)))
(ABC-21-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT "YadG and YadH are uncharacterized members of the
ABC superfamily of transporters |CITS: [99091701]|.
YadG is the putative ATP binding component, YadH is
the putative membrane compenent. Based on sequence similarity,
they probably function together as as an ATP-driven
efflux system. The genes yadg and yadh
are probably located within a single operon.")
(COMMON-NAME "YadG/YadH ABC transporter")
(COMPONENTS YADG-MONOMER YADH-MONOMER) )
((COMPONENTS YADH-MONOMER COEFFICIENT 2)
(COMPONENTS YADG-MONOMER COEFFICIENT 2)))
(ABC-22-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"OppABCDF is an ATP-dependent oligopeptide transporter that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [92149312]|. OppABCDF has not been investigated in detail in
E. coli, but the orthologous system in Salmonella typhimurium has been extensively
characterized. Binding affinity and competition assays have shown that OppABCDF will transport
oligopeptides up to five amino acids in length, but has no affinity for free amino acids |CITS: [87056967]
[8801122]|. The system has been observed to function in oligopeptide uptake, as well as recycling of cell
wall peptides |CITS: [88011222]|. Based on sequence similarity, OppB and OppC are the membrane
components of the ABC transporter, and OppD and OppF are the ATP-binding components of the ABC
transporter |CITS: [8801122][92149312]|. OppA is the periplasmic substrate-binding component that binds
oligopeptides with a Kd of approximately 1E-6 |CITS: [94261830]|. Insertion mutant of the
oppF gene has shown that OppF is required for Opp transporter function |CITS: [88011222]|. In
addition, Insertional mutants of each of the opp genes were constructed, and the opp-minus
strains were unable to utilize the peptide Pro-Gly-Gly, normally transported by the wild-type transporter
|CITS: [88011222]|.
OppA has been crystallized and its structure resolved to 2.3 A resolution showing OppA to be a bilobal,
principally beta-stranded, three-domain protein |CITS:[15299334]|.
Targeting of OppA to the Sec-translocase for transport across the inner membrane
is SecB-dependent |CITS:[16352602]|.")
(CATALYZES ABC-22-ENZRXN)
(COMMON-NAME "oligopeptide ABC transporter")
(COMPONENTS OPPC-MONOMER OPPD-MONOMER OPPF-MONOMER OPPB-MONOMER OPPA-MONOMER) )
((COMPONENTS OPPB-MONOMER COEFFICIENT 1)
(COMPONENTS OPPC-MONOMER COEFFICIENT 1)
(COMPONENTS OPPD-MONOMER COEFFICIENT 1)
(COMPONENTS OPPF-MONOMER COEFFICIENT 1)
(COMPONENTS OPPA-MONOMER COEFFICIENT 1)))
(ABC-22-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "92149312:EV-COMP-HINF-FN-FROM-SEQ:3279978248:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-22-CPLX)
(REACTION ABC-22-RXN) )
NIL)
(ABC-22-RXN NIL (
(OCELOT-GFP::PARENTS TR-13 |Protein-Modification-Reactions|)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| |Peptides|)
(LEFT ATP |Peptides| WATER)
(ENZYMATIC-REACTION TRANS-ENZRXN-219 ABC-22-ENZRXN) )
((LEFT |Peptides| COMPARTMENT CCO-PERI-BAC)))
(ABC-23-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"The PhnCDE phosphonate transporter belongs to the ATP Binding Cassette
superfamily |CITS: [94272333]|. Phosphonates (e.g. 2-aminoethylphosphate) are compounds
with direct carbon-phosphorus bonds rather than the carbon-oxygen-
phosphorus bonds of phosphates. They are used as a phosphorus source in
E. coli |CITS: [91100346]|; however, the ability to use certain phosphonates appears to
be limited by the specificity of the PhnCDE transporter |CITS: [93122525]|. The phnCDE
operon is a member of the PHO regulon and is induced many hundred-fold
during phosphate limitation. The phnCDE genes were characterized by
Tn insertion mutational analyses. Knockout mutants suggested the phn
gene products are responsible for the uptake of phosphonate, phosphite,
phosphate, and certain phosphate ester such as phosphoserine |CITS: [93122525]|. Based on
sequence similarity and mutational analysis, PhnC is the ATP-binding protein,
PhnD is the periplasmic binding protein, and PhnE is the integral membrane
protein |CITS: [91100346]|.")
(CATALYZES ABC-23-ENZRXN)
(COMMON-NAME "alkylphosphonate ABC transporter")
(COMPONENTS PHNC-MONOMER PHNE-MONOMER PHND-MONOMER) )
((COMPONENTS PHNC-MONOMER COEFFICIENT 2)
(COMPONENTS PHND-MONOMER COEFFICIENT 1)
(COMPONENTS PHNE-MONOMER COEFFICIENT 2)))
(ABC-23-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "91100346:EV-COMP-HINF-FN-FROM-SEQ:3279549768:mhance"
"93122525:EV-EXP-IMP-REACTION-BLOCKED:3276612407:ipaulsen")
(:CREATION-DATE 3059948342)
(ENZYME ABC-23-CPLX)
(REACTION TRANS-RXN-37 TRANS-RXN-34 TRANS-RXN-32 ABC-23-RXN) )
NIL)
(ABC-23-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| |Alkylphosphonates|)
(LEFT ATP |Alkylphosphonates| WATER)
(ENZYMATIC-REACTION ABC-23-ENZRXN) )
((LEFT |Alkylphosphonates| COMPARTMENT CCO-PERI-BAC)))
(ABC-24-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"PotABCD is an ATP-dependent polyamine transporter that is a member of the ATP-Binding
Cassette (ABC) Superfamily of transporters |CITS: [20053876]|. The transporter consists of a membrane
associated ATPase (PotA), two transmembrane proteins (PotB and PotC), and a periplasmic
substrate-binding protein (PotD) |CITS: [20053876]|. Knockout mutants in each of the four genes indicated
that they are all required for polyamine transport |CITS: [93374918] [20053876]|. PotA has been purified to homogeneity
and was shown to have magnesium and spermidine-dependent ATPase activity, with a Km
of 385 μM for ATP |CITS: [96029616] [20053876]|. Based on hydropathy analysis and sequence similarity, PotB and
PotC are the membrane components of the ABC transporter |CITS: [20053876]|. PotD is the periplasmic
substrate-binding protein that acts to recognize and facilitate the transport of the polyamines
|CITS: [20053876] [99315781]|. PotD preferentially binds spermidine, but will also bind putrescine with a lower affinity
(Km values of 0.1 μM and 1.5 μM for spermidine and putrescine, respectively |CITS: [20053876]|).
The dissociation constant for the binding of spermidine by PotD was found to be 3.2 μM
with an optimal spermidine concentration of 5-10 μM |CITS: [93374918]|. X-ray crystallography of
PotD showed that it has two domains with β-α -β topology, with four
acidic residues, used to recognize the positively charged nitrogen atoms of the spermidine
substrate, located in the central cleft between the two domains |CITS: [20053876] [99318982]|.
")
(CATALYZES ABC-24A-ENZRXN ABC-24-ENZRXN)
(COMMON-NAME "putrescine/spermidine ABC transporter")
(COMPONENTS POTA-MONOMER POTB-MONOMER POTC-MONOMER POTD-MONOMER) )
((COMPONENTS POTD-MONOMER COEFFICIENT 1)
(COMPONENTS POTC-MONOMER COEFFICIENT 1)
(COMPONENTS POTB-MONOMER COEFFICIENT 1)
(COMPONENTS POTA-MONOMER COEFFICIENT 2)))
(ABC-24-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059948342)
(ENZYME ABC-24-CPLX)
(REACTION ABC-24-RXN) )
NIL)
(ABC-24-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| SPERMIDINE)
(LEFT ATP SPERMIDINE WATER)
(ENZYMATIC-REACTION ABC-24-ENZRXN) )
((LEFT SPERMIDINE COMPARTMENT CCO-PERI-BAC)))
(ABC-24A-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "20053876:EV-COMP-HINF-FN-FROM-SEQ:3279981398:mhance"
"20053876:EV-EXP-IMP-REACTION-BLOCKED:3277813140:ipaulsen"
"96029616:EV-EXP-IDA-PURIFIED-PROTEIN:3277813140:ipaulsen")
(:CREATION-DATE 3059949262)
(REACTION ABC-25-RXN)
(ENZYME ABC-24-CPLX) )
NIL)
(ABC-25-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"The PotFGHI ATP-dependent putrescine transporter is a member of the ATP Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. PotFGHI is similar in sequence and subunit composition to
the PotABCD putrescine/spermidine uptake system. Based on sequence similarity, PotG is the ATP-
binding component, PotH and Pot I are the membrane components, and PotF is the periplasmic binding
component of the ABC transporter. The PotF protein possesses a high binding affinity to putrescine
(Kd=2.0 μM) |CITS: [98316327]|. Site-directed mutagenesis have shown that PotF is the
putrescine-binding protein |CITS: [98316327]|, and gel filtration studies have show that in the presence of
1mM magnesium ion and 100mM potassium ion, PotF bound putrescine, but not spermidine, in a 1:1 ratio
|CITS: [93106992]|. A high resolution structure of PotF has been determined by x-ray crystallography
|CITS: [98316327]|. Knockout and complementation studies showed that the expression of all four proteins
was necessary for maximal putrescine transport activity |CITS: [93106992]|.")
(CATALYZES ABC-25-ENZRXN)
(COMMON-NAME "putrescine ABC transporter")
(COMPONENTS POTG-MONOMER POTH-MONOMER POTI-MONOMER POTF-MONOMER) )
((COMPONENTS POTF-MONOMER COEFFICIENT 1)
(COMPONENTS POTI-MONOMER COEFFICIENT 1)
(COMPONENTS POTH-MONOMER COEFFICIENT 1)
(COMPONENTS POTG-MONOMER COEFFICIENT 2)))
(ABC-25-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279981330:mhance"
"98316327:EV-EXP-IMP-REACTION-BLOCKED:3277813488:ipaulsen"
"93106992:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279981330:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-25-CPLX)
(REACTION ABC-25-RXN) )
NIL)
(ABC-25-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| PUTRESCINE)
(LEFT ATP PUTRESCINE WATER)
(ENZYMATIC-REACTION ABC-24A-ENZRXN ABC-25-ENZRXN) )
((LEFT PUTRESCINE COMPARTMENT CCO-PERI-BAC)))
(ABC-26-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"ProVWX, the high-affinity transport system for the osmoprotectant glycine betaine, is a member of the
ATP-Binding Cassette (ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity,
ProV is the ATP-binding component of the transporter, ProW is the integral membrane component, and
ProX is the periplasmic binding component of the ABC transporter. The periplasmic protein, ProX, was
purified to homogeneity, and transport assays with the purified protein shows that it binds glycine betaine with
a high affinity (Kd of 1μM) |CITS: [87308168]|. This indicates that the ProVWX system is
well suited to scavenge glycine betaine from the environment efficiently and to achieve high intracellular
concentrations of this osmoprotectant. Many other osmoprotectants (e.g. proline, taurine, and ectoine) can
also be transported via the ProVWX transporter at lower affinities |CITS: [94280886]|. The genetic regulation
of proVWX statement has been studied using lacZ and phoA gene fusions, and it was
revealed that statement of the operon is low under regular osmotic conditions, but increases substantially at
high osmolarity |CITS: [94280886]|. The intracellular accumulation of glycine betaine by E. coli
permits growth in a high-osmolarity environment, which would otherwise strongly inhibit the proliferation of
the bacterial cells |CITS: [96381453]|. Glycine betaine is transported through both the ProVWX system and
the ProP transporter in E. coli.")
(CATALYZES ABC-26-ENZRXN)
(COMMON-NAME "proline ABC transporter")
(COMPONENTS PROV-MONOMER PROW-MONOMER PROX-MONOMER) )
((COMPONENTS PROX-MONOMER COEFFICIENT 1)
(COMPONENTS PROW-MONOMER COEFFICIENT 2)
(COMPONENTS PROV-MONOMER COEFFICIENT 2)))
(ABC-26-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279979726:mhance"
"87308168:EV-EXP-IDA-PURIFIED-PROTEIN:3278866518:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-26-CPLX)
(REACTION ABC-26-RXN) )
NIL)
(ABC-26-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| PRO)
(LEFT ATP PRO WATER)
(ENZYMATIC-REACTION ABC-26-ENZRXN) )
((LEFT PRO COMPARTMENT CCO-PERI-BAC)))
(ABC-27-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"PstABCS is an ATP-dependent phosphate uptake system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. PstABCS is responsible for inorganic phosphate (Pi)
uptake under Pi starvation conditions. Inorganic phosphate is an essential component in cellular function
since phosphorylation of nucleic acids, lipids, sugars, and proteins are important for gene regulation and
signaling |CITS: [91054431]|. Based on sequence similarity, PstA and PstC are the membrane components
of the ABC transporter, while PstS is the periplasmic phosphate binding protein |CITS: [91054431]|, and
PstB is the ATP-binding component of the ABC transporter |CITS: [91054431]|. Whole cell transport
assay indicates that the Pst system has a Km of 0.20 μM |CITS: [82030542]|. Transcription
of the Pst system is induced by Pi starvation, as opposed to the Pit phosphate transport system that is
expressed regardless of Pi level |CITS: [91054431]|.")
(CATALYZES ABC-27-ENZRXN)
(COMMON-NAME "phosphate ABC transporter")
(COMPONENTS PSTB-MONOMER PSTA-MONOMER PSTC-MONOMER PSTS-MONOMER) )
((COMPONENTS PSTS-MONOMER COEFFICIENT 1)
(COMPONENTS PSTC-MONOMER COEFFICIENT 1)
(COMPONENTS PSTA-MONOMER COEFFICIENT 1)
(COMPONENTS PSTB-MONOMER COEFFICIENT 2)))
(ABC-27-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "91054431:EV-COMP-HINF-FN-FROM-SEQ:3279979504:mhance"
"82030542:EV-EXP-IDA:3279979504:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-27-CPLX)
(REACTION ABC-27-RXN) )
NIL)
(ABC-27-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| |Pi|)
(LEFT ATP |Pi| WATER)
(ENZYMATIC-REACTION ABC-27-ENZRXN) )
((LEFT |Pi| COMPARTMENT CCO-PERI-BAC)))
(ABC-28-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"RbsABC is an ATP-dependent ribose transporter that is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [99121048]|. Based on sequence similarity, RbsA is the ATP-binding
constituent, RbsB is the periplasmic substrate-binding protein, and RbsC form the transmembrane
constituent of the transporter |CITS: [99121048]|. Mutations in each of the components eliminated transport
of ribose at external concentration of 1 μM, indicating that the components make up a transport system
that is responsible for high-affinity ribose transport. However, these mutants are able to grow normally on
high concentrations of the sugar, suggesting that there is at least a second, low-affinity transport system for
ribose in E. coli |CITS: [84212237]|. Hydrophobicity analysis has shown that RbsC contains six
transmembrane helices, while alkaline phosphatase fusions and the use of inside-out vesicles with proteolysis
have shown that the C and N termini are both on the cytoplasmic side of the membrane.")
(CATALYZES ABC-28-ENZRXN)
(COMMON-NAME "ribose ABC transporter")
(COMPONENTS RBSA-MONOMER RBSC-MONOMER RBSB-MONOMER) )
((COMPONENTS RBSB-MONOMER COEFFICIENT 1)
(COMPONENTS RBSC-MONOMER COEFFICIENT 2)
(COMPONENTS RBSA-MONOMER COEFFICIENT 2)))
(ABC-28-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "99121048:EV-COMP-HINF-FN-FROM-SEQ:3279981837:mhance"
"84212237:EV-EXP-IMP-REACTION-BLOCKED:3276265706:ipaulsen")
(:CREATION-DATE 3059948342)
(ENZYME ABC-28-CPLX)
(REACTION ABC-28-RXN) )
NIL)
(ABC-28-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| RIBOSE)
(LEFT ATP RIBOSE WATER)
(ENZYMATIC-REACTION ABC-42-ENZRXN ABC-28-ENZRXN) )
((LEFT RIBOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-29-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"SapABCDF (Sensitive to antimicrobial peptides) is a member of the ATP Binding Cassette (ABC) transporter
superfamily |CITS:[98254124]|. Disruption of the sap gene results in increased susceptibility to
endogenous antimicrobial peptides, such as protamine, mellitin, defensins and human neutrophil granules.
This suggests that the SapABCDF system may be involved in uptake of these peptides as part of a defense
degradation system |CITS:[94038887]|. Based on sequence similarity and hydrophobicity analysis, SapA is
the putative periplasmic binding protein, SapB and SapC are both transmembrane domains and SapD
and SapF are the ATP-binding proteins of the complex. Supporting this hypothesis, SapABCD are homologs
of the Salmonella typhimurium SapABCD proteins which are required for virulence and resistance to
antimicrobial peptides melittin and protamine |CITS: [94038887]| and the Sap proteins show sequence
similarity with other ABC peptide uptake systems. SapD has been implicated in an additional role in
conferring ATP dependence to the K+ uptake proteins TrkG and TrkH which are not related
to the ABC superfamily |CITS: [21557159]|. ATP binding to SapD has also been shown to be sufficient for
restoring K+ uptake in E. coli via its two Trk potassium transporters |CITS: [21557159]|.
Furthermore the previously described trkE locus |CITS: [94038887]| maps inside the
sapABCDF operon.")
(CATALYZES ABC-29-ENZRXN)
(COMMON-NAME "peptide uptake ABC transporter")
(COMPONENTS SAPF-MONOMER SAPD-MONOMER SAPB-MONOMER SAPC-MONOMER SAPA-MONOMER) )
((COMPONENTS SAPA-MONOMER COEFFICIENT 1)
(COMPONENTS SAPC-MONOMER COEFFICIENT 1)
(COMPONENTS SAPB-MONOMER COEFFICIENT 1)
(COMPONENTS SAPD-MONOMER COEFFICIENT 1)
(COMPONENTS SAPF-MONOMER COEFFICIENT 1)))
(ABC-29-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "98254124:EV-COMP-HINF-FN-FROM-SEQ:3279979272:mhance"
"94038887:EV-EXP-IMP-REACTION-BLOCKED:3279979272:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-29-CPLX)
(REACTION ABC-29-RXN) )
NIL)
(ABC-29-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| |Peptides|)
(LEFT ATP |Peptides| WATER)
(ENZYMATIC-REACTION ABC-29-ENZRXN) )
((LEFT |Peptides| COMPARTMENT CCO-PERI-BAC)))
(ABC-3-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(CATALYZES ABC-3A-ENZRXN ABC-3B-ENZRXN ABC-3-ENZRXN)
(COMMENT "Functions with HisMQP.")
(COMMON-NAME "lysine/arginine/ornithine ABC Transporter")
(COMPONENTS HISQ-MONOMER HISP-MONOMER HISM-MONOMER ARGT-MONOMER) )
((COMPONENTS HISM-MONOMER COEFFICIENT 1)
(COMPONENTS HISQ-MONOMER COEFFICIENT 1)
(COMPONENTS HISP-MONOMER COEFFICIENT 2)
(COMPONENTS ARGT-MONOMER COEFFICIENT 1)))
(ABC-3-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059948758)
(ENZYME ABC-3-CPLX)
(REACTION ABC-3-RXN) )
NIL)
(ABC-3-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT LYS ADP |Pi|)
(LEFT LYS ATP WATER)
(ENZYMATIC-REACTION ABC-3-ENZRXN) )
((LEFT LYS COMPARTMENT CCO-PERI-BAC)))
(ABC-304-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ABC-15D-ENZRXN)
(COMMENT
"LivFGHMJ and LivFGHMK are two ATP-dependent high-affinity branched-chain amino acid transport
system and are members of the ATP Binding Cassette (ABC) Superfamily of transporters |CITS: [20053876]|.
The two systems are responsible for the high affinity transport of branched-chain amino acids in
E. coli. They have shared membrane and ATP-binding components but have distinctive periplasmic
binding proteins. Due to the different periplasmic binding components, the two complexes differ in their
binding specificity: LivFGHMK is specific for the transport of leucine, while LivFGHMJ is a transporter for
leucine, isoleucine, and valine |CITS: [85288998]|. Based on sequence similarity and hydrophobicity
analysis, LivJ and LivK are the two periplasmic animo acid-binding proteins, LivH and LivM are the
membrane components, and LivG and LivF are the ATP-binding component of the ABC transport
complexes |CITS: [90307651]|. Deletions each of the liv genes resulted in the inability to transport
leucine |CITS: [90307651]|. In addition, a deletion strain that does not express any of the liv genes
was unable to carry out high-affinity transport of leucine unless one of the binding protein genes and all of
the membrane complex genes were provided on a plasmid |CITS: [90307651]|. In a separate experiment,
liv gene mutants were found to be resistant to a toxic analog of leucine, azaleucine, due to its
inability in branched-chain amino acid transport |CITS: [85288998]|.")
(COMPONENTS LIVK-MONOMER LIVM-MONOMER LIVH-MONOMER LIVG-MONOMER LIVF-MONOMER)
(COMMON-NAME "leucine ABC transporter")
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3202754430) )
((COMPONENTS LIVF-MONOMER COEFFICIENT 1)
(COMPONENTS LIVG-MONOMER COEFFICIENT 1)
(COMPONENTS LIVH-MONOMER COEFFICIENT 1)
(COMPONENTS LIVM-MONOMER COEFFICIENT 1)
(COMPONENTS LIVK-MONOMER COEFFICIENT 1)))
(ABC-32-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"The ABC transporter ThiBPQ was functionally characterized in Salmonella typhimurium where it is
required for the uptake of thiamine and thiamine pyrophosphate |CITS:[9535878]|. Its ortholog in
E. coli, SfuABC, has not been functionally characterized yet but presumably also function in
thiamine uptake. thiB (sfuA) encodes periplasmic thiamine binding protein. thiP
(sfuB) encodes inner membrane permease, and thiQ(sfuC) encodes
energy-transducing ATPase.
")
(:CREATION-DATE 3059948342)
(CATALYZES ABC-32-ENZRXN)
(COMMON-NAME "thiamin ABC transporter")
(COMPONENTS SFUC-MONOMER SFUB-MONOMER SFUA-MONOMER) )
((COMPONENTS SFUA-MONOMER COEFFICIENT 1)
(COMPONENTS SFUB-MONOMER COEFFICIENT 2)
(COMPONENTS SFUC-MONOMER COEFFICIENT 2)))
(ABC-32-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059948342)
(ENZYME ABC-32-CPLX)
(REACTION ABC-32-RXN) )
NIL)
(ABC-32-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| THIAMINE)
(LEFT ATP THIAMINE WATER)
(ENZYMATIC-REACTION ABC-32-ENZRXN) )
((LEFT THIAMINE COMPARTMENT CCO-PERI-BAC)))
(ABC-33-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"XylFGH is a D-xylose transporter belonging to the ATP Binding Cassette (ABC) Superfamily
|CITS: [96381453]|. D-xylose is the most abundant sugar in nature after glucose, and it can be utilized
by E. coli as a sole carbon source and metabolized through the pentose phosphate pathway
|CITS: [98336901]|. Sequence homology analysis suggests that XylG is the ATP-binding protein,
XylF is the periplasmic substrate-binding protein |CITS: [96117780]|, and XylH is the membrane
component of the ABC transport system |CITS: [94316500]|. The binding affinity of the receptor protein,
XylF, was studied using a mutant of xylE, which encodes the other D-Xylose transport system
in E. coli. The Km of XylF was determined to be in the range of 0.2-4 μM,
indicating that XylF is a high-affinity D-xylose transport system |CITS: [96117780]|. Transposon
mutagenesis studies suggest that XylFGH can also transport D-ribose in E.coli cells lacking
the high affinity RbsABC ribose transport system |CITS: [98336901]|.")
(CATALYZES ABC-33-ENZRXN)
(COMMON-NAME "xylose ABC transporter")
(COMPONENTS XYLG-MONOMER XYLH-MONOMER XYLF-MONOMER) )
((COMPONENTS XYLF-MONOMER COEFFICIENT 1)
(COMPONENTS XYLH-MONOMER COEFFICIENT 2)
(COMPONENTS XYLG-MONOMER COEFFICIENT 2)))
(ABC-33-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96117780:EV-COMP-HINF-FN-FROM-SEQ:3279985634:mhance"
"98336901:EV-EXP-IMP-REACTION-BLOCKED:3279985634:mhance")
(:CREATION-DATE 3059948342)
(ENZYME ABC-33-CPLX)
(REACTION ABC-33-RXN) )
NIL)
(ABC-33-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| XYLOSE)
(LEFT ATP XYLOSE WATER)
(ENZYMATIC-REACTION ABC-33-ENZRXN) )
((LEFT XYLOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-34-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMENT
"The UgpABCE glycerol-3-phosphate uptake system is a member of the ATP-Binding Cassette (ABC)
Superfamily |CITS:[96381453]|. Glycerol-3-phosphate can be used as a carbon source and a phosphate
source |CITS: [82189841]|, and is also an essential intermediate in phospholipid biosynthesis
|CITS: [98377424]|. Using 32P-labeled glycerol-3-phosphate,glycerol-3-phosphate uptake via the Ugp
system was observed in whole cell experiments |CITS: [94110221]|. Based on sequence similarity, UgpC is
the ATP-binding protein, UgpA and UgpE are the membrane components, and UgpB is the periplasmic
binding protein. Transcription of the ugp system is under the control of the pho regulon
|CITS:[94110221]|. The statement of ugp genes cloned in a plasmid were shown to be
phoB-dependent |CITS:[94012527]|. The Ugp system, even though capable of transporting glycerol-
3-phosphate, is unable to supply enough carbon for bacterial growth |CITS: [98377424]|. The concentration
of internal inorganic phosphate was monitored by nuclear magnetic resonance (NMR) imaging, and the
uptake of glycerol-3-phosphate via the Ugp system lead to a dramatic increase in the internal phosphate
concentration up to about 20 mM. This, in turn, inhibits the Ugp-mediated uptake of glycerol-3-phosphate
|CITS: [98377424]|. This feedback inhibition of Ugp by internal phosphate explains why glycerol-3-phosphate
transported by the Ugp system can only serve as the sole phosphate source but not the sole carbon source
|CITS: [98377424]|. Thus, the Ugp system is ideally geared for scavenging phosphate-containing compounds
|CITS:[98377424]|.")
(CATALYZES ABC-34-ENZRXN)
(COMMON-NAME "glycerol-3-P ABC transporter")
(COMPONENTS UGPC-MONOMER UGPA-MONOMER UGPE-MONOMER UGPB-MONOMER) )
((COMPONENTS UGPB-MONOMER COEFFICIENT 1)
(COMPONENTS UGPE-MONOMER COEFFICIENT 1)
(COMPONENTS UGPA-MONOMER COEFFICIENT 1)
(COMPONENTS UGPC-MONOMER COEFFICIENT 2)))
(ABC-34-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279561893:mhance"
"82189841:EV-EXP-IMP-REACTION-BLOCKED:3277663576:ipaulsen"
"94110221:EV-EXP-IDA:3277663576:ipaulsen")
(COMMON-NAME "tranport")
(:CREATION-DATE 3059948342)
(ENZYME ABC-34-CPLX)
(REACTION ABC-34-RXN) )
NIL)
(ABC-34-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948342)
(RIGHT ADP |Pi| GLYCEROL-3P)
(LEFT ATP GLYCEROL-3P WATER)
(ENZYMATIC-REACTION ABC-34-ENZRXN) )
((LEFT GLYCEROL-3P COMPARTMENT CCO-PERI-BAC)))
(ABC-35-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(SPECIES ECOLI)
(COMPONENT-OF CPLX0-3323)
(CATALYZES ENZRXN0-882)
(:CREATION-DATE 3059948342)
(COMMON-NAME "CcmABC ABC transporter")
(COMMENT
"The CcmABC (Cytochrome C Maturation proteins) putative transporter is a member of the ATP-Binding
Cassette (ABC) transporter superfamily |CITS: [98254124]|. Sequence analysis suggest that CcmA is the
ATP binding subunit and occurs as a homodimer and CcmB and CcmC are transmembrane domains.
CcmABC has been proposed to function as a heme exporter, which exports heme to the periplasm where it
is incorporated into cytochrome c apoproteins |CITS: [97438699]|. However, CcmC has been shown
to function independently and is essential for heme attachment to CcmE, a periplasmic heme chaperone,
that binds heme covalently in the periplasm and then acts as a heme donor for ligation to apocytochrome
c |CITS:[99272716]|. Analysis of a ccmA deletion mutant has suggested that CcmAB is not
essential for heme export |CITS: [20170685]|.")
(COMPONENTS CCMA-MONOMER CCMB-MONOMER CCMC-MONOMER) )
((COMPONENTS CCMC-MONOMER COEFFICIENT 1)
(COMPONENTS CCMB-MONOMER COEFFICIENT 1)
(COMPONENTS CCMA-MONOMER COEFFICIENT 2)))
(ABC-35-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059950155)
(RIGHT ADP |Pi| LEU)
(LEFT ATP LEU WATER)
(ENZYMATIC-REACTION ABC-15D-ENZRXN ABC-15A-ENZRXN) )
((LEFT LEU COMPARTMENT CCO-PERI-BAC)))
(ABC-36-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059950155)
(RIGHT ADP |Pi| VAL)
(LEFT ATP VAL WATER)
(ENZYMATIC-REACTION ABC-15B-ENZRXN) )
((LEFT VAL COMPARTMENT CCO-PERI-BAC)))
(ABC-37-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059950377)
(RIGHT ADP |Pi| L-ORNITHINE)
(LEFT ATP L-ORNITHINE WATER)
(ENZYMATIC-REACTION ABC-3A-ENZRXN) )
((LEFT L-ORNITHINE COMPARTMENT CCO-PERI-BAC)))
(ABC-39-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME "YddA complex")
(:CREATION-DATE 3059948342)
(COMPONENTS YDDA-MONOMER) )
((COMPONENTS YDDA-MONOMER COEFFICIENT 2)))
(ABC-3A-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059950377)
(REACTION ABC-37-RXN)
(ENZYME ABC-3-CPLX) )
NIL)
(ABC-3B-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(:CREATION-DATE 3059950377)
(REACTION ABC-4-RXN)
(ENZYME ABC-3-CPLX) )
NIL)
(ABC-4-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(COMMENT
"The ArtPMQJI arginine transporter is a member of the ATP Binding Cassette (ABC) transporter superfamily
|CITS: [98254124]|. ArtJ shows similarity to arginine-binding periplasmic protein components of other ABC
transporters. Expression studies show that ArtJ is localized to the periplasmic fractions of E. coli
and hybridization studies using radiolabeled arginine showed that part of the radioactivity co-eluted with
ArtJ, indicating that L-arginine is the natural substrate for ArtJ |CITS: [96111488]|. Furthermore, overexpression
of ArtJ resulted in stimulation of arginine uptake. In minimal medium, ArtJ was found in the periplasmic
extracts of E. coli but its presence was greatly diminished in high-arginine content medium
|CITS: [96111488]|. Sequence similarity, including a highly conserved ATP-binding consensus site, and
hydropathy analyses indicate that ArtP is highly homologous to the HisP ATP-binding protein of the
Histidine-LAO transporters (HisJQMP complexes) of S. typhimurium and E. coli . ArtQ
and ArtM are hydrophobic proteins and exhibit some homology to HisQ and HisM, membraneous
components of the Histidine-LAO ABC transport system, and to other ABC transporter integral membrane
proteins |CITS:[96111488]|. ArtQ and ArtM presumably function as integral membrane components and
couple the ATPase activity of ArtP to the transport of L-arginine across the inner membrane. ArtI exhibits
homology with a number of ABC transporter periplasmic binding proteins, but its substrate is not known
|CITS:[98254124]|.")
(CATALYZES ABC-4-ENZRXN)
(COMMON-NAME "arginine ABC transporter")
(COMPONENTS ARTP-MONOMER ARTM-MONOMER ARTQ-MONOMER ARTI-MONOMER ARTJ-MONOMER) )
((COMPONENTS ARTJ-MONOMER COEFFICIENT 1)
(COMPONENTS ARTI-MONOMER COEFFICIENT 1)
(COMPONENTS ARTQ-MONOMER COEFFICIENT 1)
(COMPONENTS ARTM-MONOMER COEFFICIENT 1)
(COMPONENTS ARTP-MONOMER COEFFICIENT 2)))
(ABC-4-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "98254124:EV-COMP-HINF-FN-FROM-SEQ:3279551538:mhance"
"96111488:EV-EXP-IDA:3278086517:ipaulsen"
"96111488:EV-EXP-IMP-REACTION-ENHANCED:3278086517:ipaulsen")
(:CREATION-DATE 3059948758)
(ENZYME ABC-4-CPLX)
(REACTION ABC-4-RXN) )
NIL)
(ABC-4-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| ARG)
(LEFT ATP ARG WATER)
(ENZYMATIC-REACTION ABC-4-ENZRXN ABC-3B-ENZRXN) )
((LEFT ARG COMPARTMENT CCO-PERI-BAC)))
(ABC-40-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS "99091701:EV-COMP-HINF-FN-FROM-SEQ:3343139507:djohnson")
(:CREATION-DATE 3059948342)
(COMMON-NAME "YehW/YehX/YehY/YehZ ABC transporter")
(COMMENT "YehX, YehW, YehY, YehZ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YehX is the putative ATP binding component, YehW and YehY
are the membrane components, and YehZ is the putative
periplasmic binding protein. Based on sequence similarity
they probably function together as an ATP-dependant
osmoprotection transporter. The yehX, yehW,
yehY, and yehZ genes are located
within a single operon.
Osmotic shock and entry into stationary phase induced transcription of the yehZYXW operon,
which was dependent upon σs |CITS:[15251200]|.")
(COMPONENTS YEHZ-MONOMER YEHX-MONOMER YEHW-MONOMER YEHY-MONOMER) )
((COMPONENTS YEHZ-MONOMER COEFFICIENT 1) (COMPONENTS EG12012 COEFFICIENT 1)
(COMPONENTS YEHY-MONOMER COEFFICIENT 1)
(COMPONENTS YEHW-MONOMER COEFFICIENT 1)
(COMPONENTS YEHX-MONOMER COEFFICIENT 2)))
(ABC-41-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(CATALYZES TRANS-ENZRXN-219)
(COMMON-NAME "YejA/YejB/YejE/YejF ABC transporter")
(COMMENT "YejF, YejB, YejE and YejA are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YejF is the putative ATP binding protein, YejB and YejE
are the putative membrane proteins, and YejA is the
putative binding protein. Based on sequence similarity
these proteins probably function together as an
ATP-dependent oligopeptide permease. The yejF,
yejB, yejE, and yejA genes are
probably in a single operon.")
(COMPONENTS YEJF-MONOMER YEJB-MONOMER YEJE-MONOMER YEJA-MONOMER) )
((COMPONENTS YEJA-MONOMER COEFFICIENT 1)
(COMPONENTS YEJE-MONOMER COEFFICIENT 1)
(COMPONENTS YEJB-MONOMER COEFFICIENT 1)
(COMPONENTS YEJF-MONOMER COEFFICIENT 2)))
(ABC-42-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMON-NAME "D-allose ABC transporter")
(CATALYZES ABC-42-ENZRXN)
(COMMENT "The AlsABC transporter belongs to the ATP-binding Cassette (ABC)
Superfamily |CITS: [94272333]|. It is responsible for the uptake of D-allose, an
all-cis hexose that can be used by E. coli as a sole carbon
source |CITS: [98062191]|. Deletion of the als genes resulted in an inability
to grow on D-allose |CITS: [98062191]|. AlsB is a periplasmic protein that binds
D-allose with a Kd of 0.33μM, as determined by
fluorescence spectroscopy |CITS: [98062191]|. Based on sequence similarity, AlsA
is the ATP-binding component, and AlsC is the membrane
component of the ABC transporter |CITS: [99165783]|. The AlsABC system also
transports ribose at low affinity |CITS: [98062191]|. Complementation analysis of
als mutants showed that the cloned als genes could
restore growth on ribose minimal media |CITS: [98062191]|. Analysis of
β-galactosidase transcriptional fusions suggest that AlsR is a
negative regulator of alsABC, and transcription of
alsR is regulated by allose |CITS: [98062191]|.")
(COMPONENTS YJCW-MONOMER YJCV-MONOMER YJCX-MONOMER) )
((COMPONENTS YJCX-MONOMER COEFFICIENT 1)
(COMPONENTS YJCV-MONOMER COEFFICIENT 2)
(COMPONENTS YJCW-MONOMER COEFFICIENT 2)))
(ABC-42-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "94272333:EV-COMP-HINF-FN-FROM-SEQ:3279556472:mhance"
"98062191:EV-EXP-IMP-REACTION-BLOCKED:3277483687:ipaulsen"
"98062191:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279556472:mhance")
(REACTION ABC-28-RXN ABC-42-RXN)
(ENZYME ABC-42-CPLX)
(:CREATOR |jchen|)
(:CREATION-DATE 3196421918) )
NIL)
(ABC-42-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(RIGHT ALLOSE ADP |Pi|)
(LEFT ALLOSE ATP WATER)
(ENZYMATIC-REACTION ABC-42-ENZRXN)
(:CREATOR |jchen|)
(:CREATION-DATE 3196422104) )
((LEFT ALLOSE COMPARTMENT CCO-PERI-BAC)))
(ABC-45-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMON-NAME "YrbF/YrbE ABC transporter")
(COMMENT "YrbF and YrbE are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YrbF is the putative ATP-binding component and YrbE
is the membrane component. Based on sequence
similarity, these proteins may function together as an
ATP-dependant toluene efflux transporter. The yrbF
and yrbE genes are probably in a single operon.
It is possible, though highly speculative, that either
YrbD or YrbC might be the periplasmic binding protein
of this complex.")
(COMPONENTS YRBF-MONOMER YRBE-MONOMER) )
((COMPONENTS YRBD-MONOMER COEFFICIENT 1)
(COMPONENTS YRBE-MONOMER COEFFICIENT 2)
(COMPONENTS YRBF-MONOMER COEFFICIENT 2)))
(ABC-46-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMON-NAME "YtfQ/YtfR/YtfS/YtfT/YjfF ABC transporter")
(COMMENT "YtfR, YtfS, YjfF, YtfT, and YtfQ are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YtfR and YtfS are the putative ATP-binding components.
YjfF and YtfT are the putative membrane components.
YtfQ is the putative binding protein. Based on sequence
similarity they probably function together as an ATP-dependant
sugar transporter. The genes ytfR, ytfS, yjfF,
ytfT, and ytfQ probably constitute a single operon.")
(COMPONENTS YJFF-MONOMER YTFR-MONOMER YTFT-MONOMER YTFQ-MONOMER) )
((COMPONENTS YJFF-MONOMER COEFFICIENT 1)
(COMPONENTS YTFQ-MONOMER COEFFICIENT 1)
(COMPONENTS YTFT-MONOMER COEFFICIENT 2)
(COMPONENTS YTFR-MONOMER COEFFICIENT 1)
(COMPONENTS YTFS-MONOMER COEFFICIENT 1)))
(ABC-48-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YnjD and YnjC are uncharacterized members of the
ABC superfamily of transporters |CITS: [99091701]|.
YnjD is the putative ATP-binding component. YnjC
is the putative membrane component. No periplasmic
binding component has yet been identified. Based on
sequence similiarity, these proteins may function
together as an ATP-dependent metabolite uptake
transporter. The genes ynjD and ynjC
are probably located within a single operon.")
(COMMON-NAME "YnjC/YnjD ABC transporter")
(COMPONENTS YNJC-MONOMER YNJD-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146931003) )
((COMPONENTS YNJD-MONOMER COEFFICIENT 2)
(COMPONENTS YNJC-MONOMER COEFFICIENT 2)))
(ABC-49-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ENZRXN0-22)
(CITATIONS "16109926:EV-EXP-IMP:3339777905:djohnson")
(COMMENT
"The GsiABCD glutathione transporter is a member of the ATP Binding Cassette (ABC) superfamily
of transporters. Based on sequence similarity, GsiA is predicted to be the ATP-binding component, GsiB
is predicted to be the periplasmic binding component, and GsiC and GsiD are predicted to be inner
membrane components. Mutation of any component impairs the ability of E. coli to transport the
glutathione molecule into the cell. Expression of the cloned genes in their respective mutants restores their
ability to transport glutathione. Transport by the glutathione ABC transporter is one of two known
mechanisms for salvage of glutathione excreted from the cell. The other involves hydrolysis of glutathione
by γ-glutamyl transpeptidase in the periplasm to yield glutamic acid and cysteinylglycine which
can be taken back into the cell |CITS:[16109926]|.")
(COMPONENTS YLIA-MONOMER YLIB-MONOMER YLID-MONOMER YLIC-MONOMER)
(COMMON-NAME "gsiABCD glutathione ABC transporter")
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146861385) )
((COMPONENTS YLIC-MONOMER COEFFICIENT 1)
(COMPONENTS YLID-MONOMER COEFFICIENT 1)
(COMPONENTS YLIB-MONOMER COEFFICIENT 1)
(COMPONENTS YLIA-MONOMER COEFFICIENT 2)))
(ABC-5-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CPLX0-1862)
(CITATIONS "12475936" "15111107")
(SPECIES ECOLI)
(:CREATION-DATE 3059864719)
(COMMENT
"BtuCDF is a vitamin B12 transport system that is a member of the ATP-Binding Cassette
(ABC) Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, BtuD is the ATP-binding
component, BtuC is the integral membrane component, and BtuF is the periplasmic substrate-binding
component of the ABC transporter |CITS: [12475936]| . Transposon insertions in the btuCand regions
conferred a deficiency in vitamin B12 utilization and transport |CITS: [86304183]|. However, there are
indications that BtuE (residing within the operon) is not required for transport. Transposon insertions in btuE were not
complemented by plasmids carrying btuE alone, whereas insertions in btuC and
btuD were effectively complemented by plasmids carrying the corresponding functional gene |CITS: [86304183] [89364713]|.
btuE mutants were also shown to have little effect on vitamin B12 binding and
transport and did not affect the utilization of vitamin B12 or other cobalamins for
methionine biosynthesis |CITS: [89364713]|.
The crystal structure of the Escherichia coli BtuCD protein has been resolved to 3.2 angstrom resolution |CITS:[12004122]|.")
(CATALYZES ABC-5-ENZRXN)
(COMMON-NAME "vitamin B12 ABC transporter")
(COMPONENTS BTUD-MONOMER BTUC-MONOMER EG12334-MONOMER) )
((COMPONENTS EG12334-MONOMER COEFFICIENT 1)
(COMPONENTS BTUE-MONOMER COEFFICIENT 1)
(COMPONENTS BTUC-MONOMER COEFFICIENT 2)
(COMPONENTS BTUD-MONOMER COEFFICIENT 2)))
(ABC-5-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279985316:mhance"
"86304183:EV-EXP-IMP-REACTION-BLOCKED:3278076574:ipaulsen"
"86304183:EV-EXP-IGI-FUNC-COMPLEMENTATION:3278076574:ipaulsen")
(:CREATION-DATE 3059948758)
(ENZYME ABC-5-CPLX)
(REACTION ABC-5-RXN) )
NIL)
(ABC-5-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| COB-I-ALAMIN)
(LEFT ATP COB-I-ALAMIN WATER)
(ENZYMATIC-REACTION ABC-5-ENZRXN) )
((LEFT COB-I-ALAMIN COMPARTMENT CCO-PERI-BAC)))
(ABC-51-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YdcS, YdcT, YdcU and YdcV are uncharacterized
members of the ABC superfamily of transporters
|CITS: [99091701]|. YdcS is the putative
periplasmic binding component, YdcT is the
putative ATP binding component, YdcU and YdcV
are the putative membrane spanning components.
Bases on sequence similarity they may function
together as an ATP-dependent spermidine/
putrecine transporter. The genes ydcS,
ydcT, ydcU, and ydcV are
probably located in a single operon.")
(COMMON-NAME "YdcS/YdcT/YdcV/YdcU ABC transporter")
(COMPONENTS YDCS-MONOMER YDCT-MONOMER YDCV-MONOMER YDCU-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146929082) )
((COMPONENTS YDCU-MONOMER COEFFICIENT 1)
(COMPONENTS YDCV-MONOMER COEFFICIENT 1)
(COMPONENTS YDCT-MONOMER COEFFICIENT 2)
(COMPONENTS YDCS-MONOMER COEFFICIENT 1)))
(ABC-52-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059948342)
(COMMON-NAME "YhdW/YhdX/YhdY/YhdZ ABC transporter")
(COMMENT "YhdZ, YhdY, YhdX and YhdW are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YhdZ is the putative ATP binding component, YhdY and YhdX
are membrane components, and YhdW is the putative binding
protein. Based on sequence similarity they probably
function together as an ATP-dependent amino acid transporter.
The genes yhdZ, yhdY, yhdX, and yhdW
probably constitute a single operon.")
(COMPONENTS YHDZ-MONOMER YHDY-MONOMER YHDX-MONOMER YHDW-MONOMER) )
((COMPONENTS YHDW-MONOMER COEFFICIENT 1)
(COMPONENTS YHDX-MONOMER COEFFICIENT 1)
(COMPONENTS YHDY-MONOMER COEFFICIENT 1)
(COMPONENTS YHDZ-MONOMER COEFFICIENT 2)))
(ABC-53-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS "99091701:EV-COMP-HINF-FN-FROM-SEQ:3343134925:djohnson")
(:CREATION-DATE 3059948342)
(COMMON-NAME "YhbG/YhbN ABC transporter")
(COMMENT "YhbG and YhbN are uncharacterized members of the
ABC superfamily of transporters |CITS: [99091701]|.
YhbG is the putative ATP binding component. YhbN is
the putative periplasmic binding protein. No membrane
protein has yet been identified. Based on sequence
similarity these proteins may function together as an
ATP-dependet uptake system. The genes yhbG and
yhbN are probably located in a single operon.
Random transposition mutagenesis showed yhbN and yhbG are essential genes
|CITS:[15380559]|.")
(COMPONENTS YHBN-MONOMER YHBG-MONOMER) )
((COMPONENTS YHBN-MONOMER COEFFICIENT 1)
(COMPONENTS YHBG-MONOMER COEFFICIENT 2)))
(ABC-54-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS "14729705:EV-EXP-IMP:3311017802:keseler")
(LOCATIONS CCO-PM-BAC-NEG)
(:CREATION-DATE 3059948342)
(COMMON-NAME "FtsE/FtsX ABC transporter")
(COMMENT
"FtsE and FtsX are members of the ABC superfamily of transporters |CITS: [99091701]|. FtsE is the putative
ATP-binding protein and FtsX is the putative membrane component. ftsE and ftsX were originally
identified as conditional lethal mutants which failed to septate at the non-permissive temperature, implying
a role in cell division |CITS: [88169472]|. FtsE and FtsX have been purified and shown to interact by
co-immunoprecipitation |CITS: [99157600]|. The FtsEX complex probably functions as an ATP-dependent
transporter which has a role in cell division and possibly salt transport.")
(COMPONENTS FTSE-MONOMER FTSX-MONOMER) )
((LOCATIONS CCO-PM-BAC-NEG CITATIONS "10048040")
(COMPONENTS FTSX-MONOMER COEFFICIENT 2)
(COMPONENTS FTSE-MONOMER COEFFICIENT 2)))
(ABC-55-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YcjO, YcjP and YcjN are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YcjO and YcjP are the putative membrane components,
YcjN is the putative periplasmic binding protein.
No ATP-binding component has yet been identified.
Based on sequence similarity, these proteins may
function together as an ATP-dependent sugar
transporter. The genes ycjO, ycjP,
ycjN are probably located in a single operon.")
(COMMON-NAME "YcjN/YcjO/YcjP ABC transporter")
(COMPONENTS YCJP-MONOMER YCJO-MONOMER YCJN-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146934785) )
((COMPONENTS YCJN-MONOMER COEFFICIENT 1)
(COMPONENTS YCJO-MONOMER COEFFICIENT 1)
(COMPONENTS YCJP-MONOMER COEFFICIENT 1)))
(ABC-56-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"Deletion mutation studies |CITS:[10506196]| indicate that the ssuEADCB gene cluster codes for proteins that enable Escherichia coli
to utilize sulfonates other than taurine as a sulfur source. Based on sequence similarity SsuABC is the ABC type transport system with
SsuA being the periplasmic substrate-binding subunit, SsuB the ATP-binding subunit and SsuC the permease. ssuD and
ssuE encode an FMNH2-dependent monooxygenase and an NAD(P)H-dependent FMN reductase, respectively.")
(COMMON-NAME "YcbE/YcbM ABC transporter")
(COMPONENTS G6478-MONOMER YCBM-MONOMER YCBE-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146937623) )
((COMPONENTS YCBE-MONOMER COEFFICIENT 2)
(COMPONENTS YCBM-MONOMER COEFFICIENT 2)))
(ABC-57-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YbhF, YbhR and YbhS are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YbhF is the putative ATP binding component, YbhR and
YbhS are the putative membrane components. Based on
sequence similarity, these proteins probably function
together as an ATP-dependent efflux pump. The genes
ybhF, ybhR, and ybhS are probably
located in a single operon.")
(COMMON-NAME "YbhF/YbhR/YbhS ABC transporter")
(COMPONENTS YBHS-MONOMER YBHR-MONOMER YBHF-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146942621) )
((COMPONENTS YBHF-MONOMER COEFFICIENT 2)
(COMPONENTS YBHR-MONOMER COEFFICIENT 1)
(COMPONENTS YBHS-MONOMER COEFFICIENT 1)))
(ABC-58-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS "99091701:EV-COMP-HINF-FN-FROM-SEQ:3343135118:djohnson")
(COMMENT "YdeX, YdeY, YdeZ and YneA are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YdeX is the putative ATP-binding component. YdeY and
YdeZ are putative membrane components. YneA is the
putative periplasmic binding component. Based on
sequence similarity, these proteins probably function
together as an ATP-dependent sugar transporter. The
genes ydeX, ydeY, ydeZ, and
yneA are probably located in a single operon.
YdeX was found, in random transposon mutagenesis studies, to be required for growth in optimum (rich
medium at 37 degrees C) growth conditions but not under cold conditions (15 degrees C) or in minimal
medium |CITS:[15380559]|.")
(COMMON-NAME "YdeX/YdeY/YdeZ/YneA ABC transporter")
(COMPONENTS YNEA-MONOMER YDEZ-MONOMER YDEY-MONOMER YDEX-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3146945007) )
((COMPONENTS YDEX-MONOMER COEFFICIENT 2)
(COMPONENTS YDEY-MONOMER COEFFICIENT 1)
(COMPONENTS YDEZ-MONOMER COEFFICIENT 1)
(COMPONENTS YNEA-MONOMER COEFFICIENT 1)))
(ABC-59-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YddO, YddP, YddQ, YddR and YddS are uncharacterized
members of the ABC superfamily of transporters |CITS: [99091701]|.
YddO and YddP are the putative ATP-binding proteins.
YddQ and YddR are the putative membrane components.
YddS is the putativeperiplasmic binding protein.
Based on sequence similarity, these proteins probably
function together as an ATP-dependent peptide transporter.
The genes yddO, yddP, yddQ, yddR,
and yddS are probably located within a single
operon.")
(COMMON-NAME "YddO/YddP/YddQ/YddR/YddS ABC transporter")
(COMPONENTS YDDR-MONOMER YDDQ-MONOMER YDDS-MONOMER YDDP-MONOMER YDDO-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3147542908) )
((COMPONENTS YDDO-MONOMER COEFFICIENT 1)
(COMPONENTS YDDP-MONOMER COEFFICIENT 1)
(COMPONENTS YDDS-MONOMER COEFFICIENT 1)
(COMPONENTS YDDQ-MONOMER COEFFICIENT 1)
(COMPONENTS YDDR-MONOMER COEFFICIENT 1)))
(ABC-6-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME "cydDC glutathione ABC transporter")
(CATALYZES ENZRXN0-4 ENZRXN0-23)
(:CREATION-DATE 3059864719)
(COMMENT
"The cydDC operon encodes two ATP-binding cassette (ABC) transporter proteins that are most
closely similar to
ABC transporters involved in export |CITS:[98254124]|. Deletion studies have shown that both of these
proteins are essential
for functional cytochrome bd and cytochrome c |CITS:[87194595], [94237457]|. Transport
assays of the heterodimeric CydDC ABC transporter show that it is responsible for transport of glutathione
|CITS:[16040611]| and, to a lesser extent, cysteine from the cytoplasm to the periplasmic space
|CITS:[15470119]|, |CITS:[16040611]|. CydDC is important for maintenance of the optimum redox balance in
the periplasm. Exogenous glutathione or cysteine has been shown to rescue cydC mutants from
temperature-sensitive and survival phenotypes |CITS:[16040611]|. Both CydD and CydC have been
shown experimentally to have six-transmembrane segments, three minor periplasmic loops, and two major
cytoplasmic loops |CITS:[15470119]|.")
(COMPONENTS CYDD-MONOMER CYDC-MONOMER) )
((COMPONENTS CYDC-MONOMER COEFFICIENT 2)
(COMPONENTS CYDD-MONOMER COEFFICIENT 2)))
(ABC-60-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(SPECIES ECOLI)
(COMMENT "YphE, YphD and YphF are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|.
YphE is the putative ATP-binding component. YphD is the
putative membrane component. YphF is the putative
periplasmic binding component. Based on sequence
similarity, these proteins probably function together
as an ATP-dependent sugar transporter. The yphE,
yphD, and yphF genes are probably located
in a single operon.")
(COMMON-NAME "YphD/YphE/YphF ABC transporter")
(COMPONENTS YPHD-MONOMER G7342-MONOMER YPHE-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3148655478) )
((COMPONENTS YPHE-MONOMER COEFFICIENT 2)
(COMPONENTS YPHF-MONOMER COEFFICIENT 1)
(COMPONENTS YPHD-MONOMER COEFFICIENT 2)))
(ABC-61-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "YbbA and YbbP are uncharacterized members
of the ABC superfamily of transporters |CITS: [99091701]|. YbbA is the putative
ATP binding component. YbbP may be the membrane
component. Based on sequence similarity, these
proteins may work together as part of an ATP
dependent metabolite uptake system. The genes
ybbA, and ybbP are probably located
within a single operon.")
(COMMON-NAME "YbbA/YbbP ABC transporter")
(COMPONENTS YBBP-MONOMER YBBA-MONOMER)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3148660780) )
((COMPONENTS YBBA-MONOMER COEFFICIENT 2)
(COMPONENTS YBBP-MONOMER COEFFICIENT 2)))
(ABC-62-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"Localization of lipoproteins to the periplasmic surface of the outer membrane in Escherichia coli requires a lipoprotein-specific sorting complex, made up of five proteins (LolABCDE) |CITS:[15221203]|.
Lipoproteins in E.coli, as well as in other bacteria, are membrane proteins that have covalently-attached lipids at their amino-terminal cysteine residue. Within the bacterial envelope of E. coli there are more than 90 species of lipoproteins, located on the periplasmic surfaces of both the inner and outer membrane, and responsible for a variety of functions. |CITS:[15221203]|.
All lipoproteins are thought to be synthesized with an N-terminal signal sequence which allows for their targeting to the Sec secretion system and subsequent translocation across the cytoplasmic membrane |CITS:[9393850]|. After translocation across the cytoplasmic membrane, the signal peptide sequence is cleaved by lipoprotein-specific signal peptidase II followed by aminoacylation of the terminal cysteine residue |CITS:[8096622]|. The mature form of the lipoprotein is then localized to either the inner or outer membrane. If the amino-acid residue next to the terminal cysteine is aspartate, then the lipoprotein is localized to the inner membrane. In all other cases, the lipoprotein is targeted for translocation across the periplasmic space to the outer membrane |CITS:[3284654]|.
LolA is a periplasmic proteinous factor which serves as a hydrophobic container, allowing for lipoproteins to become solubilized, thereby facilitating their translocation across the hydrophilic periplasmic space |CITS:[12839983]|. LolB is an outer membrane receptor for the LolA-lipoprotein complex |CITS:[10521496]|. LolCDE is a unique ABC transporter involved in the export of lipoproteins to the outer membrane |CITS:[10783239]|. Sequence analysis indicates that LolC and LolE are integral membrane proteins and LolD is an ABC ATPase. LolCDE has been shown to be capable of utilizing ATP, GTP or UTP in the release process |CITS:[9829994]|, |CITS:[1078329]|.")
(COMPONENTS YCFW-MONOMER YCFV-MONOMER YCFU-MONOMER)
(COMMON-NAME "LolCDE ABC lipoprotein transporter")
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3152305305) )
((COMPONENTS YCFU-MONOMER COEFFICIENT 1)
(COMPONENTS YCFV-MONOMER COEFFICIENT 2)
(COMPONENTS YCFW-MONOMER COEFFICIENT 1)))
(ABC-63-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS ":EV-EXP:3279377970:pkarp")
(CATALYZES ABC-63-ENZRXN)
(COMMON-NAME "ZnuA/ZnuB/ZnuC ABC transporter")
(COMMENT "ZnuABC is a high-affinity zinc uptake system that is a member
of the ATP Binding Cassette (ABC) Superfamily |CITS: [96381453]|.
znuA encodes the periplasmic zinc-binding component
of the transporter, while znuB encodes the membrane
component, and znuC encodes the ATPase subunit.
Complementation analysis of znu mutants showed that
transport of zinc (II) ion was restored in the presence of
znuABC cloned on a low-copy-number vector |CITS: [98343803]|.
The three components of ZnuABC also show high nucleotide
sequence similarity to the corresponding components of the
AdcABC zinc transporter of S. pneumoniae as well as
subunits of other ABC metal ion transporters. The high-affinity
transport of zinc ion by ZnuABC is inhibited by arsenate,
suggesting that ZnuABC-mediated transport is energized by
ATP hydrolysis |CITS: [98343803]|. Analysis of LacZ fusions indicated that
expression of znuA and znuB was regulated by
the protein Zur, which has amino acid sequence similarity to
the iron regulator Fur |CITS: [98343803]|. znuA and znuBC
are transcribed divergently |CITS: [98343803]|.")
(COMPONENTS ZNUC-MONOMER ZNUB-MONOMER ZNUA-MONOMER)
(:CREATOR |jchen|)
(:CREATION-DATE 3192192241) )
((COMPONENTS ZNUB-MONOMER COEFFICIENT 2)
(COMPONENTS ZNUC-MONOMER COEFFICIENT 2)
(COMPONENTS ZNUA-MONOMER COEFFICIENT 1)))
(ABC-63-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279994314:mhance"
"98343803:EV-EXP-IMP-REACTION-BLOCKED:3279994314:mhance")
(REACTION ABC-63-RXN)
(ENZYME ABC-63-CPLX)
(:CREATOR |jchen|)
(:CREATION-DATE 3192200835) )
NIL)
(ABC-63-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(RIGHT ZN+2 ADP |Pi|)
(LEFT ZN+2 WATER ATP)
(ENZYMATIC-REACTION ABC-63-ENZRXN)
(:CREATOR |jchen|)
(:CREATION-DATE 3192201113) )
((LEFT ZN+2 COMPARTMENT CCO-PERI-BAC)))
(ABC-64-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ABC-64-ENZRXN)
(COMMENT "The TauABC transporter belongs to the ATP Binding Cassette (ABC)
superfamily |CITS: [96381453]|, and is believed to be responsible for taurine uptake
in E. coli |CITS: [96404792]|. E. coli rely on organosulfur compounds
such as taurine as sources of sulfur when the level of inorganic sulfate
available in the invironment is low |CITS: [96404792]|. Disruption of the tauABC
genes resulted in the loss of the ability to utilize taurine
(2-aminoethanesulfonate) as a source of sulfur but did not affect the
utilization of a range of other aliphatic sulfonates as sulfur sources.
Taurine utilization was restored when the tauABC mutants
were complemented with a clone of the tauABC locus |CITS: [96404792]|. TauA
contains a N-terminal signal sequence, indicating that it is probably
located in the periplasm, and therefore may function as the substrate
binding component of the ABC transporter |CITS: [96404792]|. TauC is the membrane
component of the TauABC taurine ABC transporter |CITS:[8808933]|. Membrane topology
predictions using experimentally determined C terminus locations indicate that TauC has
6 transmembrane helices and the C-terminus is located in the cytoplasm |CITS:[15044727]|
TauB and TauC show strong sequence similarities to ATP-binding components and
membrane components, respectively, of other members of the ABC
superfamily |CITS: [96404792]|. Expression of tauABC is induced by sulfate
starvation, and analysis of LacZ fusions showed that the tauABC
operon is repressed by the presence of sulfur containing compounds, such as sulfate,
cysteine, cystine, ethanesulfonate, and lanthionine |CITS: [96404792]|.")
(COMMON-NAME "TauA/TauB/TauC ABC transporter")
(COMPONENTS TAUA-MONOMER TAUC-MONOMER TAUB-MONOMER)
(:CREATOR |jchen|)
(:CREATION-DATE 3192195678) )
((COMPONENTS TAUB-MONOMER COEFFICIENT 2)
(COMPONENTS TAUC-MONOMER COEFFICIENT 2)
(COMPONENTS TAUA-MONOMER COEFFICIENT 1)))
(ABC-64-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279982550:mhance"
"96404792:EV-EXP-IMP-REACTION-BLOCKED:3276610213:ipaulsen"
"96404792:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279982550:mhance")
(REACTION ABC-64-RXN)
(ENZYME ABC-64-CPLX)
(:CREATOR |jchen|)
(:CREATION-DATE 3192200884) )
NIL)
(ABC-64-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION ABC-64-ENZRXN)
(RIGHT TAURINE ADP |Pi|)
(LEFT TAURINE ATP WATER)
(:CREATOR |jchen|)
(:CREATION-DATE 3192201146) )
((LEFT TAURINE COMPARTMENT CCO-PERI-BAC)))
(ABC-7-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(COMMENT
"CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily of
transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component; CysT
and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component, and
Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.")
(CATALYZES ABC-7-ENZRXN)
(COMMON-NAME "thiosulfate ABC transporter")
(COMPONENTS CYSA-MONOMER CYSW-MONOMER CYST-MONOMER CYSP-MONOMER) )
((COMPONENTS CYSP-MONOMER COEFFICIENT 1)
(COMPONENTS CYST-MONOMER COEFFICIENT 1)
(COMPONENTS CYSW-MONOMER COEFFICIENT 1)
(COMPONENTS CYSA-MONOMER COEFFICIENT 2)))
(ABC-7-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "95332222:EV-COMP-HINF-FN-FROM-SEQ:3279982888:mhance"
"95332222:EV-EXP-IMP-REACTION-BLOCKED:3276615645:ipaulsen"
"95332222:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279982888:mhance")
(:CREATION-DATE 3059948758)
(ENZYME ABC-7-CPLX)
(REACTION ABC-70-RXN ABC-7-RXN) )
NIL)
(ABC-7-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| S2O3)
(LEFT ATP S2O3 WATER)
(ENZYMATIC-REACTION ABC-70-ENZRXN ABC-7-ENZRXN) )
((LEFT S2O3 COMPARTMENT CCO-PERI-BAC)))
(ABC-70-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ABC-70-ENZRXN)
(COMMON-NAME "sulfate ABC transporter")
(COMMENT
"CysATWP-Sbp is a sulfate transporter that is a member of the ATP-Binding Cassette (ABC) Superfamily
of transporters |CITS: [96381453]|. Based on sequence similarity, CysA is the ATP-binding component;
CysT and CysW are the membrane components, CysP is the periplasmic thiosulfate-binding component,
and Sbp is the periplasmic sulfate-binding component of the ABC transporter |CITS: [90264334] [95332222]|.
Single cysP and spb insertional mutants are able to utilized both sulfate and thiosulfate as a
sole sulfur source; however, both mutants have impaired growth compared with the wild-type strain,
suggesting that both proteins are required for the normal transport of these ions |CITS: [95332222]|. The
inactivation of both cysP and spb genes blocks the transport of both sulfate and thiosulfate,
and the transport activity is restored by the presence of intact copies of either the cysP or sbp
gene |CITS:[95332222]|. These results indicate that the two binding proteins have partially overlapping
activities, and that a single mutation, inactivating only one of them does not completely inactivate
thiosulfate and sulfate uptake. CysP and Sbp are therefore an example of periplasmic binding proteins
having overlapping activities and interacting with the common membrane proteins, CysATW.")
(COMPONENTS SBP-MONOMER CYSW-MONOMER CYST-MONOMER CYSA-MONOMER)
(:CREATOR |jchen|)
(:CREATION-DATE 3200844910) )
((COMPONENTS CYSA-MONOMER COEFFICIENT 2)
(COMPONENTS CYST-MONOMER COEFFICIENT 1)
(COMPONENTS CYSW-MONOMER COEFFICIENT 1)
(COMPONENTS SBP-MONOMER COEFFICIENT 1)))
(ABC-70-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "9533222:EV-COMP-HINF-FN-FROM-SEQ:3279982461:mhance"
"9533222:EV-EXP-IMP-REACTION-BLOCKED:3276615936:ipaulsen"
"95332222:EV-EXP-IGI-FUNC-COMPLEMENTATION:3279982461:mhance")
(ENZYME ABC-70-CPLX)
(REACTION ABC-7-RXN ABC-70-RXN)
(:CREATOR |jchen|)
(:CREATION-DATE 3200845353) )
NIL)
(ABC-70-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(RIGHT SULFATE |Pi| ADP)
(LEFT SULFATE WATER ATP)
(ENZYMATIC-REACTION ABC-7-ENZRXN ABC-70-ENZRXN)
(:CREATOR |jchen|)
(:CREATION-DATE 3200845384) )
((LEFT SULFATE COMPARTMENT CCO-PERI-BAC)))
(ABC-8-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3059864719)
(COMMENT
"The DppABCDF dipeptide transport system is a member of the ATP-Binding Cassette (ABC)
Superfamily of transporters |CITS: [96381453]|. Based on sequence similarity, DppA is the substrate-binding
component, while DppB and DppC are the membrane components, and DppD and DppF are the
ATP-binding components of the ABC transporter. Mutations in dpp displayed resistance to the toxic
dipeptide Lys-aminoxyAla, and the loss of ability to utilize LeuTrp as a source of its required amino acids
|CITS: [85056880]|. Substrate specificity of DppA was studied in a filter binding assay in which column
fractions were monitored for binding activity towards radioactively labeled dipeptides and tripeptides. DppA
was observed to mediate the ATP-driven uptake of dipeptides and, to a lesser extent, tripeptides from the
periplasm |CITS: [20005603]|. DppABCDF is similar in sequence and subunit composition to the oligopeptide
uptake system OppABCDF, suggesting similar subunit functions. DppA?s unbound structure has been
resolved by x-ray crystallography to 2 angstroms, and shows two domains connected by two ?hinge? segments
|CITS: [9618375]|.
")
(CATALYZES ABC-8-ENZRXN)
(COMMON-NAME "dipeptide ABC transporter")
(COMPONENTS DPPD-MONOMER DPPF-MONOMER DPPB-MONOMER DPPC-MONOMER DPPA-MONOMER) )
((COMPONENTS DPPA-MONOMER COEFFICIENT 1)
(COMPONENTS DPPC-MONOMER COEFFICIENT 1)
(COMPONENTS DPPB-MONOMER COEFFICIENT 1)
(COMPONENTS DPPF-MONOMER COEFFICIENT 1)
(COMPONENTS DPPD-MONOMER COEFFICIENT 1)))
(ABC-8-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "96381453:EV-COMP-HINF-FN-FROM-SEQ:3279557212:mhance"
"85056880:EV-EXP-IMP-REACTION-BLOCKED:3277473410:ipaulsen"
"20005603:EV-EXP-IDA-PURIFIED-PROTEIN:3277473410:ipaulsen")
(:CREATION-DATE 3059948758)
(ENZYME ABC-8-CPLX)
(REACTION ABC-8-RXN) )
NIL)
(ABC-8-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| DIPEPTIDES)
(LEFT ATP DIPEPTIDES WATER)
(ENZYMATIC-REACTION ABC-8-ENZRXN) )
((LEFT DIPEPTIDES COMPARTMENT CCO-PERI-BAC)))
(ABC-9-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CPLX0-2001)
(:CREATION-DATE 3059864719)
(COMMENT
"FecBCDE is an ATP Binding Cassette (ABC) citrate-dependent iron (III) transport system. Sequence
homology and hydropathy analyses indicate that FecB is the periplasmic binding protein, FecC and FecD
are integral membrane proteins and FecE is the ATP-binding protein |CITS: [88227855]|. Mutation and
induction studies indicate that exogenous ferric citrate induces the expression of fec transport genes
through a signaling mechanism which does not require ferric citrate to enter the cytoplasm |CITS: [82004187]|.
|CITS:[81116964]|, or to cross the outer membrane into the periplasmic space |CITS: [95246736]|. Rather,
induction of fec transport genes is a function of FecA-ferric citrate binding and is coupled through
the TonB, ExbB and ExbD proteins independent of their role in uptake |CITS:[95246736]|.")
(CATALYZES ABC-9-ENZRXN)
(COMMON-NAME "iron dicitrate ABC transporter")
(COMPONENTS FECE-MONOMER FECC-MONOMER FECD-MONOMER FECB-MONOMER) )
((COMPONENTS FECB-MONOMER COEFFICIENT 1)
(COMPONENTS FECD-MONOMER COEFFICIENT 1)
(COMPONENTS FECC-MONOMER COEFFICIENT 1)
(COMPONENTS FECE-MONOMER COEFFICIENT 2)))
(ABC-9-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "88227855:EV-COMP-HINF-FN-FROM-SEQ:3279562387:mhance"
"81116964:EV-EXP-IMP-REACTION-BLOCKED:3277470852:ipaulsen")
(:CREATION-DATE 3059948758)
(ENZYME ABC-9-CPLX)
(REACTION ABC-9-RXN) )
NIL)
(ABC-9-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059948758)
(RIGHT ADP |Pi| FERRIC-CITRATE-COMPLEX)
(LEFT ATP FERRIC-CITRATE-COMPLEX WATER)
(ENZYMATIC-REACTION ABC-9-ENZRXN) )
((RIGHT FERRIC-CITRATE-COMPLEX COMPARTMENT CCO-CYTOSOL)
(LEFT FERRIC-CITRATE-COMPLEX COMPARTMENT CCO-PERI-BAC)))
(ABC-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-3)
(MOLECULAR-WEIGHT-SEQ 37.78831699999996d0)
(:CREATION-DATE 3059864719)
(COMMENT "ATP binding component of ABC transporter")
(SYNONYMS "B0199" "MetD" "MetN" "Abc")
(DBLINKS (MODBASE "P30750" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P30750" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00005" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414741" NIL NIL NIL NIL NIL)
(UNIPROT "P30750" NIL |pkarp| 3064869797))
(COMPONENT-OF METNIQ-METHIONINE-ABC-CPLX)
(GENE EG11621)
(LOCATIONS CCO-CYTOPLASM)
(COMMON-NAME "MetN") )
NIL)
(ABGT-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-74)
(MOLECULAR-WEIGHT-SEQ 54.88576099999981d0)
(:CREATION-DATE 3143232834)
(DBLINKS (PFAM "PF03806" IN-FAMILY |pkarp| 3346700332 NIL NIL)
(ECOO157CYC "Z2431-MONOMER" |Homolog| |pick| 3278712111 NIL NIL)
(ECOO157CYC "Z2428-MONOMER" |Homolog| |pick| 3278712111 NIL NIL)
(REFSEQ "NP_415852" NIL NIL NIL NIL NIL)
(UNIPROT "P46133" NIL |paley| 3169408120))
(SYNONYMS "B1336" "YdaH" "AbgT")
(COMMON-NAME "AbgT Transporter")
(COMMENT
"The AbgT protein is a possible p-aminobenzoyl-glutamate transporter.
Overexpression of the abgT gene enables the utilisation of
p-aminobenzoyl-glutamate as a source of p-aminobenzoate, a precursor
in the synthesis of folic acid |CITS: [99047572]|. AbgT has twelve
predicted TMS and is the prototype member of the AbgT family of putative
transporters. The abgT gene is located in a probable operon with
abgAB which code for amino acid hydrolase homologues.
")
(GENE EG12853) )
NIL)
(ABSOLUTE-PLUS-1-POS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3199046812)
(:VALUE-TYPE :INTEGER)
(QUERYABLE? T)
(UNITS BASE-PAIRS)
(:DOCUMENTATION
"The absolute base pair position of the promoter on the DNA strand")
(:CARDINALITY 1)
(:DOMAIN |Promoters|) )
NIL)
(ABSTRACT NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION "The text of the abstract of the publication.")
(:DOMAIN |Publications|)
(:VALUE-TYPE :STRING) )
NIL)
(ACCCT1 NIL (
(OCELOT-GFP::PARENTS |Rho-Independent-Terminators|)
(COMPONENT-OF TU00231)
(CITATIONS "8226664")
(RIGHT-END-POSITION 3405324)
(LEFT-END-POSITION 3405308)
(:CREATOR |sgama|)
(:CREATION-DATE 3357419124) )
NIL)
(|Acceptor| T (
(OCELOT-GFP::PARENTS |Redox-Electron-Carriers|)
(MOLECULAR-WEIGHT 0.0d0)
(APPEARS-IN-LEFT-SIDE-OF RXN0-4141 RXN0-2301 RXN0-2101
HYDROXYLAMINE-REDUCTASE-RXN CYT-ACC-RXN RXN0-1
|MALATE-DEHYDROGENASE-(ACCEPTOR)-RXN| |NADPH-DEHYDROGENASE-(QUINONE)-RXN|
DAADEHYDROG-RXN GLYCOLATEDEHYDRO-RXN CHD-RXN)
(SCHEMA? T)
(APPEARS-IN-RIGHT-SIDE-OF SELENOCYSTEINE-LYASE-RXN PEROXID-RXN
CROBETREDUCT-RXN THTOREDUCT-RXN)
(SYNONYMS "an oxidized electron acceptor" "an oxidized donor" "A")
(:CREATION-DATE 3051978518)
(:CREATOR |kr|)
(COMMON-NAME "an acceptor") )
NIL)
(ACECITLY-CPLX NIL (
(OCELOT-GFP::PARENTS CITRATE-LYASE)
(:CREATION-DATE 3103560039)
(CATALYZES CITLY-ENZRXN CITTRANS-ENZRXN CITRYLY-ENZRXN)
(SYNONYMS "citrate lyase, active" "acetyl-citrate lyase")
(COMMON-NAME "citrate lyase")
(UNMODIFIED-FORM CITLY-CPLX) )
NIL)
(ACECOATRANS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "E. coli is able to utilize various fatty acids for growth
through the action of acetate CoA-transferase. The enzyme has not
been characterized and its genetics are unknown. |CITS: [69091052]|")
(REACTION ACECOATRANS-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/monday/acecoa.template")
(ENZYME ACECOATRANS-MONOMER)
(:CREATION-DATE 3041598718)
(COMMON-NAME "acetate CoA-transferase")
(SYNONYMS "acyl-CoA:acetate CoA-transferase")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(ACECOATRANS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT "Thre is no gene associated with this enzyme yet. The
subunit structure is unknown.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/monday/acecoa.template")
(CATALYZES ACECOATRANS-ENZRXN)
(:CREATION-DATE 3041598718) )
NIL)
(ACECOATRANS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.8.3)
(BALANCE-STATE :UNBALANCED-DIFFERING-R-GROUPS)
(OFFICIAL-EC? T)
(COMMENT "This reaction functions as an activiating mechanism allowing
fatty acids to function as carbon sources for growth. In catabolism
of fatty acids, the fatty acids are first activated with CoA.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/monday/acecoa.template")
(ENZYMATIC-REACTION ENZRXN0-2778 ENZRXN0-2777 ENZRXN0-2776 ACECOATRANS-ENZRXN)
(EC-NUMBER "2.8.3.8")
(:CREATION-DATE 3041598718)
(LEFT ACYL-COA ACET)
(RIGHT |a fatty acid| ACETYL-COA) )
NIL)
(ACEF-DIHYDROLIPOATE NIL (
(OCELOT-GFP::PARENTS |Pyruvate-E2|)
(MOLECULAR-WEIGHT-SEQ 66.09597599999962d0)
(DBLINKS (MODBASE "P06959" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P06959" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P06959" NIL |pick| NIL NIL NIL))
(SYNONYMS "B0115" "AceF")
(GENE EG10025)
(UNMODIFIED-FORM |lipoate-acetyltransferase|)
(COMMON-NAME "AceF-dihydrolipoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3260640985) )
NIL)
(ACEF-LIPOATE NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 66.09597599999962d0)
(DBLINKS (MODBASE "P06959" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P06959" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "3 of PF00364" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(UNIPROT "P06959" NIL |pick| 3277847086)
(REFSEQ "NP_414657" NIL NIL NIL NIL NIL))
(SYNONYMS "B0115" "AceF")
(GENE EG10025)
(UNMODIFIED-FORM |lipoate-acetyltransferase|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1139 RXN0-1130)
(COMMON-NAME "AceF-lipoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3260638393) )
NIL)
(ACEF-S-ACETYLDIHYDROLIPOATE NIL (
(OCELOT-GFP::PARENTS |Pyruvate-E2|)
(MOLECULAR-WEIGHT-SEQ 66.09597599999962d0)
(DBLINKS (MODBASE "P06959" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P06959" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P06959" NIL |pick| NIL NIL NIL))
(SYNONYMS "B0115" "AceF")
(GENE EG10025)
(UNMODIFIED-FORM |lipoate-acetyltransferase|)
(COMMON-NAME "AceF-S-acetyldihydrolipoate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3260641179) )
NIL)
(ACEKINC-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "98143432:EV-EXP:3284158212:arnaud"
"12952533:EV-COMP-HINF-FN-FROM-SEQ:3284158212:arnaud")
(:CREATION-DATE 3123853859)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETATEKIN-RXN)
(ENZYME PROPKIN-MONOMER)
(COMMENT
"The tdcD gene encodes a protein with acetate and propionate kinase activity. The tdcD protein is highly similar to
the ackA encoded acetate kinase. Propionate kinase is the major activity of the tdcD protein. |CITS: [98143432]|
Based on sequence similarity, TdcD is predicted to be an acetate kinase |CITS: [12952533]|.")
(SYNONYMS "acetokinase" "ATP:acetate phosphotransferase")
(COMMON-NAME "acetate kinase C") )
NIL)
(ACET NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF KDGALDOL-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ACETYLORNDEACET-ENZRXN NAG6PDEACET-ENZRXN
CYANLY-ENZRXN ALDOSE1EPIM-ENZRXN)
(DBLINKS (CAS "64-19-7" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C00033" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "c00033" NIL |kawakami| 3278885083 NIL NIL) (CAS "71-50-1"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -87.7d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-3962 ACETYLESTERASE-RXN RXN0-1981
PYRUVOXID-RXN CITTRANS-RXN CITLY-RXN NAG6PDEACET-RXN
UDPACYLGLCNACDEACETYL-RXN ACETOACETYL-COA-TRANSFER-RXN ACETYLORNDEACET-RXN
ACSERLY-RXN CYSSYNMULTI-RXN)
(APPEARS-IN-LEFT-SIDE-OF CITC-RXN RXN0-1981 ACECOATRANS-RXN ACETATEKIN-RXN
ACETATE--COA-LIGASE-RXN)
(MOLECULAR-WEIGHT 59.044d0)
(CHEMICAL-FORMULA (C 2) (H 3) (O 2))
(DISPLAY-COORDS-2D (0.1505d0 0.0d0) (0.71906d0 -1.0d0) (0.7291d0 0.99666d0)
(-1.0d0 0.0d0))
(STRUCTURE-BONDS (4 1 2) (3 1 1) (2 1 1))
(STRUCTURE-ATOMS C C O O)
(COMMON-NAME "acetate")
(CHARGE -1)
(SYNONYMS "acet" "acetic acid" "ethanoic acid")
(ATOM-CHARGES (3 -1)) )
((GIBBS-0 -87.7d0 CITATIONS "GibbsGroups97")))
(ACETALD NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF 4OH2OXOGLUTARALDOL-ENZRXN)
(DBLINKS (LIGAND-CPD "C00084" NIL |kr| 3346617701 NIL NIL)
(UM-BBD-CPD "c0160" NIL |kawakami| 3278871808 NIL NIL)
(LIGAND-CPD "c00084" NIL |kawakami| 3278871808 NIL NIL) (CAS "75-07-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -33.5d0)
(APPEARS-IN-LEFT-SIDE-OF RXN0-3962 RXN0-2022 ACETALD-DEHYDROG-RXN
ALCOHOL-DEHYDROG-RXN)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-986 LTAA-RXN MHPELY-RXN ETHAMLY-RXN
DEOXYRIBOSE-P-ALD-RXN)
(MOLECULAR-WEIGHT 44.053d0)
(CHEMICAL-FORMULA (C 2) (H 4) (O 1))
(DISPLAY-COORDS-2D (0.99673d0 0.71242d0) (-0.00327d0 -1.0d0)
(-0.00327d0 0.14706d0) (-1.0d0 0.71242d0))
(STRUCTURE-BONDS (4 3 1) (3 1 2) (2 3 1))
(STRUCTURE-ATOMS O H C C)
(COMMON-NAME "acetaldehyde")
(SYNONYMS "acetic aldehyde" "ethanal" "aldehyde" "ethyl aldehyde") )
((GIBBS-0 -33.5d0 CITATIONS "GibbsGroups97")))
(ACETALD-DEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ALTERNATIVE-SUBSTRATES (ACETALD BUTANAL) (ACETALD CPD-665)
(ACETALD GLYCOLALDEHYDE))
(ACTIVATORS-UNKMECH "3-pyridine-carboxaldehyde adenine dinucleotide"
"THIOLS, SUCH AS 2-MERCAPTOETHANOL OR DITHIOTHREITOL" NAD)
(INHIBITORS-UNKMECH ADENOSINE_DIPHOSPHATE_RIBOSE AMP)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COFACTORS FE+2)
(SYNONYMS "acetaldehyde:NAD+ oxidoreductase (CoA-acetylating)" "ACDH"
"coenzyme A linked aldehyde dehydrogenase")
(COMMON-NAME "acetaldehyde dehydrogenase")
(ENZYME ADHE-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETALD-DEHYDROG-RXN)
(INHIBITORS-COMPETITIVE AMP BENZALDEHYDE)
(COFACTOR-BINDING-COMMENT "There is evidence that the enzyme contains
two distinct NAD+ binding sites, an activator site and a catalytic
site. |CITS: [82113614]|")
(COMMENT "One of three reactions catalyzed by the multifunctional
enzyme coded for by the adhE gene.")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH "3-pyridine-carboxaldehyde adenine dinucleotide"
CITATIONS "[82113614]")
(ACTIVATORS-UNKMECH "THIOLS, SUCH AS 2-MERCAPTOETHANOL OR DITHIOTHREITOL"
CITATIONS "[69038537]" "[82113614]")
(ACTIVATORS-UNKMECH NAD CITATIONS "[82113614]")
(INHIBITORS-UNKMECH ADENOSINE_DIPHOSPHATE_RIBOSE COMMENT
"inhibit the enzyme by competing
for both the NAD+ and CoA binding sites. |CITS: [82113614]|")
(INHIBITORS-UNKMECH AMP COMMENT "inhibit the enzyme by competing
for both the NAD+ and CoA binding sites. |CITS: [82113614]|")
(INHIBITORS-COMPETITIVE AMP COMMENT "with respect to NAD+ under steady
state conditions")
(INHIBITORS-COMPETITIVE BENZALDEHYDE COMMENT "with respect to
acetaldehyde, uncompetitive with respect to NAD+ and CoA")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[82113614]")))
(ACETALD-DEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.2.1)
(DBLINKS (PIR "B55511" NIL |pkarp| 3199817462)
(PIR "DEEC" NIL |pkarp| 3199817462) (PIR "G64762" NIL |pkarp| 3199817462)
(PIR "H70675" NIL |pkarp| 3199817462) (PIR "S24419" NIL |pkarp| 3199817462)
(PIR "S35222" NIL |pkarp| 3199817462) (PIR "S53319" NIL |pkarp| 3199817462)
(PIR "T31270" NIL |pkarp| 3199817462))
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY-5162 FERMENTATION-PWY ETOH-ACETYLCOA-ANA-PWY)
(ENZYMATIC-REACTION MHPF-ENZRXN ACETALD-DEHYDROG-ENZRXN)
(RIGHT NADH ACETYL-COA)
(LEFT NAD CO-A ACETALD)
(EC-NUMBER "1.2.1.10")
(COMMENT "A step in the conversion of acetyl coenzyme-A to ethanol
in the fermentation pathway. The reaction is also the terminal step in the
3-(3-hydroxyphenyl)propionate catabolic pathway.")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
NIL)
(ACETAMIDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF METHYLGLYREDUCT-ENZRXN)
(DBLINKS (LIGAND-CPD "C06244" NIL |kaipa| 3311532630 NIL NIL) (CAS "60-35-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -43.0d0)
(MOLECULAR-WEIGHT 59.068d0)
(CHEMICAL-FORMULA (C 2) (H 5) (N 1) (O 1))
(DISPLAY-COORDS-2D (-0.42762d0 -0.00499d0) (-1.0d0 -1.0d0)
(0.72047d0 -0.00499d0) (-0.98669d0 0.99667d0))
(STRUCTURE-BONDS (4 1 1) (3 1 2) (2 1 1))
(STRUCTURE-ATOMS C C O N)
(COMMON-NAME "acetamide") )
((GIBBS-0 -43.0d0 CITATIONS "GibbsGroups97")))
(ACETATE--COA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS EC-6.2.1 |Small-Molecule-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY ACETATEUTIL-PWY PYRUVOX-PWY)
(ENZYMATIC-REACTION ACS-ENZRXN)
(EC-NUMBER "6.2.1.1")
(RIGHT ACETYL-COA PPI AMP)
(LEFT CO-A ACET ATP) )
NIL)
(ACETATEKIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ACETATEUTIL-PWY FERMENTATION-PWY PYRUVOX-PWY)
(ENZYMATIC-REACTION ACEKINC-ENZRXN GARTSIDE-ENZRXN ACETATEKINA-ENZRXN
ACETATEKINB-ENZRXN)
(RIGHT ACETYL-P ADP)
(LEFT ACET ATP)
(DELTAG0 -3.1d0)
(EC-NUMBER "2.7.2.1")
(COMMENT "Involved in the activation of acetate to acetyl-CoA and
utilization of acetate. During anaerobic growth it is also involved
in the generation of most of the ATP formed catabolically. |CITS:
[SwissProt]|")
(:CREATION-DATE 2976997300)
(:CREATOR |mriley|) )
((DELTAG0 -3.1d0 CITATIONS "[ColiSalII]" "[77181294]")))
(ACETATEKINA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS MG+2)
(SYNONYMS "acetokinase" "ATP:acetate phosphotransferase")
(COMMON-NAME "acetate kinase A")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETATEKIN-RXN)
(COFACTOR-BINDING-COMMENT "A phosphoenzyme intermediate is formed
during the reaction and requires enzyme-bound MgADP for phosphorylation of the
enzyme by acetylphosphate. |CITS: [77028944]|")
(COMMENT "It is unclear whether the two ack genes, ackA and ackB,
code for two distinct acetate kinase enzymes or control a single
enzyme. |CITS: [82100101]| Propanoate also acts as
acceptor, but more slowly. Acetate kinase can also catalyze acetylation of CheY, increasing signal
strength for flagellar rotation. |CITS: [98226742] [98132398]|")
(ENZYME ACETATEKINA-MONOMER)
(:CREATION-DATE 2976997300)
(:CREATOR |mriley|) )
NIL)
(ACETATEKINA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Regulation has been described |CITS: [11350954]|. Transcription is induced by the CreBC two-component system by minimal media growth conditions |CITS: [11350954]|.
")
(SYNONYMS "B2296" "AckA")
(DBLINKS (MODBASE "P0A6A3" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6A3" NIL |pkarp| 3354911363)
(PFAM "PF00871" IN-FAMILY |pkarp| 3346700358 NIL NIL)
(REFSEQ "NP_416799" NIL NIL NIL NIL NIL) (PDB "1LRG"))
(CATALYZES PROPKIN2-ENZRXN ACETATEKINA-ENZRXN)
(ISOZYME-SEQUENCE-SIMILARITY (PROPKIN-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 43.29039199999987d0)
(GENE EG10027)
(:CREATION-DATE 2976997300)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "There is no information yet on
the structure of the gene ackB to know whether or not there is any
sequence similarity with ackA.")))
(ACETATEKINB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(SYNONYMS "acetokinase" "ATP:acetate phosphotransferase")
(COMMON-NAME "acetate kinase B")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETATEKIN-RXN)
(COMMENT "It is unclear whether the two ack genes, ackA and ackB,
code for two distinct acetate kinase enzymes or control a single
enzyme. |CITS: [82100101]| Propanoate also acts as
acceptor, but more slowly. Acetate kinase can also catalyze the
acetylation of CheY, increasing signal strength for flagellar rotation.
|CITS: [98226742]|")
(ENZYME ACETATEKINB-MONOMER)
(:CREATION-DATE 2976997300)
(:CREATOR |mriley|) )
NIL)
(ACETATEKINB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "AckB")
(CATALYZES ACETATEKINB-ENZRXN)
(ISOZYME-SEQUENCE-SIMILARITY)
(NEIDHARDT-SPOT-NUMBER)
(GENE G14)
(COMMENT "There is no information available on the structure of this
gene, ackB. It has only very recently been named.")
(:CREATION-DATE 2976997300)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "There is no information yet on
the structure of the gene ackB to know whether or not there is any
sequence similarity with ackA.")))
(ACETATEUTIL-PWY NIL (
(OCELOT-GFP::PARENTS CARBOXYLATES-DEG)
(CREDITS O0-3 AU0-5)
(LAYOUT-ADVICE (:REVERSIBLE-RXNS ACETATEKIN-RXN PHOSACETYLTRANS-RXN))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(IN-PATHWAY PYRUVOX-PWY)
(SUPER-PATHWAYS PYRUVOX-PWY)
(COMMENT
"Acetate plays multiple roles in the metabolism of E. coli. It can serve as a total source of carbon
and energy. It is excreted into the medium (by a mechanism that is not yet clearly established) as a
major product of the fermentation of sugars. It is also produced and excreted in significant amounts
during aerobic growth on glucose as a carbon source, usually to be utilized later when the source of
glucose is depleted. All these uptakes and excretions of acetate flow through one or the other of the two
parallel pathways shown here.
The ack-pta pathway, which is constitutively expressed, participates the aerobic utilization of
acetate and in its excretion both aerobically and anaerobically.
In contrast the acs pathway is an inducible pathway that plays a major role in the aerobic
utilization of acetate. Mutant strains blocked in the acs pathway grow poorly on acetate. Mutants
blocked in both pathways are unable to grow on acetate. Because it is a high-affinity system, the acs
pathway is the major scavenger of acetate when extracellular concentrations of it are low. It also enables
E. coli to utilize propionate.
Review: Clark, D.P. and John E. Cronan. EcoSal module 3.4.4 |CITS: [ecosal]|
")
(ENZYME-USE (ACETATEKIN-RXN ACETATEKINB-ENZRXN)
(ACETATEKIN-RXN ACETATEKINA-ENZRXN))
(PRIMARIES (ACETATE--COA-LIGASE-RXN (ACET) (ACETYL-COA))
(PHOSACETYLTRANS-RXN (ACETYL-P) (ACETYL-COA)))
(REACTION-LIST ACETATE--COA-LIGASE-RXN PHOSACETYLTRANS-RXN ACETATEKIN-RXN)
(PREDECESSORS (ACETATE--COA-LIGASE-RXN ACETATEKIN-RXN)
(PHOSACETYLTRANS-RXN ACETATEKIN-RXN))
(COMMON-NAME "acetate utilization and formation")
(:CREATION-DATE 3122659905)
(:CREATOR |ptoole|) )
((CREDITS O0-3 REVISED 3358894037) (CREDITS AU0-5 REVISED 3358894037)))
(|Acetic-Esters| T (
(OCELOT-GFP::PARENTS |Esters|)
(APPEARS-IN-LEFT-SIDE-OF ACETYLESTERASE-RXN)
(SYNONYMS "an acetyl ester")
(CHEMICAL-FORMULA (C 2) (H 3) (O 2) (R 1))
(STRUCTURE-BONDS (4 5 1) (3 4 1) (2 5 2) (1 5 1))
(DISPLAY-COORDS-2D (3.6373d0 0.0d0) (2.4248d0 -2.1d0) (0.0d0 -0.7d0)
(1.2124d0 0.0d0) (2.4248d0 -0.7d0))
(STRUCTURE-ATOMS C O R O C)
(COMMON-NAME "an acetic ester")
(:CREATOR |paley|)
(:CREATION-DATE 3324050044) )
NIL)
(ACETOACETATE-DEG-PWY NIL (
(OCELOT-GFP::PARENTS |Fatty-Acid-Degradation|)
(PATHWAY-LINKS (ACETYL-COA TCA))
(CREDITS O0-3 AU0-5)
(COMMENT
"E. coli is able to utilize acetoacetate as a total source of carbon and energy via the two-step
pathway shown here. As end-products, the pathway yields 2 molecules of acetyl-CoA which feed into
central metabolism via the TCA cycle. Use of acetoacetate as a substrate increases the levels of these
two enzymes 200- to 300-fold. |CITS: [4563344]|
Review: Clark, D.P. and John E. Cronan. EcoSal Module 3.4.4 |CITS:[ecosal]|
")
(CITATIONS ":EV-EXP:3277587223:pkarp")
(PRIMARIES (ACETOACETYL-COA-TRANSFER-RXN NIL (ACETOACETYL-COA)))
(REACTION-LIST ACETOACETYL-COA-TRANSFER-RXN ACETYL-COA-ACETYLTRANSFER-RXN)
(PREDECESSORS (ACETYL-COA-ACETYLTRANSFER-RXN ACETOACETYL-COA-TRANSFER-RXN)
(ACETOACETYL-COA-TRANSFER-RXN))
(NET-REACTION-EQUATION "acetoacetate + 2CoA = 2acetyl-CoA")
(COMMON-NAME "acetoacetate degradation")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atopwy.template")
(:CREATION-DATE 3001088687)
(:CREATOR |mriley|) )
((CREDITS O0-3 REVISED 3361751863) (CREDITS AU0-5 REVISED 3361751863)))
(|Acetoacetyl-ACPs| T (
(OCELOT-GFP::PARENTS B-KETOACYL-ACP)
(APPEARS-IN-RIGHT-SIDE-OF 3-OXOACYL-ACP-COA-SYNTHIII-RXN
3-OXOACYL-ACP-SYNTH-BASE-RXN)
(COMMON-NAME "an acetoacetyl-ACP")
(:CREATOR |paley|)
(:CREATION-DATE 3362411292) )
NIL)
(ACETOACETYL-COA NIL (
(OCELOT-GFP::PARENTS 3-KETOACYL-COA)
(INHIBITORS-UNKMECH-OF ACETYL-COA-ACETYLTRANSFER-ENZRXN)
(DBLINKS (LIGAND-CPD "C00332" NIL |kawakami| 3276027507 NIL NIL)
(CAS "1420-36-6"))
(:CREATION-DATE 3073857204)
(SYNONYMS "acetoacetyl-S-CoA")
(SUPERATOMS COA-GROUP)
(GIBBS-0 -173.8d0)
(APPEARS-IN-RIGHT-SIDE-OF ACETYL-COA-ACETYLTRANSFER-RXN
ACETOACETYL-COA-TRANSFER-RXN)
(COMMON-NAME "acetoacetyl-CoA")
(STRUCTURE-ATOMS H H H H C C C N O O O O O O O O O O O O O C C C C C C C C C
N N N N N O O O O O S C C C C C C C C N C C C C C P P P)
(STRUCTURE-BONDS (53 55 1) (53 54 1) (52 55 1) (50 54 1) (49 51 1)
(50 48 :AROMATIC) (48 47 :AROMATIC) (47 46 :AROMATIC) (45 49 1) (41 44 1)
(40 58 1) (40 57 1) (39 56 1) (39 55 1) (38 54 1) (38 52 1) (37 58 1)
(36 57 1) (35 45 1) (34 43 1) (33 48 :AROMATIC) (47 32 :AROMATIC)
(46 31 :AROMATIC) (30 52 1) (30 37 1) (29 51 1) (29 36 1) (28 44 1)
(28 42 1) (27 43 1) (26 41 1) (25 35 1) (25 27 1) (24 34 1) (24 26 1)
(23 50 :AROMATIC) (32 23 :AROMATIC) (22 33 :AROMATIC) (31 22 :AROMATIC)
(21 58 1) (20 57 1) (19 56 1) (18 56 1) (17 53 1) (16 49 1) (15 58 2)
(14 57 2) (13 56 2) (12 45 2) (11 44 2) (10 43 2) (9 42 2) (8 46 1) (7 51 1)
(6 51 1) (5 42 1) (4 55 1) (3 54 1) (2 53 1) (1 52 1))
(DISPLAY-COORDS-2D (11.9159d0 -6.9425d0) (13.9606d0 -6.1852d0)
(14.4654d0 -6.9425d0) (12.4207d0 -6.1852d0) (11.4732d0 -11.137d0)
(3.0543d0 -6.2104d0) (3.0543d0 -3.3833d0) (12.1936d0 0.0d0)
(10.2325d0 -13.1965d0) (2.7766d0 -7.3463d0) (7.8239d0 -13.1012d0)
(1.035d0 -3.3833d0) (12.2441d0 -10.6286d0) (6.8162d0 -3.1814d0)
(9.3404d0 -3.1814d0) (2.0699d0 -6.8162d0) (13.9606d0 -7.9017d0)
(13.6576d0 -12.0421d0) (15.0712d0 -10.6286d0) (6.8162d0 -6.0085d0)
(9.3404d0 -6.0085d0) (11.1579d0 -3.2823d0) (15.2731d0 -2.6512d0)
(5.5036d0 -8.558d0) (0.0d0 -8.7606d0) (6.6648d0 -9.5432d0)
(1.6155d0 -9.6694d0) (9.0416d0 -11.0421d0) (4.0135d0 -5.4026d0)
(11.9159d0 -4.5949d0) (11.1579d0 -2.0706d0) (14.3897d0 -1.5405d0)
(12.3451d0 -3.9385d0) (4.2415d0 -9.6188d0) (0.0d0 -5.4026d0)
(5.2512d0 -4.5949d0) (10.6278d0 -4.5949d0) (13.1528d0 -5.3774d0)
(13.6576d0 -9.114d0) (7.9773d0 -4.5949d0) (6.6099d0 -10.947d0)
(10.2299d0 -11.7915d0) (2.7766d0 -8.7606d0) (7.7983d0 -11.6965d0)
(1.035d0 -4.7968d0) (12.1936d0 -1.4143d0) (13.279d0 -2.0201d0)
(13.279d0 -3.2318d0) (2.0699d0 -5.4026d0) (14.4654d0 -3.8629d0)
(3.0543d0 -4.7968d0) (11.9159d0 -6.0842d0) (13.9606d0 -7.0434d0)
(14.4654d0 -6.0842d0) (12.4207d0 -7.0434d0) (13.6576d0 -10.6286d0)
(6.8162d0 -4.5949d0) (9.3404d0 -4.5949d0))
(CHEMICAL-FORMULA (C 25) (H 40) (N 7) (O 18) (P 3) (S 1))
(MOLECULAR-WEIGHT 851.608d0)
(AROMATIC-RINGS (33 22 31 46 47 48) (23 32 47 48 50)) )
((SUPERATOMS COA-GROUP REPLACES-ATOM 41)
(SUPERATOMS COA-GROUP CONNECTED-TO 44)
(GIBBS-0 -173.8d0 CITATIONS "GibbsGroups97")))
(ACETOACETYL-COA-TRANSFER-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETOACETYL-COA-TRANSFER-ENZRXN)
(COMPONENTS ATOA-CPLX ATOD-CPLX)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
((COMPONENTS ATOD-CPLX COEFFICIENT 1) (COMPONENTS ATOA-CPLX COEFFICIENT 1)))
(ACETOACETYL-COA-TRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CPD-29)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[76060442]")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOACETYL-COA-TRANSFER-RXN)
(INHIBITORS-COMPETITIVE CO-A "epsilon-acetyl-CoA")
(COMMENT "The growth of E. coli on short-chain fatty acids (C3-C6)
requires the activation of the acids to their respective thioesters.
This activation is catalyzed by acetoacetyl-CoA transferase. |CITS:
[76060425]| The reaction takes place in two half-reactions which
involves a covalent enzyme-CoA. |CITS: [76060442]| The enzyme
undergoes two detectable conformational changes during the reaction.
|CITS: [77265490]| It is thought likely that the reaction proceeds by
a ping-pong mechanism. |CITS: [76060442]| The enzyme can utilize a
variety of short-chain acyl-CoA and carboxylic acid substrates but
exhibits maximal activity with normal and 3-keto substrates. |CITS:
[76060425]|")
(ENZYME ACETOACETYL-COA-TRANSFER-CPLX)
(SYNONYMS "CoA transferase" "acetyl-CoA:acetoacetate-CoA transferase")
(COMMON-NAME "acetoacetyl-CoA transferase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/facet.template")
(:CREATION-DATE 3001258175) )
((INHIBITORS-UNKMECH CPD-29 CITATIONS "[76060425]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "Enzyme has a fairly broad specificity
for carboxylic acid and acyl-CoA substrates |CITS: [76060425]| but
acetoacetate is the only significant inducer. |CITS: [73032600]|")
(INHIBITORS-COMPETITIVE CO-A COMMENT "with respect to acyl-CoA
substrate |CITS: [77265490]|")
(INHIBITORS-COMPETITIVE "epsilon-acetyl-CoA" COMMENT "a
competitive substrate, it inhibits acetoacetyl-CoA formation |CITS:
[76060425]|")))
(ACETOACETYL-COA-TRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.8.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ACETOACETATE-DEG-PWY)
(ENZYMATIC-REACTION ACETOACETYL-COA-TRANSFER-ENZRXN)
(RIGHT ACETOACETYL-COA ACET)
(LEFT 3-KETOBUTYRATE ACETYL-COA)
(EC-NUMBER "2.8.3.-")
(COMMENT "The first step in the degradation of short-chain fatty acid
acetoacetate.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
NIL)
(ACETOACETYL-S-ACP NIL (
(OCELOT-GFP::PARENTS |Acetoacetyl-ACPs| B-KETOACYL-ACP)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(LIGAND-CPD "C05744" NIL |kr| 3346617699 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(:CREATION-DATE 3054565679)
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(SYNONYMS "B1094" "AcpP" "acetoacetyl-S-ACP")
(CHEMICAL-FORMULA (C 4) (H 5) (O 2) (ACP 1))
(DISPLAY-COORDS-2D (0.3794d0 -2.1078d0) (-0.3351d0 -0.9787d0)
(0.3794d0 -1.3912d0) (1.0939d0 -0.9787d0) (1.8083d0 -2.2162d0)
(1.8083d0 -1.3912d0) (2.5228d0 -0.9787d0))
(STRUCTURE-BONDS (6 7 1) (6 5 2) (4 6 1) (3 4 1) (3 2 1) (3 1 2))
(STRUCTURE-ATOMS O ACP C C O C C)
(COMMON-NAME "acetoacetyl-ACP") )
NIL)
(ACETOIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00466" NIL |kaipa| 3311532628 NIL NIL)
(CAS "513-86-0") (NCI "7609"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -71.8d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2022 ACETOINDEHYDROG-A-RXN)
(COMMON-NAME "acetoin")
(MOLECULAR-WEIGHT 88.106d0)
(CHEMICAL-FORMULA (C 4) (H 8) (O 2))
(DISPLAY-COORDS-2D (0.0049d0 0.0d0) (2.7862d0 -2.4341d0) (0.0d0 -2.4242d0)
(2.9597d0 -0.1041d0) (0.704d0 -1.2146d0) (2.107d0 -1.2146d0))
(STRUCTURE-BONDS (5 6 1) (6 4 1 :UP) (3 5 2) (2 6 1) (1 5 1))
(STRUCTURE-ATOMS C C O O C C)
(SYNONYMS "(R)-acetoin" "acetylmethylcarbinol" "3-hydroxy-2-butanone"
"(R)-2-acetoin" "(R)-3-hydroxy-2-butanone" "(R)-dimethylketol"
"(R)-3-hydroxybutan-2-one" "3-hydroxybutan-2-one") )
((GIBBS-0 -71.8d0 CITATIONS "GibbsGroups97")))
(ACETOINDEHYDROG-A-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(COMMENT "This reaction converts diacetyl to acetoin.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/diacred.template")
(ENZYMATIC-REACTION ENZRXN0-2749 ENZRXN0-2748 ENZRXN0-2744
ACETOINDEHYDROG-ENZRXN)
(EC-NUMBER "1.1.1.5")
(:CREATION-DATE 3041707768)
(LEFT DIACETYL NADPH)
(RIGHT ACETOIN NADP) )
NIL)
(ACETOINDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "Diacetyl reductase has been isolated from E. coli B. The
coli enzyme is specific for NADPH as a coenzyme but otherwise has
broad substrate specificity. Its role in the cell is not conclusively
known. |CITS: [74168560]|")
(REACTION ACETOINDEHYDROG-A-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/diacred.template")
(ENZYME ACETOINDEHYDROG-MONOMER)
(ALTERNATIVE-SUBSTRATES
(DIACETYL "ethyl pyruvate" ETHYL-ACETOACETATE "ethyl thiolacetoacetate"))
(:CREATION-DATE 3041707768)
(COMMON-NAME "diacetyl reductase")
(SYNONYMS "acetoin dehydrogenase" "acetoin:NAD+ oxidoreductase")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT) )
((REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT COMMENT
"The reversibility of the reaction could not be demonstrated. |CITS: [74168560]| ")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme has broad
substrate specificity. It recognizes uncharged alpha-dicarbonyl
structure and also shows activity with beta-keto esters. However the
enzyme is highly specific for NADPH as coenzyme. |CITS: [74168560]|")))
(ACETOINDEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT "There is no gene associated with this polypeptide yet.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/diacred.template")
(CATALYZES ACETOINDEHYDROG-ENZRXN)
(:CREATION-DATE 3041707768)
(MOLECULAR-WEIGHT-SEQ 10.0d0) )
((MOLECULAR-WEIGHT-SEQ 10.0d0 CITATIONS "[74168560]")))
(ACETOL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(MOLECULAR-WEIGHT 74.079d0)
(CHEMICAL-FORMULA (C 3) (H 6) (O 2))
(STRUCTURE-BONDS (4 5 1) (3 4 1) (2 5 2) (1 5 1))
(DISPLAY-COORDS-2D (0.0d0 -2.3628d0) (1.0039d0 0.0d0) (3.0252d0 -1.3526d0)
(2.0437d0 -2.351d0) (1.0163d0 -1.3999d0))
(STRUCTURE-ATOMS C O O C C)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-4281)
(SYNONYMS "hydroxyacetone" "acetylmethanol" "1-hydroxyacetone")
(COMMON-NAME "acetol")
(:CREATOR |keseler|)
(:CREATION-DATE 3332772844) )
NIL)
(ACETOLACTREDUCTOISOM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(INHIBITORS-COMPETITIVE "2-methylphosphinoyl-2-hydroxyacetic acid")
(SYNONYMS
"(R)-2,3-dihydroxy-3-methylbutanoate:NADP(+) oxidoreductase (isomerizing)"
"2-hydroxy-3-ketol-acid reductoisomerase"
"α-acetohydroxy acid isomeroreductase" "ketol acid reductoisomerase"
"dihydroxyisovalerate dehydrogenase (isomerizing)")
(COMMON-NAME "acetohydroxy acid isomeroreductase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOLACTREDUCTOISOM-RXN)
(ENZYME KETOLREDUCTOISOM-MONOMER)
(:CREATION-DATE 2969204153)
(:CREATOR |mriley|) )
((INHIBITORS-COMPETITIVE "2-methylphosphinoyl-2-hydroxyacetic acid" CITATIONS
"[HandEnzInh]")
(INHIBITORS-COMPETITIVE "2-methylphosphinoyl-2-hydroxyacetic acid" COMMENT
"Competitive with respect to acetolactate. |CITS: [89005718]| ")))
(ACETOLACTREDUCTOISOM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY VALSYN-PWY)
(ENZYMATIC-REACTION ACETOLACTREDUCTOISOM-ENZRXN)
(RIGHT 2-ACETO-LACTATE NADPH PROTON)
(LEFT DIOH-ISOVALERATE NADP)
(EC-NUMBER "1.1.1.86")
(COMMENT "This is the second shared reaction in the valine and leucine
biosynthetic pathways. After three steps in common, the pathway forks to either
valine or leucine.")
(:CREATION-DATE 2969204153)
(:CREATOR |mriley|) )
((EC-NUMBER :FACET COMMENT "One EC number includes two reactions.")))
(ACETOLACTSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY VALSYN-PWY)
(ENZYMATIC-REACTION ACETOLACTSYNIII-ENZRXN ACETOLACTSYNII-ENZRXN
ACETOLACTSYNI-ENZRXN)
(RIGHT 2-ACETO-LACTATE CARBON-DIOXIDE)
(LEFT PYRUVATE)
(EC-NUMBER "2.2.1.6")
(COMMENT "The first of a set of shared homologous reactions in the valine,
isoleucine and leucine biosynthetic pathways.")
(:CREATION-DATE 2969204146)
(:CREATOR |mriley|) )
((LEFT PYRUVATE COEFFICIENT 2)))
(ACETOLACTSYNI-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETOOHBUTSYNI-ENZRXN ACETOLACTSYNI-ENZRXN)
(COMPONENTS LARGEILVB-MONOMER SMALLILVN-MONOMER)
(:CREATION-DATE 2969204146)
(:CREATOR |mriley|) )
((COMPONENTS SMALLILVN-MONOMER CITATIONS "[92380929]")
(COMPONENTS SMALLILVN-MONOMER COEFFICIENT 2)
(COMPONENTS LARGEILVB-MONOMER CITATIONS "[92380929]")
(COMPONENTS LARGEILVB-MONOMER COEFFICIENT 2)))
(ACETOLACTSYNI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH LEU 2-OXOBUTANOATE "sulfometuron methyl" VAL)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COFACTORS MG+2)
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE FAD)
(SYNONYMS "AHASI" "acetolactate pyruvate-lyase (carboxylating)"
"acetohydroxy-acid synthase I")
(COMMON-NAME "acetolactate synthase I")
(ALTERNATIVE-SUBSTRATES (PYRUVATE 2-OXOBUTANOATE))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOLACTSYN-RXN)
(COMMENT "There are three acetolactate synthase isozymes in E. coli
K-12. AHASI is coded by the ilvB and ilvN genes, AHASII by the
ilvG and ilvM genes and AHASIII by the ilvH and ilvI genes for the large and small subunits respectively. Both the
AHASI and III are valine sensitive in E. coli K-12. IlvGM is not but
requires mutation to be expressed in strain K-12. The AHAS
activity is required for the biosynthesis of
α-aceto-α-hydroxybutyrate for the isoleucine pathway and for
the biosynthesis of α-acetolactate for the valine pathway. Valine
inhibits activity and represses synthesis of the enzyme.
|CITS: [86111609]|")
(ENZYME ACETOLACTSYNI-CPLX)
(:CREATION-DATE 2969204146)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH LEU CITATIONS "[84000506]")
(INHIBITORS-UNKMECH 2-OXOBUTANOATE CITATIONS "DeFeliceBBA5419")
(INHIBITORS-UNKMECH VAL COMMENT "inhibition by
valine is overcome by isoleucine")
(INHIBITORS-UNKMECH VAL CITATIONS "[82075672]")
(PROSTHETIC-GROUPS FAD CITATIONS "[79130314]" "[88314835]")))
(ACETOLACTSYNII-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |shearer|)
(COMMENT "Acetohydroxyacid synthase II (AHAS II) catalyzes the biosynthesis of
α-aceto-α-hydroxybutyrate and α-acetolactate. It is not found in
E. coli K-12 due to a mutation in ilvG.
AHAS II is a bifunctional enzyme that catalyzes the biosynthesis of
α-aceto-α-hydroxybutyrate for the isoleucine pathway and
of α-acetolactate for the valine pathway |CITS: [86111609]|. Both IlvG and
IlvM are required for this activity, though the exact stoichiometry of the IlvM
subunit is unclear |CITS: [9581571][3027038]|. The kinetics of AHAS II have been evaluated |CITS: [9581571]|.
AHAS II is not present in E. coli K-12. See the entry for |FRAME: G8221-MONOMER| for more
information.")
(SYNONYMS "AHAS" "AHAS II")
(SPECIES ECOLI)
(CATALYZES ACETOOHBUTSYNII-ENZRXN ACETOLACTSYNII-ENZRXN)
(COMPONENTS G8221-MONOMER LARGEILVG-MONOMER SMALLILVM-MONOMER)
(:CREATION-DATE 2969204164)
(:CREATOR |mriley|) )
((CREDITS SRI LAST-CURATED 3349813145)
(CREDITS |shearer| LAST-CURATED 3349813145)))
(ACETOLACTSYNII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(COFACTORS FAD FAD)
(INHIBITORS-UNKMECH "sulfometuron methyl" GLYOX GLYOX "sulfometuron methyl")
(CITATIONS "9581571:EV-EXP-IDA-PURIFIED-PROTEIN:3349812545:shearer")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE THIAMINE-PYROPHOSPHATE)
(SYNONYMS "acetolactate pyruvate-lyase (carboxylating)" "AHASII"
"acetohydroxy acid synthase II")
(COMMON-NAME "acetolactate synthase II")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOLACTSYN-RXN)
(ENZYME ACETOLACTSYNII-CPLX)
(:CREATION-DATE 2969204164)
(:CREATOR |mriley|) )
((COFACTORS FAD CITATIONS "9581571")
(INHIBITORS-UNKMECH "sulfometuron methyl" CITATIONS "84264485")
(INHIBITORS-UNKMECH GLYOX CITATIONS "15958189")))
(ACETOLACTSYNIII-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-EXP 155)
(COMMENT
"Acetohydroxy acid synthase III (AHAS III) is one of two functional isozymes catalyzing the decarboxylation of
pyruvate and transfer of the resulting acetaldehyde group to either pyruvate or α-ketobutyrate, producing
α-acetolactate for the valine pathway and α-aceto-α-hydroxybutyrate for the isoleucine pathway.
This is the first common step in the biosynthesis of the branched-chain amino acids isoleucine, leucine, and valine.
A third isozyme, AHAS II, is not functional in E. coli K-12 due to the presence of a frame shift mutation in the
gene encoding the large subunit, ilvG. |CITS: [colisalII]|
In the presence of both pyruvate and α-ketobutyrate, AHAS III produces approximately 40-fold more
acetohydroxybutyrate than acetolactate, while AHAS I shows no product preference |CITS: [3301814][2675968]|.
The differential regulation of enzymatic activity and
expression of the isozymes has direct physiological consequences and has been under intense study. The end
products of the branched-chain amino acid biosynthesis pathways all inhibit AHAS III activity, although inhibition by
valine is most significant |CITS: [2675968]|. Both AHAS I and III are inhibited by valine |CITS: [Defelice78]|. Activity
of AHAS III is only partially inhibited by leucine, while AHAS I activity can be almost completely inhibited
|CITS: [6351926]|.")
(CATALYZES ACETOLACTSYNIII-ENZRXN ACETOOHBUTSYN-ENZRXN)
(COMPONENTS ACETOLACTSYNIII-ICHAIN-MONOMER ACETOLACTSYNIII-HCHAIN-MONOMER)
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 155 CITATIONS "8756689")
(CREDITS SRI LAST-CURATED 3348416812)
(CREDITS |keseler| LAST-CURATED 3348416812)
(COMPONENTS ACETOLACTSYNIII-HCHAIN-MONOMER COEFFICIENT 2)
(COMPONENTS ACETOLACTSYNIII-ICHAIN-MONOMER COEFFICIENT 2)))
(ACETOLACTSYNIII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (PYRUVATE 6000))
(PHYSIOLOGICALLY-RELEVANT ILE VAL LEU)
(PH-OPT 9)
(INHIBITORS-UNKMECH LEU VAL ILE "sulfometuron methyl")
(CITATIONS "2675968:EV-EXP-IDA-PURIFIED-PROTEIN:3348414559:keseler")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE)
(COFACTORS FAD MG+2)
(SYNONYMS "acetolactate pyruvate-lyase (carboxylating)" "AHAS III"
"acetohydroxy acid synthase III")
(COMMON-NAME "acetolactate synthase III")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOLACTSYN-RXN)
(ENZYME ACETOLACTSYNIII-CPLX)
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((KM (PYRUVATE 6000) CITATIONS "2675968")
(COFACTORS MG+2 CITATIONS "8756689") (PH-OPT 9 CITATIONS "DEFELICE78")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE CITATIONS "8756689" "DEFELICE78")
(INHIBITORS-UNKMECH VAL CITATIONS "2675968")
(INHIBITORS-UNKMECH ILE CITATIONS "[89200986]")
(INHIBITORS-UNKMECH "sulfometuron methyl" CITATIONS "[89200986]")
(COFACTORS FAD CITATIONS "8756689")))
(ACETOLACTSYNIII-HCHAIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-EXP 17)
(SYNONYMS "B0078" "BrnP" "IlvH")
(COMMON-NAME "IlvH")
(DBLINKS (MODBASE "P00894" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00894" NIL |pkarp| 3355444109 NIL NIL)
(PDB "2F1F" NIL |keseler| 3348352645 NIL NIL)
(PFAM "PF01842" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414620" NIL NIL NIL NIL NIL) (UNIPROT "P00894"))
(COMPONENT-OF ACETOLACTSYNIII-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (SMALLILVN-MONOMER YES) (SMALLILVM-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 17.97672600000001d0)
(GENE EG10499)
(COMMENT
"IlvH is the regulatory (small) subunit of acetolactate synthase III; it confers sensitivity to inhibition by valine and is
required for full catalytic activity of acetolactate synthase III holoenzyme |CITS: [8756689]|.
The crystal structure of IlvH has been determined at 1.75 Å resolution. It forms a dimer with two ferredoxin
domains in each monomer. The valine binding sites can be tentatively assigned to the interface between the two
N-terminal domains |CITS: [16458324]|.")
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((CREDITS SRI LAST-CURATED 3348417057)
(CREDITS |keseler| LAST-CURATED 3348417057)
(MOLECULAR-WEIGHT-EXP 17 CITATIONS "8756689")
(ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "There are three acetolactate
synthetase isozymes in E. coli coded by the ilvBN, ilvHI and ilvGM
genes for isozymes I, III and II, respectively. Isozyme II is only
active in E. coli K-12 when mutated. Two other isozymes coded by the
ilvJ and ilvF genes are not active and are considered cryptic.
|CITS: [85242083] [87174741] [83272971] [82271463]
[90264296]| The three isozymes show conserved
homologies with two other enzymes which require thiamine
pyrophosphate: pyruvate oxidase and pyruvate decarboxylase. |CITS:
[SwissProt]|")))
(ACETOLACTSYNIII-ICHAIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-EXP 60)
(SYNONYMS "B0077" "IlvI")
(COMMON-NAME "IlvI")
(DBLINKS (MODBASE "P00893" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02776" IN-FAMILY |pkarp| 3346700315 NIL NIL) (UNIPROT "P00893"))
(COMPONENT-OF ACETOLACTSYNIII-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (LARGEILVG-MONOMER YES) (LARGEILVB-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 62.98425399999986d0)
(GENE EG10500)
(COMMENT
"IlvI is the catalytic (large) subunit of acetolactate synthase III |CITS: [8756689]|.
")
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((CREDITS SRI LAST-CURATED 3348417042)
(CREDITS |keseler| LAST-CURATED 3348417042)
(MOLECULAR-WEIGHT-EXP 60 CITATIONS "8756689")
(ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "There are three acetolactate
synthetase isozymes in E. coli coded by the ilvBN, ilvHI and ilvGM
genes for isozymes I, III and II, respectively. Isozyme II is only
active in E. coli K-12 when mutated. Two other isozymes coded by the
ilvJ and ilvF genes are not active and are considered cryptic.
|CITS: [85242083] [87174741] [83272971] [82271463]
[90264296]| The three isozymes show conserved
homologies with two other enzymes which require thiamine
pyrophosphate: pyruvate oxidase and pyruvate decarboxylase. |CITS:
[SwissProt]|")))
(ACETOOHBUTREDUCTOISOM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(SYNONYMS "α-acetohydroxy acid isomeroreductase"
"ketol acid reductoisomerase")
(COMMON-NAME "acetohydroxy acid isomeroreductase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETOOHBUTREDUCTOISOM-RXN)
(ENZYME KETOLREDUCTOISOM-MONOMER)
(:CREATION-DATE 2969204153)
(:CREATOR |mriley|) )
NIL)
(ACETOOHBUTREDUCTOISOM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY ILEUSYN-PWY)
(ENZYMATIC-REACTION ACETOOHBUTREDUCTOISOM-ENZRXN)
(RIGHT 1-KETO-2-METHYLVALERATE NADP)
(LEFT 2-ACETO-2-HYDROXY-BUTYRATE NADPH)
(EC-NUMBER "1.1.1.86")
(COMMENT
"This is the third reaction in the isoleucine biosynthetic pathway, homologous to the second rxn for valine biosynthesis.")
(:CREATION-DATE 2969204153)
(:CREATOR |mriley|) )
((EC-NUMBER :FACET COMMENT "One EC number includes two reactions.")))
(ACETOOHBUTSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (PYRUVATE 7600))
(INHIBITORS-UNKMECH LEU VAL)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE)
(COFACTORS MG+2 FAD)
(COMMON-NAME "acetohydroxybutanoate synthase III")
(SYNONYMS "acetohydroxybutyrare pyruvate-lyase (carboxylating)" "AHASIII"
"acetohydroxy acid synthase III")
(REACTION ACETOOHBUTSYN-RXN)
(REACTION-DIRECTION REVERSIBLE)
(ENZYME ACETOLACTSYNIII-CPLX)
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((KM (PYRUVATE 7600) CITATIONS "DEFELICE78")
(INHIBITORS-UNKMECH VAL CITATIONS "2675968")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE CITATIONS "8756689")
(COFACTORS MG+2 CITATIONS "8756689")
(INHIBITORS-UNKMECH LEU CITATIONS "[84000506]")
(INHIBITORS-UNKMECH VAL COMMENT "inhibition by
valine is overcome by isoleucine")
(COFACTORS FAD CITATIONS "8756689")))
(ACETOOHBUTSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY ILEUSYN-PWY)
(ENZYMATIC-REACTION ACETOOHBUTSYNII-ENZRXN ACETOOHBUTSYNI-ENZRXN
ACETOOHBUTSYN-ENZRXN)
(RIGHT 2-ACETO-2-HYDROXY-BUTYRATE CARBON-DIOXIDE)
(LEFT PYRUVATE 2-OXOBUTANOATE)
(EC-NUMBER "2.2.1.6")
(COMMENT "The first of a set of shared homologous reactions in the valine,
isoleucine and leucine biosynthetic pathways.")
(:CREATION-DATE 2969204146)
(:CREATOR |mriley|) )
NIL)
(ACETOOHBUTSYNI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH LEU VAL)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PHYSIOLOGICALLY-RELEVANT LEU VAL)
(PROSTHETIC-GROUPS FAD THIAMINE-PYROPHOSPHATE)
(COFACTORS MG+2)
(SYNONYMS "AHASI" "acetohydroxy-acid synthase I")
(COMMON-NAME "acetohydroxybutanoate synthase I")
(REACTION ACETOOHBUTSYN-RXN)
(ALTERNATIVE-SUBSTRATES (PYRUVATE 2-OXOBUTANOATE))
(REACTION-DIRECTION REVERSIBLE)
(COMMENT "There are three acetolactate synthase isozymes in E. coli
K-12. AHASI is coded for by the ilvB and ilvN genes, AHASII by the
ilvG and ilvM genes and AHASIII by the ilvH and ilvI genes, for the large and small subunits respectively. The AHAS
activity is required for the biosynthesis of
α-aceto-α-hydroxybutyrate for the isoleucine pathway and for
the biosynthesis of α-acetolactate for the valine pathway.
|CITS: [86111609]|")
(ENZYME ACETOLACTSYNI-CPLX)
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((PROSTHETIC-GROUPS FAD CITATIONS "[79130314]" "[88314835]")))
(ACETOOHBUTSYNII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(COFACTORS FAD FAD)
(INHIBITORS-UNKMECH VAL LEU LEU VAL)
(CITATIONS "9581571:EV-EXP-IDA-PURIFIED-PROTEIN:3349812545:shearer")
(PROSTHETIC-GROUPS THIAMINE-PYROPHOSPHATE THIAMINE-PYROPHOSPHATE)
(SYNONYMS "acetolactate pyruvate-lyase (carboxylating)" "AHASII"
"acetohydroxy acid synthase II")
(COMMON-NAME "acetohydroxybutanoate synthase II")
(REACTION ACETOOHBUTSYN-RXN)
(ALTERNATIVE-SUBSTRATES (PYRUVATE 2-OXOBUTANOATE) (PYRUVATE 2-OXOBUTANOATE))
(REACTION-DIRECTION REVERSIBLE)
(ENZYME ACETOLACTSYNII-CPLX)
(:CREATION-DATE 2969204171)
(:CREATOR |mriley|) )
((COFACTORS FAD CITATIONS "9581571")))
(ACETYL-ACP NIL (
(OCELOT-GFP::PARENTS ACYL-ACP)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(:CREATION-DATE 3095444893)
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(APPEARS-IN-LEFT-SIDE-OF CITTRANS-RXN 3-OXOACYL-ACP-SYNTH-BASE-RXN)
(APPEARS-IN-RIGHT-SIDE-OF CITRYLY-RXN ACP-S-ACETYLTRANSFER-RXN
MALONYL-ACPDECARBOX-RXN)
(CHEMICAL-FORMULA (C 2) (H 3) (O 1) (ACP 1))
(DISPLAY-COORDS-2D (1.2707d0 -0.5601d0) (1.9852d0 -0.9726d0)
(2.6996d0 -0.5601d0) (1.9852d0 -1.7976d0))
(STRUCTURE-BONDS (2 3 1) (2 4 2) (1 2 1))
(STRUCTURE-ATOMS ACP C C O)
(SYNONYMS "B1094" "AcpP" "acetyl-[acyl-carrier protein]"
"acetylacylcarrier-protein")
(COMMON-NAME "acetyl-ACP") )
NIL)
(ACETYL-COA NIL (
(OCELOT-GFP::PARENTS |All-Coas|)
(INHIBITORS-ALLOSTERIC-OF MALIC-NAD-ENZRXN MALIC-NADP-ENZRXN)
(INHIBITORS-COMPETITIVE-OF MALONYL-COA-ACP-TRANSACYL-ENZRXN)
(INHIBITORS-UNKMECH-OF PYRUVATEDECARB-ENZRXN)
(ACTIVATORS-ALLOSTERIC-OF PEPCARBOX-ENZRXN CITSYN-ENZRXN)
(DBLINKS (CAS "72-89-9")
(UM-BBD-CPD "c0031" NIL |kawakami| 3278884159 NIL NIL)
(LIGAND-CPD "C00024" NIL |kawakami| 3276028395 NIL NIL))
(:CREATION-DATE 3073857204)
(APPEARS-IN-LEFT-SIDE-OF 2-ISOPROPYLMALATESYN-RXN CITSYN-RXN MALSYN-RXN
KETOACYLCOATHIOL-RXN RXN-3641 RXN0-1133 ACETYL-COA-CARBOXYLTRANSFER-RXN
RXN0-5055 DIHYDLIPACETRANS-RXN ACETYL-COA-ACETYLTRANSFER-RXN PYRUVFORMLY-RXN
AKBLIG-RXN 2.3.1.118-RXN SPERMACTRAN-RXN 2.3.1.157-RXN CYSSYNMULTI-RXN
3-OXOACYL-ACP-COA-SYNTHIII-RXN ACETOACETYL-COA-TRANSFER-RXN
TDPFUCACTRANS-RXN SERINE-O-ACETTRAN-RXN PHOSACETYLTRANS-RXN
N-ACETYLTRANSFER-RXN MALTACETYLTRAN-RXN GALACTOACETYLTRAN-RXN
DIAMACTRANS-RXN ACP-S-ACETYLTRANSFER-RXN 2.3.1.128-RXN)
(SUPERATOMS COA-GROUP)
(GIBBS-0 -148.3d0)
(APPEARS-IN-RIGHT-SIDE-OF PYRUFLAVREDUCT-RXN RXN0-2043 PYRUVDEH-RXN
ACETALD-DEHYDROG-RXN ACECOATRANS-RXN ACETATE--COA-LIGASE-RXN)
(SYNONYMS "acetyl coenzyme-A" "ac-CoA" "acetylcoenzyme-A"
"acetyl-S-CoA" "ac-S-CoA")
(COMMON-NAME "acetyl-CoA")
(STRUCTURE-ATOMS C O C H N O C O C N C O O C O O N C C C O C N C N H O O O C
O N O H C C H O C O O N P P C C P C C C C C C S O)
(STRUCTURE-BONDS (55 43 1) (54 46 1) (53 21 1) (53 3 1) (52 12 1) (52 53 1)
(51 52 1) (50 24 1) (49 19 1) (48 5 :AROMATIC) (47 31 1) (46 35 1)
(25 45 :AROMATIC) (44 40 1) (43 21 1) (42 9 :AROMATIC) (36 42 :AROMATIC)
(41 7 2) (40 51 1) (39 24 1) (38 3 1) (37 1 1) (45 36 :AROMATIC) (35 23 1)
(34 53 1) (33 50 1) (32 22 1) (31 44 1) (30 14 1) (29 43 2) (28 47 2)
(27 43 1) (26 3 1) (24 18 1) (23 20 1) (36 22 :AROMATIC) (22 10 :AROMATIC)
(20 30 1) (19 54 1) (18 16 1) (17 7 1) (16 47 1) (15 44 2) (14 17 1)
(13 19 2) (12 1 1) (11 24 1) (10 48 :AROMATIC) (9 25 :AROMATIC) (8 47 1)
(7 50 1) (6 20 2) (5 45 :AROMATIC) (4 52 1) (2 44 1) (1 25 1) (1 3 1))
(DISPLAY-COORDS-2D (0.89109d0 -0.26403d0) (0.22112d0 -0.25413d0)
(0.82508d0 -0.38944d0) (0.55776d0 -0.37624d0) (0.61386d0 0.0198d0)
(-0.63696d0 -0.42904d0) (-0.86469d0 -0.09571d0) (-0.10891d0 -0.25413d0)
(0.9967d0 0.18482d0) (0.45875d0 0.26073d0) (-0.60066d0 0.08911d0)
(0.71947d0 -0.17162d0) (0.17162d0 -0.88449d0) (-1.0d0 -0.61386d0)
(0.22112d0 0.11551d0) (-0.31353d0 -0.06931d0) (-1.0d0 -0.17492d0)
(-0.47525d0 -0.17492d0) (0.17162d0 -0.69967d0) (-0.63696d0 -0.61386d0)
(0.62376d0 -0.62046d0) (0.59406d0 0.34653d0) (-0.44554d0 -0.72607d0)
(-0.60066d0 -0.09571d0) (0.89109d0 0.0264d0) (0.82508d0 -0.27723d0)
(0.80858d0 -0.81518d0) (-0.10891d0 0.11551d0) (0.43894d0 -0.81518d0)
(-0.78878d0 -0.73267d0) (0.0429d0 -0.06931d0) (0.59406d0 0.53135d0)
(-0.72937d0 -0.35974d0) (0.62376d0 -0.27723d0) (-0.28053d0 -0.58416d0)
(0.73597d0 0.26733d0) (0.89109d0 -0.37624d0) (0.82508d0 -0.50165d0)
(-0.60066d0 -0.28053d0) (0.38944d0 -0.06931d0) (-0.86469d0 0.08911d0)
(0.88119d0 0.33003d0) (0.62376d0 -0.81518d0) (0.22112d0 -0.06931d0)
(0.73597d0 0.10891d0) (-0.12871d0 -0.71287d0) (-0.10891d0 -0.06931d0)
(0.45875d0 0.10231d0) (0.30693d0 -0.57426d0) (-0.72937d0 -0.17492d0)
(0.55776d0 -0.06931d0) (0.55776d0 -0.26403d0) (0.62376d0 -0.38944d0)
(0.0264d0 -0.57426d0) (0.62376d0 -1.0d0))
(CHEMICAL-FORMULA (C 23) (H 38) (N 7) (O 17) (P 3) (S 1))
(MOLECULAR-WEIGHT 809.571d0)
(AROMATIC-RINGS (9 42 36 45 25) (5 48 10 22 36 45)) )
((SUPERATOMS COA-GROUP CONNECTED-TO 19)
(SUPERATOMS COA-GROUP REPLACES-ATOM 54)
(GIBBS-0 -148.3d0 CITATIONS "GibbsGroups97")))
(ACETYL-COA-ACETYLTRANSFER-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETYL-COA-ACETYLTRANSFER-ENZRXN)
(COMPONENTS ACETYL-COA-ACETYLTRANSFER-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoB.template")
(:CREATION-DATE 3001088670)
(:CREATOR |mriley|) )
((COMPONENTS ACETYL-COA-ACETYLTRANSFER-MONOMER COEFFICIENT 4)))
(ACETYL-COA-ACETYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH ACETOACETYL-COA)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETYL-COA-ACETYLTRANSFER-RXN)
(COMMENT "E. coli synthesizes two distinct 3-ketoacyl-CoA thiolases.
One is a product of the fadA gene, the second is the product of the
atoB gene. This thiolase II is induced by growth on acetoacetate. It
exhibits strict substrate specificity for acetoacetyl-CoA. |CITS:
[77020548]|")
(ENZYME ACETYL-COA-ACETYLTRANSFER-CPLX)
(SYNONYMS "acetyl-CoA-C-acetyltransferase" "acetoacetyl-CoA thiolase"
"acetyl-CoA:acetyl-CoA C-acetyltransferase" "thiolase II")
(COMMON-NAME "acetyl-CoA acetyltransferase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoB.template")
(:CREATION-DATE 3001088670)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH ACETOACETYL-COA CITATIONS "[77020548]")))
(ACETYL-COA-ACETYLTRANSFER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT-INTERNAL "6/13/05 keseler removed AtoE as synonym")
(SYNONYMS "B2224" "AtoB")
(DBLINKS (MODBASE "P76461" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P76461" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00108" IN-FAMILY |pkarp| 3346700355 NIL NIL)
(REFSEQ "NP_416728" NIL NIL NIL NIL NIL)
(UNIPROT "P76461" NIL |pkarp| 3102853742))
(COMMON-NAME "AtoB")
(COMPONENT-OF ACETYL-COA-ACETYLTRANSFER-CPLX)
(MOLECULAR-WEIGHT-SEQ 40.352435999999926d0)
(GENE EG11672)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoB.template")
(:CREATION-DATE 3001088670)
(:CREATOR |mriley|) )
NIL)
(ACETYL-COA-ACETYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ACETOACETATE-DEG-PWY)
(ENZYMATIC-REACTION ACETYL-COA-ACETYLTRANSFER-ENZRXN)
(RIGHT ACETOACETYL-COA CO-A)
(LEFT ACETYL-COA)
(EC-NUMBER "2.3.1.9")
(COMMENT "The second step in the degradation of short-chain fatty acid
acetoacetate.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoB.template")
(:CREATION-DATE 3001088670)
(:CREATOR |mriley|) )
((LEFT ACETYL-COA COEFFICIENT 2)))
(ACETYL-COA-CARBOXYLMULTI-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETYL-COA-CARBOXYLMULTI-ENZRXN)
(COMPONENTS ACETYL-COA-CARBOXYLTRANSFER-CPLX BIOTIN-CARBOXYL-CPLX BCCP-CPLX)
(COMMENT
"The enzyme |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| is one of the key enzymes in the
biosynthesis of fatty acids (see |FRAME: FASYN-INITIAL-PWY|).
The enzyme belongs to the family of enzymes that catalyze
the intermolecular transfer of carboxyl groups via the transient formation of a carboxyphosphate
intermediate covalently linked to a biotin prosthetic group |CITS: [15749055]|.
The E. coli enzyme complex is composed of two catalytic units and one carrier protein,
encoded by four different genes.
The catalytic units are |FRAME:BIOTIN-CARBOXYL-CPLX| (BC), a homodimer encoded by the
|FRAME: EG10276| gene, and |FRAME:ACETYL-COA-CARBOXYLMULTI-CPLX| (ACCT), an
α2β2 tetramer, encoded by the |FRAME:EG11647| and
|FRAME: EG10217| genes.
The carrier protein is the |FRAME:BCCP-CPLX| (BCCP), a homodimer encoded by the |FRAME:EG10275| gene.
The BCCP monomer is biotinylated by the enzyme |FRAME:BIOTINLIG-ENZRXN|.
Following dimerization of the biotinylated monomers, |FRAME:BIOTIN-CARBOXYL-CPLX| (BC) catalyzes the addition
of |FRAME: CARBON-DIOXIDE| to the carrier protein dimer, forming |FRAME:Carboxybiotin-BCCP| (carboxy-BCCP).
|FRAME:Carboxybiotin-BCCP|
in turn is the substrate for ACCT, which transfers the carboxy group to |FRAME:ACETYL-COA|,
resulting in the formation of |FRAME:MALONYL-COA| and the regeneration of |FRAME:BCCP-CPLX|.
Both biotinylation and carboxylation of the carrier protein require ATP, while the last step, transfer of the carboxy
group to |FRAME: ACETYL-COA|, does not |CITS: [15749055]|.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/ACCmulti.template")
(:CREATION-DATE 3001089018)
(:CREATOR |mriley|) )
((COMPONENTS BCCP-CPLX COEFFICIENT 1)
(COMPONENTS BIOTIN-CARBOXYL-CPLX COEFFICIENT 1)
(COMPONENTS ACETYL-COA-CARBOXYLTRANSFER-CPLX COEFFICIENT 1)))
(ACETYL-COA-CARBOXYLMULTI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-OTHER "acylated derivatives of ACP")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "Acetyl-CoA carboxylase is inhibited by acylated derivatives
of ACP. The inhibition is of a mixed type, i.e. a combination
of competitive and noncompetitive inhibition. The competitive
nature of the inhibition suggests an interaction with the acetyl-CoA
binding site. This in turn suggests that the acyl-ACP is binding
with the acetyl-CoA carboxyltransferase component of the
enzyme complex. |CITS: [JBact183-1499]|")
(REACTION-DIRECTION REVERSIBLE)
(COMMON-NAME "acetyl CoA carboxylase")
(REACTION ACETYL-COA-CARBOXYLTRANSFER-RXN)
(PROSTHETIC-GROUPS BIOTIN)
(ENZYME ACETYL-COA-CARBOXYLMULTI-CPLX)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/ACCmulti.template")
(:CREATION-DATE 3001089018)
(:CREATOR |mriley|) )
((INHIBITORS-OTHER "acylated derivatives of ACP" COMMENT
"Acetyl-CoA carboxylase is inhibited by acylated derivatives
of ACP. The inhibition is of a mixed type, i.e. a combination
of competitive and noncompetitive inhibition. The competitive
nature of the inhibition suggests an interaction with the acetyl-CoA
binding site. This in turn suggests that the acyl-ACP is binding
with the acetyl-CoA carboxyltransferase component of the
enzyme complex.")
(INHIBITORS-OTHER "acylated derivatives of ACP" CITATIONS "JBact183-1499")))
(ACETYL-COA-CARBOXYLTRANSFER-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETYL-COA-CARBOXYLTRANSFER-ENZRXN)
(COMPONENT-OF ACETYL-COA-CARBOXYLMULTI-CPLX)
(COMPONENTS CARBOXYL-TRANSFERASE-ALPHA-CPLX CARBOXYL-TRANSFERASE-BETA-CPLX)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accAD.template")
(:CREATION-DATE 3001089014)
(:CREATOR |mriley|) )
((COMPONENTS CARBOXYL-TRANSFERASE-BETA-CPLX COEFFICIENT 1)
(COMPONENTS CARBOXYL-TRANSFERASE-ALPHA-CPLX COEFFICIENT 1)))
(ACETYL-COA-CARBOXYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "pyrollidine diones")
(INHIBITORS-COMPETITIVE "moiramide B")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "acetyl-CoA:carbon dioxide ligase (ADP-forming)")
(COMMON-NAME "acetyl-CoA carboxyltransferase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION RXN0-5055)
(COMMENT "The acetyl-CoA carboxylase complex is composed of four
different subunits. The overall reaction takes place in two distinct
half-reactions. Biotin carboxylase (coded for by accC) carries out
the first half, carboxylation of protein bound biotin (BCCP, coded for
by accB). The second half is the carboxyltransferase-catalyzed
transfer of the BCCP-carboxyl group to acetyl-CoA to form malonyl-CoA.
The carboxyltransferase subunits are coded for by the accA and accD
genes and are present in a α-2-β-2 complex. |CITS:
[92380982]|
Potent inhibitors with antibacterial activity have been identified |CITS: [15066985]|.")
(ENZYME ACETYL-COA-CARBOXYLTRANSFER-CPLX)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accAD.template")
(:CREATION-DATE 3001089014)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "pyrollidine diones" CITATIONS "15066985")
(INHIBITORS-COMPETITIVE "moiramide B" CITATIONS "15066985")))
(ACETYL-COA-CARBOXYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.4.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ACETYL-COA-CARBOXYLMULTI-ENZRXN)
(COMMON-NAME "Acetyl-CoA carboxylase")
(OFFICIAL-EC? T)
(IN-PATHWAY FASYN-INITIAL-PWY)
(RIGHT MALONYL-COA |Pi| ADP)
(LEFT ATP ACETYL-COA HCO3 PROTON)
(EC-NUMBER "6.4.1.2")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accAD.template")
(:CREATION-DATE 3197914854)
(:CREATOR |paley|) )
NIL)
(ACETYL-GLU NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(INHIBITORS-UNKMECH-OF N-ACETYLTRANSFER-ENZRXN)
(DBLINKS (LIGAND-CPD "C00624" NIL |kaipa| 3311532629 NIL NIL)
(CAS "1188-37-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -191.1d0)
(APPEARS-IN-RIGHT-SIDE-OF N-ACETYLTRANSFER-RXN)
(APPEARS-IN-LEFT-SIDE-OF ACETYLGLUTKIN-RXN)
(MOLECULAR-WEIGHT 189.168d0)
(CHEMICAL-FORMULA (C 7) (H 11) (N 1) (O 5))
(DISPLAY-COORDS-2D (-1.0d0 0.55224d0) (-0.53897d0 -0.05473d0)
(0.99668d0 -0.3267d0) (-0.48922d0 -0.66833d0) (-0.93367d0 -0.66833d0)
(0.62852d0 -0.07794d0) (0.2869d0 -0.33002d0) (-0.21061d0 0.29022d0)
(0.62852d0 0.3665d0) (-0.22388d0 -0.33002d0) (-0.15755d0 0.75124d0)
(-0.19403d0 -1.0d0) (-0.55556d0 0.55224d0))
(STRUCTURE-BONDS (13 8 1) (12 4 1) (11 13 1) (10 4 1) (9 6 2) (8 2 1)
(7 10 1) (6 7 1) (5 4 2) (3 6 1) (2 10 1) (1 13 2))
(STRUCTURE-ATOMS O C C C O C N C O C O O C)
(COMMON-NAME "N-acetyl-L-glutamate")
(SYNONYMS "N-acetylglutamic acid" "acetyl-glu"
"N-acetyl-glutamate" "acetyl-glutamate"
"N-acetyl L-glutamic acid" "NAG") )
((GIBBS-0 -191.1d0 CITATIONS "GibbsGroups97")))
(ACETYL-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF THI-P-SYN-ENZRXN)
(DBLINKS (CAS "19926-71-7" NIL |kr| 3346617699 NIL NIL)
(LIGAND-CPD "C00227" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3073857204)
(GIBBS-0 -88.2d0)
(APPEARS-IN-RIGHT-SIDE-OF PHOSACETYLTRANS-RXN ACETATEKIN-RXN)
(MOLECULAR-WEIGHT 140.032d0)
(CHEMICAL-FORMULA (C 2) (H 5) (O 5) (P 1))
(DISPLAY-COORDS-2D (-1.0d0 -0.44054d0) (0.44054d0 -0.44389d0)
(0.99665d0 -0.44389d0) (0.44054d0 0.11223d0) (-0.05528d0 -0.44389d0)
(0.44054d0 -1.0d0) (-0.57119d0 -0.08878d0) (-0.57119d0 0.46734d0))
(STRUCTURE-BONDS (8 7 2) (7 5 1) (6 2 1) (5 2 1) (4 2 2) (3 2 1) (1 7 1))
(STRUCTURE-ATOMS C P O O O O C O)
(COMMON-NAME "acetylphosphate")
(SYNONYMS "acetyl-P") )
((GIBBS-0 -88.2d0 CITATIONS "GibbsGroups97")))
(|Acetylated-Chitosans| T (
(OCELOT-GFP::PARENTS |Carbohydrate-Derivatives|)
(MOLECULAR-WEIGHT 907.876d0)
(CHEMICAL-FORMULA (C 34) (H 61) (N 5) (O 23))
(STRUCTURE-BONDS (60 62 2) (60 61 1) (59 60 1) (56 57 1) (55 56 1) (54 58 1)
(54 55 1) (54 59 1 :DOWN) (58 53 1 :UP) (52 58 1) (52 57 1) (57 51 1 :UP)
(55 50 1 :UP) (49 51 1) (56 48 1 :DOWN) (27 31 1) (26 30 1) (24 31 1)
(23 30 1) (22 25 1) (21 22 1) (20 29 1) (20 24 1) (19 28 1) (19 21 1)
(18 23 1) (17 18 1) (30 16 1 :DOWN) (29 16 1 :UP) (31 15 1 :DOWN)
(28 15 1 :UP) (14 29 1) (14 27 1) (13 28 1) (13 25 1) (12 26 1) (12 17 1)
(27 11 1 :UP) (26 10 1 :UP) (25 9 1 :UP) (24 8 1 :UP) (23 7 1 :UP)
(22 32 1 :DOWN) (21 6 1 :UP) (17 48 1 :UP) (5 11 1) (4 10 1) (3 9 1)
(20 2 1 :DOWN) (19 44 1 :DOWN) (18 1 1 :DOWN) (43 32 1 :UP) (39 33 1 :DOWN)
(34 37 1) (40 35 1 :UP) (41 36 1 :DOWN) (42 37 1 :UP) (38 43 1) (38 42 1)
(39 43 1) (39 40 1) (40 41 1) (41 42 1) (44 45 1) (45 47 2) (45 46 1))
(DISPLAY-COORDS-2D (10.3337d0 -3.7055d0) (7.0196d0 -1.887d0)
(0.0d0 -1.9103d0) (6.8353d0 -4.994d0) (3.4751d0 -3.107d0) (2.0485d0 0.0d0)
(8.9067d0 -2.8999d0) (5.5926d0 -1.0585d0) (0.6214d0 -2.4395d0)
(7.5029d0 -5.3393d0) (4.1888d0 -3.5212d0) (8.9067d0 -5.3393d0)
(2.0485d0 -2.4395d0) (5.5926d0 -3.5212d0) (3.7283d0 -2.0485d0)
(7.2724d0 -3.4063d0) (9.6202d0 -4.9484d0) (9.6202d0 -4.1198d0)
(2.7616d0 -1.22d0) (6.3061d0 -2.3012d0) (2.0485d0 -0.8057d0)
(1.335d0 -1.22d0) (8.9067d0 -3.7055d0) (5.5926d0 -1.887d0)
(1.335d0 -2.0485d0) (8.193d0 -4.9484d0) (4.9022d0 -3.107d0)
(2.7616d0 -2.0485d0) (6.3061d0 -3.107d0) (8.193d0 -4.1198d0)
(4.9022d0 -2.3012d0) (0.6214d0 -0.8057d0) (0.3454d0 0.437d0)
(-3.1069d0 -0.6675d0) (-1.0584d0 1.2427d0) (-2.4855d0 0.437d0)
(-2.4855d0 -1.1967d0) (-1.0584d0 -1.1967d0) (-0.3453d0 0.0227d0)
(-1.0584d0 0.437d0) (-1.7719d0 0.0227d0) (-1.7719d0 -0.8057d0)
(-0.3453d0 -0.8057d0) (3.4523d0 -0.8057d0) (3.4386d0 0.0192d0)
(2.7173d0 0.4198d0) (4.1462d0 0.4436d0) (10.3337d0 -5.3393d0)
(9.7124d0 -6.4438d0) (11.7608d0 -4.5337d0) (10.3337d0 -6.973d0)
(11.7608d0 -6.973d0) (13.4405d0 -6.582d0) (12.4738d0 -5.7536d0)
(11.7608d0 -5.3393d0) (11.0474d0 -5.7536d0) (11.0474d0 -6.582d0)
(12.4738d0 -6.582d0) (13.1645d0 -5.3393d0) (13.1508d0 -4.5145d0)
(12.4296d0 -4.1138d0) (13.8583d0 -4.09d0))
(STRUCTURE-ATOMS N N O O O O O O C C C O O O O O C C C C C C C C C C C C C C
C O N O O O C O C C C C C N C C O O O O C O O C C C C C N C C O)
(COMMON-NAME "a partly acetylated chitosan")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(|Acetylated-histones| T (
(OCELOT-GFP::PARENTS |Histones|)
(COMMON-NAME "an acetylated histone")
(:CREATOR |paley|)
(:CREATION-DATE 3347159102) )
NIL)
(|Acetylation-Modifications| T (
(OCELOT-GFP::PARENTS |Modified-Residues|)
(SCHEMA? T)
(COMMENT "Acetylation, N-terminal or other.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414656) )
NIL)
(ACETYLESTERASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2962)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3285365240)
(SYNONYMS "C-esterase (in animal tissues)")
(COMMON-NAME "Acetylesterase")
(EC-NUMBER "3.1.1.6")
(RIGHT |Alcohols| ACET)
(LEFT WATER |Acetic-Esters|) )
NIL)
(ACETYLGLUTKIN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETYLGLUTKIN-ENZRXN)
(COMPONENTS ACETYLGLUTKIN-MONOMER)
(:CREATOR |ptoole|)
(:CREATION-DATE 3152274679) )
((COMPONENTS ACETYLGLUTKIN-MONOMER COEFFICIENT 2)))
(ACETYLGLUTKIN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (ATP 300) (ACETYL-GLU 200))
(CITATIONS ":EV-EXP:3277835751:pkarp")
(COFACTORS MG+2)
(SYNONYMS "acetylglutamate kinase" "N-acetylglutamokinase" "NAG kinase" "AGK"
"ATP:N-acetyl-L-glutamate 5-phosphotransferase")
(COMMON-NAME "N-acetylglutamate kinase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETYLGLUTKIN-RXN)
(ENZYME ACETYLGLUTKIN-CPLX)
(:CREATION-DATE 2969204093)
(:CREATOR |mriley|) )
((KM (ATP 300) CITATIONS "14623187")
(KM (ACETYL-GLU 200) CITATIONS "14623187")))
(ACETYLGLUTKIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"The crystal structure of the enzyme has been determined at 1.5 Å resolution, and a catalytic mechanism has been
proposed |CITS: [99322417][12005432][12875848]|. Site-directed mutagenesis has been used to validate the model
|CITS: [14623187]|.")
(SYNONYMS "B3959" "ArgB")
(COMPONENT-OF ACETYLGLUTKIN-CPLX)
(COMMON-NAME "ArgB")
(DBLINKS (MODBASE P0A6C8 NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00696" IN-FAMILY |pkarp| 3346700427 NIL NIL)
(PDB 1GSJ NIL KESELER 3332684841 NIL NIL)
(PDB 1GS5 NIL KESELER 3332684841 NIL NIL)
(PDB 1OH9 NIL KESELER 3332684841 NIL NIL)
(PDB 1OHA NIL KESELER 3332684841 NIL NIL)
(PDB 1OHB NIL KESELER 3332684841 NIL NIL)
(UNIPROT P0A6C8 NIL KESELER 3332684721 NIL NIL)
(REFSEQ NP_418394 NIL KESELER 3310233952 NIL NIL))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 27.02831599999999d0)
(GENE EG10064)
(:CREATION-DATE 2969204093)
(:CREATOR |mriley|) )
NIL)
(ACETYLGLUTKIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLUTORN-PWY)
(ENZYMATIC-REACTION ACETYLGLUTKIN-ENZRXN)
(RIGHT N-ACETYL-GLUTAMYL-P ADP)
(LEFT ACETYL-GLU ATP)
(EC-NUMBER "2.7.2.8")
(COMMENT "This is the second step in arginine biosynthesis.")
(:CREATION-DATE 2969204093)
(:CREATOR |mriley|) )
NIL)
(ACETYLMALTOSE NIL (
(OCELOT-GFP::PARENTS |Carbohydrate-Derivatives|)
(DBLINKS (LIGAND-CPD "C02130" NIL |kr| 3346617701 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (3.4792d0 7.5548d0) (2.1868d0 6.8065d0)
(3.4791d0 5.3055d0) (1.6121d0 5.7897d0) (4.1336d0 5.6797d0)
(4.1336d0 6.428d0) (3.4791d0 6.8065d0) (2.8288d0 6.4281d0)
(2.8288d0 5.6798d0) (2.1868d0 5.3056d0) (7.4299d0 3.7723d0)
(7.4299d0 5.2731d0) (6.1251d0 6.0215d0) (4.7868d0 5.3065d0)
(6.125d0 3.7723d0) (4.258d0 4.2564d0) (6.7795d0 4.1464d0)
(6.7795d0 4.8948d0) (6.125d0 5.2732d0) (5.4747d0 4.8949d0)
(5.4747d0 4.1465d0) (4.8327d0 3.7724d0) (4.7833d0 6.8028d0)
(8.0788d0 4.1483d0) (8.7289d0 3.7744d0) (8.0776d0 4.8983d0))
(CHEMICAL-FORMULA (C 14) (H 24) (O 12))
(MOLECULAR-WEIGHT 384.336d0)
(STRUCTURE-BONDS (24 26 2) (24 25 1) (11 24 1) (6 23 1 :DOWN) (20 14 1 :DOWN)
(19 13 1 :UP) (18 12 1 :DOWN) (17 11 1 :DOWN) (21 22 1 :UP) (20 21 1)
(19 20 1) (18 19 1) (17 18 1) (15 17 1) (21 15 1) (16 22 1) (8 2 1 :DOWN)
(7 1 1 :UP) (5 14 1 :DOWN) (9 10 1 :UP) (8 9 1) (7 8 1) (6 7 1) (5 6 1)
(3 5 1) (9 3 1) (4 10 1))
(STRUCTURE-ATOMS O O O O C C C C C C O O O O O O C C C C C C O C C O)
(APPEARS-IN-RIGHT-SIDE-OF MALTACETYLTRAN-RXN)
(COMMON-NAME "acetylmaltose") )
NIL)
(ACETYLORNDEACET-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACETYLORNDEACET-ENZRXN)
(COMPONENTS ACETYLORNDEACET-MONOMER)
(:CREATION-DATE 2969204100)
(:CREATOR |mriley|) )
((COMPONENTS ACETYLORNDEACET-MONOMER COEFFICIENT 2)))
(ACETYLORNDEACET-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH GLUTATHIONE |Pi| CO+2)
(INHIBITORS-UNKMECH "N-alpha-acetyl-DL-norvaline" CU+2 NI+2 ZN+2 EDTA
"sulfhydryl reagents")
(ALTERNATIVE-SUBSTRATES (N-ALPHA-ACETYLORNITHINE "N-formylmethionine")
(N-ALPHA-ACETYLORNITHINE "acetylmethionine")
(N-ALPHA-ACETYLORNITHINE "acetylglutamate-semialdehyde")
(N-ALPHA-ACETYLORNITHINE "acetylhistidine")
(N-ALPHA-ACETYLORNITHINE "acetylarginine"))
(INHIBITORS-UNCOMPETITIVE "NaF")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "Acetylornithine deacetylase is a metalloenzyme containing
one mole of zinc per mole of enzyme. The enzyme is
activated by cobalt and may contain a second metal
binding site with a preference for cobalt. The enzyme
has broad substrate specificity but exhibits absolute
stereospecificity for acylated L-amino acids as well as
α-N-acylated amino acids. |CITS: [20150401]|")
(INHIBITORS-COMPETITIVE ACET L-ORNITHINE)
(COFACTORS ZN+2)
(SYNONYMS "acetylornithinase" "N-acetylornithinase" "AO" "NAO"
"N(2)-acetyl-L-ornithine amidohydrolase")
(COMMON-NAME "acetylornithine deacetylase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETYLORNDEACET-RXN)
(ENZYME ACETYLORNDEACET-CPLX)
(:CREATION-DATE 2969204100)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH GLUTATHIONE CITATIONS "[92331940]")
(ACTIVATORS-UNKMECH CO+2 COMMENT "When Co(II) is added to the enzyme already
containing a single mole of zinc, the activity
is increased. |CITS: [20150401]| ")
(INHIBITORS-UNKMECH "N-alpha-acetyl-DL-norvaline" COMMENT "in a
concentration of 25 mg/ml")
(INHIBITORS-UNKMECH "N-alpha-acetyl-DL-norvaline" CITATIONS "[75021016]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[VogelAdvEnzym40-71]")
(INHIBITORS-UNKMECH NI+2 CITATIONS "[VogelAdvEnzym40-71]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[VogelAdvEnzym40-71]")
(INHIBITORS-UNKMECH EDTA CITATIONS "[VogelAdvEnzym40-71]")
(INHIBITORS-UNKMECH "sulfhydryl reagents" CITATIONS "[VogelAdvEnzym40-71]")
(INHIBITORS-UNCOMPETITIVE "NaF" COMMENT
"Uncompetitive with respect to N-acetylornithine.")
(INHIBITORS-UNCOMPETITIVE "NaF" CITATIONS "20150401")
(INHIBITORS-COMPETITIVE L-ORNITHINE COMMENT
"Competitive with respect to N-acetylornithine. |CITS: [20150401]| ")
(INHIBITORS-COMPETITIVE ACET COMMENT
"Competitive with respect to N-acetylornithine. |CITS: [20150401]| ")
(COFACTORS ZN+2 COMMENT "The enzyme contains a single mole of Zn per
mole of enzyme. There is some evidence that
the enzyme contains two binding sites: a high-affinity
site binding zinc and a lower affinity site preferring
cobalt. |CITS: [20150401]| ")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT
"The enzyme exhibits broad specificity, but
exhibits absolute stereospecificity for acylated
L-amino acids. It is also specific for α-N-acylated
amino acids. |CITS: [92331940] [20150401]|")))
(ACETYLORNDEACET-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3957" "ArgE")
(COMMON-NAME "ArgE")
(DBLINKS (MODBASE "P23908" NIL |pkarp| 3355444116 NIL NIL)
(SWISSMODEL "P23908" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF01546" IN-FAMILY |pkarp| 3346700427 NIL NIL)
(REFSEQ "NP_418392" NIL |keseler| 3310234660 NIL NIL) (UNIPROT "P23908"))
(COMPONENT-OF ACETYLORNDEACET-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 42.3472969999999d0)
(GENE EG11286)
(:CREATION-DATE 2969204100)
(:CREATOR |mriley|) )
NIL)
(ACETYLORNDEACET-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLUTORN-PWY)
(ENZYMATIC-REACTION ACETYLORNDEACET-ENZRXN)
(RIGHT L-ORNITHINE ACET)
(LEFT N-ALPHA-ACETYLORNITHINE WATER)
(EC-NUMBER "3.5.1.16")
(COMMENT "This is the fifth step in arginine biosynthesis.")
(:CREATION-DATE 2969204100)
(:CREATOR |mriley|) )
NIL)
(ACETYLORNTRANSAM-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(MOLECULAR-WEIGHT-EXP 82)
(COMMENT
"The is a dual function enzyme, which participates in the biosynthesis of both lysine and arginine.
The enzyme was initially purified by Peterkofsky and Gilvarg |CITS: [13734750]|, and later by Cox et al |CITS: [Cox96]|,
as the dapC-encoded N-succinyldiaminopimelate-aminotransferase. However, searches for the
dapC gene were unsuccessful.
The gene has been independently cloned and sequenced as argD, encoding acetylornithine
transaminase, by Heimberg et al |CITS: [2199330]|. In 1999 Ledwidge and Blanchard |CITS: [10074354]|
purified and sequenced the N-succinyldiaminopimelate-aminotransferase protein,
showing that it is identical to the argD gene product.
Interestingly, the E. coli argD gene does not share sequence similarity with the dapC gene of other
organisms (such as Bordetella pertusis), even though both gene products catalyze the same reaction
|CITS: [10850974]|.")
(CATALYZES SUCCINYLDIAMINOPIMTRANS-ENZRXN ACETYLORNTRANSAM-ENZRXN)
(COMPONENTS ACETYLORNTRANSAM-MONOMER)
(:CREATION-DATE 2969204098)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 82 CITATIONS "Cox96")
(COMPONENTS ACETYLORNTRANSAM-MONOMER CITATIONS "79254656")
(COMPONENTS ACETYLORNTRANSAM-MONOMER COEFFICIENT 2)))
(ACETYLORNTRANSAM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (N-ALPHA-ACETYLORNITHINE 150))
(INHIBITORS-UNKMECH FE+2 CU+2 "sulfhydryl reagents")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT
"Acetylornithine transaminase catalyzes the fourth reaction in arginine
biosynthesis. The enzyme is the product of the argD gene. The catabolic
isozyme, the astC gene product, has a higher affinity for succinylornithine
than for acetylornithine. |CITS: [98361920] [98361921] [87039002]|")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(SYNONYMS "acetylornithine aminotransferase" "N-acetylornithine transaminase"
"N-acetylornithine-δ-transaminase" "ACOAT"
"N(2)-acetyl-L-ornithine:2-oxoglutarate aminotransferase")
(COMMON-NAME "acetylornithine transaminase")
(ALTERNATIVE-SUBSTRATES (N-ALPHA-ACETYLORNITHINE L-ORNITHINE))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETYLORNTRANSAM-RXN)
(ENZYME ACETYLORNTRANSAM-CPLX)
(:CREATION-DATE 2969204098)
(:CREATOR |mriley|) )
((KM (N-ALPHA-ACETYLORNITHINE 150) CITATIONS "10074354")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE CITATIONS "10074354")
(INHIBITORS-UNKMECH FE+2 CITATIONS "[VogelAdvEnzym40-70]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[VogelAdvEnzym40-70]")
(INHIBITORS-UNKMECH "sulfhydryl reagents" CITATIONS "[VogelAdvEnzym40-70]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "E. coli W |CITS:
[BillheimerJBact127,1315]|")))
(ACETYLORNTRANSAM-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-EXP 39.9d0)
(ISOZYME-SEQUENCE-SIMILARITY (SUCCORNTRANSAM-MONOMER YES))
(SYNONYMS "B3359" "Dtu" "DapC" "ArgD")
(COMMON-NAME "ArgD")
(DBLINKS (MODBASE "P18335" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00202" IN-FAMILY |pkarp| 3346700397 NIL NIL)
(REFSEQ "NP_417818" NIL |keseler| 3310234454 NIL NIL)
(SWISSMODEL "P18335" NIL |pkarp| 3064870651) (UNIPROT "P18335"))
(COMPONENT-OF ACETYLORNTRANSAM-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 43.766917999999876d0)
(GENE EG10066)
(:CREATION-DATE 2969204098)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 39.9d0 CITATIONS "cox96")))
(ACETYLORNTRANSAM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLUTORN-PWY)
(ENZYMATIC-REACTION ACETYLORNTRANSAM2-ENZRXN ACETYLORNTRANSAM-ENZRXN)
(RIGHT CPD-469 GLT)
(LEFT N-ALPHA-ACETYLORNITHINE 2-KETOGLUTARATE)
(EC-NUMBER "2.6.1.11")
(COMMENT "This is the fourth step in arginine biosynthesis.")
(:CREATION-DATE 2969204098)
(:CREATOR |mriley|) )
NIL)
(ACETYLORNTRANSAM2-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ALTERNATIVE-SUBSTRATES (N-ALPHA-ACETYLORNITHINE L-ORNITHINE)
(N-ALPHA-ACETYLORNITHINE N2-SUCCINYLORNITHINE))
(CITATIONS ":EV-EXP:3277835751:pkarp")
(:CREATION-DATE 3117804737)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETYLORNTRANSAM-RXN)
(COFACTORS-OR-PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(COMMENT
"The transaminase is the gene product of astC and is the catabolic version of
acetylornithine transaminase, the argD gene product. The astC enzyme shows a
higher affinity for succinylornithine than for acetylornithine.
|CITS: [98361920] [98361921] [87039002]|")
(ENZYME SUCCORNTRANSAM-CPLX)
(SYNONYMS "acetylornithine δ-aminotransferase"
"n-α-acetylornithine δ-aminotransferase"
"N2-acetyl-L-ornithine:2-oxoglutarate aminotransferase"
"carbon starvation protein C")
(COMMON-NAME "acetylornithine transaminase, catabolic") )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT
"The enzyme shows a higher affinity for succinylornithine than acetylornithine.
|CITS: [98361920]| ")
(COFACTORS-OR-PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE CITATIONS "[SwissProt]")))
(ACETYLSERINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF CPLX0-2781)
(DBLINKS (LIGAND-CPD "C00979" NIL |kr| 3346617699 NIL NIL) (CAS "66638-22-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -160.1d0)
(APPEARS-IN-LEFT-SIDE-OF RXN0-3001 RXN0-1923 ACSERLY-RXN)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-1923 SERINE-O-ACETTRAN-RXN)
(MOLECULAR-WEIGHT 147.13d0)
(CHEMICAL-FORMULA (C 5) (H 9) (N 1) (O 4))
(DISPLAY-COORDS-2D (-0.47811d0 0.07407d0) (-1.0d0 0.47138d0)
(0.12121d0 0.04377d0) (0.12121d0 -0.47811d0) (-0.47811d0 -0.47811d0)
(-0.47811d0 0.99327d0) (0.99663d0 -0.02357d0) (-0.47811d0 0.47138d0)
(0.73737d0 -0.47811d0) (0.99663d0 -0.93266d0) (0.12121d0 -1.0d0))
(STRUCTURE-BONDS (10 9 1) (8 6 1) (7 9 2) (5 4 1) (4 9 1) (4 11 1) (4 3 1)
(2 8 2) (1 5 1) (1 8 1))
(STRUCTURE-ATOMS O O H C C C O C C O N)
(SYNONYMS "O3-acetyl-L-serine" "acetylserine"
"O-acetylserine")
(COMMON-NAME "O-acetyl-L-serine")
(:CREATOR |shevelev|) )
((GIBBS-0 -160.1d0 CITATIONS "GibbsGroups97")))
(ACID-PHOSPHAT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH OXALATE)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION RXN0-1021)
(INHIBITORS-COMPETITIVE TARTRATE "sodium fluoride" "fusidic acid")
(COMMENT "Acid phosphatase catalyzes the hydrolysis of the distal
phosphoryl residues of GTP and of the regulatory nucleotide guanosine
5',3'-bisphosphate under very acidic conditions. |CITS: [82213795]|
The expression of the enzyme is subject to complex regulation. It is
induced by anoxia, influenced by the phase of growth, and the
concentration of phosphate. |CITS: [87165779] [82213795]| Although
the predominant enzymatic activity appears to be that of an acid
phosphatase, there is a second enzymatic activity associated with the
polypeptide coded for by the appA gene. This second activity is that
of a phytase. |CITS: [93256556]| The biological significance of the
pH 2.5 acid phosphatase in the periplasm of E. coli is still not
understood. The enzyme is apparently not able to supply the cell with
inorganic phosphate split from exogenous phosphorylated compounds or
polyphosphates. Its complex regulatory characteristics, and in
particular its synthesis in response to oxygen deprivation have
suggested a possible relationship with fermentation or respiration.
|CITS: [92049231]|")
(ENZYME CPLX-722)
(SYNONYMS "phosphoanhydride phosphohydrolase" "acid phosphomonoesterase"
"phosphomonoesterase" "glycerophosphatase" "acid phosphatase")
(COMMON-NAME "pH 2.5 acid phosphatase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/appA.template")
(:CREATION-DATE 3016372603)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH OXALATE COMMENT "Ethanol and dimethyl sulfoxide
inhibit the model reaction using PNPP as a substrate analog.")
(INHIBITORS-UNKMECH OXALATE CITATIONS "[82213795]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "Most monophosphorylated sugars are
barely hydrolyzed. The diphosphorylated sugars in
general are better substrates. Among the nucleoside polyphosphates GTP
was the best substrate. |CITS: [82213795]| The hydrolysis of
nucleoside triphosphate yields the corresponding nucleoside
diphosphate and in some cases the reaction proceeds to the stage of
monophosphate. However, within each base family the gamma phosphate
residue was removed much more efficiently than the beta phosphate of
the corresponding diphosphonucleoside. |CITS: [79209135]|")
(INHIBITORS-COMPETITIVE "fusidic acid" COMMENT
"competitively inhibited the hydrolysis of PNPP")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[82213795]")))
(ACID-PHOSPHATASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.3)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(ENZYMATIC-REACTION APHA-ENZRXN)
(EC-NUMBER "3.1.3.2")
(COMMON-NAME "ACID-PHOSPHATASE")
(COMMENT "WIDE SPECIFICITY. ALSO CATALYSES TRANSPHOSPHORYLATIONS.")
(RIGHT |Alcohols| |Pi|)
(LEFT WATER |Orthophosphoric-Monoesters|)
(SYNONYMS "ACID PHOSPHOMONOESTERASE" "PHOSPHOMONOESTERASE"
"GLYCEROPHOSPHATASE") )
NIL)
(ACNEULY-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/nanA.template")
(CATALYZES ACNEULY-ENZRXN)
(:CREATION-DATE 3041804876)
(COMPONENTS ACNEULY-MONOMER) )
((COMPONENTS ACNEULY-MONOMER COEFFICIENT 3)))
(ACNEULY-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH DIETHYLPYROCARBONATE N-BROMOSUCCINIMIDE CPD-29 FE+2 CU+2)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PHYSIOLOGICALLY-RELEVANT PYRUVATE DIHYDROXYACETONE "DL-glyceraldehyde")
(COMMENT "N-acetylneuraminate lyase is one of the key enzymes in
sialic acid metabolism. It is an inducible enzyme produced only in the
presence of the substrate N-acetylneuraminate. It is classified as a
Schiff-base forming Class I aldolase. Its physiological function
appears to be the breakdown of sialic acid into common metabolic
intermediates. The enzyme has been crystallized. |CITS: [91264813]|")
(REACTION ACNEULY-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/nanA.template")
(ENZYME ACNEULY-CPLX)
(:CREATION-DATE 3041804876)
(COMMON-NAME "N-acetylneuraminate lyase")
(SYNONYMS "N-acetylneuraminic acid aldolase" "NALase"
"N-acetylneuraminate pyruvate-lyase")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE PYRUVATE DIHYDROXYACETONE "DL-glyceraldehyde") )
((INHIBITORS-UNKMECH DIETHYLPYROCARBONATE CITATIONS "[91264813]")
(INHIBITORS-UNKMECH N-BROMOSUCCINIMIDE CITATIONS "[91264813]")
(INHIBITORS-UNKMECH CPD-29 CITATIONS "[91264813]")
(INHIBITORS-UNKMECH FE+2 COMMENT "slight inhibition")
(INHIBITORS-UNKMECH FE+2 CITATIONS "[91264813]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[91264813]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme shows a high degree of
specificity for sialic acids. |CITS: [91264813]|")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[91264813]")))
(ACNEULY-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Regulation has been described |CITS: [12897000]|. Transcription of the nanATEK-yhcH (sialic acid catabolic operon) is repressed by a NanR homodimer |CITS: [12897000]|.")
(SYNONYMS "B3225" "Npl" "NanA")
(COMMON-NAME "NanA")
(DBLINKS (MODBASE "P0A6L4" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6L4" NIL |pkarp| 3354911363)
(PFAM "PF00701" IN-FAMILY |pkarp| 3346700392 NIL NIL)
(PDB "1HL2" NIL |pkarp| 3346695112 NIL NIL)
(REFSEQ "NP_417692" NIL NIL NIL NIL NIL) (PDB "1NAL") (PDB "1FDZ")
(PDB "1FDY"))
(GENE EG10637)
(COMPONENT-OF ACNEULY-CPLX)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/nanA.template")
(:CREATION-DATE 3041804876)
(PI 5.91d0)
(MOLECULAR-WEIGHT-SEQ 32.59342899999992d0) )
NIL)
(ACNEULY-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLCMANNANAUT-PWY)
(COMMENT "This reaction breaks down sialic acid into common metabolic
intermediates. Sialic acid is a component of polysaccharide chains of
glycoproteins and glycolipids.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/two/nanA.template")
(ENZYMATIC-REACTION ACNEULY-ENZRXN)
(EC-NUMBER "4.1.3.3")
(:CREATION-DATE 3041804876)
(LEFT N-ACETYLNEURAMINATE)
(RIGHT N-ACETYL-D-MANNOSAMINE PYRUVATE) )
NIL)
(ACONITASE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3064871424)
(SYNONYMS "B1276" "Acn" "AcnA")
(CATALYZES ACONITATEDEHYDR-ENZRXN ACONITATEHYDR-ENZRXN)
(DBLINKS (MODBASE "P25516" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00330" IN-FAMILY |pkarp| 3346700331 NIL NIL)
(REFSEQ "NP_415792" NIL NIL NIL NIL NIL) (UNIPROT "P25516"))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 97.67709899999963d0)
(GENE EG11325)
(CITATIONS "[92174916]" "[92148368]")
(:CREATOR |mriley|) )
NIL)
(ACONITATEDEHYDR-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH NITRATE)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(ENZYME ACONITASE-MONOMER)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACONITATEDEHYDR-RXN)
(PROSTHETIC-GROUPS CPD-7)
(COMMENT "There are two aconitases in E. coli, both of which catalyze
the reversible isomerization of citrate and iso-citrate via
cis-aconitate. The acnA gene product is more stable,
has a higher affinity for citrate and is active over a wider pH
range than the acnB gene product. The main role of the acnA
enzyme is one of a maintenance or survival enzyme during
nutritional or oxidative stress. The acnB enzyme functions as the main
catabolic enzyme.
This is an iron-sulfur mediated reaction. The presence of an
iron-sulfur cluster in a hydrolase is unusual. |CITS: [20053887]|")
(SYNONYMS "aconitate hydratase" "citrate (isocitrate) hydro-lyase")
(COMMON-NAME "aconitase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/tca/acn2.template")
(:CREATION-DATE 3019237672)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH NITRATE CITATIONS "[68099840]")))
(ACONITATEDEHYDR-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ANARESP1-PWY TCA GLYOXYLATE-BYPASS)
(ENZYMATIC-REACTION ACONITATEDEHYDRB-ENZRXN ACONITATEDEHYDR-ENZRXN)
(RIGHT CIS-ACONITATE WATER)
(LEFT CIT)
(DELTAG0 2.0d0)
(EC-NUMBER "4.2.1.3")
(COMMENT "The nonoxidizable tertiary alcohol in citrate is converted
to an oxidizable secondary alcohol in isocitrate. Cis-aconitate is
the unsaturated intermediate.
The prpD gene encodes 2-methylcitrate dehydratase activity |CITS: [11782506]| and also encodes the minor aconitase activity, aconitase C |CITS: [11782506]|, which constitutes 5% or less of cellular activity and is observed in an acnA acnB double mutant |CITS: [9202458]|.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/tca/acn2.template")
(:CREATION-DATE 3019237672)
(:CREATOR |mriley|) )
NIL)
(ACONITATEDEHYDRB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "There are two aconitases in E. coli, both of which catalyze
the reversible isomerization of citrate and iso-citrate via
cis-aconitate. The acnA gene product is more stable,
has a higher affinity for citrate and is active over a wider pH
range than the acnB gene product. The main role of the acnA
enzyme is one of a maintenance or survival enzyme during
nutritional or oxidative stress. The acnB enzyme functions as the main
catabolic enzyme.
This is an iron-sulfur mediated reaction. The presence of an
iron-sulfur cluster in a hydrolase is unusual. |CITS: [95093601] [20053887]|")
(REACTION ACONITATEDEHYDR-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "~ecocyc/templates/new/acn/acnB.template")
(ENZYME ACONITATEDEHYDRB-MONOMER)
(PROSTHETIC-GROUPS CPD-7)
(:CREATION-DATE 3046611640)
(COMMON-NAME "aconitase B")
(SYNONYMS "aconitate hydratase" "citrate (isocitrate) hydro-lyase")
(REACTION-DIRECTION REVERSIBLE) )
((PROSTHETIC-GROUPS CPD-7 CITATIONS "[95093601]")))
(ACONITATEDEHYDRB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Purification of the enzyme is described |CITS: [12473114]|. Enzyme activity is sensitive to oxidation, and observations are consistent with dependence of activity on a [4Fe-4S] iron-sulfur cluster |CITS: [12473114]|.
Regulation has been described |CITS: [12473114]|.")
(MOLECULAR-WEIGHT-SEQ 93.49800499999971d0)
(MOLECULAR-WEIGHT-EXP 94)
(SYNONYMS "B0118" "YacI" "YacJ" "AcnB")
(DBLINKS (MODBASE "P36683" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF06434" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414660" NIL NIL NIL NIL NIL) (PDB "1L5J")
(UNIPROT "P36683" NIL |pkarp| 3064869797))
(GENE EG12316)
(:CREATOR |mriley|)
(TEMPLATE-FILE "~ecocyc/templates/new/acn/acnB.template")
(CATALYZES ENZRXN0-1505 ACONITATEDEHYDRB-ENZRXN ACONITATEHYDRB-ENZRXN)
(:CREATION-DATE 3046611640) )
((MOLECULAR-WEIGHT-EXP 94 CITATIONS "12473114")))
(ACONITATEHYDR-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH NITRATE)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(ENZYME ACONITASE-MONOMER)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACONITATEHYDR-RXN)
(PROSTHETIC-GROUPS FE+2)
(COMMENT "There are two aconitases in E. coli, both of which catalyze
the reversible isomerization of citrate and iso-citrate via
cis-aconitate. The acnA gene product is more stable,
has a higher affinity for citrate and is active over a wider pH
range than the acnB gene product. The main role of the acnA
enzyme is one of a maintenance or survival enzyme during
nutritional or oxidative stress. The acnB enzyme functions as the main
catabolic enzyme.
This is an iron-sulfur mediated reaction. The presence of an
iron-sulfur cluster in a hydrolase is unusual. |CITS: [20053887]|
")
(SYNONYMS "aconitate hydratase" "citrate (isocitrate) hydro-lyase")
(COMMON-NAME "aconitase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/tca/acn2.template")
(:CREATION-DATE 3019237672)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH NITRATE CITATIONS "[68099840]")))
(ACONITATEHYDR-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(EC-NUMBER "4.2.1.3")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ANARESP1-PWY TCA GLYOXYLATE-BYPASS)
(ENZYMATIC-REACTION ACONITATEHYDRB-ENZRXN ACONITATEHYDR-ENZRXN)
(RIGHT |threo-d(s)-iso-citrate|)
(LEFT CIS-ACONITATE WATER)
(DELTAG0 -0.5d0)
(COMMENT "Cis-aconitate, after dehydration of citrate, is rehydrated
to yield isocitrate.
The prpD gene encodes 2-methylcitrate dehydratase activity |CITS: [11782506]|and also encodes the minor aconitase activity, aconitase C |CITS: [11782506]|, which constitutes 5% or less of cellular activity and is observed in an acnA acnB double mutant |CITS: [9202458]|.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/tca/acn2.template")
(:CREATION-DATE 3019237672)
(:CREATOR |mriley|) )
NIL)
(ACONITATEHYDRB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "There are two aconitases in E. coli, both of which catalyze
the reversible isomerization of citrate and iso-citrate via
cis-aconitate. The acnA gene product is more stable,
has a higher affinity for citrate and is active over a wider pH
range than the acnB gene product. The main role of the acnA
enzyme is one of a maintenance or survival enzyme during
nutritional or oxidative stress. The acnB enzyme functions as the main
catabolic enzyme.
This is an iron-sulfur mediated reaction. The presence of an
iron-sulfur cluster in a hydrolase is unusual. |CITS: [95093601] [20053887]|")
(REACTION ACONITATEHYDR-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "~ecocyc/templates/new/acn/acnB.template")
(ENZYME ACONITATEDEHYDRB-MONOMER)
(PROSTHETIC-GROUPS CPD-7)
(:CREATION-DATE 3046611640)
(COMMON-NAME "aconitase B")
(SYNONYMS "aconitate hydratase" "citrate (isocitrate) hydro-lyase")
(REACTION-DIRECTION REVERSIBLE) )
((PROSTHETIC-GROUPS CPD-7 CITATIONS "[95093601]")))
(ACP NIL (
(OCELOT-GFP::PARENTS |Modified-Proteins| |All-ACPs|)
(INHIBITORS-UNKMECH-OF 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-ENZRXN
GLYCEROL-3-P-ACYLTRANSFER-ENZRXN)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(CHEMICAL-FORMULA (ACP 1))
(DISPLAY-COORDS-2D (1.7813d0 -5.4062d0))
(STRUCTURE-ATOMS ACP)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(LIGAND-CPD "C00229" NIL |kr| 3346617700 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(COMMENT
"The holo-ACP synthase enzyme (encoded by acpS) transfers the 4-phosphopantetheine
moiety of CoA to the apo-ACP to form holo-ACP, which is the active
form of the carrier in lipid synthesis |CITS: [68313114] [81215492]|.")
(:CREATION-DATE 3056125303)
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(APPEARS-IN-LEFT-SIDE-OF 3.1.4.14-RXN RXN-5741 ACYLACPSYNTH-RXN
ACP-S-ACETYLTRANSFER-RXN MALONYL-COA-ACP-TRANSACYL-RXN)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2141 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN
RXN0-1138 RXN0-1137 RXN0-1130 RXN0-947 MYRPALMTRAN-RXN PALMITOTRANS-RXN
MYRISTOYLACYLTRAN-RXN LAUROYLACYLTRAN-RXN GLYCEROL-3-P-ACYLTRANSFER-RXN
ACYLGPEACYLTRANS-RXN UDPNACETYLGLUCOSAMACYLTRANS-RXN
UDPHYDROXYMYRGLUCOSAMNACETYLTRANS-RXN 3-OXOACYL-ACP-SYNTH-RXN
HOLO-ACP-SYNTH-RXN)
(COMMON-NAME "acyl carrier protein")
(SYNONYMS "B1094" "AcpP" "holo-[acyl-carrier protein]" "ACP-SH" "ACP") )
NIL)
(ACP-MONOMER NIL (
(OCELOT-GFP::PARENTS |apo-ACP|)
(INHIBITORS-UNKMECH-OF HOLO-ACP-SYNTH-ENZRXN)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(GENE EG50003)
(MODIFIED-FORM LIPOYL-ACP OCTANOYL-ACP PALMITOLEOYL-ACP MYRISTOYL-ACP
LAUROYL-ACP TRANS-D2-DECENOYL-ACP CROTONYL-ACP SUCC-ACP MALONYL-ACP
CITRYL-ACP CIS-DELTA3-DECENOYL-ACP |cis-3,4-dehydrodecanoyl-acp|
3-OHMYRISTOYL-ACP ACETYL-ACP BUTYRYL-ACP ACETOACETYL-S-ACP
B-HYDROXYBUTYRYL-S-ACP BETA-HYDROXYDECANOYL-ACP ACP)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL) (PDB "1ACP")
(UNIPROT "P02901"))
(PI 4.14d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(COMMENT "Acyl carrier protein (ACP) plays an important role in fatty
acid biosynthesis. It carries fatty acid chains via a thioester
linkage to a phosphopantetheine prosthetic group as the chains are
elongated. There is also evidence that it has a function in the
biosynthesis of membrane-derived oligosaccharides. Therefore ACP and
its acyl forms interact with at least 12 different E. coli enzymes.
|CITS: [92210530] [89050961] [88296479]| ACP is the most abundant
protein in E. coli, with about 1.5E6 molecules per cell. |CITS: [Mathews&vanHolde]| ACP contains a
phosphopantetheine moiety (as does CoA) as the reactive unit, attached
to the ACP protein through a serine. The holo-ACP synthase enzyme
(encoded by the acpS gene) transfers the 4-phosphopantetheine
moeity of CoA to the apo-ACP to form holo-ACP, which is the active
form of the carrier in lipid synthesis |CITS: [68313114] [81215492]|.")
(SYNONYMS "apoprotein [acyl carrier protein]" "B1094" "AcpP"
"acyl carrier protein" "apo-ACP" "ACP")
(COMMON-NAME "apo-[acyl carrier protein]")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/carriers/acpP.template")
(:CREATION-DATE 2995810366)
(:CREATOR |mriley|) )
NIL)
(ACP-S-ACETYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "thiolactomycin" N-ETHYLMALEIMIDE IODOACETAMIDE)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(INHIBITORS-COMPETITIVE CPD-511 CO-A)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACP-S-ACETYLTRANSFER-RXN)
(COMMENT "Acetyl-CoA can be converted into acetyl-ACP by the ACP
S-acetyltransferase enzyme. The resulting acetyl-ACP can serve as the
primer when alternative condensing enzymes such as KASI participate in
the initiation of fatty acid production. |CITS: [94066913]| It has
been recently discovered that both transacylase and KASIII activities
are carried out by the same protein, coded for by the fabH gene.
|CITS: [92202232]|")
(ENZYME CPLX0-252)
(SYNONYMS "[acyl-carrier-protein] S-acetyltransferase"
"acetyl-CoA:[ACP] S-acetyltransferase" "acetyl-CoA:ACP transacylase")
(COMMON-NAME "acetyl-CoA:ACP transacylase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabH.template")
(:CREATION-DATE 3001089029)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "thiolactomycin" CITATIONS "[92202232]")
(INHIBITORS-UNKMECH N-ETHYLMALEIMIDE CITATIONS "[88268754]")
(INHIBITORS-UNKMECH IODOACETAMIDE CITATIONS "[88268754]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[88268754]")
(INHIBITORS-COMPETITIVE CPD-511 COMMENT "weak competitive inhibitor")
(INHIBITORS-COMPETITIVE CO-A COMMENT
"with respect to varied acetyl-CoA concentration")))
(ACP-S-ACETYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY FASYN-INITIAL-PWY)
(ENZYMATIC-REACTION ACP-S-ACETYLTRANSFER-ENZRXN)
(RIGHT ACETYL-ACP CO-A)
(LEFT ACP ACETYL-COA)
(EC-NUMBER "2.3.1.38")
(COMMENT "One of the initial reactions in fatty acid biosynthesis.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/fabH.template")
(:CREATION-DATE 3001089029)
(:CREATOR |mriley|) )
NIL)
(ACPSUB-CPLX NIL (
(OCELOT-GFP::PARENTS HOLO-CITRATE-LYASE)
(SYNONYMS "CitD acyl carrier protein")
(LOCATIONS CCO-CYTOPLASM)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-263)
(COMMENT "In the original purification of the enzyme, this subunit was
purified with a contaminant. It was thought that the enzyme existed
in an α-6 β-6 γ-1 structure. |CITS: [84024606]| Subsequent
work identified the contaminant, and the structure was recognized as
α-6 β-6 γ-6. |CITS: [87214225]|.
The prosthetic group, 2'-(5\"-phosphoribosyl)-3'-dephospho-CoA, is covalently bound to the
CitD acyl carrier protein (citrate lyase gamma subunit) |CITS: [11042274][10924139]| .
The prosthetic group is synthesized from the precursor, 2'-(5\"-triphosphoribosyl)-3'-dephospho-CoA,
which is transferred to the apo-citrate lyase
forming holo-citrate lyase and pyrophosphate |CITS: [11042274][10924139]| .
The prosthetic group precursor is synthesized from ATP and
dephospho-CoA |CITS: [11042274][10924139]| .
")
(COMPONENT-OF CITLY-CPLX)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/citly/citly.template")
(:CREATION-DATE 3042470476)
(COMMON-NAME "holo-citrate lyase")
(COMPONENTS ACPSUB-MONOMER) )
((COMPONENTS ACPSUB-MONOMER COEFFICIENT 6)))
(ACPSUB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (UNIPROT "P69330" NIL |pkarp| 3354911363)
(PFAM "PF04953" IN-FAMILY |pkarp| 3346700319 NIL NIL)
(REFSEQ "NP_415150" NIL NIL NIL NIL NIL))
(LOCATIONS CCO-CYTOPLASM)
(GENE G6343)
(COMPONENT-OF ACPSUB-CPLX)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/citly/citly.template")
(:CREATION-DATE 3042470476)
(COMMON-NAME "citrate lyase, acyl carrier γ subunit")
(MOLECULAR-WEIGHT-SEQ 10.689268999999994d0)
(SYNONYMS "B0617" "YbdX" "CitD") )
NIL)
(ACRB-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-25)
(MOLECULAR-WEIGHT-SEQ 113.57347499999933d0)
(:CREATION-DATE 3060042779)
(GENE EG11704)
(COMPONENT-OF TRANS-CPLX-201)
(COMMENT
"AcrB is an RND-type inner-membrane associate proton-substrate antiporter. It functions as a part of the AcrAB/TolC multidrug-efflux complex,
linking electrochemical-gradient energy to the efflux of drugs from the cytoplasm. The crystal structure of AcrB has been determined at 3.5 A resolution |CITS:[22262313]|.")
(SYNONYMS "AcrE" "B0462" "AcrB")
(DBLINKS (MODBASE "P31224" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00873" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_414995" NIL NIL NIL NIL NIL) (PDB "1IWG")
(UNIPROT "P31224" NIL |pkarp| 3064869797))
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AcrB RND-type permease") )
NIL)
(ACRD-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-25)
(SPECIES ECOLI)
(COMPONENT-OF CPLX0-3932)
(MOLECULAR-WEIGHT-SEQ 113.04718099999943d0)
(:CREATION-DATE 3060042779)
(COMMENT
"AcrD is a member of the resistance-nodulation-division (RND) family |CITS: [94293757]|.")
(SYNONYMS "B2470" "YffA" "AcrD")
(DBLINKS (MODBASE "P24177" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P24177" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00873" IN-FAMILY |pkarp| 3346700363 NIL NIL)
(REFSEQ "NP_416965" NIL NIL NIL NIL NIL)
(UNIPROT "P24177" NIL |pkarp| 3064869797))
(GENE EG10014)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AcrD") )
NIL)
(ACRF-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-25)
(MOLECULAR-WEIGHT-SEQ 111.45422499999935d0)
(SPECIES ECOLI)
(COMPONENT-OF CPLX0-2141)
(GENE EG10267)
(:CREATION-DATE 3060042779)
(SYNONYMS "B3266" "EnvD" "AcrF")
(DBLINKS (MODBASE "P24181" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P24181" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00873" IN-FAMILY |pkarp| 3346700393 NIL NIL)
(ECOO157CYC "ACRF_2-MONOMER" |Homolog| |pick| 3278712115 NIL NIL)
(ECOO157CYC "ACRF_1-MONOMER" |Homolog| |pick| 3278712115 NIL NIL)
(ECOO157CYC "Z2508-MONOMER" |Homolog| |pick| 3278712111 NIL NIL)
(REFSEQ "NP_417732" NIL NIL NIL NIL NIL)
(UNIPROT "P24181" NIL |pkarp| 3064869797))
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AcrF") )
NIL)
(ACS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT PROPIONATE)
(INHIBITORS-UNKMECH EDTA)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(:CREATION-DATE 3122659253)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACETATE--COA-LIGASE-RXN)
(INHIBITORS-COMPETITIVE PROPIONATE)
(COFACTORS MG+2)
(COMMENT
"There are two distinct pathways by which E. coli activates acetate to acetyl-CoA. Acetyl-CoA synthetase (ACS)
catalyzes one of them. It is thought that this ACS pathway functions in a mainly anabolic role, scavenging
acetate present in the extracellular medium. ACS also can catalyze acetylation of CheY, increasing signal
strength for flagellar rotation. |CITS: [95270608] [97151731] [98226742] [78047520]|")
(ENZYME ACS-MONOMER)
(SYNONYMS "acetate-CoA ligase" "acyl-activating"
"acetyl-coenzyme A synthetase" "acetyl activating enzyme"
"acetate thiokinase" "acetate:CoA ligase (AMP-forming)")
(COMMON-NAME "acetyl-CoA synthetase") )
((INHIBITORS-UNKMECH EDTA CITATIONS "[78047520]")
(INHIBITORS-COMPETITIVE PROPIONATE CITATIONS "[78047520]")
(COFACTORS MG+2 CITATIONS "[78047520]")))
(ACS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Acs appears to be more likely than PrpE to catalyze the first step in the propionate metabolism pathway
|CITS: [12473114]|.
Based on sequence similarity, Acs has been predicted to be a hydroxycinnamate-CoA ligase |CITS: [12952533]|.
Regulation has been described |CITS: [12473114], [14563880], [14651625]|. Gene expression is observed during
growth on acetate or propionate |CITS: [12473114]|.")
(:CREATION-DATE 3122658496)
(SYNONYMS "B4069" "AcsA" "YfaC" "Acs")
(DBLINKS (MODBASE "P27550" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P27550" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00501" IN-FAMILY |pkarp| 3346700433 NIL NIL)
(PDB "1PG4" NIL |pkarp| 3346695117 NIL NIL)
(REFSEQ "NP_418493" NIL NIL NIL NIL NIL)
(UNIPROT "P27550" NIL |paley| 3169408120))
(CATALYZES ENZRXN0-2823 ENZRXN0-1507 ACS-ENZRXN)
(MOLECULAR-WEIGHT-SEQ 72.09350499999985d0)
(GENE EG11448) )
NIL)
(ACSERLY-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY CYSTSYN-PWY)
(ENZYMATIC-REACTION ACSERLYB-ENZRXN ACSERLYA-ENZRXN)
(RIGHT CYS ACET)
(LEFT ACETYLSERINE HS)
(EC-NUMBER "2.5.1.47")
(COMMENT "This is the second reaction in the conversion of serine to
cysteine. Thioredoxin can also serve as source of sulfide.")
(:CREATION-DATE 2974150788)
(:CREATOR |mriley|) )
NIL)
(ACSERLYA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF CYSSYNMULTI-CPLX)
(CATALYZES ACSERLYA-ENZRXN)
(COMPONENTS ACSERLYA-MONOMER)
(:CREATION-DATE 2974150788)
(:CREATOR |mriley|) )
((COMPONENTS ACSERLYA-MONOMER COEFFICIENT 2)))
(ACSERLYA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(SYNONYMS "O-acetylserine sulfhydrylase A" "CSASE A"
"O3-acetyl-L-serine acetate-lyase (adding hydrogen-sulfide)"
"O-acetylserine (thiol)-lyase A" "OASS-A")
(COMMON-NAME "cysteine synthase A")
(ALTERNATIVE-SUBSTRATES (S |Thioredoxin|))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACSERLY-RXN)
(COFACTOR-BINDING-COMMENT "The native enzyme contains 2 molecules of pyridoxal
phosphate/molecule of enzyme. |CITS: [88257033]|")
(COMMENT "There are two enzymes that catalyze the reaction of
O-acetylserine with sulfide to yield cysteine, O-acetylserine
(thiol)-lyase A and B, sometimes designated as cysteine synthase A and
B. The sulfhydrylase A is coded for by the cysK gene and the
sulfhydrylase B is coded for by the cysM gene. Sulfhydrylase B can
also use thiosulfate in place of sulfide to give cysteine
thiosulfonate as a product. |CITS: [SwissProt]| Sulfhydrylase A is
found as a bifunctional complex with serine acetyltransferase |CITS:
[88009872] [91099514]| as well as free |CITS: [ColiSalII]|. The
cysteine synthase designations for acetylserine sulfhydrylases should
not be confused with the multienzyme complexes with serine acetyl
transferase. A 'Bi Bi Ping Pong' kinetic mechanism has been
demonstrated in S. typhimurium for the enzyme. |CITS:
[76190096]|")
(REQUIRED-PROTEIN-COMPLEX CYSSYNMULTI-CPLX)
(ENZYME ACSERLYA-CPLX)
(:CREATION-DATE 2974150788)
(:CREATOR |mriley|) )
NIL)
(ACSERLYA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT "Ssi5: \"sulfate starvation-induced\" |CITS: [8774726]|.
Regulation has been described |CITS: [8774726]|. Protein abundance is increased by sulfate starvation |CITS: [8774726]|.")
(SYNONYMS "B2414" "CysZ" "CysK" "Ssi5")
(COMMON-NAME "CysK")
(DBLINKS (MODBASE "P0ABK5" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0ABK5" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00291" IN-FAMILY |pkarp| 3346700361 NIL NIL)
(UNIPROT "P0ABK5" NIL |pkarp| 3338704379 NIL NIL)
(REFSEQ "NP_416909" NIL NIL NIL NIL NIL))
(COMPONENT-OF ACSERLYA-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (ACSERLYB-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 34.48960199999992d0)
(GENE EG10192)
(:CREATION-DATE 2974150788)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"Acetylserine (thiol)-lyase A (cysK) and B (cysM) carry out
the same reaction and have 40% sequence similarity. |CITS:
[90264334]| Acetylserine (thiol)-lyase A can form a multienzyme complex with
serine acetyltransferase (cysE), the cysteine synthase bifunctional
complex. Acetylserine (thiol)-lyase B does not.")))
(ACSERLYB-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-EXP 64)
(CATALYZES ACSERLYB-ENZRXN)
(COMPONENTS ACSERLYB-MONOMER)
(:CREATION-DATE 2974150799)
(:CREATOR |mriley|) )
((CREDITS SRI LAST-CURATED 3351979606)
(CREDITS |keseler| LAST-CURATED 3351979606)
(MOLECULAR-WEIGHT-EXP 64 CITATIONS "16546401")
(COMPONENTS ACSERLYB-MONOMER COEFFICIENT 2)))
(ACSERLYB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PH-OPT "7.2:9")
(KM (ACETYLSERINE 1300))
(CITATIONS "16546401:EV-EXP-IDA-PURIFIED-PROTEIN:3351979606:keseler")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(SYNONYMS "O-acetylserine (thiol)-lyase B" "O-acetylserine sulfhydrylase B"
"CSASE B" "O3-acetyl-L-serine acetate-lyase (adding hydrogen-sulfide)"
"OASS-B")
(COMMON-NAME "cysteine synthase B")
(ALTERNATIVE-SUBSTRATES (HS S2O3))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACSERLY-RXN)
(COMMENT
"The reaction follows a ping-pong bi bi mechanism |CITS: [16546401]|.")
(ENZYME ACSERLYB-CPLX)
(:CREATION-DATE 2974150799)
(:CREATOR |mriley|) )
((PH-OPT "7.2:9" CITATIONS "16546401")
(KM (ACETYLSERINE 1300) CITATIONS "16546401")))
(ACSERLYB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Cysteine synthase B is one of two isozymes in E. coli that catalyze the formation of L-cysteine from
O-acetyl-L-serine and sulfide |CITS: [colisalII]|. Unlike cysteine synthase A, cysteine synthase B does not form a
complex with serine acetyltransferase |CITS: [16546401]|. Both isozymes can also catalyze the reverse reaction,
mobilizing sulfur from cysteine and providing it for Fe-S cluster synthesis in vitro. This reaction can be driven
by removing the sulfide product or by dithiothreitol adding to the aminoacrylate |CITS: [8663055]|.
Cysteine synthase B can also use thiosulfate in place of sulfide, producing S-sulfocysteine |CITS: [12640465]|.
The broad substrate specificity of cysteine synthase was exploited for the synthesis of unnatural L-α-amino
acids |CITS: [12640465]|. Initial synthesis rates of nonproteinaceous amino acids have been determined
|CITS: [16546401]|.
Crystal structures of CysM have been solved at 2.1 and 2.7 Å resolution |CITS: [15952768]|.")
(SYNONYMS "B2421" "CysM")
(COMMON-NAME "CysM")
(DBLINKS (MODBASE "P16703" NIL |pkarp| 3355444109 NIL NIL)
(PDB "2BHS" NIL |keseler| 3351971162 NIL NIL)
(PDB "2BHT" NIL |keseler| 3351971162 NIL NIL)
(PFAM "PF00291" IN-FAMILY |pkarp| 3346700361 NIL NIL)
(REFSEQ "NP_416916" NIL NIL NIL NIL NIL) (UNIPROT "P16703"))
(COMPONENT-OF ACSERLYB-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (ACSERLYA-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 32.664111999999946d0)
(GENE EG10193)
(:CREATION-DATE 2974150799)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"O-acetylserine (thiol)-lyase A (cysK) and B (cysM) carry out
the same reaction and have 40% sequence similarity. |CITS:
[90264334]| The A enzyme can form a multienzyme complex with
serine acetyltransferase (cysE). The B enzyme does not.")))
(|Actinobacteria| T (
(OCELOT-GFP::PARENTS |Bacteria|)
(DBLINKS (NCBI-TAXONOMY-DB 201174))
(:CREATOR |paley|)
(:CREATION-DATE 3331579732) )
NIL)
(ACTION NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3276359832)
(:DOCUMENTATION "Encodes the type of action to be taken for a note.")
(:DOMAIN |Notes|) )
NIL)
(ACTIVATORS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3362411291)
(:DOMAIN |Binding-Reactions|)
(:VALUE-TYPE :SEXPR)
(:DOCUMENTATION
"Values of this slot are dotted pairs whose first element is a transcription factor
and whose second element is a DNA binding site. Presence of the transcription
factor bound to the DNA binding site activates this RNA-Polymerase binding
reaction, and therefore activates transcription.") )
NIL)
(ACTIVATORS-ALL NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3199046812)
(:VALUE-TYPE (:OR |Chemicals| :STRING))
(QUERYABLE? T)
(:DOCUMENTATION
"The computed set of all activators of the current enzymatic reaction, combined from all of the other activators slots.")
(:READ-ONLY T)
(:GET-METHODS GET-ACTIVATORS-ALL)
(:DOMAIN |Enzymatic-Reactions|) )
NIL)
(ACTIVATORS-ALLOSTERIC NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:INVERSE ACTIVATORS-ALLOSTERIC-OF)
(:CREATOR |paley|)
(:CREATION-DATE 3283182238)
(:DOCUMENTATION
"Allosteric activators increase the specified enzyme activity by binding reversibly to the
enzyme and inducing a conformational change that increases the affinity of the enzyme to
its substrates without affecting its VMAX.")
(:VALUE-TYPE (:OR |Chemicals| :STRING))
(QUERYABLE? T)
(:DOMAIN |Enzymatic-Reactions|) )
NIL)
(ACTIVATORS-ALLOSTERIC-OF NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3346770413)
(:VALUE-TYPE |Enzymatic-Reactions|)
(:INVERSE ACTIVATORS-ALLOSTERIC)
(:DOCUMENTATION
"This slot links a chemical to an enzymatic reaction frame for an enzyme that the compound allosterically activates. This slot is the inverse of slot ACTIVATORS-ALLOSTERIC.")
(:DOMAIN |Chemicals|) )
NIL)
(ACTIVATORS-NONALLOSTERIC NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:INVERSE ACTIVATORS-NONALLOSTERIC-OF)
(:CREATOR |paley|)
(:CREATION-DATE 3283182238)
(:DOCUMENTATION
"Nonallosteric activators increase the specified enzyme activity by means other than
allosteric.")
(QUERYABLE? T)
(:DOMAIN |Enzymatic-Reactions|)
(:VALUE-TYPE (:OR |Chemicals| :STRING)) )
NIL)
(ACTIVATORS-NONALLOSTERIC-OF NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3346770413)
(:VALUE-TYPE |Enzymatic-Reactions|)
(:INVERSE ACTIVATORS-NONALLOSTERIC)
(:DOCUMENTATION
"This slot links a chemical to an enzymatic reaction frame for an enzyme that the compound nonallosterically activates. This slot is the inverse of slot ACTIVATORS-NONALLOSTERIC.")
(:DOMAIN |Chemicals|) )
NIL)
(ACTIVATORS-UNKMECH NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:INVERSE ACTIVATORS-UNKMECH-OF)
(:CREATOR |paley|)
(:CREATION-DATE 3283182238)
(:DOCUMENTATION
"Compounds that activate the specified enzyme activity by an unknown
mechanism. The mechanism is defined as unknown, because either the
mechanism has yet to be elucidated in the experimental literature, or
the paper(s) curated thus far do not define the mechanism, and a full
literature search has yet to be performed.
")
(:VALUE-TYPE (:OR |Chemicals| :STRING))
(:DOMAIN |Enzymatic-Reactions|) )
NIL)
(ACTIVATORS-UNKMECH-OF NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3346770413)
(:VALUE-TYPE |Enzymatic-Reactions|)
(:INVERSE ACTIVATORS-UNKMECH)
(:DOCUMENTATION
"This slot links a chemical to an enzymatic reaction frame for an enzyme that the compound activates through an unknown mechanism. This slot is the inverse of slot ACTIVATORS-UNKMECH.")
(:DOMAIN |Chemicals|) )
NIL)
(|Active-Peptides| T (
(OCELOT-GFP::PARENTS |Protein-Segments|)
(COMMENT "Extent of a released active peptide.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414097) )
NIL)
(|Active-Sites| T (
(OCELOT-GFP::PARENTS |Amino-Acid-Sites|)
(SCHEMA? T)
(COMMENT "Amino acid(s) involved in the activity of an enzyme.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414654) )
NIL)
(ACYL-ACP T (
(OCELOT-GFP::PARENTS |Modified-Proteins| |All-ACPs|)
(INHIBITORS-OTHER-OF 3-OXOACYL-ACP-COA-SYNTHIII-ENZRXN)
(INHIBITORS-COMPETITIVE-OF 3-OXOACYL-ACP-COA-SYNTHIII-ENZRXN)
(INHIBITORS-UNKMECH-OF ENOYL-ACP-REDUCT-NADH-ENZRXN)
(DISPLAY-COORDS-2D (-3.5d0 -0.0313d0) (-2.7855d0 -0.4438d0)
(-2.0711d0 -0.0313d0) (-2.7855d0 -1.2688d0))
(CHEMICAL-FORMULA (C 1) (O 1) (ACP 1) (R 1))
(STRUCTURE-BONDS (2 3 1) (2 4 2) (1 2 1))
(STRUCTURE-ATOMS ACP C R O)
(SCHEMA? T)
(N+1-NAME "acyln+2-ACP")
(APPEARS-IN-RIGHT-SIDE-OF ACYLACPSYNTH-RXN)
(APPEARS-IN-LEFT-SIDE-OF ENOYL-ACP-REDUCT-NADPH-RXN ENOYL-ACP-REDUCT-NADH-RXN
1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN GLYCEROL-3-P-ACYLTRANSFER-RXN
ACYLGPEACYLTRANS-RXN 3-OXOACYL-ACP-SYNTH-RXN)
(SYNONYMS "acyl-[acyl carrier protein]" "CH3(CH2)xCO-S-ACP")
(COMMON-NAME "an acyl-ACP") )
NIL)
(ACYL-COA T (
(OCELOT-GFP::PARENTS |All-Coas|)
(COMPONENT-OF CPLX-126 MONOMER-51)
(SCHEMA? T)
(SUPERATOMS COA-GROUP)
(N-1-NAME "acyln-2-CoA")
(N+1-NAME "acyln+2-CoA")
(CHEMICAL-FORMULA (C 22) (H 35) (N 7) (O 17) (R 1) (P 3) (S 1))
(DISPLAY-COORDS-2D (0.65732086d0 -0.58566976d0) (-0.1775701d0 -0.42990655d0)
(-0.5607477d0 -0.84423673d0) (0.12772584d0 -0.42990655d0)
(0.76012456d0 0.08099687d0) (0.62616813d0 0.4641744d0)
(-0.87227416d0 -0.1246106d0) (0.44236755d0 -0.2679128d0)
(0.90031147d0 -5.9604645d-8) (0.12772584d0 -0.10280377d0)
(-0.635514d0 -0.2866044d0) (-1.0d0 -0.36137074d0)
(-0.25856698d0 -0.84423673d0) (0.65732086d0 -0.38006234d0)
(-0.6853583d0 -0.7788162d0) (-0.13084114d0 -0.7538941d0)
(0.62616813d0 0.29906535d0) (0.65732086d0 -0.48286605d0)
(-0.7694704d0 -0.5264798d0) (-0.635514d0 -0.44859815d0)
(0.9968847d0 0.14953268d0) (0.84112144d0 -0.47663552d0)
(0.75700927d0 -0.58566976d0) (-0.6853583d0 -0.6105919d0)
(0.84112144d0 -0.38006234d0) (0.5919002d0 -0.36448598d0)
(0.00934577d0 -0.8504673d0) (-0.8753894d0 -0.8504673d0)
(0.4984423d0 0.22118378d0) (0.65732086d0 -0.2834891d0)
(-0.635514d0 -0.1246106d0) (0.76012456d0 0.22741425d0)
(-0.1775701d0 -0.10280377d0) (-0.87227416d0 -0.2866044d0)
(-0.1775701d0 -0.2679128d0) (0.90031147d0 -0.27102804d0)
(0.84112144d0 -0.2834891d0) (0.2866043d0 -0.2679128d0)
(0.17445481d0 -0.7538941d0) (0.65732086d0 -0.6884735d0)
(-0.36448598d0 -0.2679128d0) (-0.7694704d0 -0.36137074d0)
(0.4984423d0 0.07476628d0) (0.00934577d0 -1.0d0) (0.5919002d0 -0.27102804d0)
(0.8909657d0 0.2866043d0) (0.90031147d0 -0.36448598d0)
(-0.034267962d0 -0.2679128d0) (-0.39875394d0 -0.76323986d0)
(0.55451703d0 -0.58878505d0) (0.12772584d0 -0.2679128d0)
(0.7445482d0 -0.1806854d0) (-1.0d0 -0.7788162d0)
(0.6417445d0 -0.006230533d0) (-0.5077882d0 -0.36137074d0))
(AROMATIC-RINGS (5 32 46 21 9) (54 43 29 17 32 5))
(STRUCTURE-BONDS (55 41 1) (54 5 :AROMATIC) (53 12 1) (52 36 1) (51 38 1)
(50 1 2) (49 3 1) (48 51 1) (47 36 1) (46 21 :AROMATIC) (45 52 1) (45 14 1)
(43 54 :AROMATIC) (42 11 1) (41 35 1) (40 1 1) (38 8 1) (37 25 1) (36 9 1)
(36 25 1) (35 48 1) (34 42 1) (33 35 2) (32 46 :AROMATIC) (32 17 :AROMATIC)
(31 11 1) (30 14 1) (29 43 :AROMATIC) (28 53 1) (27 44 2) (27 16 1)
(27 39 1) (26 45 1) (24 15 2) (23 1 1) (22 25 1) (21 9 :AROMATIC) (20 11 1)
(19 42 1) (17 29 :AROMATIC) (16 13 1) (15 28 1) (14 18 1) (14 25 1)
(13 49 1) (12 34 1) (11 55 1) (10 51 2) (9 5 :AROMATIC) (8 45 1) (7 34 2)
(6 17 1) (5 32 :AROMATIC) (4 51 1) (3 15 1) (2 35 1) (1 18 1))
(STRUCTURE-ATOMS P O N O C N O C N O C N C C C S C O O C C O O O C H C C N H
C C O C P C H O R O O C C O C N H O C O P O C N C)
(COMMON-NAME "an acyl-CoA")
(SYNONYMS "fatty acyl thioester-CoA" "an acyl-CoA" "RCH2CH2CO-CoA"
"acyl-Coenzyme A")
(APPEARS-IN-RIGHT-SIDE-OF ACYLCOASYN-RXN)
(APPEARS-IN-LEFT-SIDE-OF KETOACYLCOATHIOL-RXN TRANSENOYLCOARED-RXN
ACECOATRANS-RXN R135-RXN R134-RXN THIOESTER-RXN ACYLCOADEHYDROG-RXN) )
((SUPERATOMS COA-GROUP REPLACES-ATOM 16)
(SUPERATOMS COA-GROUP CONNECTED-TO 27)))
(|Acyl-L-Lysines| T (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(COMMON-NAME "an N6acyl-L-lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|Acyl-Phosphates| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(CHEMICAL-FORMULA (C 1) (H 2) (O 5) (R 1) (P 1))
(STRUCTURE-BONDS (6 8 1) (6 7 1) (5 7 1) (4 8 1) (3 8 1) (2 8 2) (1 7 2))
(DISPLAY-COORDS-2D (4.0123d0 -3.5136d0) (1.3863d0 -2.7999d0) (0.0d0 -1.39d0)
(1.3852d0 0.0d0) (5.2247d0 -1.4136d0) (2.7999d0 -1.4135d0)
(4.0123d0 -2.1136d0) (1.4d0 -1.3999d0))
(STRUCTURE-ATOMS O O O O R O C P)
(COMMON-NAME "an acyl phosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(ACYL-SN-GLYCEROL-3P T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (1.2102d0 0.0d0) (5.0309d0 -5.584d0) (6.0509d0 -1.4002d0)
(3.6131d0 -7.0191d0) (2.2302d0 -5.584d0) (0.0d0 -2.0919d0)
(3.6304d0 -1.4002d0) (4.8406d0 -3.4921d0) (2.4205d0 -2.0919d0)
(3.6304d0 -4.1838d0) (1.2102d0 -1.4002d0) (4.8406d0 -2.0919d0)
(3.6304d0 -5.584d0))
(CHEMICAL-FORMULA (C 4) (H 8) (O 7) (R 1) (P 1))
(STRUCTURE-BONDS (10 13 1) (9 11 1) (8 12 1) (8 10 1) (7 12 1) (7 9 1)
(6 11 1) (5 13 1) (4 13 1) (12 3 1 :UP) (2 13 2) (1 11 2))
(STRUCTURE-ATOMS O O O O O R C C O O C C P)
(APPEARS-IN-LEFT-SIDE-OF 1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN)
(:CREATION-DATE 3123450416)
(APPEARS-IN-RIGHT-SIDE-OF GLYCEROL-3-P-ACYLTRANSFER-RXN)
(SYNONYMS "1-acyl-sn-glycerol-3-phosphate" "acyl-sn-glycerol-3P"
"acyl-sn-glycerol-3-phosphate")
(COMMON-NAME "a 1-acyl-sn-glycerol-3P") )
NIL)
(ACYLACPSYNTH-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "salts")
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS MG+2)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACYLACPSYNTH-RXN)
(COMMENT "2-Acylglycerophosphoethanolamine (2-acyl-GPE)
acyltransferase and acyl-acyl carrier protein (acyl-ACP) synthetase
are dual catalytic activities encoded by the aas gene. Both enzymes
participate in membrane phospholipid turnover and the uptake and
incorporation of exogenous 2-acyllysophospholipids. Acyl-ACP
synthetase functions to ligate free fatty acids, with lengths of C-8
to C-18, to ACP. |CITS: [94132066] [91310656] [79216404]|")
(ENZYME AAS-MONOMER)
(SYNONYMS "acyl-acyl carrier protein synthetase"
"long chain fatty acid-[acyl-carrier protein] ligase"
"long chain fatty acid-[acyl-carrier protein] ligase (AMP-forming)")
(COMMON-NAME "acyl-ACP synthetase")
(TEMPLATE-FILE "~ecocyc/templates/new/aas/aas.template")
(:CREATION-DATE 3047852706)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "salts" COMMENT
"This inhibition is completely reversible.
|CITS: [79216404]|")
(COFACTORS MG+2 COMMENT " The enzyme has an absolute requirement for
Mg++. |CITS: [79216404]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme has broad substrate
specificity. C-12,14 and 16 fatty acids are the best substrates, the
unsaturated analogs and shorter chain acids are poorer substrates.
|CITS: [79216404]|")))
(ACYLACPSYNTH-RXN NIL (
(OCELOT-GFP::PARENTS EC-6.2.1 |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ACYLACPSYNTH-ENZRXN)
(RIGHT AMP PPI ACYL-ACP)
(LEFT ATP |a fatty acid| ACP)
(EC-NUMBER "6.2.1.20")
(COMMENT
"This reaction is part of the acyl-CoA-independent incorporation of exogenous fatty acids and 2-acyllysophospholipids into the cell. |CITS: [94132066]|")
(TEMPLATE-FILE "~ecocyc/templates/new/aas/aas.template")
(:CREATION-DATE 3047852706)
(:CREATOR |mriley|) )
NIL)
(|Acylcholines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(CHEMICAL-FORMULA (C 6) (H 13) (N 1) (O 2) (R 1))
(ATOM-CHARGES (10 1))
(STRUCTURE-BONDS (8 9 1) (7 10 1) (6 8 1) (6 7 1) (5 9 1) (4 9 2) (3 10 1)
(2 10 1) (1 10 1))
(DISPLAY-COORDS-2D (7.2746d0 -1.4d0) (6.0621d0 -2.1d0) (7.2746d0 0.0d0)
(1.2124d0 -2.1d0) (0.0d0 0.0d0) (3.6373d0 -0.7d0) (4.8497d0 0.0d0)
(2.4248d0 0.0d0) (1.2124d0 -0.7d0) (6.0621d0 -0.7d0))
(STRUCTURE-ATOMS C C C O R C C O C N)
(COMMON-NAME "an acylcholine")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(ACYLCOADEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACYLCOADEHYDROG-RXN)
(COMMENT "There is very little known about this enzyme. This is the
rate-limiting step of any one cycle of oxidation of acyl-CoA. |CITS:
[78026368]|")
(ENZYME ACYLCOADEHYDROG-MONOMER)
(SYNONYMS "medium-chain acyl-CoA dehydrogenase" "acyl dehydrogenase"
"acyl-CoA:(acceptor) 2,3-oxidoreductase")
(COMMON-NAME "acyl-CoA dehydrogenase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadE.template")
(:CREATION-DATE 3001088684)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "Ranges from short to long chain fatty
acids.")))
(ACYLCOADEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 89.22432299999988d0)
(CITATIONS "82052864")
(DBLINKS (MODBASE "Q47146" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02771" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(UNIPROT "Q47146" NIL |pick| 3277847086)
(REFSEQ "NP_414756" NIL NIL NIL NIL NIL))
(SYNONYMS "B0221" "FadE" "YafH" "FadF")
(CATALYZES ACYLCOADEHYDROG-ENZRXN)
(GENE G6105)
(COMMENT
"The previously uncharacterized yafH open reading frame has been shown to encode the FadE acyl-CoA
dehydrogenase enzyme |CITS: [11771124][12057976]|. The fadE62 mutation is a single base deletion within
yafH, resulting in a frame shift mutation, and yafH can complement the phenotype of the fadE62 mutant
strain |CITS: [12057976]|.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadE.template")
(:CREATION-DATE 3001088684)
(:CREATOR |mriley|) )
NIL)
(ACYLCOADEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.3.99)
(OFFICIAL-EC? T)
(IN-PATHWAY FAO-PWY)
(ENZYMATIC-REACTION ENZRXN0-2763 ENZRXN0-2761 ACYLCOADEHYDROG-ENZRXN)
(RIGHT FADH2 D2-ENOYL-COA)
(LEFT ACYL-COA FAD)
(EC-NUMBER "1.3.99.3")
(COMMENT "The second step in fatty acid degradation and part of the
β-oxidation cycle.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadE.template")
(:CREATION-DATE 3001088684)
(:CREATOR |mriley|) )
NIL)
(ACYLCOASYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ACYLCOASYN-ENZRXN)
(LOCATIONS CCO-CYTOPLASM)
(COMPONENTS ACYLCOASYN-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadD.template")
(:CREATION-DATE 3001088681)
(:CREATOR |mriley|) )
((COMPONENTS ACYLCOASYN-MONOMER COMMENT "probable |CITS: [SwissProt]|")
(COMPONENTS ACYLCOASYN-MONOMER COEFFICIENT 2)
(LOCATIONS :FACET COMMENT "The enzyme is partially
membrane-associated but most of the enzyme is found in cytoplasmic
fractions. |CITS: [81215484]| ")))
(ACYLCOASYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH "salts")
(INHIBITORS-UNKMECH "ClO4" "SCN")
(CITATIONS ":EV-EXP:3277835750:pkarp" "[93094273]")
(COFACTORS MG+2)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACYLCOASYN-RXN)
(COMMENT "Long chain fatty acid CoA-ligase, also known as acyl-CoA
synthetase or synthase, plays a pivotal role in the transport and
activation of exogenous fatty acids prior to their subsequent
degradation or incorporation into phospholipids. This is the rate
limiting step of β-oxidation in E. coli. |CITS: [81215484]|
The enzyme catalyzes the esterification of fatty acids into
metabolically active CoA thioesters concomitant with transport. The
reaction proceeds by a two-step mechanism. The enzyme has broad chain
length specificity, with maximal activities associated with fatty
acids ranging in length between C-12 and C-18. The enzyme appears to
be partially membrane-associated. |CITS: [93094273]|")
(ENZYME ACYLCOASYN-CPLX)
(SYNONYMS "long chain fatty acid CoA-ligase" "acyl-activating enzyme"
"acyl-CoA synthase" "fatty acid thiokinase (long-chain)"
"lignoceroyl-CoA synthase" "long-chain acyl-CoA synthetase"
"palmitoyl-CoA synthase" "arachidonyl-CoA synthetase"
"acid:CoA ligase (AMP forming)")
(COMMON-NAME "fatty acyl-CoA synthetase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadD.template")
(:CREATION-DATE 3001088681)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH "salts" COMMENT "SCN, ClO4, NO3, SO4, PO4, at low
concentrations, e.g. 50mM |CITS: [85200021]|")
(INHIBITORS-UNKMECH "ClO4" COMMENT "at >200mM
The inhibition is reversible. |CITS: [85200021]|")
(INHIBITORS-UNKMECH "SCN" COMMENT "at >200mM
The inhibition is reversible. |CITS: [85200021]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "Fatty acids ranging in length C-6 to
C-18; also a long chain carboxylic acid elaidic acid.
The enzyme activates trans fatty acids as well as cis acids
|CITS: [85200021] [81215484]|")))
(ACYLCOASYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CITATIONS "15347640")
(COMMENT
"The FadD protein, encoding fatty acyl-CoA synthetase, can transport long chain fatty acids across the inner
membrane in an in vitro system |CITS: [15067008]|.")
(MOLECULAR-WEIGHT-EXP 62)
(SYNONYMS "B1805" "OldD" "FadD")
(DBLINKS (MODBASE "P69451" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P69451" NIL |pkarp| 3354911363)
(PFAM "PF00501" IN-FAMILY |pkarp| 3346700343 NIL NIL)
(REFSEQ "NP_416319" NIL NIL NIL NIL NIL))
(COMMON-NAME "FadD")
(COMPONENT-OF ACYLCOASYN-CPLX)
(PI 6.61d0)
(MOLECULAR-WEIGHT-SEQ 62.33190099999983d0)
(GENE EG11530)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadD.template")
(:CREATION-DATE 3001088681)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 62.0d0 CITATIONS "1460045")))
(ACYLCOASYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.2.1)
(BALANCE-STATE :UNBALANCED-DIFFERING-R-GROUPS)
(OFFICIAL-EC? T)
(IN-PATHWAY FAO-PWY)
(ENZYMATIC-REACTION ENZRXN0-2570 ACYLCOASYN-ENZRXN)
(RIGHT ACYL-COA PPI AMP)
(LEFT CO-A |a fatty acid| ATP)
(EC-NUMBER "6.2.1.3")
(COMMENT "This reaction is the first step of
β-oxidation of fatty acids. R= saturated aliphatic chain.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/fadD.template")
(:CREATION-DATE 3001088681)
(:CREATOR |mriley|) )
NIL)
(ACYLGPEACYLTRANS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "LiCl")
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS MG+2)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACYLGPEACYLTRANS-RXN)
(COMMENT "2-Acylglycerophosphoethanolamine (2-acyl-GPE)
acyltransferase and acyl-acyl carrier protein (acyl-ACP) synthetase
are dual catalytic activities encoded by the aas gene. Both enzymes
participate in membrane phospholipid turnover and the uptake and
incorporation of exogenous 2-acyllysophospholipids. The function of
2-acyl-GPE acyltransferase is to regenerate phosphatidylethanolamine
(PtdEtn) from 2-acyl-GPE formed by transacylation reactions or
phospholipase A1 action. In the process enzyme-bound ACP is also
regenerated. |CITS: [94132066] [91310656]|")
(ENZYME AAS-MONOMER)
(SYNONYMS "2-acyl-GPE acyltransferase"
"acyl-[acyl-carrier protein]-phospholipid O-acyltransferase"
"acyl-[acyl-carrier protein]:O-(acyl-sn-glycero-3-phospho)-ethanolamine O-acyltransferase")
(COMMON-NAME "2-acylglycerophosphoethanolamine acyltransferase")
(TEMPLATE-FILE "~ecocyc/templates/new/aas/aas.template")
(:CREATION-DATE 3047852706)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "LiCl" COMMENT "Inhibition can be overcome by addition
of ACP. LiCl appears to affect the enzyme's ability to utilize ACP.
|CITS: [84212428]|")
(COFACTORS MG+2 CITATIONS "[84212428]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme appears to be specific for
the 1-position of the glycerol backbone. |CITS: [84212428]|")))
(ACYLGPEACYLTRANS-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.3.1 |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ACYLGPEACYLTRANS-ENZRXN)
(RIGHT ACP L-1-PHOSPHATIDYL-ETHANOLAMINE)
(LEFT ACYL-ACP 2-ACYL-GPE)
(EC-NUMBER "2.3.1.40")
(COMMENT
"This reaction is part of the acyl-CoA-independent incorporation of exogenous fatty acids and 2-acyllysophospholipids into the cell. |CITS: [94132066]|")
(TEMPLATE-FILE "~ecocyc/templates/new/aas/aas.template")
(:CREATION-DATE 3047852706)
(:CREATOR |mriley|) )
NIL)
(ADCLY-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ADCLY-ENZRXN)
(COMPONENT-OF PABSYNMULTI-CPLX)
(COMPONENTS ADCLY-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/paba/pabC2.template")
(:CREATION-DATE 3023207502)
(:CREATOR |mriley|) )
((COMPONENTS ADCLY-MONOMER COEFFICIENT 2)))
(ADCLY-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(ENZYME ADCLY-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADCLY-RXN)
(PROSTHETIC-GROUPS PYRIDOXAL)
(COMMENT "p-Aminobenzoate synthesis requires three enzymes, in a
multi-enzyme complex, acting as a glutaminase, chorismate aminase and
a 4-amino-4-deoxychorismate aromatase. PabC encodes the
4-amino-4-deoxychorismate aromatase activity; the enzyme is known as
aminochorismate lyase. |CITS: [91302313] [92355506]|")
(REQUIRED-PROTEIN-COMPLEX PABSYNMULTI-CPLX)
(SYNONYMS "ADC lyase" "4-amino-4-deoxychorismate lyase")
(COMMON-NAME "aminodeoxychorismate lyase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/paba/pabC2.template")
(:CREATION-DATE 3023207502)
(:CREATOR |mriley|) )
((PROSTHETIC-GROUPS PYRIDOXAL COMMENT "The holoenzyme
contains 1.26 mol of pyridoxal phosphate per subunit. |CITS:
[92355506]|")))
(ADCLY-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1096" "PabC")
(DBLINKS (MODBASE "P28305" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01063" IN-FAMILY |pkarp| 3346700328 NIL NIL)
(PDB "1I2L" NIL |pkarp| 3346695108 NIL NIL)
(REFSEQ "NP_415614" NIL NIL NIL NIL NIL)
(UNIPROT "P28305" NIL NIL |ouzounis| 3027899498))
(COMPONENT-OF ADCLY-CPLX)
(PI 6.47d0)
(MOLECULAR-WEIGHT-SEQ 29.71501899999998d0)
(GENE EG11493)
(COMMON-NAME "pabC")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/paba/pabC.template")
(:CREATION-DATE 3000590454)
(:CREATOR |mriley|) )
NIL)
(ADCLY-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ADCLY-ENZRXN)
(IN-PATHWAY FOLSYN-PWY)
(RIGHT P-AMINO-BENZOATE PYRUVATE)
(LEFT 4-AMINO-4-DEOXYCHORISMATE)
(EC-NUMBER "4.1.3.38")
(COMMENT "This is the second step in para-aminobenzoate biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/paba/pabC.template")
(:CREATION-DATE 3000590454)
(:CREATOR |mriley|) )
NIL)
(ADDALT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(:CREATION-DATE 3059166674)
(SYNONYMS "adenosine deaminase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADDALT-RXN)
(ENZYME ADENODEAMIN-MONOMER)
(COMMON-NAME "deoxyadenosine deaminase") )
NIL)
(ADDALT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3059166674)
(IN-PATHWAY SALVADEHYPOX-PWY)
(RIGHT AMMONIA DEOXYINOSINE)
(LEFT WATER DEOXYADENOSINE)
(COMMENT "This reaction is part of nucleotide metabolism.")
(ENZYMATIC-REACTION ADDALT-ENZRXN) )
NIL)
(ADDRESS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3355681225)
(:VALUE-TYPE :STRING)
(:DOMAIN |Organizations|)
(:DOCUMENTATION
"Stores the address of an organization, typically for use in the author crediting
system. Example usage is to store multiple values in the slot, one value
for the street address followed by one value for the city, state, and country.
") )
NIL)
(ADENINE NIL (
(OCELOT-GFP::PARENTS |Purine-Bases| |Purines|)
(INHIBITORS-UNKMECH-OF DAPASYN-ENZRXN)
(DBLINKS (LIGAND-CPD "C00147" NIL |kr| 3346617701 NIL NIL) (CAS "73-24-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 76.6d0)
(COMMON-NAME "adenine")
(SYNONYMS "2-aminopurine")
(APPEARS-IN-RIGHT-SIDE-OF ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN RXN0-1342
RXN0-986 RXN0-984 ADENOSINE-NUCLEOSIDASE-RXN RXN0-309 AMP-NUCLEOSID-RXN
ADENPRIBOSYLTRAN-RXN ADENPHOSPHOR-RXN)
(APPEARS-IN-LEFT-SIDE-OF ADENINE-DEAMINASE-RXN DEOXYADENPHOSPHOR-RXN)
(DISPLAY-COORDS-2D (-1.0869d0 -2.7101d0) (-1.8346d0 -1.4924d0)
(-0.4063d0 -1.4538d0) (-0.3838d0 -2.2784d0) (0.8739d0 -1.8315d0)
(0.3711d0 -1.1776d0) (0.4074d0 -2.5119d0) (-1.1317d0 -1.0608d0)
(-1.8124d0 -2.3172d0) (-1.0645d0 -3.5349d0))
(STRUCTURE-BONDS (1 10 1) (6 5 1) (7 5 2) (7 4 1) (3 4 :AROMATIC) (3 6 1)
(8 3 :AROMATIC) (2 8 :AROMATIC) (9 2 :AROMATIC) (1 9 :AROMATIC)
(4 1 :AROMATIC))
(STRUCTURE-ATOMS C C C C C N N N N N)
(CHEMICAL-FORMULA (C 5) (H 5) (N 5))
(MOLECULAR-WEIGHT 135.128d0)
(AROMATIC-RINGS (4 3 8 2 9 1)) )
((GIBBS-0 76.6d0 CITATIONS "GibbsGroups97")))
(ADENINE-DEAMINASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.4)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2583)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3281294643)
(SYNONYMS "Adenine aminase" "Adenase")
(COMMON-NAME "Adenine deaminase")
(EC-NUMBER "3.5.4.2")
(RIGHT AMMONIA HYPOXANTHINE)
(LEFT WATER ADENINE) )
NIL)
(ADENINE-RING NIL (
(OCELOT-GFP::PARENTS |Rings|)
(:CREATION-DATE 3074547137)
(MOLECULAR-WEIGHT 134.12d0)
(CHEMICAL-FORMULA (C 5) (H 4) (N 5))
(DISPLAY-COORDS-2D (0.50628924d0 0.6383647d0) (-1.0d0 0.35220122d0)
(-0.006289363d0 0.35220122d0) (-0.509434d0 -1.0d0)
(-0.006289363d0 -0.106918275d0) (0.99685526d0 0.10062885d0)
(-0.509434d0 0.68238986d0) (-1.0d0 -0.15408808d0)
(0.50628924d0 -0.4591195d0) (-0.509434d0 -0.4811321d0))
(STRUCTURE-BONDS (10 4 1) (10 8 :AROMATIC) (10 5 :AROMATIC) (9 5 :AROMATIC)
(8 2 :AROMATIC) (7 3 :AROMATIC) (6 9 :AROMATIC) (5 3 :AROMATIC)
(3 1 :AROMATIC) (2 7 :AROMATIC) (1 6 :AROMATIC))
(STRUCTURE-ATOMS N C C N C C N N N C)
(AROMATIC-RINGS (5 9 6 1 3) (5 10 8 2 7 3))
(COMMENT-INTERNAL "kr97-06-05: can be attached at the N1 .")
(COMMON-NAME "adenine-ring") )
NIL)
(ADENODEAMIN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH COFORMYCIN CPD-29)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(ALTERNATIVE-SUBSTRATES (ADENOSINE DEOXYADENOSINE))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENODEAMIN-RXN)
(COMMENT "Adenosine deaminase is part of a pathway which converts
adenine, adenosine and deoxyadenosine to guanine nucleotides. |CITS:
[76125643] [79010020]|")
(ENZYME ADENODEAMIN-MONOMER)
(SYNONYMS "adenosine aminohydrolase")
(COMMON-NAME "adenosine deaminase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/add.template")
(:CREATION-DATE 3010350928)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH COFORMYCIN CITATIONS "[79010020]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT
"adenosine and 2-deoxyadenosine are considered to be the natural
substrates; also serving as substrates are 6-methylaminopurine
ribonucleoside, adenine arabinoside, 3-deoxyadenosine and
2,3-dideoxyadenosine |CITS: [79010020]|")))
(ADENODEAMIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P22333" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00962" IN-FAMILY |pkarp| 3346700339 NIL NIL)
(REFSEQ "NP_416140" NIL NIL NIL NIL NIL)
(UNIPROT "P22333" NIL NIL |ouzounis| 3027899498))
(SYNONYMS "B1623" "Add")
(CATALYZES ADDALT-ENZRXN ADENODEAMIN-ENZRXN)
(PI 5.63d0)
(MOLECULAR-WEIGHT-SEQ 36.397410999999906d0)
(GENE EG10030)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/add.template")
(:CREATION-DATE 3010350928)
(:CREATOR |mriley|) )
NIL)
(ADENODEAMIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.4)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY SALVADEHYPOX-PWY)
(ENZYMATIC-REACTION ADENODEAMIN-ENZRXN)
(RIGHT AMMONIA INOSINE)
(LEFT WATER ADENOSINE)
(EC-NUMBER "3.5.4.4")
(COMMENT "This reaction is part of nucleotide metabolism.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/add.template")
(:CREATION-DATE 3010350928)
(:CREATOR |mriley|) )
NIL)
(ADENOSINE NIL (
(OCELOT-GFP::PARENTS |Ribonucleosides| |Purine-Ribonucleosides|)
(INHIBITORS-COMPETITIVE-OF DAPASYN-ENZRXN GLUTATHIONE-SYN-ENZRXN)
(INHIBITORS-UNKMECH-OF NAD-SYNTH-NH3-ENZRXN)
(DBLINKS (LIGAND-CPD "C00212" NIL |kaipa| 3311532639 NIL NIL) (CAS "58-61-7"))
(:CREATION-DATE 3064165285)
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-108A)
(GIBBS-0 -50.0d0)
(APPEARS-IN-LEFT-SIDE-OF ADENOSINE-NUCLEOSIDASE-RXN TRANS-RXN-108A
ADENODEAMIN-RXN ADENPHOSPHOR-RXN)
(SYNONYMS "adenine-D-ribose")
(COMMON-NAME "adenosine")
(STRUCTURE-ATOMS C C C O O O C C C C C N N N N N O C C)
(STRUCTURE-BONDS (17 18 1) (17 3 1) (18 1 1) (1 2 1) (2 3 1) (1 5 1 :DOWN)
(2 6 1 :DOWN) (3 12 1 :UP) (7 10 :AROMATIC) (15 7 :AROMATIC)
(8 15 :AROMATIC) (14 8 :AROMATIC) (9 14 :AROMATIC) (9 12 :AROMATIC)
(10 9 :AROMATIC) (13 10 :AROMATIC) (11 13 :AROMATIC) (12 11 :AROMATIC)
(7 16 1) (18 19 1 :UP) (19 4 1))
(DISPLAY-COORDS-2D (-2.6128d0 0.6749d0) (-1.7879d0 0.6606d0)
(-1.5467d0 -0.1282d0) (-3.0345d0 -1.4697d0) (-3.0862d0 1.3506d0)
(-1.2916d0 1.3197d0) (-0.2873d0 -2.8235d0) (-1.7125d0 -2.9268d0)
(-1.0894d0 -1.641d0) (-0.3469d0 -2.0006d0) (-0.1648d0 -0.6782d0)
(-0.9767d0 -0.8237d0) (0.2245d0 -1.4056d0) (-1.7721d0 -2.104d0)
(-0.9701d0 -3.2866d0) (0.4552d0 -3.1832d0) (-2.2224d0 -0.6015d0)
(-2.8813d0 -0.1052d0) (-3.3308d0 -0.797d0))
(CHEMICAL-FORMULA (C 10) (H 13) (N 5) (O 4))
(MOLECULAR-WEIGHT 267.244d0)
(AROMATIC-RINGS (10 7 15 8 14 9) (9 10 13 11 12)) )
((GIBBS-0 -50.0d0 CITATIONS "GibbsGroups97")))
(ADENOSINE-NUCLEOSIDASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.2)
(BALANCE-STATE :BALANCED)
(EC-NUMBER "3.2.2.7")
(ENZYMATIC-REACTION ENZRXN0-423)
(OFFICIAL-EC? T)
(RIGHT ADENINE RIBOSE)
(LEFT ADENOSINE WATER)
(:CREATOR |ptoole|)
(:CREATION-DATE 3204987204) )
NIL)
(ADENOSINE5TRIPHOSPHO5ADENOSINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C06197" NIL |sreddy| 3298323030 NIL NIL))
(DISPLAY-COORDS-2D (0.0d0 -2.8009d0) (29.517d0 -3.6695d0)
(12.0987d0 -4.6489d0) (17.699d0 -4.6489d0) (14.8981d0 -4.6489d0)
(8.5696d0 -0.6722d0) (20.3034d0 -0.9248d0) (5.5456d0 -0.7002d0)
(23.2166d0 0.0d0) (12.0987d0 -1.848d0) (17.699d0 -1.848d0)
(14.8981d0 -1.848d0) (2.7447d0 -0.3087d0) (27.669d0 -0.4491d0)
(3.8926d0 -4.7893d0) (25.2049d0 -4.3697d0) (9.4382d0 -3.8364d0)
(20.3034d0 -3.9768d0) (1.4566d0 -0.8686d0) (28.7326d0 -1.3724d0)
(3.8645d0 -1.1493d0) (26.3528d0 -0.9248d0) (2.5202d0 -4.4805d0)
(26.6039d0 -4.5086d0) (10.6983d0 -3.2485d0) (19.0994d0 -3.2485d0)
(7.0849d0 -3.9768d0) (22.7675d0 -3.5853d0) (13.4977d0 -3.2485d0)
(16.2986d0 -3.2485d0) (1.2882d0 -2.241d0) (28.4534d0 -2.7447d0)
(2.4079d0 -3.0816d0) (27.1372d0 -3.2204d0) (3.6961d0 -2.5483d0)
(26.0721d0 -2.2971d0) (7.7571d0 -1.8215d0) (21.4512d0 -1.7653d0)
(6.3566d0 -1.8215d0) (22.7675d0 -1.3443d0) (8.2062d0 -3.1377d0)
(21.4232d0 -3.1643d0) (5.9371d0 -3.1643d0) (23.58d0 -2.4655d0)
(4.6209d0 -3.5853d0) (24.8962d0 -3.0254d0) (12.0987d0 -3.2485d0)
(17.699d0 -3.2485d0) (14.8981d0 -3.2485d0))
(AROMATIC-RINGS (22 14 20 32 34 36) (16 24 34 36 46) (19 13 21 35 33 31))
(CHEMICAL-FORMULA (C 20) (H 27) (N 10) (O 16) (P 3))
(MOLECULAR-WEIGHT 756.412d0)
(STRUCTURE-BONDS (44 46 1 :UP) (43 45 1 :DOWN) (40 44 1) (39 43 1) (38 42 1)
(38 40 1) (37 41 1) (37 39 1) (46 36 :AROMATIC) (35 45 1) (36 34 :AROMATIC)
(33 35 :AROMATIC) (34 32 :AROMATIC) (31 33 :AROMATIC) (30 49 1) (30 48 1)
(29 49 1) (29 47 1) (28 44 1) (28 42 1) (27 43 1) (27 41 1) (26 48 1)
(25 47 1) (34 24 :AROMATIC) (23 33 1) (22 36 :AROMATIC) (35 21 :AROMATIC)
(32 20 :AROMATIC) (19 31 :AROMATIC) (42 18 1 :UP) (18 26 1) (41 17 1 :DOWN)
(17 25 1) (16 46 :AROMATIC) (24 16 :AROMATIC) (15 45 1) (15 23 2)
(14 22 :AROMATIC) (20 14 :AROMATIC) (21 13 :AROMATIC) (13 19 :AROMATIC)
(12 49 1) (11 48 1) (10 47 1) (40 9 1 :DOWN) (39 8 1 :UP) (38 7 1 :DOWN)
(37 6 1 :UP) (5 49 2) (4 48 2) (3 47 2) (2 32 1) (1 31 1))
(STRUCTURE-ATOMS N N O O O O O O O O O O C C C C C C N N N N N N O O O O O O
C C C C C C C C C C C C C C N N P P P)
(SYNONYMS "P1,P3-bis(5'-adenosyl)triphosphate" "5'Ap3A"
"adenosine 5'-(tetrahydrogen triphosphate), P\"-5'-ester with adenosine")
(COMMON-NAME "adenosine(5')triphospho(5')adenosine")
(:CREATOR |arnaud|)
(:CREATION-DATE 3268504944) )
NIL)
(ADENOSINE_DIPHOSPHATE_RIBOSE NIL (
(OCELOT-GFP::PARENTS |ADP-Ribose(P)|)
(INHIBITORS-UNKMECH-OF PHOSACETYLTRANS-ENZRXN ACETALD-DEHYDROG-ENZRXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-1441)
(DBLINKS (LIGAND-CPD "C00301" NIL |kr| 3346617699 NIL NIL) (CAS "20762-30-5"))
(:CREATION-DATE 3068829344)
(GIBBS-0 -183.1d0)
(APPEARS-IN-RIGHT-SIDE-OF NADNUCLEOSID-RXN)
(COMMON-NAME "ADP-ribose")
(SYNONYMS "ADP-D-ribose" "adenosine diphosphate ribose")
(STRUCTURE-ATOMS O O O C C N N O O C C C C C C C C N N P N O O O O P O C C C
C C O O O O)
(STRUCTURE-BONDS (31 34 1 :DOWN) (30 35 1 :DOWN) (32 36 1) (29 32 1 :UP)
(30 31 1) (29 30 1) (33 29 1) (33 28 1) (31 28 1) (28 27 1 :DOWN) (27 26 1)
(25 26 1) (24 26 2) (23 26 1) (16 22 1 :DOWN) (21 11 1) (1 20 2)
(15 2 1 :DOWN) (3 20 1) (6 4 :AROMATIC) (4 19 :AROMATIC) (5 8 1)
(14 5 1 :UP) (12 6 :AROMATIC) (10 7 :AROMATIC) (7 13 :AROMATIC) (8 20 1)
(9 14 1) (9 17 1) (23 20 1) (18 10 :AROMATIC) (12 11 :AROMATIC)
(11 18 :AROMATIC) (13 12 :AROMATIC) (19 13 :AROMATIC) (14 15 1) (15 16 1)
(16 17 1) (17 19 1 :UP))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (7.2769d0 -4.3761d0) (7.9875d0 -5.6161d0)
(8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0) (7.5247d0 -2.7725d0)
(7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0) (8.8524d0 -2.7725d0)
(7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0) (5.3121d0 -2.4844d0)
(7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0) (4.4916d0 -2.4844d0)
(3.6666d0 -3.3112d0) (3.6641d0 -1.6612d0) (3.6657d0 -2.4862d0)
(2.8407d0 -2.4862d0) (2.1262d0 -2.0737d0) (0.7914d0 -2.0737d0)
(1.0463d0 -1.2891d0) (1.8713d0 -1.2891d0) (0.0067d0 -2.3286d0)
(1.4588d0 -2.5586d0) (2.3562d0 -0.6217d0) (0.5614d0 -0.6217d0)
(-0.6063d0 -1.7766d0))
(CHEMICAL-FORMULA (C 15) (H 23) (N 5) (O 14) (P 2))
(MOLECULAR-WEIGHT 559.319d0)
(AROMATIC-RINGS (4 6 12 13 19) (7 10 18 11 12 13)) )
((GIBBS-0 -183.1d0 CITATIONS "GibbsGroups97")))
(ADENOSYL-HOMO-CYS NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(INHIBITORS-UNKMECH-OF ENZRXN0-3461 RIBONUCLEOSIDE-TRIP-REDUCT-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ENZRXN0-6184 CHER-ENZRXN PFLACTENZ-ENZRXN
CFA-ENZRXN ENZRXN0-2081)
(APPEARS-IN-LEFT-SIDE-OF ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN)
(DBLINKS (LIGAND-CPD "C00021" NIL |kr| 3346617699 NIL NIL) (CAS "979-92-0"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -80.3d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-5099 2.1.1.34-RXN
|RRNA-(GUANINE-N1-)-METHYLTRANSFERASE-RXN|
|RRNA-(ADENINE-N6-)-METHYLTRANSFERASE-RXN| 2.1.1.77-RXN
|RRNA-(GUANINE-N2-)-METHYLTRANSFERASE-RXN| RXN0-5063 RXN0-5053 RXN0-981
RXN0-3161 RXN0-2881 RXN0-2441 RXN0-2441 UROPORIIIMETHYLTRANSA-RXN
|DNA-(CYTOSINE-5-)-METHYLTRANSFERASE-RXN|
|TRNA-(GUANINE-N1-)-METHYLTRANSFERASE-RXN| RXN0-1361
|TRNA-(GUANINE-N7-)-METHYLTRANSFERASE-RXN| RXN0-1241 2.1.1.79-RXN
HOMOCYSTEINE-S-METHYLTRANSFERASE-RXN CHERTAPM-RXN CHERTRGM-RXN CHERTSRM-RXN
CHERTARM-RXN CHER-RXN 2.1.1.72-RXN |TRNA-(URACIL-5-)-METHYLTRANSFERASE-RXN|
DHHB-METHYLTRANSFER-RXN 2-OCTAPRENYL-6-OHPHENOL-METHY-RXN
ADOMET-DMK-METHYLTRANSFER-RXN 2-OCTAPRENYL-METHOXY-BENZOQ-METH-RXN)
(SYNONYMS "AdoHcy" "2-S-adenosyl-L-homocysteine"
"S-adenosyl-homocysteine" "S-adenosylhomocysteine"
"adenosyl-homo-cys" "adenosylhomocysteine" "adenosylhomo-cys" "SAH")
(COMMON-NAME "S-adenosyl-L-homocysteine")
(STRUCTURE-ATOMS H H H H N N O O O O C C C C C N N N O S C C C C C N C C C C)
(STRUCTURE-BONDS (29 30 1) (28 29 1) (27 28 1) (30 26 1 :UP) (24 26 1)
(24 23 :AROMATIC) (23 22 :AROMATIC) (21 25 1) (19 30 1) (19 27 1) (18 23 1)
(17 24 :AROMATIC) (22 16 :AROMATIC) (27 15 1 :UP) (15 20 1) (14 25 1)
(13 20 1) (13 14 1) (12 26 1) (12 18 2) (11 17 :AROMATIC) (16 11 :AROMATIC)
(29 10 1 :DOWN) (28 9 1 :DOWN) (8 21 1) (7 21 2) (25 6 1 :DOWN) (5 22 1)
(4 30 1) (3 29 1) (2 28 1) (1 27 1))
(DISPLAY-COORDS-2D (7.5977d0 7.9585d0) (8.19d0 7.4691d0) (10.0187d0 7.4691d0)
(10.6109d0 7.9585d0) (7.9579d0 0.0d0) (2.4466d0 8.37d0) (1.2102d0 4.9447d0)
(0.0d0 7.0055d0) (8.19d0 9.1172d0) (10.0187d0 9.1172d0) (6.6448d0 3.6317d0)
(11.6667d0 2.8845d0) (4.7904d0 6.9798d0) (3.6054d0 6.3355d0)
(7.5977d0 6.2841d0) (6.6448d0 2.138d0) (8.035d0 4.4297d0)
(10.5852d0 1.468d0) (9.0657d0 6.2584d0) (5.9748d0 6.2841d0)
(1.2102d0 6.3355d0) (7.9579d0 1.3908d0) (9.2201d0 2.0865d0)
(9.2201d0 3.5802d0) (2.4466d0 6.9798d0) (10.6109d0 4.3011d0)
(7.5977d0 7.1084d0) (8.19d0 8.2929d0) (10.0187d0 8.2929d0)
(10.6109d0 7.1084d0))
(CHEMICAL-FORMULA (C 14) (H 20) (N 6) (O 5) (S 1))
(MOLECULAR-WEIGHT 384.409d0)
(AROMATIC-RINGS (17 11 16 22 23 24)) )
((GIBBS-0 -80.3d0 CITATIONS "GibbsGroups97")))
(ADENOSYL-P4 NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C01260" NIL |kr| 3346617700 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(AROMATIC-RINGS (24 25 26 27 38) (20 21 22 23 25 24) (2 3 4 6 5 1)
(6 7 8 19 5))
(DISPLAY-COORDS-2D (-1.7198d0 -0.288d0) (-1.0561d0 -0.6461d0)
(-1.0444d0 -1.4074d0) (-1.6937d0 -1.7992d0) (-2.3441d0 -0.6922d0)
(-2.3546d0 -1.4296d0) (-3.062d0 -1.6699d0) (-3.5124d0 -1.0835d0)
(-1.6813d0 -2.645d0) (-2.6503d0 0.6774d0) (-2.4422d0 1.4008d0)
(-1.6927d0 1.4218d0) (-1.4372d0 0.7242d0) (-2.0257d0 0.2568d0)
(-2.9974d0 2.2019d0) (-1.2259d0 2.1134d0) (-0.7152d0 0.521d0)
(-0.1783d0 1.0447d0) (-3.0884d0 -0.4666d0) (7.3948d0 -0.288d0)
(6.7311d0 -0.6461d0) (6.7194d0 -1.4074d0) (7.3687d0 -1.7992d0)
(8.0441d0 -0.6964d0) (8.0296d0 -1.4296d0) (8.737d0 -1.6699d0)
(9.1874d0 -1.0835d0) (7.3563d0 -2.645d0) (8.3253d0 0.6774d0)
(8.1172d0 1.4008d0) (7.3677d0 1.4218d0) (7.1122d0 0.7242d0)
(7.7007d0 0.2568d0) (8.6724d0 2.2019d0) (6.9009d0 2.1134d0)
(6.3902d0 0.521d0) (5.8533d0 1.0447d0) (8.7634d0 -0.4666d0)
(0.5708d0 1.0417d0) (1.35d0 1.0417d0) (0.5708d0 0.2917d0)
(0.5417d0 1.7911d0) (2.1d0 1.0417d0) (2.85d0 1.0417d0) (2.1d0 0.2917d0)
(2.1d0 1.7917d0) (3.6d0 1.0417d0) (4.35d0 1.0417d0) (3.6d0 0.2917d0)
(3.6d0 1.7917d0) (5.1d0 1.0417d0) (5.1d0 0.2917d0) (5.1d0 1.7917d0))
(CHEMICAL-FORMULA (C 20) (H 28) (N 10) (O 19) (P 4))
(MOLECULAR-WEIGHT 836.392d0)
(STRUCTURE-BONDS (51 53 2) (51 52 1) (51 37 1) (48 51 1) (47 50 2) (47 49 1)
(47 48 1) (44 47 1) (43 46 2) (43 45 1) (43 44 1) (40 43 1) (39 42 2)
(39 41 1) (40 39 1) (18 39 1) (29 38 1 :UP) (36 37 1) (32 36 1 :UP)
(31 35 1 :DOWN) (30 34 1 :DOWN) (33 29 1) (32 33 1) (31 32 1) (30 31 1)
(29 30 1) (23 28 1) (24 38 :AROMATIC) (38 27 :AROMATIC) (27 26 :AROMATIC)
(26 25 :AROMATIC) (25 24 :AROMATIC) (25 23 :AROMATIC) (23 22 :AROMATIC)
(22 21 :AROMATIC) (21 20 :AROMATIC) (20 24 :AROMATIC) (10 19 1 :DOWN)
(17 18 1) (13 17 1 :DOWN) (12 16 1 :UP) (11 15 1 :UP) (14 10 1) (13 14 1)
(12 13 1) (11 12 1) (10 11 1) (4 9 1) (5 19 :AROMATIC) (19 8 :AROMATIC)
(8 7 :AROMATIC) (7 6 :AROMATIC) (5 6 :AROMATIC) (6 4 :AROMATIC)
(4 3 :AROMATIC) (3 2 :AROMATIC) (2 1 :AROMATIC) (1 5 :AROMATIC))
(STRUCTURE-ATOMS N C N C C C N C N C C C C O O O C O N N C N C C C N C N C C
C C O O O C O N P O O O P O O O P O O O P O O)
(APPEARS-IN-LEFT-SIDE-OF 3.6.1.41-RXN)
(COMMON-NAME "P(1),P(4)-bis(5'-adenosyl)tetraphosphate") )
NIL)
(ADENOSYLCOBALAMIN NIL (
(OCELOT-GFP::PARENTS |Vitamins|)
(PROSTHETIC-GROUPS-OF ETHAMLY-ENZRXN)
(HISTORY |kr-3290870141|)
(DBLINKS (LIGAND-CPD "C00194" NIL |hopkinso| 3315332465 NIL NIL)
(CAS "13870-90-1" NIL |hopkinso| 3315332465 NIL NIL))
(AROMATIC-RINGS (86 83 84 85 88 87) (101 97 100 104 105 106)
(98 102 105 106 111))
(ATOM-CHARGES (72 -1) (24 1))
(DISPLAY-COORDS-2D (3.7991d0 0.7425d0) (4.5227d0 1.155d0) (5.5619d0 1.3931d0)
(5.138d0 0.926d0) (4.5227d0 1.9892d0) (5.7211d0 2.6683d0)
(5.3145d0 1.9844d0) (5.3277d0 3.3624d0) (5.6293d0 3.9283d0)
(4.5277d0 3.3727d0) (3.0846d0 2.0121d0) (3.0846d0 1.155d0)
(2.4945d0 0.9259d0) (2.0316d0 1.4211d0) (2.3502d0 2.0119d0)
(3.2516d0 4.0625d0) (3.2676d0 3.3889d0) (2.3969d0 3.4041d0)
(2.1963d0 3.962d0) (2.6619d0 4.4588d0) (5.0303d0 4.5454d0)
(4.5385d0 4.0942d0) (3.9616d0 4.4247d0) (3.8768d0 2.6401d0)
(4.8555d0 0.347d0) (6.3751d0 1.2531d0) (5.0353d0 5.2137d0)
(2.6788d0 5.353d0) (1.6317d0 2.4154d0) (1.6133d0 0.7058d0)
(2.3109d0 0.1216d0) (3.7968d0 -0.0825d0) (6.9027d0 1.8874d0)
(7.7158d0 1.7475d0) (8.2435d0 2.3817d0) (8.0011d0 0.9734d0)
(6.3526d0 3.928d0) (6.1555d0 4.4551d0) (5.6035d0 5.4167d0)
(5.7777d0 6.0797d0) (6.5957d0 6.1577d0) (5.4148d0 6.5397d0)
(3.9634d0 5.2724d0) (2.9157d0 -0.4396d0) (2.7321d0 -1.2439d0)
(3.3369d0 -1.805d0) (1.9437d0 -1.4871d0) (1.2329d0 1.6317d0)
(5.4655d0 0.0579d0) (2.088d0 5.0917d0) (1.3858d0 4.1306d0)
(1.595d0 3.1854d0) (0.6519d0 1.0459d0) (-0.1459d0 1.2563d0)
(0.8686d0 0.2499d0) (6.2787d0 -0.1471d0) (6.3757d0 -0.9664d0)
(6.9398d0 0.3466d0) (0.6121d0 3.6674d0) (-0.0795d0 4.1173d0)
(0.5682d0 2.8435d0) (1.9633d0 5.8646d0) (1.0642d0 5.6655d0)
(0.3371d0 6.057d0) (1.0493d0 5.0425d0) (0.2826d0 7.1068d0)
(1.0868d0 7.3108d0) (2.109d0 7.2803d0) (1.0704d0 8.3087d0)
(1.6673d0 6.604d0) (2.2976d0 8.5501d0) (3.0476d0 8.0002d0)
(1.4539d0 9.2251d0) (2.4923d0 10.638d0) (3.4969d0 8.833d0)
(4.3508d0 8.7899d0) (3.9669d0 10.8443d0) (3.2726d0 10.3632d0)
(3.4988d0 9.5868d0) (4.336d0 9.5662d0) (4.6125d0 10.3424d0)
(1.8659d0 10.1012d0) (7.2669d0 7.6847d0) (7.2669d0 8.519d0)
(6.5524d0 8.9406d0) (6.5524d0 7.2722d0) (5.8287d0 7.6847d0)
(5.8287d0 8.519d0) (5.037d0 8.7709d0) (4.5512d0 8.1061d0)
(5.0659d0 7.4282d0) (7.9814d0 7.2722d0) (7.9833d0 8.9281d0)
(9.2719d0 0.5235d0) (5.5294d0 -4.2252d0) (7.0386d0 -4.2079d0)
(9.942d0 -1.6159d0) (7.2617d0 -1.1539d0) (5.0294d0 -2.1807d0)
(9.942d0 -0.8167d0) (9.3031d0 -2.0771d0) (7.7593d0 -0.4085d0)
(6.2576d0 -2.2376d0) (9.3031d0 -0.3556d0) (8.5394d0 -0.8167d0)
(8.5394d0 -1.6159d0) (5.9022d0 -3.4979d0) (6.6475d0 -3.4979d0)
(5.6231d0 -2.7795d0) (6.9137d0 -2.717d0) (7.7593d0 -1.8821d0))
(CHEMICAL-FORMULA (C 72) (H 101) (N 18) (O 17) (P 1) (COBALT 1))
(MOLECULAR-WEIGHT 1580.604d0)
(STRUCTURE-BONDS (24 99 1 :UP) (111 110 1 :DOWN) (108 110 1) (107 108 1)
(107 109 1) (111 106 :AROMATIC) (106 105 :AROMATIC) (105 104 :AROMATIC)
(103 109 1) (103 110 1) (105 102 :AROMATIC) (101 106 :AROMATIC)
(104 100 :AROMATIC) (99 109 1 :DOWN) (102 98 :AROMATIC) (98 111 :AROMATIC)
(100 97 :AROMATIC) (97 101 :AROMATIC) (108 96 1 :UP) (107 95 1 :UP)
(94 104 1) (12 1 2) (2 1 1) (2 5 2) (7 3 1) (3 4 1) (4 2 1) (5 7 1) (8 6 1)
(6 7 2) (8 10 2) (21 9 1) (9 8 1) (10 22 1) (16 23 1) (11 12 1) (12 13 1)
(13 14 1) (14 15 1) (15 11 1) (16 17 2) (17 18 1) (18 19 1) (19 20 1)
(20 16 1) (21 22 1) (22 23 2) (17 24 1) (24 5 :COORDINATION)
(24 11 :COORDINATION) (24 10 :COORDINATION) (15 18 1) (4 25 1 :DOWN)
(3 26 1 :DOWN) (21 27 1 :DOWN) (20 28 1 :DOWN) (15 29 1 :DOWN)
(14 30 1 :DOWN) (13 31 1 :DOWN) (1 32 1) (26 33 1) (33 34 1) (34 35 1)
(34 36 2) (9 37 1 :DOWN) (9 38 1 :UP) (27 39 1) (39 40 1) (40 41 1)
(40 42 2) (23 43 1) (31 44 1) (44 45 1) (45 46 2) (45 47 1) (14 48 1 :UP)
(4 49 1 :UP) (20 50 1 :UP) (19 51 1 :UP) (18 52 1 :UP) (48 53 1) (53 54 1)
(53 55 2) (49 56 1) (56 57 1) (56 58 2) (51 59 1) (59 60 1) (59 61 2)
(28 62 1) (62 63 1) (63 64 1) (63 65 2) (64 66 1) (66 67 1) (67 68 1 :UP)
(67 69 1) (67 70 1 :DOWN) (69 71 1) (71 72 1) (71 73 2) (71 75 1)
(81 77 1 :UP) (81 80 1) (78 77 1 :UP) (80 79 1) (78 79 1) (78 74 1)
(79 75 1) (80 76 1) (74 82 1) (83 86 :AROMATIC) (84 83 :AROMATIC)
(85 84 :AROMATIC) (88 85 :AROMATIC) (86 87 :AROMATIC) (87 88 :AROMATIC)
(88 89 1) (89 90 1) (90 91 2) (91 87 1) (83 92 1) (84 93 1) (81 89 1)
(24 91 1))
(STRUCTURE-ATOMS C C C C N C C C C N N C C C C C N C C C C C C COBALT C C C C
C C C C C C N O C C C C N O C C C O N C C C C H C N O C N O C N O C C N O C
C C O H P O O C O O O C C C C O C C C C C C N C N C C N O O C C C N N N O C
C C C C C C N)
(SYNONYMS "adenosylcobalamin" "Cobamide coenzyme" "Deoxyadenosylcobalamin"
"Cobamamide" "Vitamin B12 coenzyme" "Cobamamid"
"5,6-Dimethylbenzimidazolyl-5-deoxyadenosyl-cobamide"
"Cobinamide, Co-(5'-deoxyadenosine-5') derivative hydroxide, dihydrogen phosphate (ester), inner salt, 3'-ester with 5,6-dimethyl-1-a-D-ribofuranosyl-1H-benzimidazole"
"(5'-Deoxy-5'-adenosyl)cobamide coenzyme"
"(5,6-dimethylbenzimidazolyl)cobamide coenzyme"
"a-(5,6-Dimethylbenzimidazolyl)cobamide coenzyme"
"5'-Deoxy-5'-adenosylcobalamin" "5'-Deoxyadenosyl vitamin B12"
"5'-Deoxyadenosyl-5,6-dimethylbenzimidazolylcobamide"
"5'-Deoxyadenosylcobalamin"
"5,6-Dimethylbenzimidazolyl-Co-5'-deoxyadenosylcobamide" "Calomide"
"Cobalamin coenzyme" "Cobalamin, Co-(5'-deoxy-5'-adenosyl)-"
"Cobamide coenzyme, (5'-deoxy-5'-adenosyl)-"
"Cobamide coenzyme, (5,6-dimethyl-1H-benzimidazolyl)-"
"Cobinamide, Co-(5'-deoxyadenosine-5') deriv.,"
"Cobinamide, Co-(5'-deoxyadenosine-5') deriv., hydroxide, 3'-ester with 5,6-dimethyl-1-a-D-ribofuranosylbenzimidazole"
"DBC coenzyme" "Dibencozide" "Funacomide"
"Vitamin B12, Co-(5'-deoxy-5'-adenosyl) deriv.")
(APPEARS-IN-RIGHT-SIDE-OF COBALADENOSYLTRANS-RXN COBALAMINSYN-RXN)
(:CREATION-DATE 3054402666)
(:CREATOR |kr|)
(COMMON-NAME "coenzyme B12") )
NIL)
(ADENOSYLCOBALAMIN-5-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DISPLAY-COORDS-2D (1.8131d0 -2.4145d0) (5.1743d0 0.1642d0)
(2.9804d0 0.3657d0) (5.0031d0 1.3344d0) (1.7408d0 -5.8331d0)
(4.1092d0 -3.746d0) (3.9427d0 -9.1009d0) (11.7135d0 -2.506d0)
(11.7731d0 -4.1549d0) (2.2548d0 -1.9568d0) (6.3014d0 -4.5633d0)
(6.4985d0 -5.0905d0) (2.2338d0 -3.9267d0) (5.0013d0 -8.6713d0)
(1.7591d0 -8.3126d0) (1.7775d0 -6.603d0) (6.7415d0 -2.8607d0)
(8.3893d0 -6.6367d0) (2.0895d0 -10.5055d0) (0.0663d0 -4.9011d0)
(6.5216d0 -9.9849d0) (0.0d0 -7.7621d0) (9.4177d0 -8.4949d0)
(5.6856d0 -2.2911d0) (8.1469d0 -8.045d0) (3.4828d0 -10.8234d0)
(0.714d0 -6.175d0) (7.0856d0 -8.6718d0) (1.0145d0 -8.7685d0)
(1.1952d0 -3.9759d0) (1.8391d0 2.4d0) (1.5059d0 -0.2621d0)
(5.6753d0 -13.2436d0) (7.1844d0 -13.2262d0) (3.6579d0 -0.8058d0)
(4.7681d0 -0.837d0) (1.881d0 0.6861d0) (2.631d0 -1.3932d0)
(5.8669d0 -6.3501d0) (10.0878d0 -10.6343d0) (7.4076d0 -10.1723d0)
(10.3449d0 -4.2065d0) (8.3324d0 -3.4537d0) (5.7493d0 -3.6017d0)
(7.0486d0 -7.131d0) (3.0616d0 -9.4581d0) (2.1092d0 -3.1538d0)
(5.1811d0 -3.8047d0) (6.521d0 -7.7653d0) (2.4568d0 -8.8968d0)
(2.8247d0 -3.6654d0) (1.5316d0 -4.8878d0) (0.5223d0 -1.9117d0)
(3.5429d0 1.4083d0) (5.6113d0 -8.9606d0) (1.3787d0 -7.3867d0)
(5.1752d0 -11.1991d0) (10.0878d0 -9.8351d0) (9.4489d0 -11.0955d0)
(7.9051d0 -9.4268d0) (0.483d0 -2.9615d0) (2.5932d0 1.4296d0)
(6.4035d0 -11.256d0) (4.264d0 1.112d0) (1.1537d0 -0.8347d0)
(5.9235d0 -2.9387d0) (7.8616d0 -7.2709d0) (2.878d0 -10.2623d0)
(0.7579d0 -5.351d0) (6.4246d0 -9.1654d0) (0.7977d0 -7.9725d0)
(1.21d0 -3.3529d0) (4.1074d0 -4.5937d0) (3.945d0 -8.2759d0)
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(STRUCTURE-ATOMS H H H H H C C C C C C C C C C C N N N N N N N O O O O O O O
O O O O O O O O C C C C C C C C C C C C C C C C C C C N N N N O O O O C C C
C C C C C C C C C C C C C C C C C C C C C C C C C C C N N N N N N N C C C C
C C C C C C P P COBALT O C C)
(APPEARS-IN-RIGHT-SIDE-OF COBALAMIN5PSYN-RXN)
(:CREATION-DATE 3054402666)
(:CREATOR |kr|)
(COMMON-NAME "adenosylcobalamin-5'-phosphate") )
NIL)
(ADENOSYLCOBINAMIDE NIL (
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(STRUCTURE-ATOMS C C C C N C C C C N N C C C C C N C C C C C C COBALT C C C C
C C C C C C N O C C C C N O C C C O N C C C C H C N O C N O C N O C C N O C
C C O H N O O C C C N N N O C C C C C C C N)
(APPEARS-IN-RIGHT-SIDE-OF BTUR2-RXN)
(APPEARS-IN-LEFT-SIDE-OF COBINAMIDEKIN-RXN)
(:CREATION-DATE 3054402666)
(:CREATOR |kr|)
(COMMON-NAME "adenosylcobinamide") )
NIL)
(ADENOSYLCOBINAMIDE-GDP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "Adenosine-GDP-cobinamide")
(DBLINKS (PUBCHEM "5280949" NIL |keseler| 3342456579 NIL NIL)
(LIGAND-CPD "C06510" NIL |keseler| 3342456579 NIL NIL))
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(CHEMICAL-FORMULA (C 68) (H 95) (N 21) (O 21) (P 2) (COBALT 1))
(MOLECULAR-WEIGHT 1663.504d0)
(STRUCTURE-BONDS (115 116 1) (113 116 1) (109 114 1) (106 119 1) (106 116 1)
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(STRUCTURE-ATOMS H H H H H H C C C C C C C C C N N N N N N N N O O O O O O O
O O O O O O O O O C C C C C C C C C C C C C C C C C C N N N N N N O O O O O
C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C N N N N N N N
C C C C C C C C C C P P COBALT)
(APPEARS-IN-RIGHT-SIDE-OF COBINPGUANYLYLTRANS-RXN)
(APPEARS-IN-LEFT-SIDE-OF COBALAMIN5PSYN-RXN COBALAMINSYN-RXN)
(:CREATION-DATE 3054402666)
(:CREATOR |kr|)
(COMMON-NAME "adenosylcobinamide-GDP") )
NIL)
(ADENOSYLCOBINAMIDE-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C06509" NIL |kr| 3346617700 NIL NIL))
(AROMATIC-RINGS (80 76 79 83 84 85) (77 81 84 85 90))
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(5.7037d0 -12.8208d0) (6.5167d0 -12.9607d0) (7.0444d0 -12.3265d0)
(6.802d0 -13.7348d0) (5.1535d0 -10.7802d0) (4.9564d0 -10.253d0)
(4.4044d0 -9.2914d0) (4.5786d0 -8.6283d0) (5.3965d0 -8.5503d0)
(4.2157d0 -8.1683d0) (2.7642d0 -9.4357d0) (1.7165d0 -15.1479d0)
(1.5329d0 -15.9522d0) (2.1377d0 -16.5133d0) (0.7444d0 -16.1954d0)
(0.0336d0 -13.0765d0) (4.2664d0 -14.6504d0) (0.8888d0 -9.6164d0)
(0.1865d0 -10.5776d0) (0.3957d0 -11.5228d0) (-0.5474d0 -13.6623d0)
(-1.3452d0 -13.4519d0) (-0.3307d0 -14.4584d0) (5.0796d0 -14.8553d0)
(5.1766d0 -15.6748d0) (5.7407d0 -14.3617d0) (-0.5872d0 -11.0408d0)
(-1.2789d0 -10.5909d0) (-0.6311d0 -11.8647d0) (0.764d0 -8.8434d0)
(-0.1351d0 -9.0426d0) (-0.8622d0 -8.6511d0) (-0.1499d0 -9.6656d0)
(-0.8854d0 -7.6013d0) (-0.1125d0 -7.3973d0) (0.9098d0 -7.6465d0)
(-0.1914d0 -6.5243d0) (0.468d0 -8.1041d0) (1.2859d0 -7.0828d0)
(0.1608d0 -5.9517d0) (8.0729d0 -14.1848d0) (4.3303d0 -18.9337d0)
(5.8395d0 -18.9163d0) (8.7429d0 -16.3242d0) (6.0627d0 -15.8622d0)
(3.8302d0 -16.889d0) (8.7429d0 -15.525d0) (8.1041d0 -16.7854d0)
(6.5602d0 -15.1167d0) (5.0585d0 -16.9459d0) (8.1041d0 -15.0638d0)
(7.3404d0 -15.525d0) (7.3404d0 -16.3242d0) (4.703d0 -18.2063d0)
(5.4484d0 -18.2063d0) (4.424d0 -17.4879d0) (5.652d0 -17.4566d0)
(6.5602d0 -16.5904d0) (0.7545d0 -6.5329d0) (1.7191d0 -6.5891d0))
(CHEMICAL-FORMULA (C 58) (H 83) (N 16) (O 14) (P 1) (COBALT 1))
(MOLECULAR-WEIGHT 1318.296d0)
(STRUCTURE-BONDS (91 92 2) (89 90 1) (87 89 1) (86 87 1) (86 88 1)
(90 85 :AROMATIC) (85 84 :AROMATIC) (84 83 :AROMATIC) (82 88 1) (82 89 1)
(84 81 :AROMATIC) (80 85 :AROMATIC) (83 79 :AROMATIC) (78 88 1)
(81 77 :AROMATIC) (77 90 :AROMATIC) (79 76 :AROMATIC) (76 80 :AROMATIC)
(75 87 1) (74 86 1) (73 83 1) (91 71 1) (91 72 1) (69 91 1) (67 68 1 :UP)
(67 69 1) (67 70 1 :DOWN) (66 67 1) (64 66 1) (63 64 1) (63 65 2) (62 63 1)
(59 60 1) (59 61 2) (56 57 1) (56 58 2) (53 54 1) (53 55 2) (51 59 1)
(49 56 1) (48 53 1) (45 46 2) (45 47 1) (44 45 1) (40 41 1) (40 42 2)
(39 40 1) (34 35 1) (34 36 2) (33 34 1) (31 44 1) (28 62 1) (27 39 1)
(26 33 1) (24 78 1) (23 43 1) (22 23 1) (21 22 1) (21 27 1 :DOWN)
(20 28 1 :DOWN) (20 50 1 :UP) (19 20 1) (19 51 1 :UP) (18 19 1)
(18 52 1 :UP) (17 18 1) (17 24 1) (16 23 2) (16 17 1) (20 16 1) (15 18 1)
(15 29 1 :DOWN) (14 15 1) (14 30 1 :DOWN) (14 48 1 :UP) (13 14 1)
(13 31 1 :DOWN) (12 13 1) (11 12 2) (15 11 1) (24 11 :COORDINATION)
(10 22 2) (24 10 :COORDINATION) (21 9 1) (9 37 1 :DOWN) (9 38 1 :UP)
(8 10 1) (9 8 1) (8 6 2) (6 7 1) (5 7 2) (24 5 :COORDINATION) (4 25 1 :DOWN)
(4 49 1 :UP) (7 3 1) (3 4 1) (3 26 1 :DOWN) (2 5 1) (4 2 1) (12 1 1) (2 1 2)
(1 32 1))
(STRUCTURE-ATOMS C C C C N C C C C N N C C C C C N C C C C C C COBALT C C C C
C C C C C C N O C C C C N O C C C O N C C C C H C N O C N O C N O C C N O C
C C O H O O N O O C C C N N N O C C C C C C C N P O)
(SYNONYMS "adenosyl-cobinamide phosphate")
(APPEARS-IN-LEFT-SIDE-OF COBINPGUANYLYLTRANS-RXN)
(APPEARS-IN-RIGHT-SIDE-OF COBINAMIDEKIN-RXN)
(:CREATION-DATE 3054402667)
(:CREATOR |kr|)
(COMMON-NAME "adenosylcobinamide-P") )
NIL)
(ADENOSYLHOMOCYSTEINE-NUCLEOSIDASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.2)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-2245)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3277486204)
(COMMON-NAME "Adenosylhomocysteine nucleosidase")
(EC-NUMBER "3.2.2.9")
(RIGHT CPD-564 ADENINE)
(LEFT ADENOSYL-HOMO-CYS WATER) )
NIL)
(ADENPHOSPHOR-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENPHOSPHOR-RXN)
(ENZYME DEOD-CPLX)
(COMMON-NAME "adenine phosphorylase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/deoD.template")
(:CREATION-DATE 3010350973)
(:CREATOR |mriley|) )
NIL)
(ADENPHOSPHOR-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.4.2 |Small-Molecule-Reactions|)
(BALANCE-STATE :BALANCED)
(EC-NUMBER "2.4.2.-")
(OFFICIAL-EC? T)
(IN-PATHWAY SALVADEHYPOX-PWY)
(ENZYMATIC-REACTION ADENPHOSPHOR-ENZRXN)
(RIGHT RIBOSE-1P ADENINE)
(LEFT ADENOSINE |Pi|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/deoD.template")
(:CREATION-DATE 3010350973)
(:CREATOR |mriley|) )
NIL)
(ADENPRIBOSYLTRAN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ADENPRIBOSYLTRAN-ENZRXN)
(COMPONENTS ADENPRIBOSYLTRAN-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/apt.template")
(:CREATION-DATE 3010350961)
(:CREATOR |mriley|) )
((COMPONENTS ADENPRIBOSYLTRAN-MONOMER COEFFICIENT 2)))
(ADENPRIBOSYLTRAN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CA+2 BA+2 ZN+2)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(ALTERNATIVE-COFACTORS (MG+2 MN+2))
(COFACTORS MG+2)
(ALTERNATIVE-SUBSTRATES (ADENINE "26-DIAMINO-PURINE"))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENPRIBOSYLTRAN-RXN)
(INHIBITORS-COMPETITIVE PPI AMP "all 5' nucleotides" MG+2)
(COMMENT "Adenine phosphoribosyltransferase is one of the purine
salvage enzymes which play an important role in maintaining nucleotide
pool balance in E. coli. |CITS: [83054639]|")
(ENZYME ADENPRIBOSYLTRAN-CPLX)
(SYNONYMS "AMP pyrophosphorylase" "transphosphoribosidase" "APRT"
"AMP:pyrophosphate phospho-D-ribosyltransferase")
(COMMON-NAME "adenine phosphoribosyltransferase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/apt.template")
(:CREATION-DATE 3010350961)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH CA+2 CITATIONS "[79010029]")
(INHIBITORS-UNKMECH BA+2 CITATIONS "[79010029]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[79010029]")
(INHIBITORS-COMPETITIVE PPI COMMENT "competition with
PRPP may be cooperative")
(INHIBITORS-COMPETITIVE AMP COMMENT "with respect to PRPP")
(INHIBITORS-COMPETITIVE "all 5' nucleotides" COMMENT
"at high concentrations, competitive with
PRPP")
(INHIBITORS-COMPETITIVE MG+2 COMMENT "competitive with PRPP")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[79010029]")))
(ADENPRIBOSYLTRAN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0469" "Apt")
(DBLINKS (MODBASE "P69503" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P69503" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P69503" NIL |pkarp| 3354911363)
(PFAM "PF00156" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_415002" NIL NIL NIL NIL NIL))
(COMMON-NAME "Apt")
(COMPONENT-OF ADENPRIBOSYLTRAN-CPLX)
(PI 5.49d0)
(LOCATIONS CCO-OUTER-MEM)
(MOLECULAR-WEIGHT-SEQ 19.858856999999993d0)
(GENE EG10051)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/apt.template")
(:CREATION-DATE 3010350961)
(:CREATOR |mriley|) )
((LOCATIONS CCO-OUTER-MEM CITATIONS "[72004312]")))
(ADENPRIBOSYLTRAN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.4.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY SALVADEHYPOX-PWY)
(ENZYMATIC-REACTION ADENPRIBOSYLTRAN-ENZRXN)
(RIGHT PRPP ADENINE)
(LEFT PPI AMP)
(EC-NUMBER "2.4.2.7")
(COMMENT "This reaction is involved in purine salvage.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/apt.template")
(:CREATION-DATE 3010350961)
(:CREATOR |mriley|) )
NIL)
(ADENYL-KIN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "Ap5A" "P1,P5-di(adenosine-5')pentaphosphate" EDTA)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COFACTORS MG+2)
(ALTERNATIVE-SUBSTRATES
(AMP "2'-dAMP" "3'-dAMP" "ARAAMP" "TUMP" CDP GDP UDP DCDP DGDP TDP))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENYL-KIN-RXN)
(INHIBITORS-COMPETITIVE "Benzoyl2ATP")
(COMMENT "Adenylate kinase is an essential enzyme, responsible for
recycling AMP in energetically active cells. |CITS: [92084653]| The
enzyme can utilize both ribo- and deoxyribonucleotides as substrates.
Although highly specific for AMP and dAMP, detectable activity is
observed when ATP or dATP is replaced by a variety of ribonucleoside
triphosphates. |CITS: [73134598]| The enzyme has been crystallized.
|CITS: [92194314]| Inorganic triphosphate can also act as donor.
Adenylate kinase also has nucleoside diphosphate kinase activity.
Using ATP as the phosphate donor it can convert ribonucleoside
diphosphates and deoxyribonucleoside triphosphates to the respective
nucleoside triphosphate. |CITS: [96234029]|
Adenylate kinase can combine with polyphosphate kinase to catalyze
the formation of ADP from AMP and poly(Pi). This polyP:AMP phosphotransferase (PAP)
activity requires both enzymes acting together. |CITS: [20570450]|")
(ENZYME ADENYL-KIN-MONOMER)
(SYNONYMS "myokinase" "ATP-AMP transphosphorylase"
"ATP:AMP phosphotransferase")
(COMMON-NAME "adenylate kinase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/adk.template")
(:CREATION-DATE 3010350947)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "Ap5A" CITATIONS "[84005091]" "[92194314]")
(INHIBITORS-UNKMECH "P1,P5-di(adenosine-5')pentaphosphate" CITATIONS
"[84005091]")
(INHIBITORS-UNKMECH EDTA COMMENT "when present in sufficient concentration
to complex available divalent cations |CITS: [73134598]|")
(ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[96234029]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT
"The E. coli enzyme has a broad specificity for nucleoside
triphosphates and a more narrow specificity for nucleoside
monophosphates. Pyrimidine nucleoside triphosphates may replace ATP
as substrates, although the reaction rates are lower. |CITS: [87109155]|")
(INHIBITORS-COMPETITIVE "Benzoyl2ATP" COMMENT "in the presence of fixed
AMP and variable ATP concentrations |CITS: [87109155]|")
(COFACTORS MG+2 COMMENT "Mn++ will also meet the cation requirement but
less effectively |CITS: [73134598]|")))
(ADENYL-KIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P69441" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P69441" NIL |pkarp| 3354911363)
(PFAM "PF00406" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_415007" NIL NIL NIL NIL NIL) (PDB "4AKE") (PDB "2ECK")
(PDB "1E4Y") (PDB "1E4V") (PDB "1ANK") (PDB "1AKE"))
(SYNONYMS "B0474" "PlsA" "DnaW" "Adk")
(CATALYZES ADENYL-KIN-ENZRXN)
(PI 5.81d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 23.585984999999987d0)
(GENE EG10032)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/adk.template")
(:CREATION-DATE 3010350947)
(:CREATOR |mriley|) )
NIL)
(ADENYL-KIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.4)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION ADENYL-KIN-ENZRXN)
(RIGHT ADP)
(LEFT AMP ATP)
(EC-NUMBER "2.7.4.3")
(COMMENT "This reaction interconverts adenine
nucleotides.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/adk.template")
(:CREATION-DATE 3010350947)
(:CREATOR |mriley|) )
((RIGHT ADP COEFFICIENT 2)))
(ADENYLATECYC-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CA+2 GDP "methyl alpha-glucoside")
(INHIBITORS-NONCOMPETITIVE GLC GTP ADP PPI KCL NACL "K2HPO4")
(CITATIONS ":EV-EXP:3277835749:pkarp")
(ENZYME ADENYLATECYC-MONOMER)
(COMMENT "Adenylate cyclase catalyzes the intramolecular transfer of
the adenylyl group of ATP from pyrophosphate to the 3'-hydroxyl group
to form cyclic AMP. |CITS: [89008331]|")
(REACTION ADENYLATECYC-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/alone/cyaA.template")
(INHIBITORS-ALLOSTERIC ATP)
(COFACTORS MG+2)
(ALTERNATIVE-SUBSTRATES (ATP DATP))
(:CREATION-DATE 3041259517)
(COMMON-NAME "adenylate cyclase")
(SYNONYMS "adenylyl cyclase" "adenyl cyclase"
"ATP pyrophosphate-lyase (cyclizing)")
(REACTION-DIRECTION REVERSIBLE)
(ACTIVATORS-ALLOSTERIC GTP CTP UTP ATP) )
((INHIBITORS-UNKMECH CA+2 COMMENT "Ca++ is a strong inhibitor when added in
the presence of Mg++. |CITS: [83160910]|")
(INHIBITORS-UNKMECH GDP CITATIONS "[85154575]")
(INHIBITORS-UNKMECH "methyl alpha-glucoside" CITATIONS "[85154575]")
(INHIBITORS-NONCOMPETITIVE GLC COMMENT "in vivo noncompetitive inhibition
The purified enzyme is unaffected by glucose. ")
(INHIBITORS-NONCOMPETITIVE GLC CITATIONS "85154575")
(INHIBITORS-NONCOMPETITIVE GTP CITATIONS "83160910")
(INHIBITORS-NONCOMPETITIVE ADP CITATIONS "83160910")
(INHIBITORS-NONCOMPETITIVE PPI CITATIONS "83160910")
(INHIBITORS-NONCOMPETITIVE KCL CITATIONS "83160910")
(INHIBITORS-NONCOMPETITIVE NACL CITATIONS "83160910")
(INHIBITORS-NONCOMPETITIVE "K2HPO4" CITATIONS "83160910")
(INHIBITORS-ALLOSTERIC ATP CITATIONS "[83160910]")
(ACTIVATORS-ALLOSTERIC :FACET COMMENT "GTP is the most
potent activator of the triphosphate nucleosides. The activation
requires the presence of an organized complex of adenylate cyclase
with phosphoenolpyruvate:sugar phosphotransferase system proteins.
|CITS: [95345065] [85154575]|")
(COFACTORS MG+2 COMMENT "The enzyme has an absolute requirement for
a divalent cation. Mn++ will substitute for Mg++ and Co++ is
effective at low concentrations. |CITS: [83160910]|")))
(ADENYLATECYC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3806" "Cya" "CyaA")
(DBLINKS (PFAM "PF01295" IN-FAMILY |pkarp| 3346700419 NIL NIL)
(REFSEQ "NP_418250" NIL NIL NIL NIL NIL)
(UNIPROT "P00936" NIL |pkarp| 3064869797))
(CATALYZES ADENYLATECYC-ENZRXN)
(GENE EG10170)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/alone/cyaA.template")
(:CREATION-DATE 3041259517)
(PI 6.16d0)
(MOLECULAR-WEIGHT-SEQ 97.58586999999974d0) )
NIL)
(ADENYLATECYC-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(COMMENT "This reaction synthesizes cyclic AMP.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/alone/cyaA.template")
(ENZYMATIC-REACTION ADENYLATECYC-ENZRXN)
(EC-NUMBER "4.6.1.1")
(:CREATION-DATE 3041259517)
(LEFT ATP)
(RIGHT CAMP PPI) )
NIL)
(ADENYLOSUCC NIL (
(OCELOT-GFP::PARENTS |Purine-Related| |Base-Derivatives|)
(INHIBITORS-UNKMECH-OF ADENYLOSUCCINATE-SYNTHASE-ENZRXN)
(DBLINKS (LIGAND-CPD "C03794" NIL |kr| 3346617699 NIL NIL) (CAS "19240-42-7"))
(:CREATION-DATE 3073857204)
(MOLECULAR-WEIGHT 463.297d0)
(CHEMICAL-FORMULA (C 14) (H 18) (N 5) (O 11) (P 1))
(DISPLAY-COORDS-2D (5.5864d0 -10.8475d0) (4.8107d0 -12.0119d0)
(8.5378d0 -8.6395d0) (1.3539d0 -3.2711d0) (6.8155d0 -13.3547d0)
(8.3656d0 -11.0464d0) (4.6112d0 -0.0081d0) (7.5702d0 0.0d0)
(1.3499d0 -0.5662d0) (0.0d0 -1.9187d0) (4.5911d0 -5.0368d0)
(9.0432d0 -5.7136d0) (3.715d0 -2.8166d0) (6.976d0 -10.947d0)
(4.5911d0 -6.4045d0) (5.7625d0 -4.3455d0) (8.2504d0 -6.825d0)
(5.7587d0 -8.4407d0) (2.7064d0 -1.9157d0) (6.0862d0 -3.181d0)
(6.2007d0 -12.1045d0) (7.757d0 -9.7933d0) (5.7625d0 -7.0808d0)
(6.9487d0 -6.4045d0) (6.9487d0 -5.0368d0) (5.41d0 -1.0994d0)
(6.7699d0 -1.0994d0) (4.9996d0 -2.3935d0) (7.1881d0 -2.3935d0)
(8.2472d0 -4.6283d0) (6.3673d0 -9.6939d0) (1.3525d0 -1.9187d0))
(STRUCTURE-BONDS (29 30 1 :UP) (27 29 1) (26 28 1) (26 27 1)
(25 30 :AROMATIC) (24 25 :AROMATIC) (23 24 :AROMATIC) (22 31 1) (20 29 1)
(20 28 1) (19 32 1) (18 31 1) (18 23 1) (17 24 :AROMATIC) (25 16 :AROMATIC)
(15 23 :AROMATIC) (31 14 1 :UP) (14 21 1) (28 13 1 :UP) (13 19 1)
(30 12 :AROMATIC) (12 17 :AROMATIC) (16 11 :AROMATIC) (11 15 :AROMATIC)
(10 32 1) (9 32 1) (27 8 1 :DOWN) (26 7 1 :DOWN) (6 22 1) (5 21 1) (4 32 2)
(3 22 2) (2 21 2) (31 1 1 :DOWN))
(STRUCTURE-ATOMS H O O O O O O O O O C C C C N N N N O O C C C C C C C C C N
C P)
(GIBBS-0 -200.0d0)
(APPEARS-IN-LEFT-SIDE-OF AMPSYN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ADENYLOSUCCINATE-SYNTHASE-RXN)
(AROMATIC-RINGS (17 12 30 25 24) (15 11 16 25 24 23))
(COMMON-NAME "adenylo-succinate")
(SYNONYMS "N6-(1,2-dicarboxyethyl)-AMP" "adenylo-succ") )
NIL)
(ADENYLOSUCCINATE-SYN-DIMER NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ADENYLOSUCCINATE-SYNTHASE-ENZRXN)
(CITATIONS "[87269643]")
(COMPONENTS ADENYLOSUCCINATE-SYN-MONOMER)
(:CREATION-DATE 2959814168)
(:CREATOR |mriley|) )
((COMPONENTS ADENYLOSUCCINATE-SYN-MONOMER COEFFICIENT 2)))
(ADENYLOSUCCINATE-SYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4177" "AdeK" "PurA")
(COMMON-NAME "PurA")
(DBLINKS (UNIPROT "P0A7D4" NIL |pkarp| 3354911363)
(PFAM "PF00709" IN-FAMILY |pkarp| 3346700439 NIL NIL)
(REFSEQ "NP_418598" NIL NIL NIL NIL NIL) (PDB "1SOO") (PDB "1SON")
(PDB "1NHT") (PDB "1KSZ") (PDB "1KKF") (PDB "1KKB") (PDB "1KJX")
(PDB "1JUY") (PDB "1HOP") (PDB "1HOO") (PDB "1HON") (PDB "1GIN")
(PDB "1GIM") (PDB "1ADI") (PDB "1ADE"))
(COMPONENT-OF ADENYLOSUCCINATE-SYN-DIMER)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 47.34488299999988d0)
(GENE EG10790)
(CITATIONS "[89066719]" "[SwissProt]")
(:CREATION-DATE 2959814168)
(:CREATOR |mriley|) )
((GENE :FACET COMMENT
"a large ORF is present on the opposite strand |CITS: [89066719]|")))
(ADENYLOSUCCINATE-SYNTHASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH |Purine-Nucleotides| ADENYLOSUCC GUANOSINE-5DP-3DP GDP)
(INHIBITORS-NONCOMPETITIVE GMP DGMP)
(COFACTORS MG+2)
(SYNONYMS "IMP-aspartate ligase" "IMP:L-aspartate ligase (GDP-forming)"
"adenylosuccinate synthetase")
(COMMON-NAME "adenylosuccinate synthase")
(ENZYME ADENYLOSUCCINATE-SYN-DIMER)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENYLOSUCCINATE-SYNTHASE-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[79150972]" "[JBC238,1054]"
"[78242305]" "[92027780]" "[91286237]")
(INHIBITORS-COMPETITIVE DGMP AMP GDP GUANOSINE-5DP-3DP GMP)
(COMMENT
"The preferred pathway of substrate addition is aspartate followed by GTP
and IMP adding randomly. |CITS:
[92027780]| Lys140 is important for GTP binding whereas Arg147
is involved in both GTP and IMP binding. The phosphate loop near
the N-terminus is also involved in nucleotide substrate binding.
|CITS: [91286237]|
The presence of an intermediate in the reaction is suspected.
It may be an addition product between IMP and aspartate.
|CITS: [78242305]|")
(:CREATION-DATE 2959814168)
(:CREATOR |mriley|) )
((INHIBITORS-NONCOMPETITIVE DGMP COMMENT "noncompetitive against GTP")
(INHIBITORS-NONCOMPETITIVE GMP COMMENT
"noncompetitive with respect to L-aspartate")
(INHIBITORS-NONCOMPETITIVE GMP CITATIONS "[79150972]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[79150972]")
(INHIBITORS-COMPETITIVE DGMP COMMENT "competitive with IMP ")
(INHIBITORS-COMPETITIVE GMP COMMENT "with respect to GTP and IMP")
(INHIBITORS-COMPETITIVE AMP COMMENT "with respect to IMP")))
(ADENYLOSUCCINATE-SYNTHASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.3.4)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION ADENYLOSUCCINATE-SYNTHASE-ENZRXN)
(RIGHT ADENYLOSUCC |Pi| GDP)
(LEFT L-ASPARTATE IMP GTP)
(CITATIONS "[92027780]")
(EC-NUMBER "6.3.4.4")
(COMMENT
"This is the first committed step in AMP biosynthesis, converting IMP to AMP.")
(SYNONYMS "IMP-ASPARTATE LIGASE" "adenylosuccinate synthetase")
(COMMON-NAME "Adenylosuccinate synthase")
(:CREATION-DATE 2959814168)
(:CREATOR |mriley|) )
NIL)
(|Adenylyl-glutamine-synthases| T (
(OCELOT-GFP::PARENTS |Glutamine-synthases|)
(APPEARS-IN-RIGHT-SIDE-OF GSADENYLATION-RXN)
(COMMON-NAME "adenylyl-glutamine synthase")
(:CREATOR |paley|)
(:CREATION-DATE 3355688570) )
NIL)
(ADENYLYL-GS NIL (
(OCELOT-GFP::PARENTS |Gln-A|)
(MOLECULAR-WEIGHT-SEQ 51.90369399999979d0)
(:CREATION-DATE 3095444893)
(DBLINKS (SWISSMODEL "P0A9C5" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF03951" IN-FAMILY |pkarp| 3346700422 NIL NIL)
(PDB "2GLS" NIL |pkarp| 3346695117 NIL NIL)
(UNIPROT "P0A9C5" NIL |pkarp| 3338704812 NIL NIL)
(REFSEQ "NP_418306" NIL NIL NIL NIL NIL))
(STRUCTURE-ATOMS GLUTAMINESYN-OLIGOMER O O C N N H N C C C C N O C O O C C P
N H C O C O)
(GENE EG10383)
(UNMODIFIED-FORM GLUTAMINESYN-MONOMER)
(APPEARS-IN-LEFT-SIDE-OF GSDEADENYLATION-RXN)
(COMMON-NAME "adenylyl-[glutamine synthetase]")
(SYNONYMS "B3870" "GlnL" "GlnA"
"adenylyl-[L-glutamate:ammonia Ligase (ADP-forming)]" "adenylyl-GS") )
NIL)
(ADENYLYLSULFKIN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ADENYLYLSULFKIN-ENZRXN)
(COMPONENTS ADENYLYLSULFKIN-MONOMER)
(COMMENT "The enzyme exists predominantly as a homodimer, but a
tetrameric form exists when the enzyme is dephosphorylated. |CITS:
[SatischandranJBC264,15012]|")
(:CREATION-DATE 2974150691)
(:CREATOR |mriley|) )
((COMPONENTS ADENYLYLSULFKIN-MONOMER COEFFICIENT 2)))
(ADENYLYLSULFKIN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH PAPS "MGADP")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(ALTERNATIVE-COFACTORS (MG+2 MN+2 CO+2 CD+2))
(COFACTORS MG+2)
(SYNONYMS "APS kinase"
"ATP adenosine-5'-phosphosulfate 3'-phosphotransferase"
"ATP:adenylylsulfate 3'-phosphotransferase")
(COMMON-NAME "adenylylsulfate kinase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADENYLYLSULFKIN-RXN)
(INHIBITORS-COMPETITIVE APS "MGADP")
(COMMENT "The enzyme exhibits a complex steady-state kinetic
behavior, showing a combination of ping-pong and sequential pathways.
|CITS: [SatischandranJBC264,15012] [93075778]|"
"The enzyme picks up MgATP first then binds to the substrate
indicating the reaction is ordered sequential. |CITS:
[SatischandranJBC26415012]|")
(ENZYME ADENYLYLSULFKIN-CPLX)
(:CREATION-DATE 2974150691)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH PAPS COMMENT "Both inhibited the enzyme in a
noncompetitive manner at a subinhibitory concentration of APS. PAPS
was uncompetitive with MgATP when a high APS concentration was used.")
(INHIBITORS-UNKMECH PAPS CITATIONS "[SatischandranJBC26415012]")
(INHIBITORS-UNKMECH "MGADP" CITATIONS "[SatischandranJBC26415012]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[SatischandranJBC26415012]")
(COFACTORS MG+2 CITATIONS "[SatischandranJBC264,15012]")
(INHIBITORS-COMPETITIVE APS COMMENT "in the forward direction,
competitve with ATP")))
(ADENYLYLSULFKIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2750" "CysC")
(COMMON-NAME "CysC")
(DBLINKS (MODBASE "P0A6J1" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0A6J1" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6J1" NIL |pkarp| 3354911363)
(PFAM "PF01583" IN-FAMILY |pkarp| 3346700373 NIL NIL)
(REFSEQ "NP_417230" NIL NIL NIL NIL NIL))
(COMPONENT-OF ADENYLYLSULFKIN-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 22.321271999999993d0)
(GENE EG10185)
(:CREATION-DATE 2974150691)
(:CREATOR |mriley|) )
NIL)
(ADENYLYLSULFKIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY SO4ASSIM-PWY)
(ENZYMATIC-REACTION ADENYLYLSULFKIN-ENZRXN)
(RIGHT PAPS ADP)
(LEFT APS ATP)
(EC-NUMBER "2.7.1.25")
(COMMENT
"This is the second step in the activation of sulfate. The reaction occurs early in the sulfide branch of the cysteine synthesis pathway.")
(:CREATION-DATE 2974150691)
(:CREATOR |mriley|) )
NIL)
(ADHC-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "
")
(:CREATION-DATE 3122642593)
(CATALYZES FALDH-ENZRXN)
(COMPONENTS ADHC-MONOMER) )
((COMPONENTS ADHC-MONOMER COEFFICIENT 2)))
(ADHC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Glutathione-dependent formaldehyde dehydrogenase (GS-FDH) belongs to the family of class III alcohol
dehydrogenases. Glutathione and formaldehyde combine non-enzymatically to form hydroxymethylglutathione, the
true substrate of the GS-FDH catalyzed reaction. The product, S-formylglutathione, is further metabolized to formic
acid. The functional role of GS-FDH may be in the metabolism of endogenously formed formaldehyde and detoxifying
exogenous formaldehyde. |CITS: [92118844] [97472270]|
Transcription of the frmRAB operon is induced by formaldehyde, but not S-nitrosoglutathione
|CITS: [9333139][15466022]|.")
(SYNONYMS "B0356" "AdhC")
(:CREATION-DATE 3122642477)
(DBLINKS (MODBASE "P25437" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P25437" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00107" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(REFSEQ "NP_414890" NIL NIL NIL NIL NIL)
(UNIPROT "P25437" NIL |paley| 3169408120))
(COMMON-NAME "FrmA")
(COMPONENT-OF ADHC-CPLX)
(PI 4.4d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 39.358940999999916d0)
(GENE EG50010) )
((PI 4.4d0 CITATIONS "[92118844]")))
(ADHE-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES PFLDEACTIV-ENZRXN ALCOHOL-DEHYDROG-ENZRXN ACETALD-DEHYDROG-ENZRXN)
(COMPONENTS ADHE-MONOMER)
(COMMENT "A homopolymeric protein with three
Fe++-dependent catalytic functions: alcohol dehydrogenase,
acetaldehyde dehydrogenase and pyruvate formate-lyase deactivase. The
homopolymeric structure is unusual in that about 40 subunits are
helically arranged to form a rod-like ultrastructure. |CITS: [92388175]|")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
((COMPONENTS ADHE-MONOMER COMMENT
"Number of monomers in enzyme aggregate is not precisely known."
"Number of subunits is not precisely known.")
(COMPONENTS ADHE-MONOMER COEFFICIENT 40)))
(ADHE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1241" "AdhC" "Ana" "AdhE")
(COMMON-NAME "AdhE")
(DBLINKS (MODBASE "P0A9Q7" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00465" IN-FAMILY |pkarp| 3346700331 NIL NIL)
(UNIPROT "P0A9Q7" NIL |pkarp| 3338704373 NIL NIL)
(REFSEQ "NP_415757" NIL NIL NIL NIL NIL))
(COMPONENT-OF ADHE-CPLX)
(PI 6.72d0)
(MOLECULAR-WEIGHT-SEQ 96.12712999999964d0)
(GENE EG10031)
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
NIL)
(ADHP-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (ETOH 700) (ACETALD 30))
(INHIBITORS-NONCOMPETITIVE "4-methylpyrazole" PYRAZOLE)
(CITATIONS "10406936:EV-EXP-IDA-PURIFIED-PROTEIN:3335289300:keseler")
(:CREATION-DATE 3122637756)
(COMMON-NAME "ethanol dehydrogenase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALCOHOL-DEHYDROG-RXN ALCOHOL-DEHYDROG-GENERIC-RXN)
(ENZYME ADHP-MONOMER)
(SYNONYMS "ethanol dehydrogenase/acetaldehyde reductase"
"alcohol dehydrogenase, propanol-preferring" "aldehyde reductase"
"alcohol:NAD+ oxidoreductase") )
((KM (ETOH 700) CITATIONS "10406936") (KM (ACETALD 30) CITATIONS "10406936")
(INHIBITORS-NONCOMPETITIVE "4-methylpyrazole" CITATIONS "99337666")
(INHIBITORS-NONCOMPETITIVE PYRAZOLE CITATIONS "99337666")))
(ADHP-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"AdhP is an ethanol-active medium-chain alcohol dehydrogenase/reductase. The enzyme is even more efficient in
the reverse direction of acetaldehyde reduction |CITS: [99337666]|.
AdhP did not show dehydrogenase activity in a high-throughput screen of purified proteins |CITS: [15808744]|.
Expression of AdhP is inducible by ethanol |CITS: [10406936]|.")
(:CREATION-DATE 3122637183)
(SYNONYMS "B1478" "YddN" "AdhP")
(DBLINKS (MODBASE "P39451" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P39451" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00107" IN-FAMILY |pkarp| 3346700336 NIL NIL)
(REFSEQ "NP_415995" NIL NIL NIL NIL NIL)
(UNIPROT "P39451" NIL |paley| 3169408120))
(CATALYZES ADHP-ENZRXN)
(MOLECULAR-WEIGHT-SEQ 35.37952599999993d0)
(GENE G6775) )
NIL)
(ADIPATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF GLUTDECARBOXB-ENZRXN GLUTDECARBOXA-ENZRXN)
(:CREATOR |arnaud|)
(DBLINKS (CAS "124-04-9"))
(:CREATION-DATE 3252348989)
(SYNONYMS "adipic acid" "hexanedioic acid")
(GIBBS-0 -160.8d0)
(MOLECULAR-WEIGHT 146.143d0)
(CHEMICAL-FORMULA (C 6) (H 10) (O 4))
(DISPLAY-COORDS-2D (-0.42384d0 -0.80795d0) (-0.15563d0 -0.60596d0)
(-0.7351d0 -0.67219d0) (-1.0d0 -0.87417d0) (0.99669d0 -0.4702d0)
(0.72848d0 -0.66887d0) (0.14901d0 -0.7351d0) (0.41722d0 -0.53642d0)
(-0.77483d0 -0.34106d0) (0.76821d0 -1.0d0))
(STRUCTURE-BONDS (10 6 1) (9 3 2) (8 7 1) (7 2 1) (6 8 1) (5 6 2) (4 3 1)
(2 1 1) (1 3 1))
(STRUCTURE-ATOMS C C C O O C C C O O)
(COMMON-NAME "adipate") )
((GIBBS-0 -160.8d0 CITATIONS "GibbsGroups97")))
(ADOMET-DMK-METHYLTRANSFER-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT
"The ubiE gene product, a C-methyltransferase, catalyzes reactions in both
ubiquinone (Q) and menaquinone (MK) biosynthesis. Q biosynthesis and MK
biosynthesis diverge after the formation of chorismate and the pathways proceed
independently except for the C methylation step. In MK biosynthesis the ubiE
encoded enzyme catalyzes the conversion of demethylmenaquinone to menaquinone.
|CITS: [97197541] [98004566]|")
(REACTION ADOMET-DMK-METHYLTRANSFER-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/mensyn2/step72.template")
(ENZYME 2-OCTAPRENYL-METHOXY-BENZOQ-METH-MONOMER)
(:CREATION-DATE 3030979246)
(COMMON-NAME "S-adenosylmethionine:2-DMK methyltransferase")
(SYNONYMS "S-adenosylmethionine:2-demethylmenaquinone methyltransferase")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(ADOMET-DMK-METHYLTRANSFER-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION ADOMET-DMK-METHYLTRANSFER-ENZRXN)
(IN-PATHWAY MENAQUINONESYN-PWY)
(RIGHT VITAMIN_K_{2} ADENOSYL-HOMO-CYS)
(LEFT DEMETHYLMENAQUINONE S-ADENOSYLMETHIONINE)
(COMMENT "This is the seventh and final reaction in menaquinone
biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/menaq/step7.template")
(:CREATION-DATE 3000590269)
(:CREATOR |mriley|) )
NIL)
(ADOMETSYN2-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ADOMETSYN2-ENZRXN)
(COMPONENTS ADOMETSYN2-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/metX.template")
(:CREATION-DATE 3016372644)
(:CREATOR |mriley|) )
((COMPONENTS ADOMETSYN2-MONOMER CITATIONS "[94049123]")
(COMPONENTS ADOMETSYN2-MONOMER COEFFICIENT 2)))
(ADOMETSYN2-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION S-ADENMETSYN-RXN)
(REACTION-DIRECTION REVERSIBLE)
(COMMENT
"There is some uncertainty about the identity of the gene for the suspected
second methionine adenosyltransferase. This information is being left in
in the KB in case future study provides a definitive answer. There are two genes coding for methionine
adenosyltransferase in E. coli, metK and metX. The metX gene product,
methionine adenosyltransferase 2 or AdoMet synthetase 2, is expressed
in cells grown in rich media at all growth phases and in stationary
phase in minimal media. AdoMet synthetase 1 is detected only in cells
growing in minimal media. The intracellular concentration of AdoMet
is nearly constant in the cell over a variety of growth conditions. It
is unclear how the concentration is regulated. The expression of the
metK and metX gene products are also regulated so that only one gene
product predominates at any one time. AdoMet synthetase 2 has not yet
been characterized. |CITS: [94049123]|")
(ENZYME ADOMETSYN2-CPLX)
(SYNONYMS "S-adenosylmethionine synthase 2"
"ATP:L-methionine S-adenosyltransferase" "AdoMet synthase 2"
"SAM synthase 2")
(COMMON-NAME "methionine adenosyltransferase 2")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/metX.template")
(:CREATION-DATE 3016372644)
(:CREATOR |mriley|) )
NIL)
(ADOMETSYN2-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"There is some uncertainty about the identity of the gene for the suspected
methionine adenosyltransferase 2. This information is being retained in the KB
in case future study can provide a definitive answer.")
(COMPONENT-OF ADOMETSYN2-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (S-ADENMETSYN-MONOMER YES))
(PI 5.4d0)
(MOLECULAR-WEIGHT-SEQ 41.746d0)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/metX.template")
(:CREATION-DATE 3016372644)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-SEQ 41.746d0 CITATIONS "[SwissProt]")))
(ADP NIL (
(OCELOT-GFP::PARENTS |Purine-Diphosphates| |Purine-Related|)
(INHIBITORS-OTHER-OF GUANOSINEKIN-ENZRXN PRPPSYN-ENZRXN)
(INHIBITORS-ALLOSTERIC-OF PRPPSYN-ENZRXN)
(ACTIVATORS-UNKMECH-OF ICITDEHDEPHOSPH-ENZRXN)
(ACTIVATORS-ALLOSTERIC-OF 6PFRUCTPHOS-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ENZRXN0-1627 MALOX-ENZRXN GTP-CYCLOHYDRO-I-ENZRXN
NUCLEOSIDE-DIP-KIN-ENZRXN ATPPHOSPHORIBOSYLTRANS-ENZRXN
GLUTATHIONE-SYN-ENZRXN DETHIOBIOTIN-SYN-ENZRXN GLUTKIN-ENZRXN
MANNPDEHYDROG-ENZRXN PPK-ENZRXN 1PFRUCTPHOSPHN-ENZRXN GLYCEROL-KIN-ENZRXN
AIRS-ENZRXN INORGPYROPHOSPHAT-ENZRXN GLYCOGENSYN-ENZRXN)
(INHIBITORS-UNKMECH-OF GUANOSINEKIN-ENZRXN F16BDEPHOS-ENZRXN GLUTAMINB-ENZRXN
NAD-SYNTH-NH3-ENZRXN THI-P-SYN-ENZRXN ENZRXN0-5803 ICITDEHKINASE-ENZRXN
ENZRXN0-5681 ENZRXN0-5901 AIRS-ENZRXN THI-P-KIN-ENZRXN ENZRXN0-5762
ENZRXN0-402)
(INHIBITORS-NONCOMPETITIVE-OF PHOSACETYLTRANS-ENZRXN ADENYLATECYC-ENZRXN)
(DBLINKS (CAS "20398-34-9" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C00008" NIL |kr| 3346617701 NIL NIL) (CAS "58-64-0"))
(:CREATION-DATE 3054404381)
(GIBBS-0 -55.4d0)
(APPEARS-IN-LEFT-SIDE-OF RXN0-747)
(APPEARS-IN-RIGHT-SIDE-OF UDP-NACMURALGLDAPAALIG-RXN RXN0-5127 RXN0-5123
RXN0-5122 RXN0-5121 RXN0-5118 RXN0-5116 ADPREDUCT-RXN PEPDEPHOS-RXN
6PFRUCTPHOS-RXN POLYPHOSPHATE-KINASE-RXN ADENYL-KIN-RXN PROPKIN-RXN
CTPSYN-RXN RXN0-5061 RXN0-5057 3.6.3.39-RXN RXN0-5023 RXN0-3 RXN0-21 RXN0-11
2.7.1.148-RXN RXN0-4621 RXN0-4522 RXN0-4341 N-ACETYLGLUCOSAMINE-KINASE-RXN
RXN0-4261 RXN0-3901 RIBOSYLNICOTINAMIDE-KINASE-RXN GLYCOGENSYN-RXN RXN0-1402
RXN0-2921 FOLYLPOLYGLUTAMATESYNTH-RXN NANK-RXN PHOSGLYPHOS-RXN RXN0-2361
ALLOSE-KINASE-RXN FRUCTOKINASE-RXN PROTEIN-TYROSINE-KINASE-RXN
TRANS-RXN0-202 ABC-32-RXN RXN0-1401 RXN0-962 TRANS-RXN0-162 GLUCOKIN-RXN
RXN0-742 LYXK-RXN RXN0-704 GDPKIN-RXN DGDPKIN-RXN DADPKIN-RXN DUDPKIN-RXN
CDPKIN-RXN UDPKIN-RXN DTDPKIN-RXN DCDPKIN-RXN TRANS-RXN-224 ABC-2-RXN
RXN0-382 TRANS-RXN-250 TRANS-RXN-34 ABC-42-RXN ABC-70-RXN ATPSYN-RXN
ACETYL-COA-CARBOXYLTRANSFER-RXN CARBPSYN-RXN TRANS-RXN-32 TRANS-RXN-37
ABC-64-RXN ABC-63-RXN FORMYLTHFGLUSYNTH-RXN GKI-RXN DCUS-RXN PNKIN-RXN
TORS-RXN UHPB-RXN EVGS-RXN RCSF-RXN RCSC-RXN NARX-RXN NARQ-RXN ATOS-RXN
CREC-RXN PHOR-RXN BAES-RXN BASS-RXN ENVZ-RXN BARA-RXN KDPD-RXN HYDH-RXN
CPXA-RXN ARCB-RXN RSTB-RXN PHOQ-RXN CHEA-RXN NRIIPHOS-RXN TRANS-RXN-2
TRANS-RXN-7 ABC-37-RXN ABC-36-RXN ABC-35-RXN ABC-5-RXN ABC-4-RXN ABC-3-RXN
ABC-8-RXN ABC-7-RXN ABC-12-RXN ABC-11-RXN ABC-10-RXN ABC-9-RXN ABC-15-RXN
ABC-14-RXN ABC-13-RXN ABC-18-RXN ABC-16-RXN ABC-22-RXN ABC-20-RXN ABC-19-RXN
ABC-24-RXN ABC-23-RXN ABC-28-RXN ABC-27-RXN ABC-26-RXN ABC-25-RXN ABC-29-RXN
ABC-34-RXN ABC-33-RXN GMKALT-RXN COBINAMIDEKIN-RXN TAGAKIN-RXN GSPSYN-RXN
GARTRANSFORMYL2-RXN GSDEADENYLATION-RXN PYRAMKIN-RXN PROLINE-MULTI
DARABKIN-RXN GLUCONOKIN-RXN DIACYLGLYKIN-RXN THIAZOLSYN3-RXN PYRIDOXKIN-RXN
OHMETPYRKIN-RXN RIBOFLAVINKIN-RXN GLY3KIN-RXN DALADALALIG-RXN
UDP-NACMURALGLDAPLIG-RXN UDP-NACMURALA-GLU-LIG-RXN UDP-NACMUR-ALA-LIG-RXN
TETRAACYLDISACC4KIN-RXN NAD-KIN-RXN PROPIONYL-COA-CARBOXY-RXN
PEPCARBOXYKIN-RXN 3.6.1.41-RXN PHOSICITDEHASE-RXN GLUTKIN-RXN
ACETYLGLUTKIN-RXN ACETATEKIN-RXN ASPARTATEKIN-RXN GALACTOKIN-RXN THIKIN-RXN
PANTOTHENATE-KIN-RXN DEPHOSPHOCOAKIN-RXN INOSINEKIN-RXN THYKI-RXN
HOMOSERKIN-RXN GLYCEROL-KIN-RXN ADENYLYLSULFKIN-RXN MANNKIN-RXN
DEHYDDEOXGALACTKIN-RXN FUCULOKIN-RXN SHIKIMATE-KINASE-RXN XYLULOKIN-RXN
RIBOKIN-RXN 1PFRUCTPHOSN-RXN RHAMNULOKIN-RXN DEOXYGLUCONOKIN-RXN
THI-P-KIN-RXN NUCLEOSIDE-DIP-KIN-RXN CMPKI-RXN GUANYL-KIN-RXN UMPKI-RXN
PYRIMSYN3-RXN GUANOSINEKIN-RXN DURIDKI-RXN DTMPKI-RXN SUCCCOASYN-RXN
SAICARSYN-RXN DIHYDROFOLATESYNTH-RXN GLUTATHIONE-SYN-RXN GLUTCYSLIG-RXN
BIOTIN-CARBOXYL-RXN FORMATETHFLIG-RXN GLYRIBONUCSYN-RXN GLUTAMINESYN-RXN
AIRS-RXN DETHIOBIOTIN-SYN-RXN FGAMSYN-RXN)
(SYNONYMS "adenosine pyrophosphate" "adenosine 5'-pyrophosphate"
"adenosine-5'-diphosphate" "adenosine-diphosphate" "adenosine-5-diphosphate")
(CHARGE -3)
(COMMON-NAME "ADP")
(STRUCTURE-ATOMS O O O C C N N O O C C C C C C C C N N P N O O O O P O)
(STRUCTURE-BONDS (27 26 1) (25 26 1) (24 26 2) (23 26 1) (16 22 1 :DOWN)
(21 11 1) (1 20 2) (15 2 1 :DOWN) (3 20 1) (6 4 :AROMATIC) (4 19 :AROMATIC)
(5 8 1) (14 5 1 :UP) (12 6 :AROMATIC) (10 7 :AROMATIC) (7 13 :AROMATIC)
(8 20 1) (9 14 1) (9 17 1) (23 20 1) (18 10 :AROMATIC) (12 11 :AROMATIC)
(11 18 :AROMATIC) (13 12 :AROMATIC) (19 13 :AROMATIC) (14 15 1) (15 16 1)
(16 17 1) (17 19 1 :UP))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (7.2769d0 -4.3761d0) (7.9875d0 -5.6161d0)
(8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0) (7.5247d0 -2.7725d0)
(7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0) (8.8524d0 -2.7725d0)
(7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0) (5.3121d0 -2.4844d0)
(7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0) (4.4916d0 -2.4844d0)
(3.6666d0 -3.3112d0) (3.6641d0 -1.6612d0) (3.6657d0 -2.4862d0)
(2.8407d0 -2.4862d0))
(CHEMICAL-FORMULA (C 10) (H 15) (N 5) (O 10) (P 2))
(MOLECULAR-WEIGHT 427.203d0)
(AROMATIC-RINGS (4 6 12 13 19) (7 10 18 11 12 13)) )
((GIBBS-0 -55.4d0 CITATIONS "GibbsGroups97")))
(|ADP-Aldoses| T (
(OCELOT-GFP::PARENTS |Aldoses|)
(COMMON-NAME "an ADP-aldose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(ADP-D-GLUCOSE NIL (
(OCELOT-GFP::PARENTS ADP-SUGARS |NDP-glucoses|)
(OVERVIEW-NODE-SHAPE :ELLIPSE-VERT)
(INHIBITORS-COMPETITIVE-OF UDPSUGARHYDRO-ENZRXN)
(INHIBITORS-UNKMECH-OF ENZRXN0-5762)
(APPEARS-IN-LEFT-SIDE-OF GLYCOGENSYN-RXN)
(DBLINKS (LIGAND-CPD "C00498" NIL |kr| 3346617701 NIL NIL) (CAS "2140-58-1"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -214.6d0)
(APPEARS-IN-RIGHT-SIDE-OF GLUC1PADENYLTRANS-RXN)
(SYNONYMS "adenosine diphosphate glucose" "ADP-glucose")
(COMMON-NAME "ADP-D-glucose")
(STRUCTURE-ATOMS O O O O C C C C C C O O P P O O O O O O C C O C C O O C C C
C C N N N N C N)
(STRUCTURE-BONDS (37 38 1) (31 30 :AROMATIC) (32 35 :AROMATIC)
(31 37 :AROMATIC) (36 32 :AROMATIC) (37 36 :AROMATIC) (35 30 :AROMATIC)
(34 29 :AROMATIC) (30 34 :AROMATIC) (29 33 :AROMATIC) (33 31 :AROMATIC)
(28 33 1 :UP) (25 27 1 :DOWN) (24 26 1 :DOWN) (21 22 1 :UP) (25 28 1)
(24 25 1) (23 28 1) (21 24 1) (23 21 1) (20 22 1) (14 18 1) (13 17 1)
(13 16 2) (14 15 2) (13 20 1) (19 13 1) (14 19 1) (12 14 1) (10 11 1)
(5 12 1 :DOWN) (6 1 1 :DOWN) (7 2 1 :UP) (8 3 1 :DOWN) (9 10 1 :UP) (4 5 1)
(4 9 1) (5 6 1) (6 7 1) (7 8 1) (8 9 1))
(DISPLAY-COORDS-2D (5.2046d0 -0.831d0) (3.7713d0 0.0d0) (2.3506d0 -0.8329d0)
(3.7736d0 -2.4795d0) (4.4932d0 -2.0693d0) (4.4932d0 -1.2398d0)
(3.7736d0 -0.8205d0) (3.0631d0 -1.2398d0) (3.0631d0 -2.0693d0)
(2.3525d0 -2.4795d0) (1.638d0 -2.067d0) (5.2026d0 -2.4815d0)
(7.6776d0 -2.4815d0) (6.0276d0 -2.4815d0) (6.0276d0 -3.3065d0)
(7.6776d0 -3.3065d0) (7.6776d0 -1.6565d0) (6.0276d0 -1.6565d0)
(6.8526d0 -2.4815d0) (8.5026d0 -2.4815d0) (9.9316d0 -2.4815d0)
(9.2171d0 -2.894d0) (10.599d0 -2.9665d0) (10.1865d0 -1.6969d0)
(11.0115d0 -1.6969d0) (9.6031d0 -1.1136d0) (11.424d0 -0.9825d0)
(11.2664d0 -2.4815d0) (12.6733d0 -2.4455d0) (13.0173d0 -3.7353d0)
(12.1935d0 -3.6911d0) (12.9407d0 -5.1622d0) (11.9809d0 -2.894d0)
(13.3138d0 -2.9654d0) (13.3909d0 -4.4708d0) (12.1169d0 -5.118d0)
(11.7433d0 -4.3825d0) (10.9183d0 -4.3825d0))
(CHEMICAL-FORMULA (C 16) (H 25) (N 5) (O 15) (P 2))
(MOLECULAR-WEIGHT 589.345d0)
(AROMATIC-RINGS (29 34 30 31 33) (30 35 32 36 37 31)) )
((GIBBS-0 -214.6d0 CITATIONS "GibbsGroups97")))
(ADP-D-GLYCERO-D-MANNO-HEPTOSE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (CAS "119-61-9" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C06397" NIL |kr| 3346617701 NIL NIL))
(APPEARS-IN-RIGHT-SIDE-OF RXN0-4342)
(APPEARS-IN-LEFT-SIDE-OF 5.1.3.20-RXN)
(:CREATOR |keseler|)
(:CREATION-DATE 3333293211)
(COMMON-NAME "ADP-D-glycero-D-manno-heptose")
(SYNONYMS
" 2-[[[5-[(6-amino-9H-purin-9-yl)]-3,4-dihydroxy-tetrahydrofuran- 2-yl]methoxy-hydroxy-phosphinoyl]oxy-hydroxy-phosphinoyl]oxy-6- (1,2-dihydroxyethyl)tetrahydropyran-3,4,5-triol"
"ADP-D-β-D-heptose")
(STRUCTURE-ATOMS C C C C C N N N N N C C C C C P P O O O O O O O C C C C C C
O O O O O O O O O C)
(DISPLAY-COORDS-2D (6.2883d0 -2.5667d0) (5.2696d0 -3.5688d0)
(4.6911d0 -2.9807d0) (4.9111d0 -2.1855d0) (3.5776d0 -2.2445d0)
(5.0496d0 -4.3639d0) (3.8669d0 -3.0171d0) (4.2229d0 -1.7306d0)
(5.7098d0 -1.9785d0) (6.0682d0 -3.3618d0) (4.1865d0 -0.9064d0)
(4.1276d0 0.4272d0) (4.6415d0 -0.2182d0) (3.355d0 0.1378d0)
(2.6668d0 0.5928d0) (1.2405d0 0.6793d0) (-0.1884d0 0.691d0)
(3.3914d0 -0.6863d0) (1.6773d0 1.3792d0) (-0.5951d0 1.4088d0)
(0.2182d0 -0.0268d0) (0.8036d0 -0.0206d0) (0.5294d0 1.0976d0)
(-0.9063d0 0.2844d0) (-1.6173d0 0.7027d0) (-2.3754d0 1.9141d0)
(-1.6467d0 1.5272d0) (-3.0454d0 0.6519d0) (-3.0747d0 1.4764d0)
(-3.7154d0 -0.6102d0) (-2.4047d0 2.7385d0) (-3.8034d0 1.8632d0)
(-4.4734d0 0.6011d0) (-4.4147d0 -1.0479d0) (-2.3167d0 0.2651d0)
(4.3476d0 1.2223d0) (5.4657d0 -0.1818d0) (-0.9473d0 1.9649d0)
(1.9287d0 0.2243d0) (-3.7447d0 0.2143d0))
(STRUCTURE-BONDS (27 38 1 :UP) (30 34 1) (40 30 1) (40 33 1 :DOWN) (28 40 1)
(29 32 1 :DOWN) (26 31 1 :UP) (28 29 1) (35 28 1) (26 29 1) (26 27 1)
(25 35 1) (27 25 1) (25 24 1 :DOWN) (13 37 1 :DOWN) (12 36 1 :DOWN)
(17 20 1) (17 21 2) (17 24 1) (23 17 1) (16 22 2) (16 19 1) (16 23 1)
(39 16 1) (15 39 1) (14 15 1 :UP) (18 14 1) (12 14 1) (12 13 1) (11 18 1)
(13 11 1) (11 8 1 :UP) (2 6 1) (7 5 2) (8 5 1) (8 4 1) (3 4 :AROMATIC)
(3 7 1) (2 3 :AROMATIC) (10 2 :AROMATIC) (1 10 :AROMATIC) (4 9 :AROMATIC)
(9 1 :AROMATIC))
(CHEMICAL-FORMULA (C 17) (H 27) (N 5) (O 16) (P 2))
(MOLECULAR-WEIGHT 619.372d0)
(AROMATIC-RINGS (9 4 3 2 10 1)) )
NIL)
(|ADP-D-ribosyl-nitrogen-reductases| T (
(OCELOT-GFP::PARENTS |Nitrogen-reductases|)
(AROMATIC-RINGS (4 6 12 13 19) (7 10 18 11 12 13))
(CHEMICAL-FORMULA (C 15) (H 22) (N 5) (O 13) (|Protein| 1) (P 2))
(STRUCTURE-BONDS (31 34 1 :DOWN) (30 35 1 :DOWN) (32 36 1) (29 32 1 :UP)
(30 31 1) (29 30 1) (33 29 1) (33 28 1) (31 28 1) (28 27 1 :DOWN) (27 26 1)
(25 26 1) (24 26 2) (23 26 1) (16 22 1 :DOWN) (21 11 1) (1 20 2)
(15 2 1 :DOWN) (3 20 1) (6 4 :AROMATIC) (4 19 :AROMATIC) (5 8 1)
(14 5 1 :UP) (12 6 :AROMATIC) (10 7 :AROMATIC) (7 13 :AROMATIC) (8 20 1)
(9 14 1) (9 17 1) (23 20 1) (18 10 :AROMATIC) (12 11 :AROMATIC)
(11 18 :AROMATIC) (13 12 :AROMATIC) (19 13 :AROMATIC) (14 15 1) (15 16 1)
(16 17 1) (17 19 1 :UP))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (7.2769d0 -4.3761d0) (7.9875d0 -5.6161d0)
(8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0) (7.5247d0 -2.7725d0)
(7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0) (8.8524d0 -2.7725d0)
(7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0) (5.3121d0 -2.4844d0)
(7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0) (4.4916d0 -2.4844d0)
(3.6666d0 -3.3112d0) (3.6641d0 -1.6612d0) (3.6657d0 -2.4862d0)
(2.8407d0 -2.4862d0) (2.1262d0 -2.0737d0) (0.7914d0 -2.0737d0)
(1.0463d0 -1.2891d0) (1.8713d0 -1.2891d0) (0.0067d0 -2.3286d0)
(1.4588d0 -2.5586d0) (2.3562d0 -0.6217d0) (0.5614d0 -0.6217d0)
(-0.6063d0 -1.7766d0))
(STRUCTURE-ATOMS O O O C C N N O O C C C C C C C C N N P N O O O O P O C C C
C C O O O |Protein|)
(COMMON-NAME "ADP-D-ribosyl-(dinitrogen reductase)")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(ADP-GROUP NIL (
(OCELOT-GFP::PARENTS |Coenzyme-Groups|)
(MOLECULAR-WEIGHT 427.203d0)
(CHEMICAL-FORMULA (C 10) (H 15) (N 5) (O 10) (P 2))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (7.2769d0 -4.3761d0) (7.9875d0 -5.6161d0)
(8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0) (7.5247d0 -2.7725d0)
(7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0) (8.8524d0 -2.7725d0)
(7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0) (5.3121d0 -2.4844d0)
(7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0) (4.4916d0 -2.4844d0)
(3.6666d0 -3.3112d0) (3.6641d0 -1.6612d0) (3.6657d0 -2.4862d0)
(2.8407d0 -2.4862d0))
(STRUCTURE-BONDS (27 26 1) (25 26 1) (24 26 2) (23 26 1) (16 22 1 :DOWN)
(21 11 1) (1 20 2) (15 2 1 :DOWN) (3 20 1) (6 4 :AROMATIC) (4 19 :AROMATIC)
(5 8 1) (14 5 1 :UP) (12 6 :AROMATIC) (10 7 :AROMATIC) (7 13 :AROMATIC)
(8 20 1) (9 14 1) (9 17 1) (23 20 1) (18 10 :AROMATIC) (12 11 :AROMATIC)
(11 18 :AROMATIC) (13 12 :AROMATIC) (19 13 :AROMATIC) (14 15 1) (15 16 1)
(16 17 1) (17 19 1 :UP))
(STRUCTURE-ATOMS O O O C C N N O O C C C C C C C C N N P N O O O O P O)
(AROMATIC-RINGS (4 6 12 13 19) (7 10 18 11 12 13))
(:CREATOR |kr|)
(COMMON-NAME "ADP group")
(:CREATION-DATE 3084133996) )
NIL)
(ADP-L-GLYCERO-D-MANNO-HEPTOSE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-5127 RXN0-5122 RXN0-5118 RXN0-5061 RXN0-5057)
(DBLINKS (LIGAND-CPD "C06398" NIL |kr| 3346617701 NIL NIL))
(APPEARS-IN-RIGHT-SIDE-OF 5.1.3.20-RXN)
(:CREATOR |keseler|)
(:CREATION-DATE 3333293210)
(COMMON-NAME "ADP-L-glycero-D-manno-heptose")
(SYNONYMS
"2-[[[5-[(6-amino-9H-purin-9-yl)]-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphinoyl]oxy-hydroxy-phosphinoyl]oxy-6-(1,2-dihydroxyethyl)tetrahydropyran-3,4,5-triol"
"ADP-L-glycero-D-manno-heptose")
(STRUCTURE-ATOMS C C C C C N N N N N C C C C C P P O O O O O O O C C C C C C
O O O O O O O O O C)
(DISPLAY-COORDS-2D (6.2883d0 -2.5667d0) (5.2696d0 -3.5688d0)
(4.6911d0 -2.9807d0) (4.9111d0 -2.1855d0) (3.5776d0 -2.2445d0)
(5.0496d0 -4.3639d0) (3.8669d0 -3.0171d0) (4.2229d0 -1.7306d0)
(5.7098d0 -1.9785d0) (6.0682d0 -3.3618d0) (4.1865d0 -0.9064d0)
(4.1276d0 0.4272d0) (4.6415d0 -0.2182d0) (3.355d0 0.1378d0)
(2.6668d0 0.5928d0) (1.2405d0 0.6793d0) (-0.1884d0 0.691d0)
(3.3914d0 -0.6863d0) (1.6773d0 1.3792d0) (-0.5951d0 1.4088d0)
(0.2182d0 -0.0268d0) (0.8036d0 -0.0206d0) (0.5294d0 1.0976d0)
(-0.9063d0 0.2844d0) (-1.6173d0 0.7027d0) (-2.3754d0 1.9141d0)
(-1.6467d0 1.5272d0) (-3.0454d0 0.6519d0) (-3.0747d0 1.4764d0)
(-3.7154d0 -0.6102d0) (-2.4047d0 2.7385d0) (-3.8034d0 1.8632d0)
(-4.4734d0 0.6011d0) (-4.4147d0 -1.0479d0) (-2.3167d0 0.2651d0)
(4.3476d0 1.2223d0) (5.4657d0 -0.1818d0) (-0.9473d0 1.9649d0)
(1.9287d0 0.2243d0) (-3.7447d0 0.2143d0))
(STRUCTURE-BONDS (27 38 1 :UP) (30 34 1) (40 30 1) (40 33 1 :UP) (28 40 1)
(29 32 1 :DOWN) (26 31 1 :UP) (28 29 1) (35 28 1) (26 29 1) (26 27 1)
(25 35 1) (27 25 1) (25 24 1 :DOWN) (13 37 1 :DOWN) (12 36 1 :DOWN)
(17 20 1) (17 21 2) (17 24 1) (23 17 1) (16 22 2) (16 19 1) (16 23 1)
(39 16 1) (15 39 1) (14 15 1 :UP) (18 14 1) (12 14 1) (12 13 1) (11 18 1)
(13 11 1) (11 8 1 :UP) (2 6 1) (7 5 2) (8 5 1) (8 4 1) (3 4 :AROMATIC)
(3 7 1) (2 3 :AROMATIC) (10 2 :AROMATIC) (1 10 :AROMATIC) (4 9 :AROMATIC)
(9 1 :AROMATIC))
(CHEMICAL-FORMULA (C 17) (H 27) (N 5) (O 16) (P 2))
(MOLECULAR-WEIGHT 619.372d0)
(AROMATIC-RINGS (9 4 3 2 10 1)) )
NIL)
(ADP-MANNOSE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "ADP-mannose")
(:CREATOR |keseler|)
(:CREATION-DATE 3333729302) )
NIL)
(|ADP-Ribose(P)| T (
(OCELOT-GFP::PARENTS ADP-SUGARS)
(COMMON-NAME "an ADP-ribose")
(SCHEMA? T) )
NIL)
(ADP-SUGARS T (
(OCELOT-GFP::PARENTS NUCLEOTIDE-SUGARS |Purine-Related|)
(SYNONYMS "an ADP-sugar")
(APPEARS-IN-LEFT-SIDE-OF ADPSUGPPHOSPHAT-RXN)
(COMMON-NAME "an ADP-sugar")
(:CREATOR |paley|)
(:CREATION-DATE 3355617747) )
NIL)
(ADPREDUCT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "Glutaredoxin may substitute for thioredoxin in the reaction.")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ADPREDUCT-RXN)
(ENZYME RIBONUCLEOSIDE-DIP-REDUCTI-CPLX)
(COMMON-NAME "ADP reductase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/pyrnusal/nrdAB.template")
(:CREATION-DATE 3010324856)
(:CREATOR |mriley|) )
NIL)
(ADPREDUCT-RXN NIL (
(OCELOT-GFP::PARENTS EC-1.17.4 |Protein-Modification-Reactions|)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY DENOVOPURINE2-PWY)
(OFFICIAL-EC? NIL)
(EC-NUMBER "1.17.4.1")
(ENZYMATIC-REACTION ADPREDUCT-ENZRXN)
(RIGHT ADP |Red-Thioredoxin|)
(LEFT DADP |Ox-Thioredoxin| WATER)
(COMMENT "Necessary for DNA synthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/pyrnusal/nrdAB.template")
(:CREATION-DATE 3010324856)
(:CREATOR |mriley|) )
NIL)
(ADPSUGPPHOSPHAT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.6.1)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ENZRXN0-5822 ENZRXN0-5803)
(RIGHT AMP |Alpha-D-aldose-1-phosphates|)
(LEFT ADP-SUGARS WATER)
(EC-NUMBER "3.6.1.21")
(COMMENT "This reaction is a part of the breakdown of ADP-sugars.")
(TEMPLATE-FILE "~ecocyc/templates/new/onlies/adpsug.template")
(:CREATION-DATE 3054505279)
(:CREATOR |mriley|) )
NIL)
(AERESPDON-PWY NIL (
(OCELOT-GFP::PARENTS AEROBIC-RESPIRATION)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3064091736)
(PRIMARIES (|SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN| (SUC) (FUM))
(HYDROG-RXN (PROTON) (HYDROGEN-MOLECULE)) (NADH-DEHYDROG-A-RXN (NADH) (NAD)))
(ENZYME-USE (HYDROG-RXN FORMHYDROGI-ENZRXN)
(GLYC3PDEHYDROG-RXN AERGLYC3PDEHYDROG-ENZRXN))
(REACTION-LIST NADH-DEHYDROG-A-RXN L-LACTDEHYDROGFMN-RXN DLACTDEHYDROGFAD-RXN
|SUCCINATE-DEHYDROGENASE-(UBIQUINONE)-RXN| GLYC3PDEHYDROG-RXN)
(COMMON-NAME "aerobic respiration -- electron donors reaction list") )
NIL)
(AERGLYC3PDEHYDROG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"The aerobic glycerol 3-phosphate dehydrogenase is a homodimeric enzyme associated
with the cytoplasmic membrane through binding to negatively-charged phopholipids |CITS: [11955283]|. It is
essential for utilization of glycerol-3-phosphate or its precursors, glycerol and glycerophosphodiesters. Under
anaerobic conditions the anaerobic glycerol-3-phosphate dehydrogenase fulfills the same function. Optimal
intracellular levels of glycerol-3-phosphate are maintained for biosynthesis of phospholipids. Oxidation of
glycerol-3-phosphate results in concurrent reduction of its noncovalently-bound FAD cofactor, which passes
electrons on to ubiquinone.
GlpD is encoded by the glpD gene |CITS:[87109031] [91100269]|. Expression of glpD (along with other
members of the glp regulon |CITS: [825019]|) is repressed by GlpR and induced by glycerol-3-phosphate.
Anaerobically glpD expression is repressed by the two-component regulatory system arcA and
arcB.
")
(SYNONYMS "GlpD")
(CATALYZES AERGLYC3PDEHYDROG-ENZRXN)
(LOCATIONS CCO-MEMBRANE)
(COMPONENTS AERGLYC3PDEHYDROG-MONOMER)
(:CREATION-DATE 2974211043)
(:CREATOR |mriley|) )
((COMPONENTS AERGLYC3PDEHYDROG-MONOMER COEFFICIENT 2)))
(AERGLYC3PDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "POTASSIUM PHOSPHATE")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "G3P dehydrogenase"
"sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase")
(COMMON-NAME "glycerol 3-phosphate dehydrogenase, aerobic")
(REACTION-DIRECTION REVERSIBLE)
(REACTION GLYC3PDEHYDROG-RXN)
(INHIBITORS-COMPETITIVE DIHYDROXY-ACETONE-PHOSPHATE PHOSPHO-ENOL-PYRUVATE
CPD-67 GAP "D-2- AND D-3-PHOSPHOGLYCERIC ACID")
(COFACTOR-BINDING-COMMENT
"The enzyme contains 0.5 mol of FAD/mol of monomer. |CITS: [SchryversJBC253,783]|")
(REQUIRED-PROTEIN-COMPLEX)
(ENZYME AERGLYC3PDEHYDROG-CPLX)
(:CREATION-DATE 2974211043)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "POTASSIUM PHOSPHATE" COMMENT
"non-competitive |CITS:[WeinerBBRC47,1360]|")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[SchryversJBC253783]")))
(AERGLYC3PDEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3426" "GlyD" "GlvD" "GlpD")
(COMMON-NAME "GlpD")
(DBLINKS (MODBASE "P13035" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01266" IN-FAMILY |pkarp| 3346700400 NIL NIL)
(REFSEQ "NP_417884" NIL NIL NIL NIL NIL) (UNIPROT "P13035"))
(COMPONENT-OF AERGLYC3PDEHYDROG-CPLX)
(PI 6.33d0)
(MOLECULAR-WEIGHT-SEQ 56.750465999999825d0)
(GENE EG10394)
(:CREATION-DATE 2974211043)
(:CREATOR |mriley|) )
NIL)
(AEROBIC-RESPIRATION T (
(OCELOT-GFP::PARENTS |Respiration|)
(COMMENT
"This class contains pathways through which electrons flow from various organic and inorganic electron donors to oxygen as the terminal electron acceptor. The passage of electrons through intermediates of the pathway, which are membrane-bound, generates a trans-membrane ion gradient, which serves as a source of metabolic energy. ")
(COMMON-NAME "Aerobic")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(AFFILIATES NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |kr|)
(:CREATION-DATE 3339519670)
(:DOMAIN |Organizations|)
(:VALUE-TYPE |People|)
(:INVERSE AFFILIATIONS)
(:DOCUMENTATION
"This slot records individual people that are affiliated with the organization.") )
NIL)
(AFFILIATIONS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |kr|)
(:CREATION-DATE 3339519669)
(:DOMAIN |People|)
(:VALUE-TYPE |Organizations|)
(:INVERSE AFFILIATES)
(:DOCUMENTATION
"This slot records the organizations with which the individual person is affiliated.") )
NIL)
(AG NIL (
(OCELOT-GFP::PARENTS |Elements|)
(VALENCE 2 1)
(SYNONYMS "silver")
(COMMON-NAME "Ag")
(ATOMIC-WEIGHT 107.87d0)
(ATOMIC-NUMBER 47)
(:CREATOR |paley|)
(:CREATION-DATE 3301322514) )
NIL)
(AG+ NIL (
(OCELOT-GFP::PARENTS |Cations|)
(INHIBITORS-UNKMECH-OF PANTOATE-BETA-ALANINE-LIG-ENZRXN)
(SYNONYMS "silver")
(DBLINKS (CAS "7440-22-4" NIL |kr| 3346617701 NIL NIL)
(LIGAND-CPD "C06710" NIL |kr| 3346617701 NIL NIL))
(CHEMICAL-FORMULA (AG 1))
(CHARGE 1)
(COMMON-NAME "Ag+")
(:CREATOR |paley|)
(:CREATION-DATE 3233673360) )
NIL)
(AGAA-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 17.519299999999998d0)
(:CREATION-DATE 3060117329)
(CITATIONS "[97086503]")
(SPECIES ECOLI)
(COMMENT "putative deacetylase")
(SYNONYMS "B3135" "YraA" "AgaA")
(DBLINKS (MODBASE "P42906" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P42906" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF01979" IN-FAMILY |pkarp| 3346700388 NIL NIL)
(ECOO157CYC "Z4489-MONOMER" |Homolog| |pick| 3278712115 NIL NIL)
(REFSEQ "NP_417604" NIL NIL NIL NIL NIL)
(UNIPROT "P42906" NIL |pkarp| 3064869797))
(GENE EG12766)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME
"predicted truncated N-acetylgalactosamine-6-phosphate deacetylase") )
NIL)
(AGAB-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 17.622242000000014d0)
(:CREATION-DATE 3060117329)
(CITATIONS "[97086503]")
(SPECIES ECOLI)
(COMMENT "contains a PTS Enzyme IIB domain")
(SYNONYMS "B3138" "YraD" "AgaB")
(DBLINKS (MODBASE "P42909" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF03830" IN-FAMILY |pkarp| 3346700388 NIL NIL)
(REFSEQ "NP_417607" NIL NIL NIL NIL NIL)
(UNIPROT "P42909" NIL |pkarp| 3064869797))
(COMPONENT-OF CPLX-170)
(GENE EG12769)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AgaB") )
NIL)
(AGAC-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 28.644833999999996d0)
(:CREATION-DATE 3060117329)
(CITATIONS "[97086503]")
(SPECIES ECOLI)
(COMMENT "contains a PTS Enzyme IIC domain")
(SYNONYMS "B3139" "YraE" "AgaC")
(DBLINKS (PFAM "PF03609" IN-FAMILY |pkarp| 3346700388 NIL NIL)
(REFSEQ "NP_417608" NIL NIL NIL NIL NIL)
(UNIPROT "P42910" NIL |pkarp| 3064869797))
(COMPONENT-OF CPLX-170)
(GENE EG12770)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AgaC") )
NIL)
(AGAD-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 29.00133499999997d0)
(CITATIONS "[97086503]")
(SPECIES ECOLI)
(DBLINKS (PFAM "PF03613" IN-FAMILY |pkarp| 3346700388 NIL NIL)
(REFSEQ "NP_417609" NIL NIL NIL NIL NIL)
(UNIPROT "P42911" NIL |paley| 3169408120))
(COMMENT "contains a PTS Enzyme IID domain")
(SYNONYMS "B3140" "YraF" "AgaD")
(COMPONENT-OF CPLX-170)
(GENE G7635)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3131301657) )
NIL)
(AGAX-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 16.540033000000008d0)
(DBLINKS (MODBASE "P36881" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF03610" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414671" NIL NIL NIL NIL NIL)
(UNIPROT "P36881" NIL |paley| 3169408120))
(COMMENT "contains a PTS Enzyme IIA domain")
(SYNONYMS "B0129" "YadI" "AgaX")
(COMPONENT-OF CPLX-170)
(GENE EG12322)
(:CREATOR |ipaulsen|)
(:CREATION-DATE 3131301689) )
NIL)
(AGMATHINE NIL (
(OCELOT-GFP::PARENTS |Aliphatic-Amines|)
(DBLINKS (LIGAND-CPD "C00179" NIL |kr| 3346617701 NIL NIL) (CAS "306-60-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 10.8d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2162 ARGDECARBOX-RXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2162 AGMATIN-RXN)
(MOLECULAR-WEIGHT 130.192d0)
(CHEMICAL-FORMULA (C 5) (H 14) (N 4))
(DISPLAY-COORDS-2D (-0.42669d0 -0.99671d0) (0.99671d0 -0.83196d0)
(0.14003d0 -0.99671d0) (-1.0d0 -1.0d0) (-0.14333d0 -0.83196d0)
(0.42669d0 -0.83196d0) (0.71005d0 -0.99671d0) (-0.71334d0 -0.83196d0)
(-0.71334d0 -0.50247d0))
(STRUCTURE-BONDS (9 8 1) (7 6 1) (6 3 1) (5 1 1) (4 8 2) (3 5 1) (2 7 1)
(1 8 1))
(STRUCTURE-ATOMS N N C N C C C C N)
(COMMON-NAME "agmatine")
(SYSTEMATIC-NAME "guanidine, (4-aminobutyl)-") )
((GIBBS-0 10.8d0 CITATIONS "GibbsGroups97")))
(AGMATIN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENTS AGMATIN-MONOMER)
(CATALYZES AGMATIN-ENZRXN)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speB.template")
(:CREATION-DATE 3000591065)
(:CREATOR |mriley|) )
((COMPONENTS AGMATIN-MONOMER COEFFICIENT 2)
(COMPONENTS AGMATIN-MONOMER CITATIONS "[86139896]")))
(AGMATIN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH L-ORNITHINE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(ENZYME AGMATIN-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION AGMATIN-RXN)
(INHIBITORS-COMPETITIVE ARG)
(COMMENT "Agmatinase is part of the second putresine biosynthetic
pathway. It also represents the only pathway for urea biosynthesis in
E. coli as no urease is present. |CITS: [86139896] [85163236]|")
(SYNONYMS "agmatine ureohydrolase" "AUH" "agmatine amidinohydrolase")
(COMMON-NAME "agmatinase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speB.template")
(:CREATION-DATE 3000591065)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH L-ORNITHINE COMMENT "noncompetitive inhibitor |CITS:
[86139896]|")
(INHIBITORS-COMPETITIVE ARG CITATIONS "[86139896]")))
(AGMATIN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2937" "SpeB")
(COMMON-NAME "SpeB")
(COMPONENT-OF AGMATIN-CPLX)
(DBLINKS (MODBASE "P60651" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P60651" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P60651" NIL |pkarp| 3354911363)
(PFAM "PF00491" IN-FAMILY |pkarp| 3346700380 NIL NIL)
(REFSEQ "NP_417412" NIL NIL NIL NIL NIL))
(PI 5.44d0)
(MOLECULAR-WEIGHT-SEQ 33.55700599999991d0)
(GENE EG10960)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speB.template")
(:CREATION-DATE 3000591065)
(:CREATOR |mriley|) )
NIL)
(AGMATIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY-40 ARGDEG-PWY PWY0-823)
(ENZYMATIC-REACTION AGMATIN-ENZRXN)
(RIGHT UREA PUTRESCINE)
(LEFT WATER AGMATHINE)
(EC-NUMBER "3.5.3.11")
(COMMENT "This reaction is part of putrescine and spermidine biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speB.template")
(:CREATION-DATE 3000591065)
(:CREATOR |mriley|) )
NIL)
(AGNO3 NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF DCYSDESULF-ENZRXN GLUTAMINA-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979810)
(COMMON-NAME "AgNO3")
(SYNONYMS "silver nitrate" "nitric acid, silver(1+) salt" "lunar caustic"
"argerol" "argenti nitras" "silver mononitrate")
(STRUCTURE-ATOMS O O O N AG)
(DISPLAY-COORDS-2D (2.4248d0 0.0d0) (0.0d0 0.0d0) (1.2124d0 -2.1d0)
(1.2124d0 -0.7d0) (4.4048d0 -1.204d0))
(STRUCTURE-BONDS (3 4 1) (2 4 2) (1 4 2))
(ATOM-CHARGES (5 1) (3 -1))
(CHEMICAL-FORMULA (N 1) (O 3) (AG 1))
(MOLECULAR-WEIGHT 169.875d0) )
NIL)
(AICAR NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04677" NIL |keseler| 3341780225 NIL NIL)
(CAS "3031-94-5"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -127.4d0)
(APPEARS-IN-LEFT-SIDE-OF AICARTRANSFORM-RXN)
(APPEARS-IN-RIGHT-SIDE-OF AICARSYN-RXN GLUTAMIDOTRANS-RXN)
(MOLECULAR-WEIGHT 338.213d0)
(CHEMICAL-FORMULA (C 9) (H 15) (N 4) (O 8) (P 1))
(DISPLAY-COORDS-2D (-0.01254d0 0.54545d0) (-0.01254d0 -0.66144d0)
(0.22884d0 -0.32288d0) (-0.15674d0 -0.53918d0) (-0.01254d0 -1.0d0)
(-0.15674d0 -0.35737d0) (0.60815d0 -0.66458d0) (0.60815d0 0.15674d0)
(0.45455d0 -0.83072d0) (0.34483d0 0.5768d0) (0.60815d0 -0.4953d0)
(-0.01254d0 -0.83072d0) (-0.44828d0 -0.35737d0) (0.21317d0 0.99687d0)
(0.80251d0 0.42633d0) (0.45455d0 -0.66144d0) (-0.71787d0 -0.63009d0)
(0.34483d0 0.29467d0) (0.21317d0 0.71473d0) (-0.71787d0 -0.35737d0)
(0.60188d0 0.68652d0) (-0.15674d0 -0.70846d0) (0.0815d0 0.19122d0)
(0.45455d0 -1.0d0) (-0.71787d0 -0.06583d0) (-1.0d0 -0.35737d0))
(STRUCTURE-BONDS (26 20 1) (25 20 2) (24 9 1) (23 18 1) (22 4 1)
(21 15 :AROMATIC) (20 13 1) (19 10 1) (8 18 :AROMATIC) (17 20 1) (16 9 1)
(15 8 :AROMATIC) (14 19 2) (13 6 1) (12 9 1) (11 9 1) (11 8 1)
(10 21 :AROMATIC) (18 10 :AROMATIC) (7 11 1) (6 4 1) (5 12 1) (4 12 1)
(4 3 1) (3 11 1) (2 12 1) (1 19 1))
(STRUCTURE-ATOMS N H O C O C H N C C C C O O C H O C C P N H N O O O)
(SYSTEMATIC-NAME
"Imidazole-4-carboxamide, 5-amino-1-beta-D-ribofuranosyl-, 5-(dihydrogen phosphate)")
(SYNONYMS "Z-nucleotide" "aminoimidazole carboxamide ribonucleotide"
"AICA ribonucleotide" "5'-phosphoribosyl-5-amino-4-imidazole carboxamide"
"5-amino-4-imidazolecarboxamide ribotide"
"5'-P-ribosyl-5-amino-4-imidazole carboxamide")
(COMMON-NAME "AICAR")
(AROMATIC-RINGS (18 8 15 21 10)) )
((GIBBS-0 -127.4d0 CITATIONS "GibbsGroups97")))
(AICARSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(COMMON-NAME
"5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase")
(REACTION AICARSYN-RXN)
(COMMENT "Adenylosuccinate lyase is a bifunctional enzyme that
catalyzes the removal of fumarate from
5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole and from
succinyl-AMP to form AICAR and AMP, respectively.")
(ENZYME ASL-MONOMER)
(:CREATION-DATE 2959814156)
(:CREATOR |mriley|) )
NIL)
(AICARSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION AICARSYN-ENZRXN)
(RIGHT FUM AICAR)
(LEFT P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE)
(CITATIONS "[92104952]")
(EC-NUMBER "4.3.2.2")
(COMMENT "This is the eighth step in the de novo purine biosynthesis.")
(:CREATION-DATE 2959814156)
(:CREATOR |mriley|) )
NIL)
(AICARTRANSFORM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(REACTION-DIRECTION REVERSIBLE)
(COMMON-NAME "AICAR transformylase")
(REACTION AICARTRANSFORM-RXN)
(CITATIONS ":EV-EXP:3277835749:pkarp" "[90286915]")
(COMMENT "The ninth and tenth reactions of the de novo purine
biosynthetic pathway for IMP biosynthesis are sequentially catalysed
by AICAR transformylase and IMP cyclohydrolase. This is the second of
two transformylation reactions in the de novo biosynthesis of purine
nucleotides and like the glycineamide-ribonucleotide (GAR)transformylase,
AICAR transformylase also utilizes N10-formyl-THF as the formyl donor.
The synthesis of IMP in both E. coli and S. typhimurium, is under
the control of a common regulatory protein, the product of the purR
locus. Recent studies have concluded that AICAR transformylase and IMP
cyclohydrolase form a bifunctional enzyme with both activities
residing on a single polypeptide. The two activities reside in two
distinct domains of a single polypeptide which requires dimerization
for maximum activity of both reactions.|CITS:[90286915]|")
(ENZYME AICARTRANSIMPCYCLO-CPLX)
(:CREATION-DATE 2955471181)
(:CREATOR |mriley|) )
NIL)
(AICARTRANSFORM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.1.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION AICARTRANSFORM-ENZRXN)
(RIGHT THF PHOSPHORIBOSYL-FORMAMIDO-CARBOXAMIDE)
(LEFT 10-FORMYL-THF AICAR)
(EC-NUMBER "2.1.2.3")
(COMMENT "This is the ninth step in purine biosynthesis")
(:CREATION-DATE 2955471181)
(:CREATOR |mriley|) )
NIL)
(AICARTRANSIMPCYCLO-CPLX NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4006" "PurH")
(DBLINKS (MODBASE "P15639" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02142" IN-FAMILY |pkarp| 3346700429 NIL NIL)
(REFSEQ "NP_418434" NIL |hopkinso| 3309630841 NIL NIL) (UNIPROT "P15639"))
(CATALYZES AICARTRANSFORM-ENZRXN IMPCYCLOCYDROLASE-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 57.329132999999786d0)
(GENE EG10795)
(COMMENT "From the earliest studies an association between AICAR
transformylase and IMP cyclohydrolase has been shown.")
(:CREATION-DATE 2955471181)
(:CREATOR |mriley|) )
NIL)
(AIRS-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES AIRS-ENZRXN)
(COMPONENTS AIRS-MONOMER)
(:CREATION-DATE 2955471200)
(:CREATOR |mriley|) )
((COMPONENTS AIRS-MONOMER COEFFICIENT 2)))
(AIRS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH ADP |Pi| 5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE)
(COFACTORS K+ MG+2)
(SYNONYMS "AIR synthetase" "AIRS" "AIR synthase"
"phosphoribosyl-aminoimidazole synthetase"
"5'-Phosphoribosyl-5-aminoimidazole synthetase"
"aminoimidazole ribonucleotide synthetase")
(COMMON-NAME "phosphoribosylformylglycinamide cyclo-ligase")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(REACTION AIRS-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[87000552]" "[86278135]" "[90126847]")
(INHIBITORS-COMPETITIVE ADP)
(COFACTOR-BINDING-COMMENT "Both K and Mg ions were found to be
absolutely required for catalytic activity.
|CITS: [87000552]| ")
(COMMENT "AIR synthetase from E. coli, as in the case of the chicken
liver protein, catalyzes transfer of the oxygen of the formyl group to
inorganic phosphate. Both K and Mg ions were found to be
absolutely required for catalytic activity. Kinetic studies are available. |CITS:[87000552]|")
(ENZYME AIRS-CPLX)
(:CREATION-DATE 2955471200)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH ADP COMMENT "ADP versus FGAM")
(INHIBITORS-UNKMECH |Pi| COMMENT "Pi versus FGAM")
(INHIBITORS-UNKMECH 5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE COMMENT
"AIR versus FGAM")
(INHIBITORS-COMPETITIVE ADP COMMENT "versus ATP")))
(AIRS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2499" "PurI" "PurG" "PurM")
(COMMON-NAME "PurM")
(DBLINKS (MODBASE "P08178" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00586" IN-FAMILY |pkarp| 3346700364 NIL NIL)
(REFSEQ "NP_416994" NIL NIL NIL NIL NIL) (UNIPROT "P08178"))
(COMPONENT-OF AIRS-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 36.85399299999993d0)
(GENE EG10798)
(:CREATION-DATE 2955471200)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT " to purI from Salmonella")))
(AIRS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.3.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION AIRS-ENZRXN)
(RIGHT ADP |Pi| 5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE)
(LEFT ATP 5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE)
(EC-NUMBER "6.3.3.1")
(COMMENT "This is the fifth step (the imidazole ring closure) in de
novo purine biosynthesis")
(:CREATION-DATE 2955471200)
(:CREATOR |mriley|) )
NIL)
(AKBLIG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES AKBLIG-ENZRXN)
(COMPONENTS AKBLIG-MONOMER)
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/kbl.template")
(:CREATION-DATE 3044212596)
(:CREATOR |mriley|) )
((COMPONENTS AKBLIG-MONOMER COEFFICIENT 2)))
(AKBLIG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CO-A "aminomethylphosphonic acid" GLUTATHIONE
DITHIOTHREITOL CYS CD+2 CU+2 HG+2)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(ALTERNATIVE-SUBSTRATES (ACETYL-COA "n-propionyl-CoA"))
(REACTION-DIRECTION REVERSIBLE)
(REACTION AKBLIG-RXN)
(PHYSIOLOGICALLY-RELEVANT CYS GLUTATHIONE CO-A "aminomalonic acid")
(INHIBITORS-COMPETITIVE "aminomalonic acid")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(COMMENT "2-Amino-3-ketobutyrate CoA ligase (AKB ligase) catalyzes
the reversible cleavage/condensation reaction between
2-amino-3-ketobutyrate and glycine plus acetyl-CoA. It is the second
reaction in the threonine dehydrogenase-initiated pathway by which
threonine is converted to glycine (hence serine). It is the primary
route for threonine utilization in prokaryotes and is a highly
efficient alternate pathway for serine biosynthesis in E. coli. As
2-amino-3-ketobutyrate can spontaneously decarboxylate, study
continues on the metabolic role of this product/substrate and enzyme.
|CITS: [88032988] [90105507]|")
(ENZYME AKBLIG-CPLX)
(SYNONYMS "glycine C-acetyltransferase" "AKB ligase" "aminoacetone synthase"
"aminoacetone synthetase" "acetyl-CoA:glycine C-acetyltransferase")
(COMMON-NAME "2-amino-3-ketobutyrate CoA ligase")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/kbl.template")
(:CREATION-DATE 3044212596)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH CO-A COMMENT
"exhibits strong product inhibition |CITS: [88032988]|")
(INHIBITORS-UNKMECH "aminomethylphosphonic acid" CITATIONS "[88032988]")
(INHIBITORS-UNKMECH GLUTATHIONE CITATIONS "[88032988]")
(INHIBITORS-UNKMECH DITHIOTHREITOL CITATIONS "[88032988]")
(INHIBITORS-UNKMECH CYS CITATIONS "[88032988]")
(INHIBITORS-UNKMECH CD+2 CITATIONS "[88032988]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[88032988]")
(INHIBITORS-UNKMECH HG+2 CITATIONS "[88032988]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The
enzyme is strictly specific for glycine. |CITS: [88032988]|")
(INHIBITORS-COMPETITIVE "aminomalonic acid" COMMENT "competitive with
respect to glycine |CITS: [88032988]|")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE COMMENT "1 mol of pyridoxal
phosphate is bound/enzyme subunit. |CITS: [90105507]|")))
(AKBLIG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3617" "Kbl")
(COMMON-NAME "Kbl")
(DBLINKS (MODBASE "P0AB77" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00155" IN-FAMILY |pkarp| 3346700409 NIL NIL)
(UNIPROT "P0AB77" NIL |pkarp| 3338704378 NIL NIL)
(REFSEQ "NP_418074" NIL NIL NIL NIL NIL) (PDB "1FC4"))
(COMPONENT-OF AKBLIG-CPLX)
(PI 5.99d0)
(MOLECULAR-WEIGHT-SEQ 43.116983999999846d0)
(GENE EG10512)
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/kbl.template")
(:CREATION-DATE 3044212596)
(:CREATOR |mriley|) )
NIL)
(AKBLIG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY THREOCAT-PWY)
(ENZYMATIC-REACTION AKBLIG-ENZRXN)
(RIGHT AMINO-OXOBUT CO-A)
(LEFT GLY ACETYL-COA)
(EC-NUMBER "2.3.1.29")
(COMMENT "This reaction is part of the primary route of threonine
utilization, and is also a highly efficient alternate pathway for
glycine and serine biosynthesis.")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/kbl.template")
(:CREATION-DATE 3044212596)
(:CREATOR |mriley|) )
NIL)
(AL NIL (
(OCELOT-GFP::PARENTS |Elements|)
(VALENCE 3)
(SYNONYMS "aluminum")
(COMMON-NAME "Al")
(ATOMIC-WEIGHT 26.98d0)
(ATOMIC-NUMBER 13)
(:CREATOR |paley|)
(:CREATION-DATE 3301322514) )
NIL)
(|ALA-tRNAs| T (
(OCELOT-GFP::PARENTS |tRNAs|)
(DBLINKS (LIGAND-CPD "C01635" NIL |kr| 3346617699 NIL NIL))
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF ALANINE--TRNA-LIGASE-RXN)
(SYNONYMS "TRNA(ALA)")
(COMMON-NAME "tRNAala") )
NIL)
(ALADEG-PWY NIL (
(OCELOT-GFP::PARENTS ALANINE-DEG)
(PATHWAY-LINKS (PYRUVATE GLYCOLYSIS))
(COMMENT
"Through this single pathway either L- or D-alanine can be degraded to pyruvate which
enters central metabolism, and thereby, can serve as a growth-supporting, total source of carbon and energy.
This pathway is unque among those through which L-amino acids are degraded in that the L form must first be
converted to the D form. This first step of the pathway, which can be catalyzed by either of two racemases, also
serves an essential role in biosynthesis because its product, D-alanine is an essential component of cell wall
peptidoglycan (murein). The role of the ala racemase is predominately biosynthetic: it is produced constitutively in
small amounts. The role of the dsdX racemase is degradative: it is induced to high levels by alanine and
is subject to catabolite repression.")
(LAYOUT-ADVICE (:REVERSIBLE-RXNS ALARACECAT-RXN))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(SYNONYMS "L-alanine degradation")
(REACTION-LIST DALADEHYDROG-RXN ALARACECAT-RXN)
(PATHWAY-INTERACTIONS)
(ENZYME-USE (DAADEHYDROG-RXN DAADEHYDROGA-MONOMER)
(DAADEHYDROG-RXN DAADEHYDROGB-MONOMER))
(PREDECESSORS (ALARACECAT-RXN) (DALADEHYDROG-RXN ALARACECAT-RXN))
(NET-REACTION-EQUATION "L-alpha-alanine = pyruvate + NH3")
(COMMON-NAME "alanine degradation I")
(:CREATION-DATE 2976548471)
(:CREATOR |mriley|) )
((PATHWAY-INTERACTIONS :FACET COMMENT "This is one of many reactions
that generate pyruvate. D-alanine appears in murein.")))
(ALADEHYDCHLORO-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALADEHYDCHLORO-RXN)
(COMMENT "The purified enzyme catalyzes this reaction, but it is not
known to occur in vivo. |CITS: [88251237]|")
(ENZYME DCYSDESULF-CPLX)
(COMMON-NAME "3-chloro-D-alanine dehydrochlorinase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/june/dcysdesul.template")
(:CREATION-DATE 3042991144)
(:CREATOR |mriley|) )
NIL)
(ALADEHYDCHLORO-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.5.1)
(EC-NUMBER "4.5.1.2")
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(ENZYMATIC-REACTION ALADEHYDCHLORO-ENZRXN)
(RIGHT S-CARBOXYMETHYL-D-CYSTEINE CL-)
(LEFT 3-CHLORO-D-ALANINE THIOGLYCOLATE)
(COMMENT "This is an alternate substrate reaction of D-cysteine
desulfhydrase. It may be identical with EC number 4.5.1.2.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/june/dcysdesul.template")
(:CREATION-DATE 3042991144)
(:CREATOR |mriley|) )
NIL)
(ALANINE--TRNA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS |tRNA-Charging-Reactions| EC-6.1.1)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY TRNA-CHARGING-PWY)
(ENZYMATIC-REACTION ALAS-ENZRXN)
(EC-NUMBER "6.1.1.7")
(COMMON-NAME "ALANINE--TRNA-LIGASE")
(RIGHT |Charged-ALA-tRNAs| PPI AMP)
(LEFT |ALA-tRNAs| L-ALPHA-ALANINE ATP)
(SYNONYMS "ALANYL-TRNA SYNTHETASE") )
NIL)
(ALANINE-AMINOTRANSFERASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY ALANINE-SYN2-PWY)
(ENZYMATIC-REACTION ENZRXN0-3401)
(:CREATOR |ingraham|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3288034478)
(SYNONYMS "Glutamic--alanine transaminase" "Glutamic--pyruvic transaminase")
(COMMON-NAME "Alanine aminotransferase")
(EC-NUMBER "2.6.1.2")
(RIGHT GLT PYRUVATE)
(LEFT 2-KETOGLUTARATE L-ALPHA-ALANINE) )
NIL)
(ALANINE-DEG T (
(OCELOT-GFP::PARENTS |Amino-Acid-Degradation|)
(COMMENT
"This class contains pathways of the degradation of D- and L- forms of the amino acid, alanine, that permit the cell to use this amino acid, when exogenously supplied, as a source of carbon and nitrogen. ")
(SCHEMA? T)
(COMMON-NAME "Alanine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104625) )
NIL)
(ALANINE-SYN T (
(OCELOT-GFP::PARENTS IND-AMINO-ACID-SYN)
(COMMENT
"This class contains pathways of the biosynthesis of L-alanine de novo (from intermediates of central metabolism) and from other amino acids or their biosynthetic intermediates; L-alanine is a constituent of protein and peptidoglycan. It is a source of D-alanine, which is also a constituent of peptidoglycan. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Alanine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104632) )
NIL)
(ALANINE-SYN2-PWY NIL (
(OCELOT-GFP::PARENTS ALANINE-SYN)
(PRIMARIES (ALANINE-AMINOTRANSFERASE-RXN NIL (L-ALPHA-ALANINE)))
(IN-PATHWAY PWY0-1061)
(SUPER-PATHWAYS PWY0-1061)
(COMMENT
"L-alanine is an essential component of protein and peptidoglycan. The later also contains about three molecules of
D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan.
At least three pathways (alanine biosynthesis I, alanine biosynthesis II, and alanine biosynthesis III) contribute
to the synthesis of alanine. Alanine biosynthesis I is established only by existence of the relevant enzymes. Its contribution to
alanine synthesis remains speculative because alanine auxotrophs have not yet been isolated. Because alanine but
not valine represses AvtA, its primary purpose is probably synthesis of L-alanine |CITS: [396446]|, |CITS: [7040341]|.Existence of the Alanine biosyntheis II pathways rests on the evidence that glutamate-pyruvate
aminotransferase acitivity is found in crude cell extracts; the enzymes has not been purified nor have mutant
alleles of its designated encoding gene (alaB) been isolated |CITS: [396446]|, |CITS: [4146872]|. The conversion
can also be mediated as a side reaction of alanine racemase |CITS: [9832621]| . The alanine biosyntheis III pathway, mediated by cysteine desulfurase activity is required to donate sulfane sulfur
for the synthesis of Fe-S clusters, thiamine, thionucleosides in tRNAs, biotin, lipoic acid, and molybdopterin
|CITS: [12382038]| probably contributes only a minor amount of the cell's alanine requirement, as judged by the
cell's total requirement for sulfane sulfur.
Review:|CITS: [ECOSAL]| Reitzer, L. Biosynthesis of glutamate, aspartate, asparagine, L-alanine and D-alanine. EcoSal, ASM Press,
WashingtonD.C.
")
(LAYOUT-ADVICE (:REVERSIBLE-RXNS ALANINE-AMINOTRANSFERASE-RXN))
(REACTION-LIST ALANINE-AMINOTRANSFERASE-RXN)
(PREDECESSORS (ALANINE-AMINOTRANSFERASE-RXN))
(CITATIONS "ECOSAL" ":EV-EXP:3288034841:ingraham")
(COMMON-NAME "alanine biosynthesis II")
(:CREATOR |ingraham|)
(:CREATION-DATE 3288034698) )
NIL)
(ALANINE-VALINESYN-PWY NIL (
(OCELOT-GFP::PARENTS ALANINE-SYN)
(IN-PATHWAY PWY0-1061)
(SUPER-PATHWAYS PWY0-1061)
(LAYOUT-ADVICE (:REVERSIBLE-RXNS ALARACECAT-RXN))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(COMMON-NAME "alanine biosynthesis I")
(REACTION-LIST VALINE-PYRUVATE-AMINOTRANSFER-RXN ALARACECAT-RXN
BRANCHED-CHAINAMINOTRANSFERVAL-RXN)
(PATHWAY-INTERACTIONS)
(PREDECESSORS (ALARACECAT-RXN VALINE-PYRUVATE-AMINOTRANSFER-RXN)
(VALINE-PYRUVATE-AMINOTRANSFER-RXN
BRANCHED-CHAINAMINOTRANSFERVAL-RXN)
(BRANCHED-CHAINAMINOTRANSFERVAL-RXN))
(NET-REACTION-EQUATION "pyruvate + glutamate = L-alanine + 2-ketoglutarate")
(COMMENT
"L-alanine is an essential component of protein and peptidoglycan. The later also contains about three molecules of
D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan.
At least three pathways (alanine biosynthesis I, alanine biosynthesis II, and alanine biosynthesis III) contribute
to the synthesis of alanine.
Alanine biosynthesis I is established only by existence of the relevant enzymes. Its contribution to
alanine synthesis remains speculative because alanine auxotrophs have not yet been isolated. Because alanine but
not valine represses expression of AvtA, its primary purpose is probably synthesis of L-alanine |CITS: [396446]|,
|CITS: [7040341]|. Existence of the Alanine biosyntheis II pathways rests on the evidence that glutamate-pyruvate
aminotransferase acitivity is found in crude cell extracts; the enzymes has not been purified nor have mutant
alleles of its designated encoding gene (alaB) been isolated |CITS: [396446]| , |CITS: [4146872]|. The conversion
can also be mediated as a side reaction of alanine racemase |CITS: [9832621]| .
The alanine biosyntheis III pathway, mediated by cysteine desulfurase activity is required to donate sulfane sulfur
for the synthesis of Fe-S clusters, thiamine, thionucleosides in tRNAs, biotin, lipoic acid, and molybdopterin
|CITS: [12382038]| probably contributes only a minor amount of the cell's alanine requirement, as judged by the
cell's total requirement for sulfane sulfur.
Review:|CITS: [ECOSAL]| Reitzer, L. Biosynthesis of glutamate, aspartate, asparagine, L-alanine and D-alanine. EcoSal, ASM Press,
Washington D.C.")
(:CREATION-DATE 2976548485)
(:CREATOR |mriley|) )
((PATHWAY-INTERACTIONS :FACET COMMENT "Enzymes used in common link
alanine synthesis with the branched-chain amino acids. L-alanine is
used in synthesis of both protein and murein.")))
(ALARACEBIOSYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(SPECIES ECOLI)
(CATALYZES ALARACEBIOSYN-ENZRXN)
(COMPONENTS ALARACEBIOSYN-MONOMER)
(:CREATION-DATE 2976548324)
(:CREATOR |mriley|) )
((COMPONENTS ALARACEBIOSYN-MONOMER CITATIONS "[78187250]")
(COMPONENTS ALARACEBIOSYN-MONOMER COEFFICIENT 2)))
(ALARACEBIOSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(SYNONYMS "Alr" "alanine racemase")
(INHIBITORS-IRREVERSIBLE "D-chlorovinylglycine" "L-chlorovinylglycine"
"DL-fluorovinylglycine" "3-fluoroalanine")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(COMMON-NAME "alanine racemase, minor")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALARACECAT-RXN)
(INHIBITORS-COMPETITIVE CPD-2482 "O-CARBAMOYL-D-SERINE")
(COFACTOR-BINDING-COMMENT "The enzyme contains 1 mol of pyridoxal
phosphate per monomer. |CITS: [ColiSalII]|")
(COMMENT "Activity of alanine racemase in E. coli is due to two
distinct gene products |CITS: [85162992]|. One alanine racemase (Alr)
is constitutive |CITS: [3920477]|; it is encode by alr. The other DadX is induced by D- or L-alanine and repressed by glucose;
it is , and is encoded by the dadX |CITS: [ColiSalII]|. Alr is less abundant than DadX. The enzymes from Salmonella
typhimurium are the only enteric alanine racemases that have been purified and characterized |CITS: [2644260]|
|CITS: [3920477]|.")
(ENZYME ALARACEBIOSYN-CPLX)
(:CREATION-DATE 2976548324)
(:CREATOR |mriley|) )
((INHIBITORS-IRREVERSIBLE "D-chlorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "L-chlorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "DL-fluorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "3-fluoroalanine" CITATIONS "[HandEnzInh]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[78187250]")))
(ALARACEBIOSYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SPECIES ECOLI)
(GENE EG10001)
(SYNONYMS "B4053" "Alr")
(DBLINKS (MODBASE "P0A6B4" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6B4" NIL |pkarp| 3354911363)
(PFAM "PF01168" IN-FAMILY |pkarp| 3346700432 NIL NIL)
(REFSEQ "NP_418477" NIL NIL NIL NIL NIL))
(COMMON-NAME "Alr")
(COMPONENT-OF ALARACEBIOSYN-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 39.152888999999924d0)
(:CREATION-DATE 2976548324)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"The biosynthetic alanine racemase
(alr) is similar to the catabolic racemase (dadX).")))
(ALARACECAT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-IRREVERSIBLE "D-chlorovinylglycine" "L-chlorovinylglycine"
"DL-fluorovinylglycine" "3-fluoroalanine")
(CITATIONS ":EV-EXP:3277835749:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(COMMON-NAME "alanine racemase, major")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALARACECAT-RXN)
(INHIBITORS-COMPETITIVE CPD-2482 "O-CARBAMOYL-D-SERINE")
(COFACTOR-BINDING-COMMENT "The enzyme contains 1 mol of pyridoxal
phosphate per monomer. |CITS: [ColiSalII]|")
(COMMENT "Activity of alanine racemase in E. coli is due to two
distinct gene products |CITS: [85162992]|. One alanine racemase (Alr)
is constitutive |CITS: [3920477]|; it is encode by alr. The other DadX is induced by D- or L-alanine and repressed by glucose;
it is , and is encoded by the dadX |CITS: [ColiSalII]|. Alr is less abundant than DadX. The enzymes from Salmonella
typhimurium are the only enteric alanine racemases that have been purified and characterized |CITS: [2644260]|
|CITS: [3920477]|.")
(ENZYME ALARACECAT-MONOMER)
(:CREATION-DATE 2976548338)
(:CREATOR |mriley|) )
((INHIBITORS-IRREVERSIBLE "D-chlorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "L-chlorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "DL-fluorovinylglycine" CITATIONS
"[JAmChemSoc109-7543]")
(INHIBITORS-IRREVERSIBLE "3-fluoroalanine" CITATIONS "[HandEnzInh]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[78187250]")))
(ALARACECAT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1190" "DadB" "AlnB" "AlnA" "DadX" "alanine racemase")
(GENE EG11408)
(DBLINKS (MODBASE "P29012" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P29012" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01168" IN-FAMILY |pkarp| 3346700329 NIL NIL)
(REFSEQ "NP_415708" NIL NIL NIL NIL NIL)
(UNIPROT "P29012" NIL NIL |ouzounis| 3027899498))
(CATALYZES ALARACECAT-ENZRXN)
(ISOZYME-SEQUENCE-SIMILARITY)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 38.844572999999954d0)
(:CREATION-DATE 2976548338)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "The catabolic alanine racemase
(dadX)is similar to the biosynthetic racemase (alr).")))
(ALARACECAT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ALADEG-PWY ALANINE-VALINESYN-PWY)
(ENZYMATIC-REACTION ALARACEBIOSYN-ENZRXN ALARACECAT-ENZRXN)
(RIGHT D-ALANINE)
(LEFT L-ALPHA-ALANINE)
(EC-NUMBER "5.1.1.1")
(COMMENT "A step in the breakdown of L-alanine.")
(:CREATION-DATE 2976548338)
(:CREATOR |mriley|) )
NIL)
(ALAS-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(PI 4.9d0)
(:CREATION-DATE 3067804951)
(CATALYZES ALAS-ENZRXN)
(COMPONENTS ALAS-MONOMER) )
((CREDITS SRI LAST-CURATED 3360617031)
(CREDITS |keseler| LAST-CURATED 3360617031) (PI 4.9d0 CITATIONS "8645007")
(COMPONENTS ALAS-MONOMER CITATIONS "[ColiSalII]")
(COMPONENTS ALAS-MONOMER COEFFICIENT 2)))
(ALAS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (L-ALPHA-ALANINE 190) (|ALA-tRNAs| 0.29d0) (ATP 4.4d0))
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT)
(INHIBITORS-UNKMECH O-PHENANTHROLINE)
(COFACTORS ZN+2)
(CITATIONS "7005211:EV-EXP-IDA-PURIFIED-PROTEIN:3358519305:keseler")
(ENZYME ALAS-CPLX)
(REACTION ALANINE--TRNA-LIGASE-RXN)
(:CREATION-DATE 3067730803)
(:CREATOR |kr|)
(COMMON-NAME "alanyl-tRNA synthetase") )
((KM (L-ALPHA-ALANINE 190) CITATIONS "340903")
(KM (|ALA-tRNAs| 0.29d0) CITATIONS "340903")
(KM (ATP 4.4d0) CITATIONS "340903")
(INHIBITORS-UNKMECH O-PHENANTHROLINE CITATIONS "1712632")
(COFACTORS ZN+2 CITATIONS "1712632")))
(ALAS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Alanyl-tRNA synthetase (AlaRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AlaRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971][1852601]|.
AlaRS is a homotetramer in solution |CITS: [7005211]|. Later experiments determined that AlaRS exists in an
equilibrium between a homodimeric and a homodecameric state, depending on temperature
|CITS: [8645007][9343380]|. The enzyme contains one molecule of zinc per AlaS polypeptide |CITS: [1712632]|; zinc
binds cooperatively and induces a conformational change in AlaRS |CITS: [8024549][10441391]|. Zinc is important for
tRNA recognition |CITS: [1549561]|.
Specificity determinants within tRNAAla that are important for recognition by AlaRS have been
identified |CITS: [3053691][8539617][8601277][10390340][10889033][11983895][12022232]|. A single nucleotide
base pair in the acceptor helix of tRNAAla, G3-U70, is necessary and sufficient for aminoacylation of
that tRNA with alanine |CITS: [3285220][2452483][2462282][1608452][9294178][10518524]|. A mutation in alaS
which compensates for a mutant tRNAAla containing a G3-C70 base pair has been isolated
|CITS: [2001352]|. Discrimination of the G3-U70 base pair maps to a 76 amino acid region outside the catalytic
center of AlaRS |CITS: [7742303]|. The nucleotide at position 73 modulates the efficiency of the transfer step of
aminoacylation |CITS: [1692733][1704363][10601268][10871402]|.
Specificity determinants and residues within AlaRS that are important for catalytic activity have been investigated
|CITS: [2271589][9736622]|. An N-terminal 461 amino acid fragment of the AlaS polypeptide was shown to
complement a temperature-sensitive alaS allele in vivo; the C-terminal portion of the enzyme appears to
be dispensable for catalytic activity, but is required for formation of the tetramer
|CITS: [7005211][7025207][6358898][3882689]|. The C-terminal domain plays a role in activating the catalytic sites
of the N-terminal domain |CITS: [6200234]|. Mutagenesis of an N-terminal domain peptide reveals residues that
increase catalytic activity of the fragment |CITS: [3892692]|.
A central region of AlaRS is essential for interaction with alanine-specific tRNA |CITS: [2435005]|. Site-directed
mutagenesis has identified the Arg69 residue within motif 2 |CITS: [8163518][8060998]|, the Cys665 residue
|CITS: [7918446]| and the Asp232 residue |CITS: [8172905]| as important for catalysis. The Lys73 residue is
important for recognition of tRNAAla |CITS: [2543446][8239663]|.
Kinetic parameters for binding of AlaRS to tmRNA have been determined |CITS: [10704215]|.
Many aminoacyl tRNA synthetases have been shown to have editing functions. AlaRS misactivates glycine and
serine, but has a pre-transfer editing function, hydrolyzing the non-cognate amino acid before transfer to
tRNAAla, and/or a post-transfer editing function that deacetylates mischarged tRNAAla
|CITS: [6117825]|. The covalently continuous two-domain structure of the tRNA is required to enable editing
|CITS: [12949076]|.
AlaRS represses transcription of the alaS gene by binding to a region flanking the transcription start site, and
thus autoregulates its own expression. The autoregulatory effect depends on the concentration of alanine, with higher
concentrations leading to lower levels of alaS transcription. At physiological levels of AlaRS, repression of
alaS transcription is solely mediated by alanine levels |CITS: [6264314]|.
The alaS21 allele leads to increased resistance to novobiocin |CITS: [10217798]|. Mutations in ribosomal
proteins S5 and S20 partially suppresses the temperature sensitive growth defect of an alaS mutation
|CITS: [4280505]|. The mechanism of suppression is thought to be a reduction in the rate of polypeptide synthesis
|CITS: [796671]|.
Reviews: |CITS: [10966471][2669241][1379318]|
")
(MOLECULAR-WEIGHT-EXP 95)
(MOLECULAR-WEIGHT-SEQ 96.03227199999938d0)
(DBLINKS (MODBASE "P00957" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00957" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01411" IN-FAMILY |pkarp| 3346700371 NIL NIL)
(REFSEQ "NP_417177" NIL NIL NIL NIL NIL)
(UNIPROT "P00957" NIL |pkarp| 3102853742))
(COMPONENT-OF ALAS-CPLX)
(GENE EG10034)
(SYNONYMS "Act" "B2697" "LovB" "AlaS" "ala-act")
(:CREATION-DATE 3067730817)
(:CREATOR |kr|)
(COMMON-NAME "alanyl-tRNA synthetase") )
((MOLECULAR-WEIGHT-EXP 95 CITATIONS "7005211")))
(|alaT-tRNA| NIL (
(OCELOT-GFP::PARENTS |ALA-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(alaT) is one of five alanine tRNAs.
tRNA(alaT) interacts with |FRAME: SSRA-RNA| |CITS: [11387229]|.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.
Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the
G3-U70 pairing in the acceptor stem |CITS: [1799462][9153306]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "UGC")
(MODIFIED-FORM |charged-alaT-tRNA|)
(COMMON-NAME "tRNAalaT")
(GENE EG30008) )
((CREDITS SRI LAST-CURATED 3355075384)
(CREDITS |shearer| LAST-CURATED 3355075384)))
(|alaU-tRNA| NIL (
(OCELOT-GFP::PARENTS |ALA-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(alaU) is one of five alanine tRNAs.
tRNA(alaU) interacts with |FRAME: SSRA-RNA| |CITS: [11387229]|.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.
Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the
G3-U70 pairing in the acceptor stem |CITS: [1799462][9153306]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "UGC")
(MODIFIED-FORM |charged-alaU-tRNA|)
(COMMON-NAME "tRNAalaU")
(GENE EG30009) )
((CREDITS SRI LAST-CURATED 3355075413)
(CREDITS |shearer| LAST-CURATED 3355075413)))
(|alaV-tRNA| NIL (
(OCELOT-GFP::PARENTS |ALA-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(alaV) is one of five alanine tRNAs.
tRNA(alaV) interacts with |FRAME: SSRA-RNA||CITS: [11387229]|.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.
Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the
G3-U70 pairing in the acceptor stem |CITS: [1799462][9153306]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "UGC")
(MODIFIED-FORM |charged-alaV-tRNA|)
(COMMON-NAME "tRNAalaV")
(GENE EG30010) )
((CREDITS SRI LAST-CURATED 3355075439)
(CREDITS |shearer| LAST-CURATED 3355075439)))
(|alaW-tRNA| NIL (
(OCELOT-GFP::PARENTS |ALA-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(alaW) is one of five alanine tRNAs.
tRNA(alaW) interacts with |FRAME: SSRA-RNA||CITS: [11387229]|.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.
Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the
G3-U70 pairing in the acceptor stem |CITS: [1799462][9153306]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GGC")
(MODIFIED-FORM |charged-alaW-tRNA|)
(COMMON-NAME "tRNAalaW")
(GENE EG30011) )
((CREDITS SRI LAST-CURATED 3355075456)
(CREDITS |shearer| LAST-CURATED 3355075456)))
(|alaX-tRNA| NIL (
(OCELOT-GFP::PARENTS |ALA-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(alaX) is one of five alanine tRNAs.
tRNA(alaX) interacts with |FRAME: SSRA-RNA||CITS: [11387229]|.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.
Bases A73 and G20 are key determinants of tRNA(ala) identity, as is the
G3-U70 pairing in the acceptor stem |CITS: [1799462][9153306]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GGC")
(MODIFIED-FORM |charged-alaX-tRNA|)
(COMMON-NAME "tRNAalaX")
(GENE EG30012) )
((CREDITS SRI LAST-CURATED 3355075491)
(CREDITS |shearer| LAST-CURATED 3355075491)))
(|Alcohol-Degradation| T (
(OCELOT-GFP::PARENTS |Degradation|)
(COMMENT
"This class contains pathways of degradation of various monohydric, dihydric, and trihydric alcohols, yielding a source of nutrients and energy. Pathways of degradation of polyhydric alcohols are shown under the class, \"Sugar alcohols\". ")
(COMMON-NAME "Alcohols")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(ALCOHOL-DEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ALTERNATIVE-SUBSTRATES (ETOH BUTANOL) (ETOH PROPANOL))
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COFACTORS FE+2)
(SYNONYMS "ADH" "alcohol:NAD+ oxidoreductase" "aldehyde reductase")
(COMMON-NAME "alcohol dehydrogenase")
(ENZYME ADHE-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALCOHOL-DEHYDROG-GENERIC-RXN ALCOHOL-DEHYDROG-RXN)
(COMMENT "One of three reactions catalyzed by the multifunctional
enzyme coded for by the adhE gene. Fermentative alcohol
dehydrogenase, ADH, works well with ethanol, n-propanol and n-butanol,
shows poor activity with pentanol and is ineffective with methanol or
branched alcohols. |CITS: [90198524]|")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
NIL)
(ALCOHOL-DEHYDROG-GENERIC-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ADHP-ENZRXN ALCOHOL-DEHYDROG-ENZRXN)
(RIGHT NADH |an aldehyde or ketone|)
(LEFT |Alcohols| NAD)
(EC-NUMBER "1.1.1.1")
(COMMENT "Acts on primary or secondary alcohols or hemiacetals.")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
NIL)
(ALCOHOL-DEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(EC-NUMBER "1.1.1.1")
(IN-PATHWAY FERMENTATION-PWY ETOH-ACETYLCOA-ANA-PWY)
(ENZYMATIC-REACTION ADHP-ENZRXN ALCOHOL-DEHYDROG-ENZRXN)
(RIGHT ETOH NAD)
(LEFT ACETALD NADH)
(COMMENT "The final reaction in the fermentation pathway leading to ethanol.")
(:CREATION-DATE 2976997311)
(:CREATOR |mriley|) )
NIL)
(|Alcohol-group| T (
(OCELOT-GFP::PARENTS |Simple-Groups| |Alcohols|)
(CHEMICAL-FORMULA (C 1) (H 1) (O 1) (R1 1) (R2 1))
(STRUCTURE-BONDS (1 2 1) (1 3 2) (1 5 1) (1 4 1))
(DISPLAY-COORDS-2D (-1.0625d0 -0.4375d0) (-1.0625d0 0.3875d0)
(-1.0625d0 -1.2625d0) (-1.8875d0 -0.4375d0) (-0.2375d0 -0.4375d0))
(STRUCTURE-ATOMS C H O R1 R2)
(COMMON-NAME "an alcohol group")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|Alcohols| T (
(OCELOT-GFP::PARENTS |Compounds|)
(APPEARS-IN-LEFT-SIDE-OF ALCOHOL-DEHYDROG-GENERIC-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ACETYLESTERASE-RXN CARBOXYLESTERASE-RXN
ACID-PHOSPHATASE-RXN R4-RXN GLYCPDIESTER-RXN BETA-GLUCURONID-RXN
ALKAPHOSPHA-RXN)
(N-NAME "ROH")
(CHEMICAL-FORMULA (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(DISPLAY-COORDS-2D (1.2124d0 0.0d0) (0.0d0 -0.7d0))
(STRUCTURE-ATOMS O R)
(SCHEMA? T)
(SYNONYMS "an alcohol" "alcohol" "ROH")
(:CREATION-DATE 3355619197)
(:CREATOR |paley|)
(COMMON-NAME "an alcohol") )
NIL)
(ALD-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME "aldehyde dehydrogenase A, NAD-linked")
(COMMENT-INTERNAL "subunit composition not discussed in |CITS: [12952533]|")
(CATALYZES ENZRXN0-2755 GLYCOLALD-DEHYDROG-ENZRXN LACTALDDEHYDROG-ENZRXN)
(COMPONENTS LACTALDDEHYDROG-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycolate/ald2.template")
(:CREATION-DATE 3027797948)
(:CREATOR |mriley|) )
((COMPONENTS LACTALDDEHYDROG-MONOMER CITATIONS "[92011371]")
(COMPONENTS LACTALDDEHYDROG-MONOMER COEFFICIENT 4)))
(ALDDEHYDROGB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SPECIES ECOLI)
(COMPONENT-OF CPLX0-3482)
(GENE EG12292)
(SYNONYMS "B3588" "YiaX" "AldB")
(DBLINKS (MODBASE "P37685" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00171" IN-FAMILY |pkarp| 3346700408 NIL NIL)
(REFSEQ "NP_418045" NIL NIL NIL NIL NIL)
(UNIPROT "P37685" NIL |pkarp| 3064869797))
(ISOZYME-SEQUENCE-SIMILARITY (LACTALDDEHYDROG-MONOMER YES))
(MOLECULAR-WEIGHT-SEQ 56.306281999999854d0)
(TEMPLATE-FILE "~ecocyc/templates/new/aldB/aldB.template")
(:CREATION-DATE 3047831111)
(:CREATOR |mriley|) )
NIL)
(ALDHDEHYDROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (MODBASE "P23883" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P23883" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00171" IN-FAMILY |pkarp| 3346700332 NIL NIL)
(UNIPROT "P23883" NIL |keseler| 3324744246 NIL NIL)
(REFSEQ "NP_415816" NIL |keseler| 3324744246 NIL NIL))
(CATALYZES ENZRXN0-5303)
(COMMON-NAME "γ-glutamyl-γ-aminobutyraldehyde dehydrogenase")
(CITATIONS "15590624:EV-EXP:3324408228:keseler")
(SYNONYMS "B1300" "AldH" "PuuC")
(GENE EG10036)
(COMMENT
"PuuC is inferred to be the γ-glutamyl-γ-aminobutyraldehyde dehydrogenase in a putrescine
utilization pathway; together with PuuB, γ-glutamyl-γ-aminobutyrate is produced from
γ-glutamylputrescine |CITS: [15590624]|.
The function of genes in the puu gene cluster was initially inferred by similarity with the ipuABCDEGFH
operon in Pseudomonas sp. |CITS: [15590624]|
The puuC, puuB, and puuE genes may form an operon |CITS: [9150200][1840553]|.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/indies/aldH.template")
(:CREATION-DATE 3041782456)
(PI 6.14d0)
(MOLECULAR-WEIGHT-SEQ 53.41856799999985d0) )
NIL)
(|Aldohexoses| T (
(OCELOT-GFP::PARENTS |Aldoses|)
(COMMON-NAME "an aldohexose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(|Aldonic-Acids| T (
(OCELOT-GFP::PARENTS |All-Carbohydrates|)
(SYNONYMS "an aldonic acid")
(COMMENT
"Sugars that had their terminal aldehyde oxydized to a carboxylic acid.")
(COMMON-NAME "an aldonate")
(:CREATOR |kr|)
(:CREATION-DATE 3262615600) )
NIL)
(|Aldopentoses| T (
(OCELOT-GFP::PARENTS |Aldoses|)
(COMMON-NAME "an aldopentose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(ALDOSE1EPIM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(ALTERNATIVE-SUBSTRATES
(ALPHA-D-GALACTOSE ARABINOSE XYLOSE GLC MALTOSE LACTOSE "D-FUCOSE" FRU))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ALDOSE1EPIM-RXN)
(INHIBITORS-COMPETITIVE MANNOSE |Glycosides| ACET 2-DEOXY-D-GLUCOSE GLC)
(COMMENT "This enzymatic reaction links the metabolism of lactose and
galactose. Before the discovery of aldose-1-epimerase the
intracellular mutarotation of α- and β-galactose was believed
to be spontaneous. The mutarotase activity has been recently
identified with the galM gene. |CITS: [95055764]| The enzymatic
reaction appears to follow a bifunctional mechanism, a simultaneous
attack of a nucleophilic and electrophilic group of the enzyme on the
substrate. The reaction proceeds from the pyranose form via the open
chain intermediate, producing either pyranose or furanose products.
|CITS: [67136046] [72097688]|")
(ENZYME ALDOSE1EPIM-MONOMER)
(SYNONYMS "mutarotase" "aldose mutarotase" "galactose-1-epimerase")
(COMMON-NAME "aldose-1-epimerase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/gala/galM.template")
(:CREATION-DATE 3016310120)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "The specificity
of the enzyme is not very pronounced, it is capable of activity with
several structurally different substrates. However, aldonolactones
are not hydrolyzed. |CITS: [95055764] [72097688]|")
(INHIBITORS-COMPETITIVE MANNOSE CITATIONS "[72097688]")
(INHIBITORS-COMPETITIVE |Glycosides| COMMENT
"alpha-O-methylglycoside, alpha- and
beta-dinitrophenyl-O-galactosides were tested |CITS: [67136046]|")
(INHIBITORS-COMPETITIVE ACET CITATIONS "[67136046]")
(INHIBITORS-COMPETITIVE 2-DEOXY-D-GLUCOSE CITATIONS "[72097688]")
(INHIBITORS-COMPETITIVE GLC CITATIONS "[67136046]")))
(ALDOSE1EPIM-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0756" "GalM")
(DBLINKS (MODBASE "P0A9C3" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01263" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(UNIPROT "P0A9C3" NIL |pkarp| 3338704367 NIL NIL)
(REFSEQ "NP_415277" NIL NIL NIL NIL NIL))
(CATALYZES ALDOSE1EPIM-ENZRXN)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 38.190424999999905d0)
(GENE EG11698)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/gala/galM.template")
(:CREATION-DATE 3016310120)
(:CREATOR |mriley|) )
((LOCATIONS CCO-PERI-BAC CITATIONS "[95055764]")))
(ALDOSE1EPIM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(COMMON-NAME "ALDOSE-1-EPIMERASE")
(ENZYMATIC-REACTION ALDOSE1EPIM-ENZRXN)
(RIGHT ALPHA-D-GALACTOSE)
(LEFT GALACTOSE)
(DELTAG0 11.9d0)
(EC-NUMBER "5.1.3.3")
(COMMENT "This reaction is involved in galactose metabolism. It
funnels β-galactose into reactions of α-galactose catabolism.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/gala/galM.template")
(:CREATION-DATE 3016310120)
(:CREATOR |mriley|) )
((DELTAG0 :FACET COMMENT "for mutarotation of glucose |CITS:
[72097688]|")))
(|Aldoses| T (
(OCELOT-GFP::PARENTS |Monosaccharides|)
(COMMON-NAME "an aldose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(|Aldoxime| T (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(COMMON-NAME "an aldoxime")
(CHEMICAL-FORMULA (C 1) (H 2) (N 1) (O 1) (R 1))
(DISPLAY-COORDS-2D (-1.0d0 -1.0d0) (0.32876706d0 -1.0d0)
(-0.32876712d0 -1.0d0) (0.9863013d0 -1.0d0))
(STRUCTURE-BONDS (3 2 2) (2 4 1) (1 3 1))
(STRUCTURE-ATOMS R N C O)
(:CREATOR |paley|)
(:CREATION-DATE 3276359851) )
NIL)
(|Aliphatic-Aldoximes| T (
(OCELOT-GFP::PARENTS |Aldoxime|)
(CHEMICAL-FORMULA (C 1) (H 2) (N 1) (O 1) (R 1))
(STRUCTURE-BONDS (1 2 1) (4 5 1) (1 4 2) (1 3 1))
(DISPLAY-COORDS-2D (-0.0625d0 -0.5938d0) (-0.777d0 -1.0063d0)
(0.652d0 -1.0063d0) (-0.0625d0 0.2312d0) (0.5209d0 0.8146d0))
(STRUCTURE-ATOMS C R H N O)
(COMMON-NAME "an aliphatic aldoxime")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|Aliphatic-Alpha-Omega-Diamines| T (
(OCELOT-GFP::PARENTS |Aliphatic-Diamines|)
(APPEARS-IN-LEFT-SIDE-OF DIAMTRANSAM-RXN DIAMACTRANS-RXN)
(SYNONYMS "an aliphatic α,ω-diamine"
"aliphatic α,ω-diamine" "an α,ω-diamine"
"α,ω-diamine")
(COMMENT
"This compound class stands for generic and unspecified α,ω-diamines.")
(:CREATOR |kr|)
(:CREATION-DATE 3265062735) )
NIL)
(|Aliphatic-Amides| T (
(OCELOT-GFP::PARENTS |Amides|)
(COMMON-NAME "an aliphatic amide")
(CHEMICAL-FORMULA (C 1) (H 1) (N 1) (O 1) (R 2))
(SYNONYMS "an aliphatic amide")
(STRUCTURE-BONDS (4 5 1) (3 5 1) (2 4 1) (1 5 2))
(DISPLAY-COORDS-2D (1.2124d0 -2.1d0) (3.6373d0 -0.7d0) (0.0d0 0.0d0)
(2.4248d0 0.0d0) (1.2124d0 -0.7d0))
(STRUCTURE-ATOMS O R R N C)
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Aliphatic-Amines| T (
(OCELOT-GFP::PARENTS |All-Amines|)
(COMMON-NAME "an aliphatic amine")
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF AMINEOXID-RXN)
(SYNONYMS "RCH2NH2" "RCH(2)NH(2)")
(:CREATION-DATE 3052674235)
(:CREATOR |kr|) )
NIL)
(|Aliphatic-Diamines| T (
(OCELOT-GFP::PARENTS |Aliphatic-Amines|)
(COMMON-NAME "an aliphatic diamine")
(SYNONYMS "aliphatic diamine")
(COMMENT "This compound class collects various aliphatic diamines.")
(:CREATOR |kr|)
(:CREATION-DATE 3265062352) )
NIL)
(|Aliphatic-N-Acetyl-Diamines| T (
(OCELOT-GFP::PARENTS |Aliphatic-Diamines|)
(APPEARS-IN-RIGHT-SIDE-OF DIAMACTRANS-RXN)
(SYNONYMS "an aliphatic N-acetyl-diamine"
"aliphatic N-acetyl-diamine" "an N-acetyl-diamine"
"N-acetyl-diamine")
(COMMENT
"This compound class stands for generic and unspecified N-acetyl-diamines.")
(:CREATOR |kr|)
(:CREATION-DATE 3265119692) )
NIL)
(|Aliphatic-Nitriles| T (
(OCELOT-GFP::PARENTS |Nitriles|)
(CHEMICAL-FORMULA (C 1) (N 1) (R 1))
(STRUCTURE-BONDS (3 2 1) (3 1 3))
(DISPLAY-COORDS-2D (6.2625d0 2.7187d0) (4.6125d0 2.7187d0)
(5.4375d0 2.7187d0))
(STRUCTURE-ATOMS N R C)
(COMMON-NAME "an aliphatic nitrile")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Aliphatic-Omega-Amino-Aldehydes| T (
(OCELOT-GFP::PARENTS |Aliphatic-Amines|)
(APPEARS-IN-RIGHT-SIDE-OF DIAMTRANSAM-RXN)
(SYNONYMS "an aliphatic ω-aminoaldehyde"
"aliphatic ω-aminoaldehyde" "an ω-aminoaldehyde"
"ω-aminoaldehyde")
(COMMENT
"This compound class collects various aliphatic ω-aminoaldehydes.")
(:CREATOR |kr|)
(:CREATION-DATE 3265123084) )
NIL)
(ALKALOIDS-SYN T (
(OCELOT-GFP::PARENTS N-CONTAINING-SECONDARY-CMPD-SYN)
(COMMENT
"This class contains biosynthetic pathways of alkaloids. Most alkaloids contain cyclic nitrogen. They function as defense compounds. Many alkaloids, including morphine and cocaine, have a high affinity for receptors of neurotransmitters and have pharmacological activities. ")
(COMMON-NAME "Alkaloids")
(:CREATOR |paley|)
(:CREATION-DATE 3347159102) )
NIL)
(ALKANEMONOX-PWY NIL (
(OCELOT-GFP::PARENTS |Sulfur-Assimilation|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(PRIMARIES (RXN0-280 (|Alkanesulfonates|) (|an aldehyde|)))
(PREDECESSORS (FMNREDUCT-RXN RXN0-280) (RXN0-280 FMNREDUCT-RXN))
(COMMENT "E. coli can utilize alkanesulfonates as a sulfur source
for growth. The ssuD gene encodes a FMN-dependent
alkanesulfonate monooxygenase. The monooxygenase has
a broad substrate range. It is able to desulfonate C-2 to
C-10 unsubstituted alkanesulfonates, substituted ethanesulfonic
acids, N-phenyltaurine, 4-phenyl-1-butanesulfonic acid and
certain sulfonated buffers. The best substrates for the monooxygenase
were decanesulfonic acid, octanesulfonic acid and
1,3-dioxo-2-isoindolineethanesulfonic acid.
The ssuE-encoded NAD(P)H-dependent FMN reductase provides the alkanesulfonate
monooxygenase with FMNH2. The reductase
and monooxygenase act as a two-component system.
|CITS: [99410391]|")
(ENZYME-USE (FMNREDUCT-RXN ENZRXN0-277))
(REACTION-LIST RXN0-280 FMNREDUCT-RXN)
(COMMON-NAME "alkanesulfonate monooxygenase two-component system")
(:CREATOR |ptoole|)
(:CREATION-DATE 3156164753) )
NIL)
(|Alkanesulfonates| T (
(OCELOT-GFP::PARENTS SULFONATES)
(COMMON-NAME "an alkanesulfonate")
(APPEARS-IN-LEFT-SIDE-OF RXN0-280)
(SYNONYMS "an alkanesulfonate" "alkanesulfonate" "alkylsulfonate")
(COMMENT
"This compound class stands for generic and unspecified alkanesulfonate compounds.")
(:CREATOR |kr|)
(:CREATION-DATE 3266186775) )
NIL)
(ALKAPHOSPHA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/phoA.template")
(CATALYZES ALKAPHOSPHA-ENZRXN)
(:CREATION-DATE 3041707788)
(COMPONENTS ALKAPHOSPHA-MONOMER) )
((COMPONENTS ALKAPHOSPHA-MONOMER COEFFICIENT 2)))
(ALKAPHOSPHA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CYS)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "Alkaline phosphatase catalyzes the hydrolysis of a wide
variety of phosphomonoesters. The reaction proceeds through a
phosphoseryl intermediate. The enzyme will also catalyze a
transphosphorylation reaction with the transfer of the phosphoryl
group to the alcohol in the presence of certain phosphate acceptors.
Alkaline phosphatase is a metalloenzyme, binding two zinc atoms and
one magnesium ion per monomer. The enzyme has been crystallized.
|CITS: [86115281] [91329345] [93160199] [92399963]|")
(REACTION ALKAPHOSPHA-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/phoA.template")
(ENZYME ALKAPHOSPHA-CPLX)
(PROSTHETIC-GROUPS ZN+2 MG+2)
(:CREATION-DATE 3041707788)
(COMMON-NAME "alkaline phosphatase")
(SYNONYMS "APase" "AP" "alkaline phosphomonoesterase" "phosphomonoesterase"
"glycerophosphatase"
"orthophosphoric-monoester phosphohydrolase (alkaline optimum)")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE TUNGSTATE CPD-3 CPD-4422 CPD-4584 THIOGLYCOLATE
ARSENATE |Pi|) )
((INHIBITORS-UNKMECH CYS CITATIONS "[MalamyBiochem3-1893]")
(INHIBITORS-COMPETITIVE THIOGLYCOLATE CITATIONS "[MalamyBiochem3-1893]")
(INHIBITORS-COMPETITIVE CPD-4422 CITATIONS "[88163569]")
(INHIBITORS-COMPETITIVE CPD-3 CITATIONS "[88163569]")
(INHIBITORS-COMPETITIVE TUNGSTATE CITATIONS "[88163569]")
(INHIBITORS-COMPETITIVE CPD-4584 COMMENT
"The vanadate inhibition is enhanced by phenol. |CITS: [88163569]| ")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme exhibits broad substrate
specificity, it will hydrolyze phosphate monoesters (ROP) regardless
of the size and the chemical nature of the R. The enzyme also
hydrolyzes a variety of O- and S-phosphorothiolates, phosphoramidates,
thiophosphates and phosphates. |CITS: [86115281] [92399963]|")
(INHIBITORS-COMPETITIVE ARSENATE CITATIONS "[86115281]")
(INHIBITORS-COMPETITIVE |Pi| CITATIONS "[91186406]")
(PROSTHETIC-GROUPS ZN+2 COMMENT "The enzyme binds 2 atoms per
monomer. |CITS: [86115281]|")
(PROSTHETIC-GROUPS MG+2 COMMENT "The enzyme binds 1 atom
per monomer. In the absence of Mg++ this binding site can be filled
by Zn. |CITS: [86115281]|")
(PROSTHETIC-GROUPS :FACET COMMENT "The metal-ligand interactions
have been determined. |CITS: [91186406]|")))
(ALKAPHOSPHA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0383" "PsiF" "PsiA" "PhoA")
(COMMON-NAME "PhoA")
(DBLINKS (MODBASE "P00634" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00245" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(REFSEQ "NP_414917" NIL |keseler| 3306089400 NIL NIL) (PDB "2ANH")
(PDB "1URB") (PDB "1URA") (PDB "1KHN") (PDB "1KHL") (PDB "1KHK")
(PDB "1KHJ") (PDB "1KH9") (PDB "1KH7") (PDB "1KH5") (PDB "1KH4")
(PDB "1HQA") (PDB "1HJK") (PDB "1EW9") (PDB "1EW8") (PDB "1ELZ")
(PDB "1ELY") (PDB "1ELX") (PDB "1ED9") (PDB "1ED8") (PDB "1ANJ")
(PDB "1ANI") (PDB "1ALK") (PDB "1ALJ") (PDB "1ALI") (PDB "1ALH")
(PDB "1AJD") (PDB "1AJC") (PDB "1AJB") (PDB "1AJA")
(UNIPROT "P00634" NIL |pkarp| 3064869797))
(GENE EG10727)
(COMMENT
"Alkaline phosphatase is a dimer that occurs in three forms, depending upon the growth conditions of the cell. These
forms have been designated isozymes 1, 2 and 3. They differ by the presence of an NH2-terminal arginine residue on
the subunits of isozyme 1, the absence of this residue on isozyme 3 and isozyme 2 being a heterodimer
of one subunit each of isozymes 1 and 3 |CITS: [81273081]|.
The precursor polypeptide is secreted across the inner membrane to the periplasmic space concommitant with
removal of the signal sequence |CITS: [87031576]|.
Transposon mutagenesis and biochemical assays showed that the PhoA protein oxidizes phosphite to phosphate,
producing molecular H2 |CITS: [15148399]|.")
(COMPONENT-OF ALKAPHOSPHA-CPLX)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/phoA.template")
(:CREATION-DATE 3041707788)
(PI 6.09d0)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 49.43855099999987d0) )
NIL)
(ALKAPHOSPHA-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.3)
(OFFICIAL-EC? T)
(COMMENT "This reaction is part of the phosphate acquisition and
transport system in the cell.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/centmet/phoA.template")
(ENZYMATIC-REACTION ALKAPHOSPHA-ENZRXN)
(EC-NUMBER "3.1.3.1")
(:CREATION-DATE 3041707788)
(LEFT |Orthophosphoric-Monoesters| WATER)
(RIGHT |Alcohols| |Pi|) )
NIL)
(|Alkyl-acetyl-glycero-phosphocholines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "a 2-acetyl-1-alkyl-sn-glycero-3-phosphocholine")
(COMMON-NAME "a 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine")
(CHEMICAL-FORMULA (C 10) (H 22) (N 1) (O 7) (R1 1) (P 1))
(ATOM-CHARGES (19 1))
(STRUCTURE-BONDS (1 17 1) (2 19 1) (3 19 1) (4 19 1) (5 17 2) (6 20 2)
(7 20 1) (8 13 1) (9 12 1) (9 14 1) (10 13 1) (10 18 1) (11 15 1) (11 18 1)
(12 19 1) (14 20 1) (15 20 1) (16 17 1) (16 18 1))
(DISPLAY-COORDS-2D (2.1435d0 -4.5393d0) (3.6005d0 -0.4216d0)
(3.5899d0 -1.2466d0) (2.8913d0 0.0d0) (2.8579d0 -5.7768d0)
(2.2813d0 -3.3145d0) (0.6319d0 -3.3303d0) (0.7144d0 -7.0142d0)
(2.1505d0 -2.0532d0) (0.0d0 -5.7768d0) (0.7145d0 -4.5393d0)
(2.1611d0 -1.2282d0) (0.0d0 -6.6018d0) (1.4429d0 -2.4773d0)
(1.429d0 -4.1268d0) (1.429d0 -5.7768d0) (2.1434d0 -5.3643d0)
(0.7145d0 -5.3643d0) (2.8808d0 -0.8249d0) (1.4564d0 -3.3022d0))
(STRUCTURE-ATOMS C C C C O O O R1 C C C C O O O O C C N P)
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Alkyl-acyl-gly-P-EtOH-amines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME
"an O-1-alkyl-2-acyl-sn-glycero-3-phosphoethanolamine")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Alkyl-enyl-acyl-gly-P-EtOH-amines| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME
"an O-1-alk-1-enyl-2-acyl-sn-glycero-3-phosphoethanolamine")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Alkyl-Hydro-Peroxides| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(APPEARS-IN-LEFT-SIDE-OF R4-RXN)
(SYNONYMS "ROOH")
(COMMENT
"This compound class stands for generic and unspecified alkylhydroperoxides.")
(COMMON-NAME "an alkylhydroperoxide")
(:CREATOR |kr|)
(:CREATION-DATE 3264452162) )
NIL)
(|Alkyl-Sulfenates| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SYNONYMS "an alkyl sulfenate")
(CHEMICAL-FORMULA (H 1) (O 1) (R1 1) (S 1))
(STRUCTURE-BONDS (1 2 1) (1 3 1))
(DISPLAY-COORDS-2D (0.1605d0 -3.1063d0) (-0.6364d0 -3.3198d0)
(0.1605d0 -2.2813d0))
(STRUCTURE-ATOMS S O R1)
(COMMON-NAME "an S-alkylsulfenate")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Alkyl-Thiols| T (
(OCELOT-GFP::PARENTS |Thiols|)
(CHEMICAL-FORMULA (H 1) (R 1) (S 1))
(STRUCTURE-BONDS (1 2 1))
(DISPLAY-COORDS-2D (1.2124d0 0.0d0) (0.0d0 -0.7d0))
(STRUCTURE-ATOMS S R)
(COMMON-NAME "an alkyl-thiol")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Alkylamines| T (
(OCELOT-GFP::PARENTS |All-Amines|)
(CHEMICAL-FORMULA (H 2) (N 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(DISPLAY-COORDS-2D (0.0d0 -0.7d0) (1.2124d0 0.0d0))
(STRUCTURE-ATOMS N R)
(COMMON-NAME "an alkylamine")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Alkylphosphonates| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "an alkylphosphate")
(APPEARS-IN-LEFT-SIDE-OF ABC-23-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ABC-23-RXN)
(SYNONYMS "an alkylphosphonate" "alkylphosphonate" "alkanephosphonate")
(COMMENT
"This compound class stands for generic and unspecified alkylphosphonate compounds.")
(:CREATOR |kr|)
(:CREATION-DATE 3266186788) )
NIL)
(|All-ACPs| T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(APPEARS-IN-RIGHT-SIDE-OF 3-OXOACYL-ACP-SYNTH-BASE-RXN)
(COMMON-NAME "an acyl carrier protein") )
NIL)
(|All-Amines| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMON-NAME "an amine")
(:CREATOR |kr|)
(:CREATION-DATE 3265049000) )
NIL)
(|All-Amino-Acids| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMON-NAME "an amino acid or its derivative")
(SCHEMA? T) )
NIL)
(|All-Biopterines| T (
(OCELOT-GFP::PARENTS |Coenzymes|)
(COMMON-NAME "a biopterin") )
NIL)
(|All-Carbohydrates| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMON-NAME "all carbohydrates")
(SCHEMA? T)
(OVERVIEW-NODE-SHAPE :SQUARE) )
NIL)
(|All-Carboxy-Acids| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMON-NAME "all carboxy acids")
(:CREATOR |kr|)
(:CREATION-DATE 3264456060) )
NIL)
(ALL-CHORISMATE-PWY NIL (
(OCELOT-GFP::PARENTS |Super-Pathways|)
(:CREATION-DATE 3067198692)
(COMMON-NAME "superpathway of chorismate")
(SUB-PATHWAYS ENTBACSYN-PWY COMPLETE-ARO-PWY FOLSYN-PWY UBISYN-PWY)
(PREDECESSORS (ISOCHORSYN-RXN CHORISMATE-SYNTHASE-RXN) ENTBACSYN-PWY
UBISYN-PWY FOLSYN-PWY COMPLETE-ARO-PWY
(PABASYN-RXN CHORISMATE-SYNTHASE-RXN)
(CHORPYRLY-RXN CHORISMATE-SYNTHASE-RXN))
(REACTION-LIST ENTBACSYN-PWY COMPLETE-ARO-PWY UBISYN-PWY FOLSYN-PWY) )
NIL)
(|All-Coas| T (
(OCELOT-GFP::PARENTS |Coenzyme-Groups|)
(COMMON-NAME "a CoA derivative")
(SCHEMA? T) )
NIL)
(|All-Elements| T (
(OCELOT-GFP::PARENTS |Compounds-And-Elements|)
(COMMON-NAME "All Elements")
(SCHEMA? T)
(COMMENT
"This class exists for historical reasons. It used to differ from the Elements class,
but currently it does not.
") )
NIL)
(|All-Folates| T (
(OCELOT-GFP::PARENTS |Coenzymes|)
(COMMON-NAME "a folate")
(SCHEMA? T) )
NIL)
(|All-Genes| T (
(OCELOT-GFP::PARENTS |DNA-Segments|)
(:INSTANCE-NAME-TEMPLATE "G-*")
(COMMENT
"The class All-Genes includes as its subclasses the set of true genes (class Genes), as
well as sets of gene-like sequences. The latter includes class Phantom-Genes
(sequences that were predicted to be genes by computational gene-finding
programs, but that were later determined not to be genes, such as through
experimentation), and class Pseudo-Genes. Therefore, to enumerate all true
genes in an organism, query the instances of class Genes, not class All-Genes.
")
(:CREATOR |pkarp|)
(:CREATION-DATE 3242753274) )
NIL)
(|All-Glutathiones| T (
(OCELOT-GFP::PARENTS ORGANOSULFUR)
(COMMON-NAME "all glutathiones")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|All-Nucleosides| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMENT
"This class includes several classes of compounds that form components
of nucleic acids, and serves as a way of grouping those classes together.
It does not strictly speaking define a structurally defined set of compounds.")
(COMMON-NAME "a nucleic acid component")
(SCHEMA? T) )
NIL)
(|All-tRNAs| T (
(OCELOT-GFP::PARENTS RNA)
(:KEY-SLOT COMMON-NAME)
(OVERVIEW-NODE-SHAPE :TEE)
(SCHEMA? T) )
NIL)
(ALLANTOATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00499" NIL |kr| 3346617701 NIL NIL) (CAS "99-16-1"))
(:CREATION-DATE 3073857204)
(APPEARS-IN-LEFT-SIDE-OF ALLANTOICASE-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ALLANTOINASE-RXN)
(GIBBS-0 -160.6d0)
(MOLECULAR-WEIGHT 176.132d0)
(CHEMICAL-FORMULA (C 4) (H 8) (N 4) (O 4))
(DISPLAY-COORDS-2D (-1.0d0 -0.99667d0) (-0.29118d0 -0.19135d0)
(0.00166d0 -0.80366d0) (0.00166d0 -0.43095d0) (-0.67388d0 -0.80366d0)
(-0.33444d0 -1.0d0) (-0.67388d0 -0.42429d0) (0.99667d0 -0.99334d0)
(0.33444d0 -1.0d0) (0.3178d0 -0.21797d0) (0.67055d0 -0.42429d0)
(0.67055d0 -0.80366d0))
(STRUCTURE-BONDS (12 9 1) (11 12 1) (10 4 1) (9 3 1) (8 12 2) (7 5 1) (6 3 1)
(5 6 1) (4 3 1) (2 4 2) (1 5 2))
(STRUCTURE-ATOMS O O C C C N N O N O N C)
(COMMON-NAME "allantoate")
(SYSTEMATIC-NAME "acetic acid, bis((aminocarbonyl)amino)-") )
((GIBBS-0 -160.6d0 CITATIONS "GibbsGroups97")))
(ALLANTOICASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.3)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY PWY0-41)
(ENZYMATIC-REACTION ENZRXN-323)
(OFFICIAL-EC? T)
(EC-NUMBER "3.5.3.4")
(RIGHT CPD-1091 UREA)
(LEFT ALLANTOATE WATER)
(:CREATOR |ptoole|)
(:CREATION-DATE 3160741710) )
NIL)
(ALLANTOIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER0-2221)
(DBLINKS (LIGAND-CPD "C01551" NIL |kaipa| 3311532631 NIL NIL) (CAS "97-59-6"))
(:CREATION-DATE 3073857204)
(APPEARS-IN-LEFT-SIDE-OF RXN0-4481 ALLANTOINASE-RXN)
(GIBBS-0 -112.5d0)
(MOLECULAR-WEIGHT 158.116d0)
(CHEMICAL-FORMULA (C 4) (H 6) (N 4) (O 3))
(DISPLAY-COORDS-2D (0.99674d0 -0.16938d0) (-0.29967d0 -1.0d0)
(0.66775d0 -0.76547d0) (-0.28339d0 -0.19544d0) (0.02606d0 -0.40391d0)
(0.35179d0 -0.1759d0) (-0.64169d0 -0.78827d0) (-0.64169d0 -0.38436d0)
(0.66775d0 -0.40391d0) (-1.0d0 -0.20195d0) (0.02606d0 -0.76547d0))
(STRUCTURE-BONDS (11 3 1) (10 8 1) (9 3 1) (8 4 1) (7 8 2) (6 9 1) (5 6 1)
(5 11 1) (4 5 1) (2 11 2) (1 9 2))
(STRUCTURE-ATOMS O O N N C N O C C N C)
(COMMON-NAME "allantoin") )
((GIBBS-0 -112.5d0 CITATIONS "GibbsGroups97")))
(ALLANTOINASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.2)
(BALANCE-STATE :BALANCED)
(IN-PATHWAY PWY0-41)
(ENZYMATIC-REACTION ENZRXN0-268)
(:CREATOR |paley|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3251055122)
(COMMON-NAME "Allantoinase")
(EC-NUMBER "3.5.2.5")
(RIGHT ALLANTOATE)
(LEFT WATER ALLANTOIN) )
NIL)
(ALLO-THR NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(INHIBITORS-UNKMECH-OF DSERDEAM-ENZRXN)
(DBLINKS (CAS "2676-21-3"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -125.0d0)
(HISTORY |kr-6| |kr-5|)
(MOLECULAR-WEIGHT 119.12d0)
(CHEMICAL-FORMULA (C 4) (H 9) (N 1) (O 3))
(DISPLAY-COORDS-2D (-1.0d0 -0.42475d0) (0.0d0 -0.43478d0)
(0.99666d0 -0.42475d0) (-0.50836d0 -0.14381d0) (0.50502d0 -0.14381d0)
(-0.50836d0 0.4214d0) (0.50502d0 0.4214d0) (0.0d0 -1.0d0))
(STRUCTURE-BONDS (8 2 1) (7 5 2) (6 4 1) (5 2 1) (4 2 1) (3 5 1) (1 4 1))
(STRUCTURE-ATOMS C C O C C O O N)
(COMMON-NAME "allothreonine")
(SYNONYMS "DL-allothreonine" "allo-thr") )
((GIBBS-0 -125.0d0 CITATIONS "GibbsGroups97")))
(ALLOLACTOSE NIL (
(OCELOT-GFP::PARENTS |Disaccharides|)
(COMPONENT-OF MONOMER0-159)
(GIBBS-0 -366.6d0)
(DISPLAY-COORDS-2D (-4.7457d0 -0.5688d0) (-4.7457d0 0.2563d0)
(-4.0313d0 0.6688d0) (-3.3168d0 0.2563d0) (-3.3168d0 -0.5688d0)
(-5.4602d0 -0.9813d0) (-1.5273d0 -0.95d0) (-0.8128d0 -0.5375d0)
(-0.8128d0 0.2875d0) (-0.0984d0 0.7d0) (0.6161d0 0.2875d0)
(0.6161d0 -0.5375d0) (-6.1747d0 -0.5687d0) (-5.4602d0 0.6688d0)
(-4.0313d0 1.4938d0) (-4.0313d0 -0.9813d0) (-2.6023d0 0.6688d0)
(-1.5273d0 0.7d0) (-2.6023d0 -0.9813d0) (-0.0984d0 -0.95d0)
(-0.0984d0 1.525d0) (1.3306d0 0.7d0) (1.3306d0 -0.95d0))
(STRUCTURE-BONDS (9 18 1 :UP) (10 21 1 :UP) (11 22 1 :DOWN) (12 23 1 :UP)
(11 12 1) (10 11 1) (9 10 1) (20 12 1) (8 9 1) (20 8 1) (8 7 1 :UP) (19 7 1)
(5 19 1 :UP) (4 17 1 :DOWN) (3 15 1 :UP) (2 14 1 :UP) (6 13 1) (1 6 1 :UP)
(4 5 1) (3 4 1) (2 3 1) (1 2 1) (16 5 1) (16 1 1))
(STRUCTURE-ATOMS C C C C C C C C C C C C O O O O O O O O O O O)
(DBLINKS (CAS "28447-39-4"))
(APPEARS-IN-LEFT-SIDE-OF R167-RXN)
(COMMON-NAME "allolactose")
(:CREATOR |paley|)
(:CREATION-DATE 3189471494) )
NIL)
(ALLOSE NIL (
(OCELOT-GFP::PARENTS |D-Hexoses|)
(DBLINKS (CAS "2595-97-3" NIL |kr| 3346617700 NIL NIL)
(LIGAND-CPD "C01487" NIL |kr| 3346617700 NIL NIL))
(APPEARS-IN-RIGHT-SIDE-OF ABC-42-RXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-4942 ALLOSE-KINASE-RXN ABC-42-RXN)
(:CREATOR |paley|)
(:CREATION-DATE 3201460851)
(SYNONYMS "allose" "β-D-allose")
(MOLECULAR-WEIGHT 180.157d0)
(CHEMICAL-FORMULA (C 6) (H 12) (O 6))
(DISPLAY-COORDS-2D (0.9969605d0 -0.31610942d0) (0.44984806d0 -0.48024315d0)
(-1.0d0 -0.31610942d0) (0.44984806d0 0.5653496d0) (-1.0d0 0.37386024d0)
(0.44984806d0 0.19148934d0) (0.44984806d0 0.90577507d0)
(0.9969605d0 0.024316072d0) (-0.4407295d0 -0.12765956d0)
(-0.4407295d0 0.5653496d0) (-1.0d0 0.024316072d0)
(-0.4407295d0 -0.8237082d0) (-0.9848024d0 -1.0d0)
(-0.4407295d0 0.19148934d0) (0.9969605d0 0.37386024d0)
(-0.4407295d0 0.90577507d0) (-0.4407295d0 -0.48024315d0))
(STRUCTURE-BONDS (17 9 1) (17 2 1) (12 13 1) (12 17 1) (11 5 1) (11 3 1)
(11 17 1) (10 16 1) (10 14 1) (10 11 1) (8 15 1) (8 1 1) (8 4 1) (4 7 1)
(4 6 1) (4 10 1) (2 8 1))
(STRUCTURE-ATOMS O O H C O H O C H C C C O H H O C)
(COMMON-NAME "D-allose")
(GIBBS-0 -216.2d0)
(OVERVIEW-NODE-SHAPE :SQUARE) )
NIL)
(ALLOSE-KINASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-3241)
(:CREATOR |arnaud|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3286815403)
(SYNONYMS "Allokinase")
(COMMON-NAME "Allose kinase")
(EC-NUMBER "2.7.1.55")
(RIGHT D-ALLOSE-6-PHOSPHATE ADP)
(LEFT ALLOSE ATP) )
NIL)
(ALPHA-ACIDS T (
(OCELOT-GFP::PARENTS BITTER-ACIDS)
(COMMON-NAME "an α-acid")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(ALPHA-AMYL-CYTO-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "There are two α-amylases present in E. coli, one located
in the cytoplasm, coded for by the amyA gene, and one located in the
periplasm coded for by the malS gene. The cytoplasmic amylase has
been recently identified in E. coli. Its physiological role is still
uncertain. Under experimental conditions glycogen was a poor substrate
for the enzyme, however it is the most likely natural substrate since
it is the only polysaccharide present in appreciable amounts in the
cytoplasm. It has been hypothesized that in the absence of exogenous
oligosaccharides to act as primers for glycogen synthesis the
cytoplasmic amylase might provide oligosaccharides, through catabolism
of existing cellular glycogen, which would then act as the source of
primers for the synthesis of more molecules of glycogen. |CITS:
[93015717]|")
(REACTION ALPHA-AMYL-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/amyA.template")
(ENZYME ALPHA-AMYL-CYTO-MONOMER)
(:CREATION-DATE 3028482500)
(COMMON-NAME "α-amylase, cytoplasmic")
(SYNONYMS "glycogenase" "1,4-α-D-glucan glucanohydrolase")
(REACTION-DIRECTION REVERSIBLE) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme was capable under
experimental conditions of utilizing amylose, starch, amylopectin and
maltodextrins of size G-6 or larger. Glycogen was utilized much more
slowly. The enzyme is specific for the alpha-anomeric linkage.
|CITS: [93015717]|")))
(ALPHA-AMYL-CYTO-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1927" "YedC" "AmyA")
(DBLINKS (MODBASE "P26612" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00128" IN-FAMILY |pkarp| 3346700346 NIL NIL)
(REFSEQ "NP_416437" NIL NIL NIL NIL NIL)
(UNIPROT "P26612" NIL |pkarp| 3031948485))
(GENE EG11387)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/amyA.template")
(CATALYZES ALPHA-AMYL-CYTO-ENZRXN)
(:CREATION-DATE 3028482500)
(PI 4.71d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 56.63931299999982d0) )
NIL)
(ALPHA-AMYL-PERI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "There are two α-amylases present in E. coli, one
located in the cytoplasm, coded for by the amyA gene, and one located
in the periplasm coded for by the malS gene. The periplasmic
α-amylase degrades maltooligosaccharides with chain lengths longer
than 6 glucose units, which can then be transported through the
cytoplasmic membrane. |CITS: [92184757]| The enzyme hydrolyzes
internal 1,4-glucosidic linkages."
"The enzyme is thought to contain Ca++ binding
sites. |CITS: [92184757]|")
(REACTION ALPHA-AMYL-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/malS.template")
(ENZYME ALPHA-AMYL-PERI-MONOMER)
(:CREATION-DATE 3028482521)
(COMMON-NAME "α-amylase, periplasmic")
(SYNONYMS "1,4-α-D-glucan glucanohydrolase" "glycogenase")
(REACTION-DIRECTION REVERSIBLE) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme is able to hydrolyze
maltodextrins longer than maltose including cyclic dextrins. |CITS:
[86140052]|")))
(ALPHA-AMYL-PERI-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3571" "MalS")
(DBLINKS (MODBASE "P25718" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00128" IN-FAMILY |pkarp| 3346700407 NIL NIL)
(REFSEQ "NP_418028" NIL NIL NIL NIL NIL)
(UNIPROT "P25718" NIL |pkarp| 3031948485))
(GENE EG11316)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/malS.template")
(CATALYZES ALPHA-AMYL-PERI-ENZRXN)
(:CREATION-DATE 3028482521)
(PI 5.67d0)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 75.71260699999976d0) )
NIL)
(ALPHA-AMYL-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(OFFICIAL-EC? YES)
(IN-PATHWAY GLYCOCAT-PWY)
(COMMENT
"In general the reaction is the enhydrolysis of 1,4-α-D-glucosidic linkages in polysaccharides containing three or more 1,4-α-linked D-glucose units.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/amyA.template")
(ENZYMATIC-REACTION ALPHA-AMYL-PERI-ENZRXN ALPHA-AMYL-CYTO-ENZRXN)
(EC-NUMBER "3.2.1.1")
(:CREATION-DATE 3028482500)
(LEFT |1-4-alpha-D-Glucan|)
(RIGHT CPD-1790) )
NIL)
(|Alpha-D-aldose-1-phosphates| T (
(OCELOT-GFP::PARENTS |D-Aldose-1-phosphates|)
(APPEARS-IN-RIGHT-SIDE-OF UDPSUGARHYDRO-RXN ADPSUGPPHOSPHAT-RXN)
(COMMON-NAME "an α-D-aldose-1-phosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(ALPHA-D-GALACTOSE NIL (
(OCELOT-GFP::PARENTS |D-Galactose|)
(APPEARS-IN-RIGHT-SIDE-OF ALDOSE1EPIM-RXN)
(:CREATION-DATE 3073857204)
(GIBBS-0 -214.5d0)
(MOLECULAR-WEIGHT 180.157d0)
(CHEMICAL-FORMULA (C 6) (H 12) (O 6))
(DISPLAY-COORDS-2D (0.0d0 -5.6d0) (4.8497d0 -4.2d0) (4.8497d0 -1.4d0)
(2.4249d0 0.0d0) (0.0d0 -1.4d0) (0.0d0 -4.2d0) (2.4249d0 -4.2d0)
(3.6373d0 -3.5d0) (3.6373d0 -2.1d0) (2.4249d0 -1.4d0) (1.2124d0 -2.1d0)
(1.2124d0 -3.5d0))
(STRUCTURE-BONDS (11 12 1) (10 11 1) (9 10 1) (8 9 1) (7 12 1) (7 8 1)
(12 6 1 :UP) (11 5 1 :UP) (10 4 1 :UP) (9 3 1 :DOWN) (8 2 1 :DOWN) (1 6 1))
(STRUCTURE-ATOMS O O O O O C O C C C C C)
(SYNONYMS "α-galactose"
"6-(hydroxymethyl)tetrahydropyran-2,3,4,5-tetraol")
(COMMON-NAME "α-D-galactose") )
((GIBBS-0 -214.5d0 CITATIONS "GibbsGroups97")))
(|Alpha-D-Glucuronides| T (
(OCELOT-GFP::PARENTS |Glucuronides|)
(COMMON-NAME "an α-D-glucuronoside")
(CHEMICAL-FORMULA (C 6) (H 9) (O 7) (R 1))
(STRUCTURE-BONDS (12 14 1) (11 13 1) (10 12 1) (10 11 1) (14 9 1 :UP)
(8 14 1) (8 13 1) (13 7 1 :DOWN) (6 7 1) (12 5 1 :DOWN) (11 4 1 :DOWN)
(10 3 1 :UP) (2 9 1) (1 9 2))
(DISPLAY-COORDS-2D (1.2124d0 -5.6d0) (0.0d0 -3.5d0) (3.6373d0 0.0d0)
(6.0622d0 -1.4d0) (1.2124d0 -1.4d0) (7.2746d0 -3.5d0) (6.0622d0 -4.2d0)
(3.6373d0 -4.2d0) (1.2124d0 -4.2d0) (3.6373d0 -1.4d0) (4.8497d0 -2.1d0)
(2.4249d0 -2.1d0) (4.8497d0 -3.5d0) (2.4249d0 -3.5d0))
(STRUCTURE-ATOMS O O O O O R O O C C C C C C)
(:CREATOR |paley|)
(:CREATION-DATE 3324143238) )
NIL)
(ALPHA-D-MANNOSYL-3-PHOSPHOGLYCERATE NIL (
(OCELOT-GFP::PARENTS |Glycerates|)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2522)
(:CREATOR |caspi|)
(:CREATION-DATE 3342281781)
(COMMON-NAME "2-(α-D-mannosyl)-3-phosphoglycerate")
(STRUCTURE-ATOMS O O O O O O O O O C C O O O C C C C C C C P)
(DISPLAY-COORDS-2D (4.8497d0 -7.7d0) (9.8975d0 -7.0d0) (0.0d0 -3.5d0)
(3.6373d0 -5.6d0) (1.2124d0 -1.4d0) (3.6373d0 0.0d0) (6.0622d0 -1.4d0)
(9.9191d0 -4.2004d0) (11.287d0 -5.6d0) (1.2124d0 -4.2d0) (7.2746d0 -6.3d0)
(8.487d0 -5.6d0) (6.0622d0 -4.2d0) (3.6373d0 -4.2d0) (4.8497d0 -6.3d0)
(6.0622d0 -5.6d0) (2.4249d0 -3.5d0) (2.4249d0 -2.1d0) (3.6373d0 -1.4d0)
(4.8497d0 -2.1d0) (4.8497d0 -3.5d0) (9.887d0 -5.6d0))
(STRUCTURE-BONDS (20 21 1) (19 20 1) (18 19 1) (17 18 1) (15 16 1) (14 21 1)
(14 17 1) (21 13 1 :DOWN) (13 16 1) (12 22 1) (11 16 1) (11 12 1)
(17 10 1 :UP) (9 22 1) (8 22 1) (20 7 1 :UP) (19 6 1 :UP) (18 5 1 :DOWN)
(4 15 1) (3 10 1) (2 22 2) (1 15 2))
(CHEMICAL-FORMULA (C 9) (H 17) (O 12) (P 1))
(MOLECULAR-WEIGHT 348.2d0)
(DBLINKS (PUBCHEM "443242" NIL |hopkinso| 3317070996 NIL NIL))
(COMMENT-INTERNAL "This structure was imported from PubChem on Feb-15-2005") )
NIL)
(ALPHA-GLC-6-P NIL (
(OCELOT-GFP::PARENTS HEXOSE-6-PHOSPHATES)
(DBLINKS (CAS "56-73-5" NIL |keseler| 3349791794 NIL NIL)
(LIGAND-CPD "C00668" NIL |kr| 3345587433 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF TREHALOSE6PSYN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF PHOSPHOGLUCMUT-RXN)
(:CREATOR |caspi|)
(:CREATION-DATE 3314471473)
(GIBBS-0 -214.7d0)
(MOLECULAR-WEIGHT 260.137d0)
(CHEMICAL-FORMULA (C 6) (H 13) (O 9) (P 1))
(DISPLAY-COORDS-2D (1.3935d0 -2.1239d0) (8.8478d0 -4.2202d0)
(8.8512d0 -1.4132d0) (6.4136d0 0.0d0) (3.9975d0 -1.4165d0)
(1.3953d0 -4.9145d0) (0.0d0 -3.5192d0) (4.0007d0 -4.2168d0)
(2.7923d0 -3.5192d0) (6.4175d0 -4.2168d0) (7.6413d0 -3.5192d0)
(7.6413d0 -2.1084d0) (6.4175d0 -1.3953d0) (5.2092d0 -2.1084d0)
(5.2092d0 -3.5192d0) (1.3953d0 -3.5192d0))
(STRUCTURE-BONDS (14 15 1) (13 14 1) (12 13 1) (11 12 1) (10 15 1) (10 11 1)
(9 16 1) (15 8 1 :UP) (8 9 1) (7 16 1) (6 16 1) (14 5 1 :DOWN) (13 4 1 :UP)
(12 3 1 :DOWN) (11 2 1 :DOWN) (1 16 2))
(STRUCTURE-ATOMS O O O O O O O C O O C C C C C P)
(COMMON-NAME "α-D-glucose-6-phosphate")
(SYNONYMS "α-glucose-6-phosphate" "α-D-glucose-6-P") )
((GIBBS-0 -214.7d0 CITATIONS "GibbsGroups97")))
(ALPHA-GLUCOSE NIL (
(OCELOT-GFP::PARENTS |D-Glucose|)
(APPEARS-IN-RIGHT-SIDE-OF MALTODEXGLUCOSID-RXN)
(:CREATOR |paley|)
(:CREATION-DATE 3355687775)
(STRUCTURE-ATOMS O O O O O O C C C C C C)
(DISPLAY-COORDS-2D (3.0506d0 -0.2195d0) (3.0506d0 1.2814d0)
(1.7458d0 2.0298d0) (0.4534d0 1.2815d0) (1.7457d0 -0.2195d0)
(-0.1212d0 0.2647d0) (2.4003d0 0.1547d0) (2.4003d0 0.903d0)
(1.7457d0 1.2815d0) (1.0955d0 0.9031d0) (1.0955d0 0.1548d0)
(0.4534d0 -0.2194d0))
(STRUCTURE-BONDS (10 4 1 :DOWN) (9 3 1 :UP) (8 2 1 :DOWN) (7 1 1 :DOWN)
(11 12 1 :UP) (10 11 1) (9 10 1) (8 9 1) (7 8 1) (5 7 1) (11 5 1) (6 12 1))
(CHEMICAL-FORMULA (C 6) (H 12) (O 6))
(MOLECULAR-WEIGHT 180.157d0)
(COMMON-NAME "α-D-glucose")
(SYNONYMS "α-glucose" "D-glucose" "glucose"
"6-(hydroxymethyl)tetrahydropyran-2,3,4,5-tetraol") )
NIL)
(ALPHA-GLUCOSE-16-BISPHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(ACTIVATORS-UNKMECH-OF PHOSPHOGLUCMUT-ENZRXN)
(INHIBITORS-COMPETITIVE-OF PHOSPHOGLUCMUT-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3324149440)
(COMMON-NAME "α-glucose-1,6-bisphosphate")
(SYSTEMATIC-NAME "alpha-D-glucopyranose, 1,6-bis(dihydrogen phosphate)")
(STRUCTURE-ATOMS O O O O O C C C C C C P O O O O P O O O)
(STRUCTURE-BONDS (17 20 1) (17 19 1) (17 18 2) (1 17 1) (12 16 1) (12 15 1)
(12 14 2) (12 13 1) (11 13 1) (10 11 1 :UP) (9 4 1 :DOWN) (8 3 1 :UP)
(7 2 1 :DOWN) (6 1 1 :DOWN) (9 10 1) (8 9 1) (7 8 1) (6 7 1) (5 6 1)
(10 5 1))
(DISPLAY-COORDS-2D (5.0321d0 1.5233d0) (5.0452d0 3.0242d0)
(3.7469d0 3.7839d0) (2.4481d0 3.0469d0) (3.7272d0 1.5348d0)
(4.385d0 1.9032d0) (4.3916d0 2.6515d0) (3.7403d0 3.0356d0)
(3.0868d0 2.663d0) (3.0803d0 1.9147d0) (2.3052d0 1.4967d0)
(1.2583d0 0.8083d0) (2.0125d0 0.8083d0) (1.2499d0 0.0583d0)
(0.5083d0 0.8042d0) (1.2499d0 1.5583d0) (5.7792d0 1.5208d0)
(5.7792d0 2.2708d0) (5.7792d0 0.7708d0) (6.5292d0 1.5184d0))
(GIBBS-0 -212.2d0)
(DBLINKS (CAS "10139-18-1"))
(SYNONYMS "α-D-glucose-1,6-P2" "glucose-1,6-diphosphate"
"D-Glucose 1,6-bisphosphate" "D-glucose 1,6-biphosphate"
"α-D-glucopyranose, 1,6-bis(dihydrogen phosphate)"
"glucose-1,6-bisphosphate")
(CHEMICAL-FORMULA (C 6) (H 14) (O 12) (P 2))
(MOLECULAR-WEIGHT 340.117d0) )
((GIBBS-0 -212.2d0 CITATIONS "GibbsGroups97")))
(|Alpha-Hexose-1-Phosphate| T (
(OCELOT-GFP::PARENTS |Hexose-1-Phosphate|)
(MOLECULAR-WEIGHT 260.137d0)
(CHEMICAL-FORMULA (C 6) (H 13) (O 9) (P 1))
(STRUCTURE-BONDS (13 15 1) (12 14 1) (11 13 1) (11 12 1) (10 16 1)
(15 10 1 :DOWN) (9 15 1) (9 14 1) (8 14 1) (7 16 1) (6 16 1) (5 13 1)
(4 12 1) (3 11 1) (2 8 1) (1 16 2))
(DISPLAY-COORDS-2D (6.2497d0 -5.6d0) (0.0d0 -5.6d0) (2.4249d0 0.0d0)
(0.0d0 -1.4d0) (4.8497d0 -1.4d0) (6.2497d0 -2.8d0) (7.6497d0 -4.2d0)
(0.0d0 -4.2d0) (2.4249d0 -4.2d0) (4.8497d0 -4.2d0) (2.4249d0 -1.4d0)
(1.2124d0 -2.1d0) (3.6373d0 -2.1d0) (1.2124d0 -3.5d0) (3.6373d0 -3.5d0)
(6.2497d0 -4.2d0))
(STRUCTURE-ATOMS O O O O O O O C O O C C C C C P)
(COMMON-NAME "α-hexose-1-phosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(ALPHA-METHYLMETHIONINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF HOMSUCTRAN-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979799)
(COMMON-NAME "α-methylmethionine")
(SYNONYMS "2-methylmethionine") )
NIL)
(|alpha-N-Peptidyl-LGlutamate| T (
(OCELOT-GFP::PARENTS |Protein-Glutamates|)
(CHEMICAL-FORMULA (C 6) (H 8) (N 1) (O 5) (|Peptides| 1))
(STRUCTURE-BONDS (13 9 2) (12 11 2) (11 10 1) (11 6 1) (8 7 1) (7 5 1)
(6 5 1) (5 3 1 :DOWN) (4 9 1) (2 7 2) (1 3 1) (1 9 1))
(DISPLAY-COORDS-2D (0.54591835d0 0.3316326d0) (0.54591835d0 -1.0d0)
(0.15816319d0 0.107142806d0) (0.92857134d0 0.99489796d0)
(0.15816319d0 -0.33163267d0) (-0.22448981d0 -0.5561224d0)
(0.54591835d0 -0.5561224d0) (0.92857134d0 -0.33163267d0)
(0.54591835d0 0.7755102d0) (-1.0d0 -0.60714287d0)
(-0.60714287d0 -0.33163267d0) (-0.60714287d0 0.107142806d0)
(0.15816319d0 0.99489796d0))
(STRUCTURE-ATOMS C O C O C N C O C |Peptides| C O O)
(COMMON-NAME "an α-N-peptidyl-L-glutamate")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|alpha-N-Peptidyl-LGlutamine| T (
(OCELOT-GFP::PARENTS |Protein-Amino-Acids|)
(CHEMICAL-FORMULA (C 6) (H 9) (N 2) (O 4) (|Peptides| 1))
(STRUCTURE-BONDS (13 8 1) (11 6 1) (10 12 1) (9 6 2) (7 10 1) (7 3 1) (6 3 1)
(5 8 2) (3 4 1 :DOWN) (2 10 2) (1 4 1) (1 8 1))
(DISPLAY-COORDS-2D (0.49489796d0 0.3316326d0) (-0.6581633d0 0.107142806d0)
(0.112244844d0 -0.33163267d0) (0.112244844d0 0.107142806d0)
(0.112244844d0 0.99489796d0) (0.49489796d0 -0.5561224d0)
(-0.2755102d0 -0.5561224d0) (0.49489796d0 0.7755102d0) (0.49489796d0 -1.0d0)
(-0.6581633d0 -0.33163267d0) (0.87755096d0 -0.33163267d0)
(-1.0d0 -0.6683674d0) (0.87755096d0 0.99489796d0))
(STRUCTURE-ATOMS C O C C O C N C O C O |Peptides| N)
(COMMON-NAME "an α-N-peptidyl-L-glutamine")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(ALPHA-NAPHTHYL-ACETATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "α-naphthyl acetate")
(:CREATOR |keseler|)
(:CREATION-DATE 3352663049) )
NIL)
(|Alpha-omega-dicarboxylates| T (
(OCELOT-GFP::PARENTS |dicarboxylate|)
(SYNONYMS "an α ω dicarboxylic acid")
(COMMON-NAME "an α ω dicarboxylate")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(ALPHA-RIBAZOLE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C05775" NIL |kr| 3346617700 NIL NIL))
(HISTORY |kr-3290870141|)
(AROMATIC-RINGS (2 3 4 8 7 1) (7 11 10 9 8))
(DISPLAY-COORDS-2D (-0.8567d0 -0.9089d0) (-0.276d0 -1.2428d0)
(-0.2718d0 -1.9136d0) (-0.8484d0 -2.2547d0) (0.3042d0 -2.2583d0)
(0.3d0 -0.9083d0) (-1.4375d0 -1.25d0) (-1.4333d0 -1.9208d0)
(-2.0532d0 -2.1989d0) (-2.5574d0 -1.5447d0) (-2.0599d0 -0.9161d0)
(-3.2446d0 -0.0748d0) (-2.5774d0 -0.0743d0) (-2.1055d0 0.5606d0)
(-2.8929d0 0.8822d0) (-3.709d0 0.5432d0) (-3.7167d0 1.2125d0)
(-2.5833d0 -0.7458d0) (-3.25d0 -0.7458d0) (-4.3d0 1.5458d0))
(CHEMICAL-FORMULA (C 14) (H 18) (N 2) (O 4))
(MOLECULAR-WEIGHT 278.307d0)
(STRUCTURE-BONDS (11 14 1) (17 20 1) (7 8 :AROMATIC) (12 19 1) (13 18 1)
(8 4 :AROMATIC) (16 17 1) (4 3 :AROMATIC) (16 12 1) (16 15 1 :UP)
(14 15 1 :UP) (13 14 1) (12 13 1) (3 2 :AROMATIC) (2 1 :AROMATIC) (2 6 1)
(1 7 :AROMATIC) (3 5 1) (8 9 :AROMATIC) (11 7 :AROMATIC) (10 11 :AROMATIC)
(9 10 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C C C N C N C C C O C C O O O)
(APPEARS-IN-RIGHT-SIDE-OF RIBAZOLEPHOSPHAT-RXN)
(APPEARS-IN-LEFT-SIDE-OF COBALAMINSYN-RXN)
(SYNONYMS "N1-(α-D-ribosyl)-5,6-dimethylbenzimidazole")
(:CREATION-DATE 3054402667)
(:CREATOR |kr|)
(COMMON-NAME "α-ribazole") )
NIL)
(ALPHA-RIBAZOLE-5-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04778" NIL |kr| 3346617699 NIL NIL))
(HISTORY |kr-3290870141|)
(AROMATIC-RINGS (6 7 8 9 5) (2 3 5 6 4 1))
(DISPLAY-COORDS-2D (-1.6917d0 2.9917d0) (-1.6917d0 3.75d0)
(-1.0421d0 4.1333d0) (-1.0421d0 2.6167d0) (-0.3843d0 3.75d0)
(-0.3843d0 2.9917d0) (0.9284d0 2.9917d0) (0.9284d0 3.75d0)
(0.272d0 4.1315d0) (-0.55d0 5.8334d0) (-0.3182d0 5.1159d0)
(-0.9292d0 4.6792d0) (-1.5317d0 5.1159d0) (-1.3042d0 5.8334d0)
(-2.2441d0 4.8812d0) (-1.7472d0 6.4386d0) (-0.1087d0 6.4398d0)
(-2.9387d0 5.3345d0) (-3.6917d0 5.3292d0) (-4.4417d0 5.3292d0)
(-3.689d0 4.5792d0) (-3.6973d0 6.0791d0) (-2.3412d0 2.6167d0)
(-2.343d0 4.1219d0))
(CHEMICAL-FORMULA (C 14) (H 19) (N 2) (O 7) (P 1))
(MOLECULAR-WEIGHT 358.287d0)
(STRUCTURE-BONDS (2 24 1) (1 23 1) (19 22 2) (19 21 1) (19 20 1) (18 19 1)
(15 18 1) (10 17 1 :DOWN) (14 16 1 :DOWN) (11 9 1 :UP) (13 15 1 :UP)
(14 10 1) (13 14 1) (12 13 1) (11 12 1) (10 11 1) (7 6 :AROMATIC)
(5 9 :AROMATIC) (9 8 :AROMATIC) (8 7 :AROMATIC) (6 5 :AROMATIC)
(4 6 :AROMATIC) (5 3 :AROMATIC) (3 2 :AROMATIC) (2 1 :AROMATIC)
(1 4 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C N C N C C O C C C O O O P O O O C C)
(APPEARS-IN-LEFT-SIDE-OF RIBAZOLEPHOSPHAT-RXN COBALAMIN5PSYN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF DMBPPRIBOSYLTRANS-RXN)
(SYNONYMS "N1-(5'-phospho-α-D-ribosyl)-5,6-dimethylbenzimidazole"
"DMB-ribose-5'-P")
(:CREATION-DATE 3054402716)
(:CREATOR |kr|)
(COMMON-NAME "α-ribazole-5'-P") )
NIL)
(ALPHA-SIALYL-GROUPS T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "an α-sialyl group")
(:CREATOR |paley|)
(:CREATION-DATE 3330790565) )
NIL)
(ALPHA-SUBUNIT-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME
"trimer complex of formate dehydrogenase-N α, β and γ subunits")
(COMPONENT-OF FORMATEDEHYDROGN-CPLX)
(LOCATIONS)
(COMPONENTS FDNI-MONOMER FDNH-MONOMER FDNG-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/anaresp/fdnGHI.template")
(:CREATION-DATE 2995810116)
(:CREATOR |mriley|) )
((LOCATIONS :FACET COMMENT "inner membrane")
(COMPONENTS FDNI-MONOMER COEFFICIENT 1)
(COMPONENTS FDNH-MONOMER COEFFICIENT 1)
(COMPONENTS FDNG-MONOMER COEFFICIENT 1)))
(|Alpha-tubulins| T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMON-NAME "α-tubulin")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(ALPHAALPHA-DIPYRIDYL NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF RHAMNULPALDOL-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979835)
(COMMON-NAME "α,α'-dipyridyl") )
NIL)
(ALPHACOMP-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2764" "CysJ")
(DBLINKS (MODBASE "P38038" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00258" IN-FAMILY |pkarp| 3346700373 NIL NIL)
(REFSEQ "NP_417244" NIL NIL NIL NIL NIL) (UNIPROT "P38038"))
(COMPONENT-OF SULFITE-REDUCT-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 66.26975399999984d0)
(GENE EG10191)
(CITATIONS "[74127024]" "[89380164]")
(COMMENT "The subunit binds one FMN and one FAD per chain.")
(COMMON-NAME "sulfite reductase flavoprotein subunit")
(:CREATION-DATE 2974150781)
(:CREATOR |mriley|) )
NIL)
(ALPHAGALACTOSID-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/galactocat2/melA2.template")
(CATALYZES ALPHAGALACTOSID-ENZRXN)
(:CREATION-DATE 3037559203)
(COMPONENTS ALPHAGALACTOSID-MONOMER) )
((COMPONENTS ALPHAGALACTOSID-MONOMER COEFFICIENT 2)))
(ALPHAGALACTOSID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH "thiol compounds" 2-MERCAPTOETHANOL NAD)
(INHIBITORS-UNKMECH PHMB CPD-1490 ZN+2 CD+2 NI+2
5-AMINO-5-DEOXY-D-GALACTOPYRANOSIDE 15-DIDEOXY-15-IMINO-D-GALACTITOL
D-GALACTOSYLAMINE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COFACTORS MN+2)
(COMMENT "α-galactosidase is required for utilization of
α-galactosides as nutrients in E. coli. |CITS: [88162811]|")
(REACTION ALPHAGALACTOSID-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/galactocat2/melA2.template")
(ENZYME ALPHAGALACTOSID-CPLX)
(:CREATION-DATE 3037559203)
(COMMON-NAME "α-galactosidase")
(SYNONYMS "melibiase" "α-D-galactoside galactohydrolase")
(REACTION-DIRECTION REVERSIBLE) )
((ACTIVATORS-UNKMECH "thiol compounds" CITATIONS "[71110316]")
(ACTIVATORS-UNKMECH 2-MERCAPTOETHANOL CITATIONS "[71110316]")
(ACTIVATORS-UNKMECH NAD COMMENT " The requirement of a
hydrolytic enzyme for NAD+, usually a coenzyme for oxidoreduction is
presently unexplained. |CITS: [71110316] [88162811]|")
(INHIBITORS-UNKMECH PHMB CITATIONS "[71110316]")
(INHIBITORS-UNKMECH CPD-1490 CITATIONS "[71110316]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[71110316]")
(INHIBITORS-UNKMECH CD+2 CITATIONS "[71110316]")
(INHIBITORS-UNKMECH NI+2 CITATIONS "[71110316]")
(INHIBITORS-UNKMECH 5-AMINO-5-DEOXY-D-GALACTOPYRANOSIDE CITATIONS
"[HandEnzInh]")
(INHIBITORS-UNKMECH 15-DIDEOXY-15-IMINO-D-GALACTITOL CITATIONS
"[HandEnzInh]")
(INHIBITORS-UNKMECH D-GALACTOSYLAMINE CITATIONS "[HandEnzInh]")
(COFACTORS MN+2 CITATIONS "[71110316]" "[88162811]")))
(ALPHAGALACTOSID-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Alpha-galactosidase was previously thought to be a tetramer, but is now believed to be a
dimer. |CITS: [88162811]|
An amber mutation has been generated |CITS: [12853150]|.")
(COMPONENT-OF ALPHAGALACTOSID-CPLX)
(DBLINKS (MODBASE "P06720" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02056" IN-FAMILY |pkarp| 3346700436 NIL NIL)
(REFSEQ "NP_418543" NIL NIL NIL NIL NIL) (UNIPROT "P06720"))
(PI 5.83d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 50.65701299999984d0)
(GENE EG10577)
(SYNONYMS "B4119" "MelA" "melibiase" "α-D-galactoside galactohydrolase")
(COMMON-NAME "α-galactosidase monomer")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/galactocat/melA.template")
(:CREATION-DATE 2988132852)
(:CREATOR |mriley|) )
NIL)
(ALPHAGALACTOSID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ALPHAGALACTOSID-ENZRXN)
(RIGHT GLC GALACTOSE)
(LEFT WATER MELIBIOSE)
(EC-NUMBER "3.2.1.22")
(COMMENT "Part of galactose, galactoside and glucose catabolism.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/galactocat/melA.template")
(:CREATION-DATE 2988132852)
(:CREATOR |mriley|) )
NIL)
(ALTARCA-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3087821485)
(SPECIES ECOLI)
(CITATIONS "[98348461]" "[98352006]" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(IN-PATHWAY ARCB-PWY)
(RIGHT PHOSPHO-ARCA ARCB-MONOMER)
(LEFT ARCA-MONOMER PHOSPHO-ARCB717)
(COMMENT
"In this reaction respiration control protein ArcA is phosphorylated by sensor
kinase-phosphotransferase ArcB-his717-P. This is an alternative route to ArcA
activation."
"The respiration control protein ArcA can be phosphorylated by either the
phospho-ArcB-his292 protein or the phospho-ArcB-his717 protein depending upon
the cytosolic environment. In vitro studies indicated that the
phospho-ArcB-his717 protein was the more active phosphoryl donor. When activated
respiration control protein ArcA acts mainly as a negative regulator of aerobic
gene expression. However it can also function as a positive activator in a few
instances.
|CITS: [97431492] [94043221]
[Hoch&Silhavy] [95045412] [ColiSalII] [92380937] [95158706] [96422482]|") )
NIL)
(ALTERNATIVE-COFACTORS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3199046812)
(QUERYABLE? T)
(:DOCUMENTATION "This slot records variability in the cofactors that
have been observed for this enzymatic reaction. If, for example, the
literature indicates that Mn+2 can substitute for Mg+2 as a cofactor
in this reaction, we would list the following as a value: (Mg+2 Mn+2).")
(:DOMAIN |Enzymatic-Reactions|)
(:VALUE-TYPE :LIST) )
NIL)
(ALTERNATIVE-SUBSTRATES NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3243015060)
(:DOCUMENTATION "This slot records variability in the substrates that
have been observed for this enzymatic reaction. If, for example, the
literature indicates that X can substitute for Y as a substrate
in this reaction, we would list the following as a value: (Y X), where
X and Y are the frame IDs for the corresponding substrates.")
(QUERYABLE? T)
(:DOMAIN |Enzymatic-Reactions|)
(:VALUE-TYPE :LIST) )
NIL)
(ALTRO-OXIDOREDUCT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CPD-29)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "Altronate oxidoreductase is an enzyme of the galacturonate
catabolism pathway, inducible by galacturonate, tagaturonate,
glucuronate and fructuronate. |CITS: [72233233]| The reaction proceeds
as an ordered bi-bi mechanism. |CITS: [73203082]|")
(REACTION ALTRO-OXIDOREDUCT-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/glugalcat2/uxaB2.template")
(ENZYME ALTRO-OXIDOREDUCT-MONOMER)
(:CREATION-DATE 3037378159)
(COMMON-NAME "altronate oxidoreductase")
(SYNONYMS "tagaturonate reductase" "tagaturonate dehydrogenase"
"D-altronate:NAD+ 3-oxidoreductase")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE D-MANNONATE FRUCTURONATE) )
((INHIBITORS-UNKMECH CPD-29 COMMENT "non-competitive
|CITS: [72233233]|")
(INHIBITORS-COMPETITIVE D-MANNONATE COMMENT "with respect to
tagaturonate |CITS: [72233233]|")
(INHIBITORS-COMPETITIVE FRUCTURONATE COMMENT "with respect
to tagaturonate |CITS: [72233233]|")))
(ALTRO-OXIDOREDUCT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CATALYZES ALTRO-OXIDOREDUCT-ENZRXN)
(DBLINKS (MODBASE "P0A6L7" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6L7" NIL |pkarp| 3354911363)
(PFAM "PF01232" IN-FAMILY |pkarp| 3346700336 NIL NIL)
(REFSEQ "NP_416038" NIL NIL NIL NIL NIL))
(PI 5.25d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 54.80824099999976d0)
(GENE EG11065)
(SYNONYMS "B1521" "UxaB" "tagaturonate reductase"
"tagaturonate dehydrogenase" "D-altronate:NAD+ 3-oxidoreductase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uxaB.template")
(:CREATION-DATE 2988132858)
(:CREATOR |mriley|) )
NIL)
(ALTRO-OXIDOREDUCT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ALTRO-OXIDOREDUCT-ENZRXN)
(IN-PATHWAY GALACTUROCAT-PWY)
(RIGHT NADH D-TAGATURONATE)
(LEFT NAD D-ALTRONATE)
(EC-NUMBER "1.1.1.58")
(COMMENT "Part of the galacturonate pathway.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uxaB.template")
(:CREATION-DATE 2988132858)
(:CREATOR |mriley|) )
NIL)
(ALTRODEHYDRAT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH FE+2)
(INHIBITORS-UNKMECH D-GLUCARATE)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "Altronate dehydratase catalyzes the final reaction of the
galaturonate branch of the hexuronate pathway. |CITS: [83114543]|")
(REACTION ALTRODEHYDRAT-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/glugalcat2/uxaA2.template")
(ENZYME ALTRODEHYDRAT-MONOMER)
(:CREATION-DATE 3037378159)
(COMMON-NAME "altronate dehydratase")
(SYNONYMS "altronate hydrolase" "D-altronate hydro-lyase")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(INHIBITORS-COMPETITIVE "D-arabonate") )
((ACTIVATORS-UNKMECH FE+2 CITATIONS "[83114543]")
(INHIBITORS-UNKMECH D-GLUCARATE COMMENT "weakly inhibitory |CITS:
[83114543]|")
(INHIBITORS-COMPETITIVE "D-arabonate" CITATIONS "[83114543]")))
(ALTRODEHYDRAT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 54.09302399999987d0)
(DBLINKS (PFAM "PF04292" IN-FAMILY |pkarp| 3346700386 NIL NIL)
(REFSEQ "NP_417562" NIL NIL NIL NIL NIL)
(UNIPROT "P42604" NIL |pkarp| 3064869797))
(CATALYZES ALTRODEHYDRAT-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(GENE EG12734)
(SYNONYMS "B3091" "YgjW" "UxaA")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uxaA.template")
(:CREATION-DATE 2988132857)
(:CREATOR |mriley|) )
NIL)
(ALTRODEHYDRAT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ALTRODEHYDRAT-ENZRXN)
(IN-PATHWAY GALACTUROCAT-PWY)
(RIGHT WATER 2-DEHYDRO-3-DEOXY-D-GLUCONATE)
(LEFT D-ALTRONATE)
(EC-NUMBER "4.2.1.7")
(COMMENT "Part of the galacturonate pathway.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uxaA.template")
(:CREATION-DATE 2988132857)
(:CREATOR |mriley|) )
NIL)
(ALTROSE NIL (
(OCELOT-GFP::PARENTS |Aldohexoses|)
(:CREATOR |kaipa|)
(:CREATION-DATE 3346525588)
(DBLINKS (CAS "5987-68-8"))
(GIBBS-0 -216.2d0)
(SYNONYMS "D-altropyranose" "D-altrose")
(MOLECULAR-WEIGHT 180.157d0)
(CHEMICAL-FORMULA (C 6) (H 12) (O 6))
(DISPLAY-COORDS-2D (-0.14667d0 0.2d0) (-1.0d0 -0.60333d0) (-0.56667d0 -0.2d0)
(-0.56667d0 -1.0d0) (-0.56667d0 0.59d0) (-0.56667d0 0.2d0)
(-0.14333d0 0.59d0) (-0.14d0 -0.2d0) (-0.56667d0 -0.60333d0)
(-0.56667d0 0.99667d0) (-0.14667d0 0.99667d0) (-0.14d0 -1.0d0))
(STRUCTURE-BONDS (12 4 2) (11 10 1) (10 5 1) (9 3 1) (8 3 1) (7 5 1) (6 3 1)
(5 6 1) (4 9 1) (2 9 1) (1 6 1))
(STRUCTURE-ATOMS O O C C C C O O C C O O)
(COMMON-NAME "altrose") )
((GIBBS-0 -216.2d0 CITATIONS "GibbsGroups97")))
(AMACETOXID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION AMACETOXID-RXN)
(COMMENT "This is a specific activity of the enzyme.")
(ENZYME AMINEOXID-CPLX)
(COMMON-NAME "aminoacetone oxidase")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
NIL)
(AMACETOXID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY THREOCAT-PWY)
(ENZYMATIC-REACTION AMACETOXID-ENZRXN)
(RIGHT METHYL-GLYOXAL AMMONIA HYDROGEN-PEROXIDE)
(LEFT AMINO-ACETONE WATER OXYGEN-MOLECULE)
(COMMENT "This is a specific substrate reaction of the general amine
oxidase reaction.")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
NIL)
(|Amidation-Modifications| T (
(OCELOT-GFP::PARENTS |Modified-Residues|)
(SCHEMA? T)
(COMMENT "Amidation, generally at the C-terminal of a mature active peptide.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414656) )
NIL)
(|Amides| T (
(OCELOT-GFP::PARENTS |Compounds|)
(COMMON-NAME "an amide")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(AMINE-DEG T (
(OCELOT-GFP::PARENTS |Degradation|)
(COMMENT
"This class contains pathways of degradation of various amines (primary, secondary, quaternary, aliphatic, and aromatic) with the exception of amino acids, to utilize them as sources of nutrients and energy. Pathways of the degradation of amino acids are shown in a separate class; those involving degradation of aromatic amines are also included in the \"Aromatic compounds\" class. ")
(COMMON-NAME "Amines and Polyamines")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(AMINE-SYN T (
(OCELOT-GFP::PARENTS N-CONTAINING-SECONDARY-CMPD-SYN)
(COMMENT
"This class contains pathways of the biosynthesis of amines that are widely found in plants and can occur as independent products involved in a variety of functions (attractant, defense compound, antibacterial, antifungal), or as intermediates in the biosynthesis of alkaloids.")
(COMMON-NAME "Amines")
(:CREATOR |paley|)
(:CREATION-DATE 3324143236) )
NIL)
(AMINEOXID-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES AMINEPHEN-ENZRXN AMACETOXID-ENZRXN AMINEOXID-ENZRXN)
(COMPONENTS AMINEOXID-MONOMER)
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
((COMPONENTS AMINEOXID-MONOMER COEFFICIENT 2)))
(AMINEOXID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH SEMICARBAZIDE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION AMINEOXID-RXN)
(PROSTHETIC-GROUPS CU+2 TOPAQUINONE)
(COMMENT "Amine oxidase catalyzes the conversion of an aliphatic amine
to an aldehyde, followed by a two-electron reduction of O2 to H2O2 to
regenerate the oxidized enzyme. |CITS: [95284034]| It has been
recently proven that the oxidase coded for by the maoA gene uses
copper and topaquinone as prosthetic groups. The topaquinone is a
part of the polypeptide chain. |CITS: [93098778]| The topaquinone is
generated through the post-translational modification of a protein
tyrosine residue, that occurs as a copper-dependent, probably
autocatalytic reaction. |CITS: [95284034] [95217132]| The enzyme has
been crystallized. |CITS: [94231582]|")
(ENZYME AMINEOXID-CPLX)
(SYNONYMS "diamine oxidase" "diamino oxhydrase" "histiminase"
"amine:oxygen oxidoreductase (deaminating) (Cu containing)"
"monoamine oxidase" "aromatic amine oxidase")
(COMMON-NAME "amine oxidase (Cu containing)")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH SEMICARBAZIDE COMMENT "inhibits the activated enzyme
|CITS: [95217132]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme has very broad substrate
specificity.")
(PROSTHETIC-GROUPS :FACET COMMENT "The enzyme contains
one atom of Cu and one molecule of topaquinone per subunit. |CITS:
[95352083]|")))
(AMINEOXID-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1386" "MaoA" "FeaA" "TynA")
(COMMON-NAME "TynA")
(DBLINKS (MODBASE "P46883" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF07833" IN-FAMILY |pkarp| 3346700333 NIL NIL)
(REFSEQ "NP_415904" NIL NIL NIL NIL NIL) (PDB "1SPU") (PDB "1OAC")
(PDB "1JRQ") (PDB "1DYU") (UNIPROT "P46883" NIL |pkarp| 3064869797))
(COMPONENT-OF AMINEOXID-CPLX)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 84.37857299999979d0)
(GENE EG13139)
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
NIL)
(AMINEOXID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.4.3)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION AMINEOXID-ENZRXN)
(RIGHT |an aldehyde| AMMONIA HYDROGEN-PEROXIDE)
(LEFT |Aliphatic-Amines| WATER OXYGEN-MOLECULE)
(EC-NUMBER "1.4.3.6")
(COMMENT "This reaction converts an aliphatic amine to an aldehyde.")
(TEMPLATE-FILE "~ecocyc/templates/new/threocat/maoA.template")
(:CREATION-DATE 3044212616)
(:CREATOR |mriley|) )
NIL)
(AMINEPHEN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(:CREATION-DATE 3077461617)
(SYNONYMS "2-phenylethylamine oxidase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION AMINEPHEN-RXN)
(COMMENT
"E. coli K-12 is capable of growth on phenylethylamine as the sole carbon and
energy source. Phenylethylamine oxidase catalyzes the first step in the
degradation pathway. This is a particular instance of a reaction catalyzed by
the amine oxidase enzyme. |CITS: [97263463] [88009860]|")
(ENZYME AMINEOXID-CPLX)
(COMMON-NAME "phenylethylamine oxidase") )
NIL)
(AMINEPHEN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| |Chemical-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(:CREATION-DATE 3077461617)
(IN-PATHWAY 2PHENDEG-PWY)
(ENZYMATIC-REACTION AMINEPHEN-ENZRXN)
(RIGHT HYDROGEN-PEROXIDE AMMONIA PHENYLACETALDEHYDE)
(LEFT WATER OXYGEN-MOLECULE PHENYLETHYLAMINE)
(COMMENT
"This is a specific substrate reaction of the general amine oxidase reaction.
This reaction is involved in the catabolism of 2-phenylethylamine.") )
NIL)
(AMINO-ACETONE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C01888" NIL |kr| 3346617701 NIL NIL) (CAS "298-08-8"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -36.9d0)
(APPEARS-IN-RIGHT-SIDE-OF AMINOPROPDEHYDROG-RXN THREOSPON-RXN)
(APPEARS-IN-LEFT-SIDE-OF AMACETOXID-RXN)
(MOLECULAR-WEIGHT 73.094d0)
(CHEMICAL-FORMULA (C 3) (H 7) (N 1) (O 1))
(DISPLAY-COORDS-2D (0.33779d0 -1.0d0) (-0.33445d0 0.14716d0)
(0.33779d0 -0.23746d0) (-1.0d0 -0.22742d0) (0.99666d0 0.14381d0))
(STRUCTURE-BONDS (5 3 1) (4 2 1) (3 1 2) (2 3 1))
(STRUCTURE-ATOMS O C C N C)
(COMMON-NAME "aminoacetone") )
((GIBBS-0 -36.9d0 CITATIONS "GibbsGroups97")))
(|Amino-Acid| T (
(OCELOT-GFP::PARENTS |Amino-Acids|)
(DISPLAY-COORDS-2D (1.2892d0 0.0d0) (2.395d0 -3.3859d0) (3.6236d0 -1.324d0)
(0.0d0 -1.9859d0) (2.4041d0 -1.9859d0) (1.2892d0 -1.2195d0))
(CHEMICAL-FORMULA (C 2) (H 4) (N 1) (O 2) (R 1))
(STRUCTURE-BONDS (5 6 1) (4 6 1) (3 5 1) (2 5 2) (1 6 1))
(STRUCTURE-ATOMS N O O R C C)
(APPEARS-IN-LEFT-SIDE-OF GAMMA-GLUTAMYLTRANSFERASE-RXN)
(SYNONYMS "amino acid" "L-amino acid")
(COMMENT
"This compound class stands for generic but unspecified amino acids, which includes the standard L-amino acids plus glycine.")
(APPEARS-IN-RIGHT-SIDE-OF 3.4.11.1-RXN N-METHYL-L-AMINO-ACID-OXIDASE-RXN)
(COMMON-NAME "an amino acid")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104643) )
NIL)
(|Amino-Acid-Binding-Sites| T (
(OCELOT-GFP::PARENTS |Amino-Acid-Sites| |Protein-Binding-Features|)
(SCHEMA? T)
(COMMENT "This class describes binding (covalent or otherwise) to
specific residues of a polypeptide.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414652) )
NIL)
(|Amino-Acid-Biosynthesis| T (
(OCELOT-GFP::PARENTS |Biosynthesis|)
(COMMENT
"This class contains the pathways of biosynthesis of each of the 21 amino acids present normally in proteins. ")
(SCHEMA? T)
(COMMON-NAME "Amino acids") )
NIL)
(|Amino-Acid-Degradation| T (
(OCELOT-GFP::PARENTS |Degradation|)
(COMMENT
"This class contains pathways of the degradation of various amino acids, not all of which occur in proteins, to utilize them as sources of nutrients and energy. ")
(SCHEMA? T)
(COMMON-NAME "Amino Acids") )
NIL)
(|Amino-Acid-Derivatives| T (
(OCELOT-GFP::PARENTS |All-Amino-Acids|)
(COMMON-NAME "an amino acid derivative")
(SCHEMA? T) )
NIL)
(AMINO-ACID-FAMILY-SYN T (
(OCELOT-GFP::PARENTS |Amino-Acid-Biosynthesis| |Super-Pathways|)
(COMMENT
"This class contains pathways of the synthesis of those groups of amino acids that share common steps in their biosynthesis or steps catalyzed by the same enzymes.")
(SCHEMA? T)
(COMMON-NAME "Amino acid families") )
NIL)
(|Amino-Acid-Sites| T (
(OCELOT-GFP::PARENTS |Protein-Features|)
(SCHEMA? T)
(COMMENT "Members of this class describe modifications to, binding to,or
other interesting features of one or more specific (and generally
non-contiguous) amino acid residues in a polypeptide, as
opposed to a larger bounded region. The set of residues
defining the feature is encoded using slots RESIDUE-NUMBER
(which lists the index within the amino-acid sequence of the
indicated residue), and RESIDUE-TYPE (which lists the
one-letter code of that residue). The values of these two
slots must be in parallel order. The second slot is needed in
cases where the full amino-acid sequence of the protein is not available.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414652) )
NIL)
(|Amino-Acids| T (
(OCELOT-GFP::PARENTS |All-Amino-Acids|)
(COMMON-NAME "an amino acid")
(SCHEMA? T)
(OVERVIEW-NODE-SHAPE :TRIANGLE) )
NIL)
(AMINO-GROUP NIL (
(OCELOT-GFP::PARENTS |Simple-Groups|)
(COMMON-NAME "amino-group")
(MOLECULAR-WEIGHT 28.033d0)
(CHEMICAL-FORMULA (C 1) (H 2) (N 1))
(DISPLAY-COORDS-2D (-1.0d0 -1.0d0) (0.9967d0 -1.0d0))
(STRUCTURE-BONDS (1 2 1))
(STRUCTURE-ATOMS C N)
(ATOM-CHARGES (1 -3)) )
NIL)
(AMINO-HYDROXYMETHYL-METHYL-PYR-P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04556" NIL |kr| 3346617699 NIL NIL))
(:CREATION-DATE 3105713036)
(AROMATIC-RINGS (10 2 13 1 12 11))
(DISPLAY-COORDS-2D (0.72294366d0 -0.5266955d0) (0.44588745d0 -0.05339104d0)
(-0.6854257d0 -0.52380955d0) (0.99711394d0 -0.047619045d0)
(-0.099567115d0 -0.6825397d0) (-0.6883117d0 -0.83838385d0)
(-0.3708514d0 -0.52380955d0) (-0.6854257d0 -0.20923519d0)
(-1.0d0 -0.52380955d0) (0.17171717d0 -0.20923519d0)
(0.17171717d0 -0.5266955d0) (0.44588745d0 -0.6854257d0)
(0.72294366d0 -0.20923519d0) (0.44588745d0 -1.0d0))
(CHEMICAL-FORMULA (C 6) (H 10) (N 3) (O 4) (P 1))
(MOLECULAR-WEIGHT 219.136d0)
(STRUCTURE-BONDS (13 1 :AROMATIC) (13 4 1) (12 11 :AROMATIC) (12 14 1)
(11 10 :AROMATIC) (11 5 1) (10 2 :AROMATIC) (7 3 1) (5 7 1) (3 9 1) (3 8 1)
(3 6 2) (2 13 :AROMATIC) (1 12 :AROMATIC))
(STRUCTURE-ATOMS N N P C C O O O O C C C C N)
(APPEARS-IN-RIGHT-SIDE-OF PYRIMSYN1-RXN OHMETPYRKIN-RXN)
(APPEARS-IN-LEFT-SIDE-OF PYRIMSYN3-RXN)
(SYNONYMS "4-amino-2-methyl-5-phosphomethylpyrimidine"
"4-amino-5-phosphomethyl-2-methylpyrimidine" "HMP-P"
"4-amino-5-hydroxymethyl-2-methylpyrimidine-P"
"4-amino-5-hydroxymethyl-2-methylpyrimidine-phosphate")
(COMMON-NAME "hydroxymethylpyrimidine phosphate") )
NIL)
(AMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(HISTORY |kr-3290870141|)
(DBLINKS (CAS "745-65-3" NIL |kr| 3346617700 NIL NIL)
(LIGAND-CPD "C04752" NIL |kr| 3346617700 NIL NIL) (CAS "841-01-0"))
(:CREATION-DATE 3115390701)
(AROMATIC-RINGS (2 3 4 5 6 1))
(DISPLAY-COORDS-2D (3.0917d0 1.3417d0) (3.0917d0 2.1d0) (3.7412d0 2.4833d0)
(4.399d0 2.1d0) (4.399d0 1.3417d0) (3.7412d0 0.9667d0) (5.0475d0 0.9649d0)
(3.7391d0 3.2333d0) (2.4404d0 2.4719d0) (1.7926d0 2.0938d0)
(1.0417d0 2.0917d0) (1.0427d0 1.3417d0) (1.0396d0 2.8417d0)
(0.2926d0 2.0938d0) (-0.4583d0 2.0917d0) (-1.2083d0 2.0917d0)
(-0.4573d0 1.3417d0) (-0.4604d0 2.8417d0))
(CHEMICAL-FORMULA (C 6) (H 11) (N 3) (O 7) (P 2))
(MOLECULAR-WEIGHT 299.116d0)
(STRUCTURE-BONDS (15 18 2) (15 17 1) (15 16 1) (14 15 1) (11 13 2) (11 12 1)
(11 14 1) (10 11 1) (9 10 1) (2 9 1) (3 8 1) (5 7 1) (6 5 :AROMATIC)
(5 4 :AROMATIC) (4 3 :AROMATIC) (3 2 :AROMATIC) (2 1 :AROMATIC)
(1 6 :AROMATIC))
(STRUCTURE-ATOMS C C C N C N C N C O P O O O P O O O)
(APPEARS-IN-LEFT-SIDE-OF THI-P-SYN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF PYRIMSYN3-RXN)
(SYNONYMS "4-amino-2-methyl-5-diphosphomethylpyrimidine"
"2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate" "HMP-PP"
"4-amino-5-hydroxymethyl-2-methylpyrimidine-PP")
(COMMON-NAME "4-amino-5-hydroxymethyl-2-methylpyrimidine-pyrophosphate") )
NIL)
(AMINO-OH-HYDROXYMETHYL-DIHYDROPTERIDINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(:CREATION-DATE 3115390701)
(AROMATIC-RINGS (6 7 8 9 10 5))
(DISPLAY-COORDS-2D (0.2417d0 -2.5083d0) (0.2417d0 -3.2667d0)
(0.8912d0 -3.65d0) (0.8912d0 -2.1333d0) (1.549d0 -3.2667d0)
(2.2116d0 -3.6474d0) (2.8741d0 -3.2698d0) (2.8689d0 -2.5035d0)
(2.2063d0 -2.1228d0) (1.549d0 -2.5083d0) (-0.4096d0 -3.6386d0)
(-1.0574d0 -3.2605d0) (2.2103d0 -4.3974d0) (3.5167d0 -2.1256d0))
(CHEMICAL-FORMULA (C 7) (H 9) (N 5) (O 2))
(MOLECULAR-WEIGHT 195.18d0)
(STRUCTURE-BONDS (8 14 1) (6 13 1) (11 12 1) (2 11 1) (10 9 :AROMATIC)
(9 8 :AROMATIC) (8 7 :AROMATIC) (7 6 :AROMATIC) (6 5 :AROMATIC)
(5 10 :AROMATIC) (10 4 1) (3 5 1) (2 3 2) (1 2 1) (1 4 1))
(STRUCTURE-ATOMS C C N N C C N C N C C O O N)
(APPEARS-IN-RIGHT-SIDE-OF H2NEOPTERINALDOL-RXN)
(APPEARS-IN-LEFT-SIDE-OF H2PTERIDINEPYROPHOSPHOKIN-RXN)
(SYNONYMS "dihydropterin-CH2OH"
"2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine")
(COMMON-NAME "6-hydroxymethyl-dihydropterin") )
NIL)
(AMINO-OXOBUT NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C03508" NIL |kr| 3346617701 NIL NIL))
(:CREATION-DATE 3082488681)
(MOLECULAR-WEIGHT 117.104d0)
(CHEMICAL-FORMULA (C 4) (H 7) (N 1) (O 3))
(DISPLAY-COORDS-2D (-0.006369412d0 -0.4299363d0)
(-0.009554148d0 0.70382166d0) (-1.0d0 0.13057327d0)
(-0.34076434d0 0.13057327d0) (0.99044585d0 0.1433121d0)
(0.6592357d0 -0.4299363d0) (0.9968153d0 -1.0d0) (-0.3821656d0 -1.0d0))
(STRUCTURE-BONDS (8 1 1) (7 6 2) (6 1 1) (5 6 1) (4 1 1) (3 4 2) (2 4 1))
(STRUCTURE-ATOMS C O O C C C O N)
(APPEARS-IN-LEFT-SIDE-OF THREOSPON-RXN)
(APPEARS-IN-RIGHT-SIDE-OF AKBLIG-RXN THREODEHYD-RXN)
(COMMON-NAME "2-amino-3-oxobutanoate")
(SYNONYMS "2-amino-acetoacetate" "2-amino-3-ketobutyrate"
"2-amino-3-oxobutyrate" "α-amino-β-ketobutyrate"
"L-2-amino-3-oxobutanoate") )
NIL)
(AMINO-RIBOSYLAMINO-1H-3H-PYR-DIONE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04732" NIL |kr| 3346617700 NIL NIL))
(AROMATIC-RINGS (14 13 15 21 16 20))
(:CREATION-DATE 3115390701)
(CITATIONS "colisalII")
(SYNONYMS "4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine"
"4-(1-D-ribitylamino)-5-aminouracil" "compound 6")
(DISPLAY-COORDS-2D (3.8346d0 -3.6487d0) (6.382d0 -8.0443d0)
(1.1168d0 -8.3292d0) (3.8157d0 -9.6088d0) (6.3749d0 -4.9094d0)
(1.3263d0 0.0d0) (1.3263d0 -1.1399d0) (1.3263d0 -3.3037d0)
(1.3263d0 -2.1869d0) (0.0d0 0.0d0) (0.0d0 -4.5135d0) (1.3263d0 -4.9094d0)
(2.5361d0 -7.352d0) (2.5361d0 -5.8167d0) (3.8157d0 -8.1197d0)
(5.1651d0 -5.8167d0) (0.0d0 -1.1399d0) (0.0d0 -3.3037d0) (0.0d0 -2.1869d0)
(3.8157d0 -5.0485d0) (5.1651d0 -7.352d0))
(CHEMICAL-FORMULA (C 9) (H 16) (N 4) (O 6))
(MOLECULAR-WEIGHT 276.249d0)
(STRUCTURE-BONDS (18 19 1) (17 19 1) (16 21 :AROMATIC) (20 16 :AROMATIC)
(21 15 :AROMATIC) (14 20 :AROMATIC) (15 13 :AROMATIC) (13 14 :AROMATIC)
(12 14 1) (11 18 1) (11 12 1) (10 17 1) (9 19 1) (8 18 1) (7 17 1) (6 10 1)
(5 16 2) (4 15 2) (3 13 1) (2 21 1) (1 20 1))
(STRUCTURE-ATOMS H H N O O O O O O C C N C C C C C C C N N)
(APPEARS-IN-RIGHT-SIDE-OF RIBOPHOSPHAT-RXN RIBOFLAVIN-SYN-RXN)
(APPEARS-IN-LEFT-SIDE-OF LUMAZINESYN-RXN)
(COMMON-NAME "5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione") )
NIL)
(|Aminoacyl-tRNAs| T (
(OCELOT-GFP::PARENTS |Biosynthesis|)
(COMMENT
"This class contains the set of reactions by which the various amino acids become bonded to their corresponding tRNAs; the products of these reactions recognize cognate codons in mRNAs present in ribosomes and react there, forming peptide bonds, thereby, lengthening a growing polypeptide. ")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(AMINOBUTDEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(COMMENT "This is the second reaction in a putrescine degradative pathway.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "~ecocyc/templates/new/putcat/ambutdehyd.template")
(ENZYMATIC-REACTION ENZRXN0-5382)
(EC-NUMBER "1.2.1.19")
(:CREATION-DATE 3046644080)
(IN-PATHWAY PUTDEG-PWY)
(LEFT 4-AMINO-BUTYRALDEHYDE NAD WATER)
(RIGHT 4-AMINO-BUTYRATE NADH) )
NIL)
(AMINOCYL-TRNA-HYDROLASE-RXN NIL (
(OCELOT-GFP::PARENTS EC-3.1.1 |tRNA-Reactions|)
(ENZYMATIC-REACTION ENZRXN0-1628)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "3.1.1.29")
(COMMON-NAME "AMINOCYL-TRNA-HYDROLASE")
(RIGHT |Some-tRNA| |N-Substituted-Amino-Acids|)
(LEFT WATER |N-Substituted-Aminoacyl-tRNA|) )
NIL)
(AMINOMETHYLDIHYDROLIPOYL-GCVH NIL (
(OCELOT-GFP::PARENTS |Gcv-H|)
(SYNONYMS "Gcv" "B2904" "GcvH")
(DISPLAY-COORDS-2D (-0.99d0 1.4759d0) (-0.2756d0 1.0634d0)
(0.4389d0 1.4759d0) (1.1535d0 1.0634d0) (1.868d0 1.4759d0)
(-1.7045d0 1.0634d0) (2.5824d0 1.0634d0) (3.2969d0 1.4759d0)
(4.0113d0 1.0634d0) (4.7244d0 1.4782d0) (4.027d0 0.2886d0)
(0.4389d0 2.3009d0) (-0.2756d0 2.7134d0) (-0.2756d0 3.5384d0))
(CHEMICAL-FORMULA (C 9) (H 18) (N 1) (O 1) (|Apo-GcvH| 1) (S 2))
(STRUCTURE-BONDS (13 14 1) (12 13 1) (8 9 1) (9 11 2) (9 10 1) (7 8 1)
(5 7 1) (3 12 1) (1 6 1) (4 5 1) (3 4 1 :UP) (2 3 1) (1 2 1))
(STRUCTURE-ATOMS C C C C C S C C C |Apo-GcvH| O S C N)
(MOLECULAR-WEIGHT-SEQ 13.811178d0)
(DBLINKS (MODBASE "P23884" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P23884" NIL |pick| NIL NIL NIL))
(APPEARS-IN-RIGHT-SIDE-OF GCVP-RXN)
(:CREATION-DATE 3055532636)
(GENE EG10371)
(UNMODIFIED-FORM GCVH-MONOMER)
(APPEARS-IN-LEFT-SIDE-OF GCVT-RXN)
(COMMON-NAME "H-protein-S-(aminomethyldihydrolipoyl)lysine") )
NIL)
(AMINOPROPDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (1-AMINO-PROPAN-2-OL 14500))
(ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" BUTANEDIOL)
("D-1-aminopropanol-2-ol" 3-AMINO-12-PROPANEDIOL)
("D-1-aminopropanol-2-ol" "3-mercapto-1,2-propanediol")
("D-1-aminopropanol-2-ol" "3-chloro-1,2-propanediol")
("D-1-aminopropanol-2-ol" BUTANEDIOL)
("D-1-aminopropanol-2-ol" |PROPANE-1,2-DIOL|)
("D-1-aminopropanol-2-ol" GLYCEROL))
(INHIBITORS-UNKMECH HG+2 CO+2 CU+2 MN+2 FE+2 NI+2 ZN+2 RB+ K+ NA+ LI+)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "D-aminopropanol dehydrogenase continues the degradation of
threonine. The enzyme has broad substrate specificity. |CITS:
[84135662] [85157403]|")
(REACTION AMINOPROPDEHYDROG-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/threocat/ampropdehyd.template")
(ENZYME GLYCDEH-CPLX)
(:CREATION-DATE 3045249147)
(COMMON-NAME "D-aminopropanol dehydrogenase")
(SYNONYMS "D-1-amino-2-propanol oxidoreductase"
"D-1-aminopropan-2-ol:NAD+ oxidoreductase")
(REACTION-DIRECTION REVERSIBLE) )
((ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" BUTANEDIOL) CITATIONS
"[84135662]")
(ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" 3-AMINO-12-PROPANEDIOL)
CITATIONS "[84135662]")
(ALTERNATIVE-SUBSTRATES
("D-1-aminopropanol-2-ol" "3-mercapto-1,2-propanediol") CITATIONS
"[84135662]")
(ALTERNATIVE-SUBSTRATES
("D-1-aminopropanol-2-ol" "3-chloro-1,2-propanediol") CITATIONS
"[84135662]")
(ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" BUTANEDIOL) CITATIONS
"[84135662]")
(ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" |PROPANE-1,2-DIOL|)
CITATIONS "[84135662]")
(ALTERNATIVE-SUBSTRATES ("D-1-aminopropanol-2-ol" GLYCEROL) CITATIONS
"[84135662]")
(INHIBITORS-UNKMECH HG+2 COMMENT "completely blocked activity")
(INHIBITORS-UNKMECH HG+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH CO+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH MN+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH FE+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH NI+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[84135662]")
(INHIBITORS-UNKMECH RB+ COMMENT "slight inhibition")
(INHIBITORS-UNKMECH RB+ CITATIONS "[84135662]")
(INHIBITORS-UNKMECH K+ COMMENT "slight inhibition")
(INHIBITORS-UNKMECH K+ CITATIONS "[84135662]")
(INHIBITORS-UNKMECH NA+ COMMENT "slight inhibition")
(INHIBITORS-UNKMECH NA+ CITATIONS "[84135662]")
(INHIBITORS-UNKMECH LI+ COMMENT "slight inhibition")
(INHIBITORS-UNKMECH LI+ CITATIONS "[84135662]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT
"In the oxidation reaction only NAD+ will function
as a cosubstrate. However, both NADH and NADPH serve as a cosubstrate
in the reduction of hydroxyacetone. |CITS: [84135662]| The enzyme may
also function as a glycerol dehydrogenase, EC# 1.1.1.6. |CITS:
[85157403]|")))
(AMINOPROPDEHYDROG-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY THREOCAT-PWY)
(COMMENT "This reaction is part of the degradation of threonine.")
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/threocat/ampropdehyd.template")
(ENZYMATIC-REACTION AMINOPROPDEHYDROG-ENZRXN)
(EC-NUMBER "1.1.1.75")
(:CREATION-DATE 3045249147)
(LEFT 1-AMINO-PROPAN-2-OL NAD)
(RIGHT AMINO-ACETONE NADH) )
NIL)
(AMMASSIM-PWY NIL (
(OCELOT-GFP::PARENTS NITROGEN-DEG)
(SUB-PATHWAYS GLUTSYN-PWY GLNSYN-PWY)
(SYNONYMS "ammonium assimilation" "ammonia assimilation cycle")
(CITATIONS ":EV-EXP:3277587223:pkarp")
(COMMENT
"In an energy-rich (glucose-containing), nitrogen-poor environment glutamine
synthetase and glutamate synthase form an ammonia assimilatory cycle. This
ATP-dependent cycle is essential for nitrogen-limited growth and for
steady-state growth with some sources of nitrogen. |CITS: [ColiSalII]|")
(PRIMARIES (GLUTAMINESYN-RXN (GLT) (GLN)))
(REACTION-LIST GLUTSYN-PWY GLNSYN-PWY)
(PREDECESSORS (GLUTAMATESYN-RXN GLUTAMINESYN-RXN) GLNSYN-PWY GLUTSYN-PWY)
(COMMON-NAME "superpathway of glutamate biosynthesis")
(:CREATION-DATE 3121601554)
(:CREATOR |ptoole|) )
NIL)
(AMMONIA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(STRUCTURE-BONDS (4 1 1) (4 2 1) (3 4 1))
(DBLINKS (CAS "7664-41-7"))
(:CREATION-DATE 3057679256)
(GIBBS-0 -8.6d0)
(APPEARS-IN-RIGHT-SIDE-OF HOMOSERDEAM-RXN 4.3.1.17-RXN
GLUCOSAMINE-6-P-DEAMIN-RXN RIBOFLAVINSYNDEAM-RXN THREDEHYD-RXN
ADENINE-DEAMINASE-RXN 4.3.1.15-RXN GLUTDEHYD-RXN GCVMULTI-RXN RXN0-1081
UREIDOGLYCOLATE-HYDROLASE-RXN CYTIDEAM-RXN CYSTAGLY-RXN SUCCARGDIHYDRO-RXN
GUANINE-DEAMINASE-RXN TRANS-RXN-149 PYRAZIN-RXN CHEBTARD-RXN CHEBTSRD-RXN
CHEBTRGD-RXN CHEBTAPD-RXN CHEBDEAMID-RXN AMINEPHEN-RXN NMNAMIDOHYDRO-RXN
NICOTINAMID-RXN ADDALT-RXN AMINEOXID-RXN DCYSDESULF-RXN AMACETOXID-RXN
LCYSDESULF-RXN GLUTAMIN-RXN ETHAMLY-RXN DSERDEAM-RXN TRYPTOPHAN-RXN
OHMETHYLBILANESYN-RXN ASPARTASE-RXN CYSTATHIONINE-BETA-LYASE-RXN
CYTIDEAM2-RXN ADENODEAMIN-RXN CYTDEAM-RXN DCTP-DEAM-RXN ASPARAGHYD-RXN
DAADEHYDROG-RXN PMPOXI-RXN GCVT-RXN DALADEHYDROG-RXN)
(APPEARS-IN-LEFT-SIDE-OF CTPSYN-RXN 1.7.7.2-RXN ASNSYNA-RXN
HYDROXYLAMINE-REDUCTASE-RXN GMP-REDUCT-RXN TRANS-RXN-149 METBALT-RXN
GMP-SYN-NH3-RXN GLUTAMINESYN-RXN NAD-SYNTH-NH3-RXN)
(COMMON-NAME "ammonia")
(DISPLAY-COORDS-2D (-1.0d0 -1.0d0) (0.99489796d0 -1.0d0)
(-0.020408154d0 -0.2755102d0) (-0.020408154d0 -1.0d0))
(STRUCTURE-ATOMS H H H N)
(CHEMICAL-FORMULA (H 3) (N 1))
(MOLECULAR-WEIGHT 17.03d0)
(SYNONYMS "NH3") )
((GIBBS-0 -8.6d0 CITATIONS "GibbsGroups97")))
(AMMONIUM NIL (
(OCELOT-GFP::PARENTS |Cations|)
(COFACTORS-OF PPPGPPHYDRO-ENZRXN ENZRXN0-4921)
(ACTIVATORS-ALLOSTERIC-OF CARBPSYN-ENZRXN)
(ACTIVATORS-UNKMECH-OF UDPNACETYLMURAMATEDEHYDROG-ENZRXN GUANYL-KIN-ENZRXN
ENZRXN0-5101 TRYPTOPHAN-ENZRXN THIKIN-ENZRXN MALIC-NADP-ENZRXN
IMP-DEHYDROG-ENZRXN GLYCDEH-ENZRXN)
(INHIBITORS-UNKMECH-OF ASP-SEMIALDEHYDE-DEHYDROGENASE-ENZRXN DTMPKI-ENZRXN)
(DBLINKS (LIGAND-CPD "C01342" NIL |kr| 3346617701 NIL NIL) (CAS "14798-03-9"))
(:CREATION-DATE 3074889411)
(GIBBS-0 -18.1d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-3921 NIRBD-RXN)
(MOLECULAR-WEIGHT 18.038d0)
(CHEMICAL-FORMULA (H 4) (N 1))
(DISPLAY-COORDS-2D (0.99399d0 -0.003d0) (-0.003d0 -1.0d0) (-0.003d0 -0.003d0)
(-1.0d0 -0.003d0) (-0.003d0 0.99399d0))
(STRUCTURE-BONDS (5 3 1) (4 3 1) (3 1 1) (3 2 1))
(STRUCTURE-ATOMS H H N H H)
(COMMON-NAME "NH4+")
(CHARGE 1)
(SYNONYMS "ammonium")
(ATOM-CHARGES (3 1)) )
((GIBBS-0 -18.1d0 CITATIONS "GibbsGroups97")))
(AMP NIL (
(OCELOT-GFP::PARENTS |Ribonucleoside-Monophosphates| |Purine-Related|)
(ACTIVATORS-ALLOSTERIC-OF PEPDEPHOSII-ENZRXN THREDEHYDCAT-ENZRXN)
(INHIBITORS-ALLOSTERIC-OF GLUC1PADENYLTRANS-ENZRXN PRPPAMIDOTRANS-ENZRXN)
(INHIBITORS-NONCOMPETITIVE-OF F16BDEPHOS-ENZRXN FMNREDUCT-ENZRXN
THI-P-KIN-ENZRXN)
(INHIBITORS-UNKMECH-OF GLUTAMINESYN-ENZRXN PEPSYNTH-ENZRXN GUANYL-KIN-ENZRXN
ACETALD-DEHYDROG-ENZRXN ENZRXN0-5803 ICITDEHKINASE-ENZRXN RIB5PISOMA-ENZRXN)
(ACTIVATORS-UNKMECH-OF GLUTAMINB-ENZRXN GLYCOPHOSPHORYL-ENZRXN
ICITDEHDEPHOSPH-ENZRXN 6PFRUCTPHOS-ENZRXN CDPDIGLYSYN-ENZRXN
PYRUVATEDECARB-ENZRXN)
(INHIBITORS-COMPETITIVE-OF MALOX-ENZRXN ADENYLOSUCCINATE-SYNTHASE-ENZRXN
ATPPHOSPHORIBOSYLTRANS-ENZRXN GLUTATHIONE-SYN-ENZRXN ACETALD-DEHYDROG-ENZRXN
CDPDIGLYPYPHOSPHA-ENZRXN MANNPDEHYDROG-ENZRXN FMNREDUCT-ENZRXN
ADENPRIBOSYLTRAN-ENZRXN PRPPAMIDOTRANS-ENZRXN ENZRXN0-253 ASNSYNA-ENZRXN)
(DBLINKS (LIGAND-CPD "C00020" NIL |kr| 3346617700 NIL NIL) (CAS "61-19-8")
(NCI "20264"))
(:CREATION-DATE 3056125303)
(GIBBS-0 -50.2d0)
(APPEARS-IN-LEFT-SIDE-OF AMP-NUCLEOSID-RXN ADENYL-KIN-RXN
ADENPRIBOSYLTRAN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF THIFIS-RXN RXN0-5098 ADPSUGPPHOSPHAT-RXN CITC-RXN
RXN0-5038 RXN0-4401 RXN-5741 RXN0-2161 ENTG-RXN ASNSYNA-RXN ASNSYNB-RXN
RXN0-1961 RXN0-1139 RXN0-1140 RXN0-1141 4-COUMARATE--COA-LIGASE-RXN
RXN0-2023 RXN0-1441 RXN0-948 BIOTINLIG-RXN PHENYLACETATE--COA-LIGASE-RXN
2.7.9.3-RXN ENTMULTI-RXN PROPIONATE--COA-LIGASE-RXN
|RNA-3'-PHOSPHATE-CYCLASE-RXN| NADPYROPHOSPHAT-RXN GDPPYPHOSKIN-RXN
ACYLACPSYNTH-RXN GTPPYPHOSKIN-RXN GLURS-RXN PRPPSYN-RXN AMPSYN-RXN
H2PTERIDINEPYROPHOSPHOKIN-RXN PEPSYNTH-RXN O-SUCCINYLBENZOATE-COA-LIG-RXN
ACETATE--COA-LIGASE-RXN ACYLCOASYN-RXN VALINE--TRNA-LIGASE-RXN
TRYPTOPHAN--TRNA-LIGASE-RXN THREONINE--TRNA-LIGASE-RXN
CYSTEINE--TRNA-LIGASE-RXN GLYCINE--TRNA-LIGASE-RXN ARGININE--TRNA-LIGASE-RXN
ISOLEUCINE--TRNA-LIGASE-RXN PROLINE--TRNA-LIGASE-RXN
TYROSINE--TRNA-LIGASE-RXN HISTIDINE--TRNA-LIGASE-RXN SERINE--TRNA-LIGASE-RXN
ALANINE--TRNA-LIGASE-RXN ASPARTATE--TRNA-LIGASE-RXN
GLUTAMINE--TRNA-LIGASE-RXN LYSINE--TRNA-LIGASE-RXN
ASPARAGINE--TRNA-LIGASE-RXN LEUCINE--TRNA-LIGASE-RXN
METHIONINE--TRNA-LIGASE-RXN PHENYLALANINE--TRNA-LIGASE-RXN
|DNA-LIGASE-(NAD(+))-RXN| PANTOATE-BETA-ALANINE-LIG-RXN GMP-SYN-NH3-RXN
ARGSUCCINSYN-RXN NAD-SYNTH-NH3-RXN NAD-SYNTH-GLN-RXN GMP-SYN-GLUT-RXN)
(SYNONYMS "adenosine-5'-phosphate" "adenosine-phosphate" "5'-AMP"
"adenosine-monophosphate" "adenylic acid" "AMP" "adenosine 5'-monophosphate"
"adenylate" "5'-adenylic acid" "5'-adenosine monophosphate"
"adenosine 5'-phosphate")
(CHARGE -2)
(COMMON-NAME "AMP")
(STRUCTURE-ATOMS O O O C C N N O O O C C C C C C C C N N P N O)
(STRUCTURE-BONDS (17 23 1 :DOWN) (22 12 1) (1 21 2) (16 2 1 :DOWN) (3 21 1)
(6 4 :AROMATIC) (4 20 :AROMATIC) (5 8 1) (15 5 1 :UP) (13 6 :AROMATIC)
(11 7 :AROMATIC) (7 14 :AROMATIC) (8 21 1) (9 15 1) (9 18 1) (10 21 1)
(19 11 :AROMATIC) (13 12 :AROMATIC) (12 19 :AROMATIC) (14 13 :AROMATIC)
(20 14 :AROMATIC) (15 16 1) (16 17 1) (17 18 1) (18 20 1 :UP))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (4.4916d0 -2.4844d0) (7.2769d0 -4.3761d0)
(7.9875d0 -5.6161d0) (8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0)
(7.5247d0 -2.7725d0) (7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0)
(8.8524d0 -2.7725d0) (7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0)
(5.3121d0 -2.4844d0) (7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0))
(CHEMICAL-FORMULA (C 10) (H 14) (N 5) (O 7) (P 1))
(MOLECULAR-WEIGHT 347.224d0)
(AROMATIC-RINGS (4 6 13 14 20) (7 11 19 12 13 14)) )
((GIBBS-0 -50.2d0 CITATIONS "GibbsGroups97")))
(AMP-GROUP NIL (
(OCELOT-GFP::PARENTS |Coenzyme-Groups|)
(MOLECULAR-WEIGHT 347.224d0)
(CHEMICAL-FORMULA (C 10) (H 14) (N 5) (O 7) (P 1))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (4.4916d0 -2.4844d0) (7.2769d0 -4.3761d0)
(7.9875d0 -5.6161d0) (8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0)
(7.5247d0 -2.7725d0) (7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0)
(8.8524d0 -2.7725d0) (7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0)
(5.3121d0 -2.4844d0) (7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0))
(STRUCTURE-BONDS (17 23 1 :DOWN) (22 12 1) (1 21 2) (16 2 1 :DOWN) (3 21 1)
(6 4 :AROMATIC) (4 20 :AROMATIC) (5 8 1) (15 5 1 :UP) (13 6 :AROMATIC)
(11 7 :AROMATIC) (7 14 :AROMATIC) (8 21 1) (9 15 1) (9 18 1) (10 21 1)
(19 11 :AROMATIC) (13 12 :AROMATIC) (12 19 :AROMATIC) (14 13 :AROMATIC)
(20 14 :AROMATIC) (15 16 1) (16 17 1) (17 18 1) (18 20 1 :UP))
(STRUCTURE-ATOMS O O O C C N N O O O C C C C C C C C N N P N O)
(AROMATIC-RINGS (4 6 13 14 20) (7 11 19 12 13 14))
(:CREATOR |kr|)
(COMMON-NAME "AMP group")
(:CREATION-DATE 3084128989) )
NIL)
(AMP-LYSINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "AMP-lysine")
(:CREATOR |keseler|)
(:CREATION-DATE 3329656689) )
NIL)
(AMP-MOR NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "AMP-Mor")
(:CREATOR |keseler|)
(:CREATION-DATE 3329656763) )
NIL)
(AMP-NH2 NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "AMP-NH2")
(:CREATOR |keseler|)
(:CREATION-DATE 3329656734) )
NIL)
(AMP-NUCLEOSID-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(MOLECULAR-WEIGHT-EXP 280)
(CATALYZES AMP-NUCLEOSID-ENZRXN)
(COMPONENTS AMP-NUCLEOSID-MONOMER)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/amn.template")
(:CREATION-DATE 3010350952)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 280 CITATIONS "81046949")
(COMPONENTS :FACET COMMENT "The active enzyme has a polymeric
structure with 4 to 6 subunits. There is some evidence for the
formation of higher polymers which also have catalytic activity.
|CITS: [81046949]|")
(COMPONENTS AMP-NUCLEOSID-MONOMER COEFFICIENT 6)))
(AMP-NUCLEOSID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION AMP-NUCLEOSID-RXN)
(INHIBITORS-ALLOSTERIC |Pi|)
(INHIBITORS-COMPETITIVE "formycin 5'-PO4")
(ACTIVATORS-ALLOSTERIC "MgATP")
(ENZYME AMP-NUCLEOSID-CPLX)
(SYNONYMS "AMP phosphoribohydrolase" "adenosine monophosphate nucleosidase")
(COMMON-NAME "AMP nucleosidase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/amn.template")
(:CREATION-DATE 3010350952)
(:CREATOR |mriley|) )
((ACTIVATORS-ALLOSTERIC "MgATP" CITATIONS "[79009981]" "[81046949]")
(INHIBITORS-ALLOSTERIC |Pi| COMMENT "phosphate inhibition is
competitve with MgATP |CITS: [79009981] [81046949]|")
(INHIBITORS-COMPETITIVE "formycin 5'-PO4" COMMENT "competitive with
respect to AMP |CITS: [81046949]|")))
(AMP-NUCLEOSID-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"AMP nucleosidase is the primary intracellular mechanism for AMP degradation in E. coli. The adenine which
is produced in the nucleosidase reaction can be reincorporated into the purine pool |CITS: [81046949] [90105402]|.
An amp mutant carrying a small deletion has been studied |CITS: [8473316]|.
Expression of amp is induced under limiting phosphate conditions |CITS: [2690948]|.
Crystal structures of AMP nucleosidase in the unliganded form and in complex with formycin 5'-monophosphate or
inorganic phosphate have been determined |CITS: [2670945][15296732]|. The enzyme is a homohexamer
|CITS: [2670945][15296732]|, and each monomer consists of a catalytic and a proposed regulatory domain. The
catalytic domain resembles nucleoside phosphorylases |CITS: [15296732][7920254]|.")
(MOLECULAR-WEIGHT-EXP 54)
(SYNONYMS "B1982" "Amn")
(DBLINKS (MODBASE "P0AE12" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0AE12" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01048" IN-FAMILY |pkarp| 3346700348 NIL NIL)
(UNIPROT "P0AE12" NIL |pkarp| 3343984410 NIL NIL)
(PDB "1T8Y" NIL |keseler| 3329761495 NIL NIL)
(PDB "1T8W" NIL |keseler| 3329761495 NIL NIL)
(PDB "1T8S" NIL |keseler| 3329761462 NIL NIL)
(PDB "1T8R" NIL |keseler| 3329761462 NIL NIL)
(REFSEQ "NP_416489" NIL NIL NIL NIL NIL))
(COMMON-NAME "Amn")
(COMPONENT-OF AMP-NUCLEOSID-CPLX)
(PI 6.56d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 53.99485299999985d0)
(GENE EG10039)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/amn.template")
(:CREATION-DATE 3010350952)
(:CREATOR |mriley|) )
((MOLECULAR-WEIGHT-EXP 54 CITATIONS "81046949")))
(AMP-NUCLEOSID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY SALVADEHYPOX-PWY)
(ENZYMATIC-REACTION AMP-NUCLEOSID-ENZRXN)
(RIGHT RIBOSE-5P ADENINE)
(LEFT WATER AMP)
(EC-NUMBER "3.2.2.4")
(COMMENT "This reaction regulates AMP concentrations through the
hydrolysis of the N-glycosidic bond of AMP.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/nucleomet/amn.template")
(:CREATION-DATE 3010350952)
(:CREATOR |mriley|) )
NIL)
(AMPG-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 53.24510799999986d0)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(:CREATION-DATE 3060042779)
(COMMENT
"AmpG is a member of the major facilitator superfamily of transporters,
and together with AmpD, is essential for induction of the AmpC Β-lactamase
and is involved in the recycling of cell wall peptides
|CITS: [90120556] [94049112] [95291453] [96100441]|.
Mutants in ampG are unable to induce ampC and display greatly
increased cell wall turnover |CITS: [95009971]|.
AmpG is responsible for the transport of precursors of the anhMurNAc tripeptide into the cytoplasm
|CITS:[8878601]|. These precursors are the products of peptidoglycan degradation and include the
disaccharide GlcNAc-anhMurNAc as well as GlcNAc-anhMurNAc-oligopeptides (tri-, tetra-, and
pentapeptides). Transport is dependent on the proton motive force |CITS:[12426329]|.
Following uptake of these muropeptides, they are degraded, releasing the components which can
subsequently be used in cell wall synthesis |CITS: [95302966]|.
Experiments with β-lactamase fusions show AmpG contains two large cytoplasmic loops and 10
transmembrane segments |CITS:[15728916]|.
Cytosolic muramyl peptides probably induce expression of ampC by binding
to its regulator AmpR |CITS: [97302495]|.")
(SYNONYMS "B0433" "AmpG")
(DBLINKS (MODBASE "P0AE16" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(UNIPROT "P0AE16" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_414967" NIL NIL NIL NIL NIL))
(GENE EG12183)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AmpG muropeptide MFS transporter") )
NIL)
(AMPSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(REACTION-DIRECTION REVERSIBLE)
(SYNONYMS "adenylosuccinase" "asl")
(COMMON-NAME "adenylosuccinate lyase")
(REACTION AMPSYN-RXN)
(CITATIONS ":EV-EXP:3277835749:pkarp" "[92104952]")
(COMMENT
"Adenylosuccinate lyase (ASL), the product of the gene purB in E. coli,
catalyzes two reactions in de novo purine nucleotide biosynthesis. In
addition to catalyzing step 8 in the pathway to IMP, conversion of
phosphoribosylsuccinocarboxamideaminoimidazole to
phosphoribosylaminoimidazole carboxamide, the enzyme (ASL) also converts
adenylosuccinate to AMP. Very little work has been done on this
enzyme in E. coli. |CITS:[92104952]|")
(ENZYME ASL-MONOMER)
(:CREATION-DATE 2959814156)
(:CREATOR |mriley|) )
NIL)
(AMPSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DENOVOPURINE2-PWY)
(ENZYMATIC-REACTION AMPSYN-ENZRXN)
(RIGHT FUM AMP)
(LEFT ADENYLOSUCC)
(EC-NUMBER "4.3.2.2")
(COMMENT "The final step in the de novo
biosynthesis of purines, the second of the
two step sequence from IMP to AMP.")
(:CREATION-DATE 2959814156)
(:CREATOR |mriley|) )
NIL)
(AMTB-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-63)
(MOLECULAR-WEIGHT-SEQ 44.514614999999935d0)
(:CREATION-DATE 3060112802)
(CITATIONS "[97000355]")
(SPECIES ECOLI)
(COMMENT
"The AmtB transporter is responsible for uptake of either ammonium or
ammonia. Disruption of the amtB gene impairs growth on ammonium
only under acidic growth conditions, and this defect could be complemented
by the cloned amtB gene |CITS: [98284052]|. Whole cell transport
experiments have shown that AmtB mediates transport of the ammonium
analogue, methylammonium and have suggested that transport is dependent
on rapid metabolism of the transported substrate |CITS: [98284052]|.
Whether AmtB mediates transport of ammonium ions or the uncharged species,
ammonia, remains unclear. The energy coupling mechanism is also unclear.
Amt has been proposed to mediate ammonia uniport in an energy independent,
non-concentrative process |CITS: [98284052]|, but homologues of AmtB in other
organisms have been proposed to function as ammonium/proton symporters
|CITS: [96214991]|. AmtB is a member of the Amt family of ammonium/ammonia
transporters.
The amtB forms an operon with the glnK gene, and expression
of this operon occurs under nitrogen-limiting conditions and is
dependent on the NtrC regulatory protein |CITS: [97000355]|.
GlnK and AmtB have been shown to directly interact after ammonium shock.
This reversible sequestration of GlnK by AmtB is rapidly responsive to μM
concentrations of ammonium. The deuridylylated form of GlnK has been shown
to be sequestered by AmtB and to inhibit transport of ammonium by AmtB.
Deletion or mutation of amtB was shown to prevent deuridylylation of GlnK.
The internal glutamine pool, which is increased upon rapid increases in
ammonium availability to nitrogen-limited cells, is responsible for deuridylylation
of GlnK due to its interaction with uridylyltransferase. From these results it has
been suggested that AmtB acts as a sensor of external ammonium concentration
as part of the Ntr system |CITS:[14668330]|.
Imported
ammonia/ammonium is rapidly metabolised to glutamine and glutamate.
The crystal structure has been resolved in two forms at 1.8 and 2.1 A |CITS:[15563598]|. A 12 A resolution projection map of AmtB was determined by cryoelectron microscopy, and
high-resolution topographs were acquired using atomic force microscopy. As determined by
both techniques, AmtB was found to be trimeric in the native cell membrane |CITS:[15568015]|.")
(SYNONYMS "B0451" "YbaG" "AmtB")
(DBLINKS (UNIPROT "P69681" NIL |pkarp| 3354911363)
(PFAM "PF00909" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_414985" NIL NIL NIL NIL NIL))
(CATALYZES TRANS-ENZRXN-149)
(GENE EG11821)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AmtB ammonium Amt transporter") )
NIL)
(AMYLOMALT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CPD-29 ZN+2 CU+2 NI+2 HG+2)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "Amylomaltase recognizes maltotriose and larger
maltodextrins (donors), cleaving off the reducing glucose residue and
transferring the remaining dextrinyl residue onto the nonreducing end
of maltodextrin (acceptors), including maltose and glucose.
Amylomaltase thus produces glucose and longer maltodextrins from
maltotriose, the smallest donor substrate, as well as from longer
linear maltodextrins. |CITS: [93374863]| In the cytoplasm this
synthesis of longer maltodextrins is the major pathway supporting
growth on short malto-oligosaccharides. |CITS: [92011742]|")
(REACTION AMYLOMALT-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/malQ.template")
(ENZYME AMYLOMALT-MONOMER)
(:CREATION-DATE 3028482515)
(COMMON-NAME "amylomaltase")
(SYNONYMS "4-α-glucanotransferase" "disproportionating enzyme"
"D-enzyme" "dextrin glycosyltransferase"
"1,4-α-D-glucan 4-α-D-glycosyltransferase")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE "methyl-alpha-D-glucose" "methyl-beta-D-glucose"
"phenyl-alpha-D-glucose" "phenyl-beta-D-glucose" "beta-methyl maltoside") )
((INHIBITORS-UNKMECH CPD-29 CITATIONS "[WiesmeyerBBA39,427]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[WiesmeyerBBA39,427]")
(INHIBITORS-UNKMECH CU+2 CITATIONS "[WiesmeyerBBA39,427]")
(INHIBITORS-UNKMECH NI+2 CITATIONS "[WiesmeyerBBA39,427]")
(INHIBITORS-UNKMECH HG+2 CITATIONS "[WiesmeyerBBA39,427]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[WiesmeyerBBA39,427]")))
(AMYLOMALT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3416" "MalA" "MalQ")
(DBLINKS (MODBASE "P15977" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02446" IN-FAMILY |pkarp| 3346700400 NIL NIL)
(REFSEQ "NP_417875" NIL NIL NIL NIL NIL)
(UNIPROT "P15977" NIL |pkarp| 3031948485))
(GENE EG10561)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/malQ.template")
(CATALYZES MALTODEG-ENZRXN MALTDEG-ENZRXN AMYLOMALT-ENZRXN)
(:CREATION-DATE 3028482515)
(PI 6.71d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 78.5034069999998d0) )
NIL)
(AMYLOMALT-RXN NIL (
(OCELOT-GFP::PARENTS EC-2.4.1 |Small-Molecule-Reactions|)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(COMMENT
"This reaction synthesizes maltodextrins of longer length. In general the reaction transfers
a segment of a 1,4-α-D-glucan to a new 4-position in an acceptor, which may be glucose or 1,4-α-D-glucan.")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/glycdeg/malQ.template")
(ENZYMATIC-REACTION AMYLOMALT-ENZRXN)
(EC-NUMBER "2.4.1.25")
(:CREATION-DATE 3028482515)
(IN-PATHWAY GLYCOCAT-PWY)
(LEFT MALTOTRIOSE MALTOSE)
(RIGHT MALTOTETRAOSE GLC) )
NIL)
(|an acid| T (
(OCELOT-GFP::PARENTS |All-Carboxy-Acids| |Holder-Class|)
(DISPLAY-COORDS-2D (1.2124d0 -2.1d0) (2.4248d0 0.0d0) (0.0d0 0.0d0)
(1.2124d0 -0.7d0))
(CHEMICAL-FORMULA (C 1) (H 1) (O 2) (R 1))
(STRUCTURE-BONDS (3 4 1) (2 4 1) (1 4 2))
(STRUCTURE-ATOMS O O R C)
(COMMENT
"This special compound collects under one roof a number of synonyms that occur in the ENZYME db v.23.")
(SCHEMA? T)
(SYNONYMS "a carboxylate" "a carboxylic anion" "acid" "RCOOH")
(:CREATION-DATE 3106947099)
(:CREATOR |kr|)
(COMMON-NAME "an acid") )
NIL)
(|an aldehyde| T (
(OCELOT-GFP::PARENTS |an aldehyde or ketone|)
(DISPLAY-COORDS-2D (2.458d0 -0.2485d0) (1.1627d0 -2.1798d0) (0.0d0 0.0d0)
(1.1627d0 -0.7798d0))
(CHEMICAL-FORMULA (C 1) (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (3 4 1) (2 4 2) (1 4 1))
(STRUCTURE-ATOMS H O R C)
(SCHEMA? T)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-280 AMINEOXID-RXN)
(SYNONYMS "aldehyde" "RCHO")
(:CREATION-DATE 3052002273)
(:CREATOR |kr|)
(COMMON-NAME "an aldehyde") )
NIL)
(|an aldehyde or ketone| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(SCHEMA? T)
(APPEARS-IN-RIGHT-SIDE-OF ALCOHOL-DEHYDROG-GENERIC-RXN)
(SYNONYMS "aldehyde or ketone")
(:CREATION-DATE 3051978518)
(:CREATOR |kr|)
(COMMON-NAME "an aldehyde or ketone") )
NIL)
(|an alkane| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "an alkane")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104637) )
NIL)
(ANA-ELECT-TRANS-PWY NIL (
(OCELOT-GFP::PARENTS ANAEROBIC-RESPIRATION)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(PRIMARIES (FAD-RED-RXN (|NAD(P)H|) NIL) (FMN-RED-RXN (|NAD(P)H|) NIL))
(:CREATION-DATE 3063973628)
(SYNONYMS "anaerobic electron transfer")
(COMMENT
"A series of reactions passes electrons derived from oxidation from one electron
carrier to another. The electron carriers are classes of proteins, not
unique proteins. Each class differs in electron potential. A chain passes
from low values to higher, the highest being the capture of electrons by electron
acceptor compounds. Not all possible members of the chain of electron transfer
are used for any one oxidation. Electron carriers often are integral parts of
dehydrogenase enzymes. For example, succinate dehydrogenase subunits contain
iron-sulfur centers, FAD and a cytochrome b. Electron transfer from the
quinones is catalyzed by quinone oxidoreductases and from cytochromes to other
cytochromes. During the chain of electron transfer, protons (H+) are transported
outside the cytoplasmic membrane, generating a proton motive force. Upon passage
of protons back into the cytoplasm, the PMF is captured as ATP, catalyzed by a
multisubunit ATPase.")
(REACTION-LIST CYT-ACC-RXN DMKCYT-RXN MENCYT-RXN DMK-FE-RXN MEN-FE-RXN
FMN-OX-RXN FAD-OX-RXN FAD-RED-RXN FMN-RED-RXN)
(PREDECESSORS (FAD-OX-RXN FAD-RED-RXN) (MEN-FE-RXN FAD-OX-RXN)
(CYT-ACC-RXN MENCYT-RXN) (MENCYT-RXN MEN-FE-RXN)
(CYT-ACC-RXN DMKCYT-RXN) (DMKCYT-RXN DMK-FE-RXN)
(DMK-FE-RXN FMN-OX-RXN) (MEN-FE-RXN FMN-OX-RXN)
(FMN-OX-RXN FMN-RED-RXN))
(COMMON-NAME "electron transfer (anaerobic)") )
NIL)
(ANAEROBIC-RESPIRATION T (
(OCELOT-GFP::PARENTS |Respiration|)
(COMMENT
"This class contains pathways of the various electron flows of anaerobic respiration including, from various compounds donating electron to the electron transport chain, through the chain itself, and to compounds serving as terminal acceptors of electrons from the chain. The passage of electrons through components of the electron-transport chain, which are membrane-bound, generates a trans-membrane ion gradient, which serves as a source of energy. ")
(COMMON-NAME "Anaerobic")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(ANARESP1-PWY NIL (
(OCELOT-GFP::PARENTS ANAEROBIC-RESPIRATION)
(PRIMARIES (R601-RXN NIL (SUC)))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3064091736)
(SYNONYMS "anaerobic respiration")
(COMMENT
"Respiration is an ATP-generating process in which organic compounds act as
electron donors (see anaerobic respiration electron donor list) through a chain
of electron transfer to electron acceptors. Anaerobic respiration uses several
compounds, both organic and inorganic, as acceptors such as fumarate,
nitrate and hydrogen (see anaerobic respiration electron acceptor list). By
contrast, aerobic respiration uses oxygen as the final acceptor.
During the chain of electron transfer, protons (H+) are transported outside the
cytoplasmic membrane, generating a proton motive force. Upon passage of protons
back into the cytoplasm, the PMF energy is captured as ATP, catalyzed by a
multisubunit ATPase.")
(ENZYME-USE (CITSYN-RXN CITSYN-ENZRXN)
(SUCC-FUM-OXRED-A-RXN FUMARATE-REDN-ENZRXN))
(REACTION-LIST R601-RXN FHLMULTI-RXN 2PGADEHYDRAT-RXN PYRUVFORMLY-RXN
FUMHYDR-RXN MALATE-DEH-RXN PEPCARBOX-RXN ISOCITDEH-RXN ACONITATEHYDR-RXN
ACONITATEDEHYDR-RXN CITSYN-RXN PYRUVDEH-RXN PEPDEPHOS-RXN)
(PREDECESSORS (R601-RXN FUMHYDR-RXN) (FHLMULTI-RXN PYRUVFORMLY-RXN)
(MALATE-DEH-RXN PEPCARBOX-RXN) (PEPCARBOX-RXN 2PGADEHYDRAT-RXN)
(PYRUVFORMLY-RXN PEPDEPHOS-RXN) (FUMHYDR-RXN MALATE-DEH-RXN)
(ISOCITDEH-RXN ACONITATEHYDR-RXN)
(ACONITATEHYDR-RXN ACONITATEDEHYDR-RXN)
(ACONITATEDEHYDR-RXN CITSYN-RXN) (CITSYN-RXN PYRUVDEH-RXN)
(PYRUVDEH-RXN PEPDEPHOS-RXN))
(COMMON-NAME "respiration (anaerobic)") )
NIL)
(ANARESPACC-PWY NIL (
(OCELOT-GFP::PARENTS ANAEROBIC-RESPIRATION)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3064091736)
(SYNONYMS "anaerobic respiration -- electron acceptors reaction list")
(PRIMARIES (R601-RXN (FUM) (SUC)) (1.7.7.2-RXN (NITRITE) (AMMONIA))
(1.7.2.3-RXN (TRIMENTHLAMINE-N-O) (TRIMETHYLAMINE))
(NIRBD-RXN (NITRITE) (AMMONIUM)) (RXN0-2081 (NITRATE) (NITRITE))
(SUCC-FUM-OXRED-A-RXN (FUM) (SUC)))
(ENZYME-USE (SUCC-FUM-OXRED-A-RXN FUMARATE-REDN-ENZRXN))
(REACTION-LIST R601-RXN 1.7.2.3-RXN RXN0-2081 NIRBD-RXN 1.7.7.2-RXN
THTOREDUCT-RXN TMAOREDUCT-RXN DIMESULFREDUCT-RXN)
(COMMON-NAME "respiration (anaerobic)-- electron acceptors reaction list") )
NIL)
(ANARESPDON-PWY NIL (
(OCELOT-GFP::PARENTS ANAEROBIC-RESPIRATION)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3064091736)
(SYNONYMS "anaerobic respiration -- electron donors reaction list")
(ENZYME-USE
(FORMATEDEHYDROG-RXN FORMATEDEHYDROGN-ENZRXN FORMATEDEHYDROGO-ENZRXN)
(GLYC3PDEHYDROG-RXN ANGLYC3PDEHYDROG-ENZRXN))
(REACTION-LIST RXN0-4141 NADH-DEHYDROG-A-RXN FORMATEDEHYDROG-RXN
L-LACTDEHYDROGFMN-RXN GLYC3PDEHYDROG-RXN)
(COMMON-NAME "respiration (anaerobic)-- electron donors reaction list") )
NIL)
(ANGLYC3PDEHYDROG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"The GlpABC enzyme is loosely associated with the cell membrane. A functional two subunit form, GlpAC, has been
isolated, and it is assumed that the third subunit (GlpB) is responsible for membrane anchoring.
The GlpA subunit contains noncovalently bound FAD, and the GlpC subunit is thought to bind flavin mononucleotide
|CITS: [3286606]|.
The GlpB subunit contains two iron-sulfur clusters, and does not contain any transmembrane helices, so
the mechanism by which it acts as the membrane anchor for the complex is not clear
|CITS: [3286606][7576488]|.
Please note: reference |CITS: [6363389]| and reference |CITS: [3286606]| utilize different terminologies for the
members of the glpACB operons. The former names the genes A,B,C, while the later names them A,C and B,
respectively. Throughout this discussion we have used the nomenclature of the later.
This three-subunit enzyme converts glycerol-3-phosphate to dihydroxyacetone phosphate (DHAP) using
electron acceptors other than oxygen, and functions mostly under anaerobic conditions.
The anaerobic dehydrogenase protein complex is encoded by the glpACB operon,
and is regulated by glycerol and catabolite repression |CITS: [6363389]|.
The reducing equivalents are passed through a simple electron transport chain which terminates with
fumarate or nitrate as the electron acceptor |CITS:[82007833]|.
Expression of glpABC (along with other members of the glp regulon |CITS: [825019]| is repressed by
GlpR and induced by glycerol-3-phosphate. Optimal intracellular levels of glycerol-3-phosphate are maintained for
biosynthesis of phospholipids. The glpTQ operon, which encodes glycerol-3-phosphate transporter and
phosphodiesterase is adjacent to glpABC. The two operons are divergently transcribed; the operators to
which GlpR binds overlap the ,glpA promoter |CITS: [9179845]|.
")
(SYNONYMS "G3P dehydrogenase"
"sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase")
(SPECIES ECOLI)
(CATALYZES ANGLYC3PDEHYDROG-ENZRXN)
(LOCATIONS)
(COMPONENTS ANGLYC3PDEHYDROGSUBUNITA-MONOMER ANGLYC3PDEHYDROGSUBUNITB-MONOMER
ANGLYC3PDEHYDROGSUBUNITC-MONOMER)
(:CREATION-DATE 2974210982)
(:CREATOR |mriley|) )
((COMPONENTS ANGLYC3PDEHYDROGSUBUNITC-MONOMER COEFFICIENT 1)
(COMPONENTS ANGLYC3PDEHYDROGSUBUNITB-MONOMER COEFFICIENT 1)
(COMPONENTS ANGLYC3PDEHYDROGSUBUNITA-MONOMER COEFFICIENT 1)
(LOCATIONS :FACET COMMENT "loosely bound to the cytoplasmic membrane |CITS:
[SwissProt]|")))
(ANGLYC3PDEHYDROG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH 55-DITHIO-BIS2-NITROBENZOIC-ACID "PCMS")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS FMN)
(SYNONYMS "G3P dehydrogenase"
"sn-glycerol-3-phosphate:(acceptor) 2-oxidoreductase"
"anaerobic glycerol-3-phosphate dehydrogenase")
(COMMON-NAME "glycerol-3-phosphate-dehydrogenase, anaerobic")
(REACTION-DIRECTION REVERSIBLE)
(REACTION GLYC3PDEHYDROG-RXN)
(COFACTOR-BINDING-COMMENT "The FAD is said to be associated with the
glpA subunit and the FMN is said to be associated with the glpB
subunit. |CITS: [SwissProt]|")
(REQUIRED-PROTEIN-COMPLEX)
(ENZYME ANGLYC3PDEHYDROG-CPLX)
(:CREATION-DATE 2974210982)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH 55-DITHIO-BIS2-NITROBENZOIC-ACID CITATIONS "[82007833]")
(INHIBITORS-UNKMECH "PCMS" CITATIONS "[82007833]")))
(ANGLYC3PDEHYDROGSUBUNITA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SPECIES ECOLI)
(GENE EG10391)
(SYNONYMS "B2241" "GlpA")
(COMMON-NAME "GlpA")
(DBLINKS (MODBASE "P0A9C0" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01266" IN-FAMILY |pkarp| 3346700356 NIL NIL)
(UNIPROT "P0A9C0" NIL |pkarp| 3338704367 NIL NIL)
(REFSEQ "NP_416744" NIL NIL NIL NIL NIL))
(COMPONENT-OF ANGLYC3PDEHYDROG-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 58.95817499999982d0)
(:CREATION-DATE 2974210982)
(:CREATOR |mriley|) )
NIL)
(ANGLYC3PDEHYDROGSUBUNITB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SPECIES ECOLI)
(GENE EG10392)
(SYNONYMS "B2242" "GlpB")
(COMMON-NAME "GlpB")
(DBLINKS (PFAM "PF06982" IN-FAMILY |pkarp| 3346700356 NIL NIL)
(REFSEQ "NP_416745" NIL NIL NIL NIL NIL) (UNIPROT "P13033"))
(COMPONENT-OF ANGLYC3PDEHYDROG-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 45.357182999999914d0)
(:CREATION-DATE 2974210982)
(:CREATOR |mriley|) )
NIL)
(ANGLYC3PDEHYDROGSUBUNITC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SPECIES ECOLI)
(GENE EG10393)
(SYNONYMS "B2243" "GlpC")
(COMMON-NAME "GlpC")
(DBLINKS (MODBASE "P0A996" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00037" IN-FAMILY |pkarp| 3346700356 NIL NIL)
(UNIPROT "P0A996" NIL |pkarp| 3338704367 NIL NIL)
(REFSEQ "NP_416746" NIL NIL NIL NIL NIL))
(COMPONENT-OF ANGLYC3PDEHYDROG-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 44.10798999999994d0)
(:CREATION-DATE 2974210982)
(:CREATOR |mriley|) )
NIL)
(|Anions| T (
(OCELOT-GFP::PARENTS |Ions|)
(COMMON-NAME "an anion")
(SCHEMA? T) )
NIL)
(ANSA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPARAGHYDA-ENZRXN)
(CITATIONS "[86168005]" "[89357501]")
(LOCATIONS CCO-CYTOPLASM)
(COMPONENTS ANSA-MONOMER)
(COMMENT "Coli synthesizes two L-asparaginases, I and II, which are
distinct in a number of ways. First, asparaginase I is located in the
cytoplasm, whereas asparaginase II is secreted. Asparaginase II in
contrast to asparaginase I is dramatically regulated by oxygen; under
anaerobic conditions the levels of asparaginase II are considerably
higher than in aerated cultures. Finally, whereas asparaginase I has a
relativly low affinity for its substrate, asparaginase II has a much
higher affinity, and has found widespread use in the treatment of
childhood acute lymphocytic leukemia. |CITS:[86168005]|")
(:CREATION-DATE 2963847690)
(:CREATOR |mriley|) )
((COMPONENTS ANSA-MONOMER CITATIONS "[89357501]")
(COMPONENTS ANSA-MONOMER COEFFICIENT 2)))
(ANSA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1767" "AnsA")
(COMMON-NAME "AnsA")
(DBLINKS (MODBASE "P0A962" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00710" IN-FAMILY |pkarp| 3346700342 NIL NIL)
(UNIPROT "P0A962" NIL |pkarp| 3338704337 NIL NIL)
(REFSEQ "NP_416281" NIL NIL NIL NIL NIL))
(COMPONENT-OF ANSA-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 37.12719599999997d0)
(GENE EG10045)
(:CREATION-DATE 2963847690)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"Although most of the proteins in coli are of a single
molecular species coded by a single gene, several instances are known
where two or more genes code for enzymes which catalyze the same reaction.
The two asparaginases of coli have markedly
different affinities for asparagine and pH optima.
|CITS: [80182029]| There is a distant sequence similarity between
asparaginases I and II.")))
(ANSB-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPARAGHYDB-ENZRXN)
(CITATIONS "[90170867]" "[90382683]" "[89357501]")
(LOCATIONS CCO-PERI-BAC)
(COMPONENTS ANSB-MONOMER)
(COMMENT
"There are two asparaginase enzymes in E. coli, I and II. The synthesis of L-asparaginase
II in E. coli is subject to regulation by cyclic AMP receptor protein (CRP) and is
also induced by anaerobiosis. The latter form of regulation involves
the fnr gene product , which also activates a number of other
anaerobically regulated genes. |CITS:[90170867]| AnsII has a higher
affinity for substrate than AnsI. In humans, AnsII causes
rapid decline of plasma and cerebrospinal fluid L-asparagine levels
when administered to patients with lymphoblastic leukemia, resulting
in selective toxicity to malignant lymphoblasts, which have a relatively
high nutritional requirement for this amino acid |CITS:[90382683]|.
A signal peptide effects secretion |CITS:[90382683]|.")
(:CREATION-DATE 2963847690)
(:CREATOR |mriley|) )
((COMPONENTS ANSB-MONOMER COEFFICIENT 4)
(LOCATIONS :FACET COMMENT "and secreted")))
(ANSB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2957" "AnsB")
(COMMON-NAME "AnsB")
(DBLINKS (MODBASE "P00805" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00710" IN-FAMILY |pkarp| 3346700381 NIL NIL)
(REFSEQ "NP_417432" NIL NIL NIL NIL NIL) (PDB "4ECA") (PDB "1HO3")
(PDB "3ECA") (UNIPROT "P00805"))
(COMPONENT-OF ANSB-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 36.85065699999994d0)
(GENE EG10046)
(:CREATION-DATE 2963847690)
(:CREATOR |mriley|) )
NIL)
(ANSP-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 54.2329889999998d0)
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700335 NIL NIL)
(REFSEQ "NP_415970" NIL NIL NIL NIL NIL)
(UNIPROT "P77610" NIL |paley| 3169408120))
(CATALYZES TRANS-ENZRXN-216)
(SYNONYMS "B1453" "YncF" "AnsP")
(COMMENT "AnsP is a probable L-asparagine transporter. The equivalent gene to
ansP in Salmonella enterica has been expressed and shown
to confer L-asparagine uptake |CITS: [95202072]|. AnsP is a member of
the APC superfamily of transporters and based on sequence similarity
probably functions as an L-asparagine/proton symporter.")
(COMMON-NAME "AnsP L-asparagine APC Transporter")
(GENE G6764)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160741) )
NIL)
(|Anthocyanidin-3-O-beta-D-glucosides| T (
(OCELOT-GFP::PARENTS |Anthocyanidins|)
(COMMON-NAME "an anthocyanidin-3-O-β-D-glucoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Anthocyanidin-malonyl-beta-D-glucosides| T (
(OCELOT-GFP::PARENTS |Anthocyanidins|)
(COMMON-NAME
"an anthocyanidin-3-O-(6-O-malonyl-β-D-glucoside)")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Anthocyanidins| T (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(AROMATIC-RINGS (11 14 20 12 21 22) (8 16 18 17 9 19) (7 15 22 21 10 13))
(CHEMICAL-FORMULA (C 15) (H 9) (O 5) (R1 2))
(ATOM-CHARGES (12 1))
(STRUCTURE-BONDS (1 13 1) (2 14 1) (3 15 1) (4 18 1) (5 16 1) (6 17 1)
(7 13 :AROMATIC) (15 7 :AROMATIC) (16 8 :AROMATIC) (8 19 :AROMATIC)
(9 17 :AROMATIC) (19 9 :AROMATIC) (13 10 :AROMATIC) (10 21 :AROMATIC)
(14 11 :AROMATIC) (11 22 :AROMATIC) (12 20 :AROMATIC) (21 12 :AROMATIC)
(20 14 :AROMATIC) (22 15 :AROMATIC) (18 16 :AROMATIC) (17 18 :AROMATIC)
(19 20 1) (22 21 :AROMATIC))
(DISPLAY-COORDS-2D (6.4302d0 -2.475d0) (2.1434d0 -0.825d0) (5.0013d0 0.0d0)
(0.0d0 -3.7125d0) (1.429d0 -4.5375d0) (0.0d0 -2.0625d0) (5.7158d0 -1.2375d0)
(2.1434d0 -3.3d0) (1.429d0 -2.0625d0) (5.0013d0 -2.475d0)
(3.5724d0 -0.825d0) (3.5724d0 -2.475d0) (5.7158d0 -2.0625d0)
(2.8579d0 -1.2375d0) (5.0013d0 -0.825d0) (1.429d0 -3.7125d0)
(0.7145d0 -2.475d0) (0.7145d0 -3.3d0) (2.1434d0 -2.475d0)
(2.8579d0 -2.0625d0) (4.2868d0 -2.0625d0) (4.2868d0 -1.2375d0))
(STRUCTURE-ATOMS O O O O R1 R1 C C C C C O C C C C C C C C C C)
(COMMON-NAME "an anthocyanidin")
(:CREATOR |paley|)
(:CREATION-DATE 3355681266) )
NIL)
(|Anthocyanin-3-O-beta-D-glucosides| T (
(OCELOT-GFP::PARENTS |Anthocyanins|)
(COMMON-NAME "an anthocyanin 3'-O-β-D glucoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(ANTHOCYANIN-SYN T (
(OCELOT-GFP::PARENTS FLAVONOID-SYN)
(COMMENT
"This class contains pathways of biosynthesis of anthocyanins, which are water soluble, mostly glucosylated pigments in fruits, leaves and flowers responsible for displaying red to blue colors. Anthocyanins are powerful antioxidants and involved in UV-B protection and inter-species interactions.")
(COMMON-NAME "Anthocyanins")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(|Anthocyanins| T (
(OCELOT-GFP::PARENTS |Flavonoids|)
(COMMON-NAME "an anthocyanin")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(ANTHRANILATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF IGPSYN-ENZRXN)
(DBLINKS (LIGAND-CPD "C00108" NIL |kr| 3346617701 NIL NIL) (CAS "118-92-3"))
(SYNONYMS "anthranilic acid" "2-aminobenzoic acid" "vitamin L1"
"o-aminobenzoic acid" "2-aminobenzoate")
(:CREATION-DATE 3073857204)
(GIBBS-0 -48.7d0)
(APPEARS-IN-RIGHT-SIDE-OF PRTRANS-RXN ANTHRANSYN-RXN)
(COMMON-NAME "anthranilate")
(STRUCTURE-ATOMS C C C N O C C C C O)
(STRUCTURE-BONDS (10 6 1) (9 3 :AROMATIC) (3 8 :AROMATIC) (7 1 :AROMATIC)
(2 7 :AROMATIC) (6 3 1) (5 6 2) (4 9 1) (8 2 :AROMATIC) (1 9 :AROMATIC))
(DISPLAY-COORDS-2D (-0.49254d0 -1.0d0) (-1.0d0 -0.13765d0)
(0.00166d0 -0.14428d0) (0.49917d0 -0.99668d0) (0.49917d0 0.73134d0)
(0.49917d0 0.15423d0) (-1.0d0 -0.71476d0) (-0.49585d0 0.15091d0)
(0.00166d0 -0.70813d0) (0.99668d0 -0.13433d0))
(CHEMICAL-FORMULA (C 7) (H 7) (N 1) (O 2))
(MOLECULAR-WEIGHT 137.138d0)
(AROMATIC-RINGS (7 2 8 3 9 1)) )
((GIBBS-0 -48.7d0 CITATIONS "GibbsGroups97")))
(ANTHRANSYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ANTHRANSYN-ENZRXN)
(CITATIONS "[74173403]" "[81267360]" "[82150258]")
(COMPONENTS ANTHRANSYNCOMPI-MONOMER ANTHRANSYNCOMPII-MONOMER)
(COMMENT
"The native anthranilate synthase enzyme exists as a tetrameric complex of two subunits each of the TrpE (Component I) and TrpD (Component II) proteins |CITS: [5331787] [74173403]|.
The TrpD protein is bifunctional; it also catalyzes the second reaction in the biosynthesis of tryptophan from chorismate |CITS:[81267360]|.
")
(:CREATION-DATE 2945294071)
(:CREATOR |mriley|) )
((COMPONENTS ANTHRANSYNCOMPII-MONOMER COEFFICIENT 2)
(COMPONENTS ANTHRANSYNCOMPI-MONOMER COEFFICIENT 2)))
(ANTHRANSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT TRP)
(INHIBITORS-NONCOMPETITIVE TRP)
(ALTERNATIVE-COFACTORS (MG+2 CO+2 FE+2))
(REACTION-DIRECTION REVERSIBLE)
(COFACTORS MG+2)
(COMMON-NAME "anthranilate synthase")
(SYNONYMS "ASase")
(ALTERNATIVE-SUBSTRATES (GLN AMMONIA))
(REACTION ANTHRANSYN-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[81267360]" "[90024964]"
"[Ito&CoxJbact97-725-69]")
(INHIBITORS-COMPETITIVE TRP)
(COMMENT
"The complex of the TrpE (Component I) and TrpD (Component II) proteins uses either glutamine or NH3 as the
amino donor for the anthranilate synthase reaction. TrpE contains the binding site for chorismate. In the absence of
TrpD it cannot catalyze the formation of anthranilate with glutamine as the nitrogen source. In vitro, purified
TrpE can form anthranilate using ammonia instead of glutamine as the amino donor |CITS: [4886289]|.
Anthranilate synthase activity is subject to feedback inhibition and thus, is responsive to changes in the free
tryptophan concentration |CITS:[81267360]|.")
(ENZYME ANTHRANSYN-CPLX)
(:CREATION-DATE 2945294071)
(:CREATOR |mriley|) )
((INHIBITORS-NONCOMPETITIVE TRP COMMENT
"Noncompetitive with respect to ammonium sulfate concentration")
(COFACTORS MG+2 CITATIONS "[69130186]")
(INHIBITORS-COMPETITIVE TRP COMMENT
"Competitive with respect to chorismate|CITS:[Ito&CoxJBact97-725-69]|")))
(ANTHRANSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY TRPSYN-PWY)
(ENZYMATIC-REACTION ANTHRANSYN-ENZRXN)
(RIGHT ANTHRANILATE PYRUVATE GLT)
(LEFT CHORISMATE GLN)
(EC-NUMBER "4.1.3.27")
(COMMON-NAME "anthranilate synthesis")
(:CREATION-DATE 2945294071)
(:CREATOR |mriley|) )
NIL)
(ANTHRANSYNCOMPI-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(LOCATIONS CCO-CYTOPLASM)
(DBLINKS (MODBASE "P00895" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00895" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF04715" IN-FAMILY |pkarp| 3346700331 NIL NIL)
(REFSEQ "NP_415780" NIL NIL NIL NIL NIL) (UNIPROT "P00895"))
(COMPONENT-OF ANTHRANSYN-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY)
(PI 5.57d0)
(MOLECULAR-WEIGHT-SEQ 57.4943869999998d0)
(GENE EG11028)
(CITATIONS "[74173403]" "[84239604]" "[81267360]")
(COMMENT
"The TrpE protein is also called Component I of the anthranilate synthase enzyme complex. In vitro in the
absence of the TrpD (Component II) protein, TrpE can use ammonia as the amino donor for the synthesis of
anthranilate from chorismate at approximately 20% efficiency |CITS: [4886289]|. As a component of the anthranilate
synthase complex, TrpD (Component II) provides the glutamine amidotransferase function that allows glutamine to
serve as the amino donor in anthranilate formation.
The TrpE subunit contains the tryptophan binding site for feedback inhibition |CITS:[90024964]|. Both the TrpE and
TrpA polypeptides in the trp operon lack tryptophan residues |CITS:[7021857][81267360]|.")
(SYNONYMS "B1264" "TryD" "TrpE" "α subunit")
(COMMON-NAME "anthranilate synthase component I")
(:CREATION-DATE 2945294071)
(:CREATOR |mriley|) )
((GENE EG11028 COMMENT
"Expression of trpE (Component I of the complex) and trpD (Component II) is co-ordinately regulated at both the transcriptional and
translational levels. Transcriptional co-ordination is achieved by the polycistronic nature of trp messenger RNA: expression is regulated by
the intracellular concentrations of both free tryptophan (via repression) and tryptophanyl-transfer RNA (via attenuation).
Translational co-ordination is mediated through the specialized intercistronic sequence found between trpE and trpD: in the absence of
translation of the distal portion of trpE mRNA, trpD mRNA translation is markedly reduced|CITS:[81267360]|.")
(ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"It has been proposed that pabB and trpE, although not isozymes, arose from a common ancestor and hence that there is a common ancestry of genes encoding
p-aminobenzoate synthetase and anthranilate synthetase|CITS:[84239604]|")))
(ANTHRANSYNCOMPII NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES PRTRANS-ENZRXN)
(CITATIONS "[74173403]" "[82216842]")
(COMPONENTS ANTHRANSYNCOMPII-MONOMER)
(COMMENT "Component II of anthranilate synthase also provides PRTase
activity. The amino terminal 1/3 provides the glutamine amidotransferase
function. The carboxyl terminal 2/3 of the polypeptide carries out
the PRTase reaction |CITS:[74173403]| Anthranilate synthase is a
tetramer composed of 2 component I polypeptides and 2 component II polypeptides. In E. coli
component II is larger and its C-terminal 2/3 has the 2.4.2.18
activity |CITS:[82216842]|.")
(:CREATION-DATE 2945294047) )
((COMPONENTS ANTHRANSYNCOMPII-MONOMER COEFFICIENT 2)))
(ANTHRANSYNCOMPII-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1263" "TrpD" "TrpGD")
(DBLINKS (MODBASE "P00904" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00904" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00117" IN-FAMILY |pkarp| 3346700331 NIL NIL)
(REFSEQ "NP_415779" NIL NIL NIL NIL NIL) (UNIPROT "P00904"))
(COMPONENT-OF ANTHRANSYN-CPLX ANTHRANSYNCOMPII)
(PI 6.47d0)
(MOLECULAR-WEIGHT-SEQ 56.86987799999981d0)
(GENE EG11027)
(CITATIONS "[84239604]" "[74173403]" "[84183611]" "[81267360]" "[82216842]")
(COMMENT
"The trpD gene encodes a bifunctional protein that participates in both of the two first steps of tryptophan biosynthesis
from chorismate: it contains a glutamine amidotransferase (GATase) activity which, along with the TrpE protein, forms
the anthranilate synthase complex that catalyzes the first step of the pathway, and an anthranilate phosphoribosyl
transferase (PRTase) activity which catalyzes the second step. The two activities are encoded as separate
polypeptides (TrpD and TrpG) in other organisms |CITS:[84183611]|; in them, the gene encoding GATase is
designated trpD and the one encoding anthranilate PRTase is designated trpG. For this reason, the domain of the
E. coli TrpD protein with anthranilate PRTase activity is sometimes termed the TrpG domain.
The TrpD protein is also called Component II of the anthranilate synthase enzyme complex, where its TrpD domain
provides the glutamine amidotransferase function that allows glutamine to serve as the amino donor in anthranilate
formation, channelling the nitrogen from glutamine to the active site of the anthranilate synthase enzyme complex.
|CITS: [ColiSalII]|
The TrpG domain of the TrpD protein catalyzes the second step in the tryptophan biosynthesis pathway, converting
anthranilate + PRPP to phosphoribosylanthranilate |CITS:[82150258]|. This activity can be carried out by the purified
TrpD protein and is thus independent of TrpE, the second component of the anthranilate synthase complex.
Genetic and biochemical studies have shown that the glutamine amidotransferase function resides in the
amino-terminal third of the TrpD protein. The carboxyl-terminal two thirds of the polypeptide is sufficient to perform
the phosphoribosyltransferase reaction, since deletion mutants lacking the first 1/3 of the trpD gene retain
phosphoribosyltransferase activity |CITS:[368647]|.
The protein is unusual in having only one tryptophan residue. This should be advantageous, since translation of
message coding for an enzyme required for tryptophan biosynthesis would be impeded in cases of severe tryptophan
starvation if it contained a significant number of tryptophan codons |CITS:[82216842]|.
")
(COMMON-NAME "anthranilate synthase component II")
(:CREATION-DATE 2945294071)
(:CREATOR |mriley|) )
NIL)
(|Antibiotics| T (
(OCELOT-GFP::PARENTS |Secondary-Metabolites|)
(COMMON-NAME "an antibiotic")
(:CREATOR |suzannep|)
(:CREATION-DATE 3129397675) )
NIL)
(ANTICODON NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3199046812)
(:DOCUMENTATION
"The three bases of the tRNA, which make up the anticodon. The direction is 5' to 3' of the tRNA.
This is the reverse and complementary to the sequence of the recognized codons.")
(:CARDINALITY 1)
(:VALUE-TYPE :STRING)
(:DOMAIN |tRNAs|) )
NIL)
(ANTIMONITE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMMON-NAME "antimonite")
(:CREATOR |caspi|)
(:CREATION-DATE 3335032978) )
NIL)
(AP-ENDONUCLEASES T (
(OCELOT-GFP::PARENTS BASE-EXCISION-REPAIR)
(COMMON-NAME "an AP endonuclease")
(:CREATOR |paley|)
(:CREATION-DATE 3314378978) )
NIL)
(APHA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES APHA-ENZRXN)
(COMPONENTS APHA-MONOMER)
(:CREATOR |ptoole|)
(:CREATION-DATE 3145714030) )
((COMPONENTS APHA-MONOMER COEFFICIENT 4)))
(APHA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH ETOH)
(INHIBITORS-UNKMECH EDTA |Nucleosides| |Pi| CA+2)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(PHYSIOLOGICALLY-RELEVANT |Pi| |Nucleosides| CA+2)
(COFACTORS MG+2)
(COMMENT "E. coli contains a periplasmic acid phosphatase/phosphotransferase.
It is capable of dephosphorylating several organic phosphomonoesters,
such as 5'- and 3'-nucleotides, 2'-deoxy-5'-nucleotides, pNPP,
phenyl phosphate, glycerol 2-phosphate, O-phospho-L-amino acids
and phytic acid. There is a marked preference for aryl phosphoesters.
There is also a phosphotransferase activity, with the enzyme catalyzing
the transfer of low-energy phosphate groups from an organic
phosphomonoester donor to organic acceptors carrying free hydroxyl groups.
|CITS: [97164349]|")
(SYNONYMS "class B acid phosphatase/phosphotransferase" "acid phosphatase"
"non-specific acid phosphatase" "NAP" "acid phosphomonoesterase"
"phosphomonoesterase" "glycerophosphatase"
"orthophosphoric-monoester phosphohydrolase (acid optimum)")
(COMMON-NAME "acid phosphatase/phosphotransferase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ACID-PHOSPHATASE-RXN)
(ENZYME APHA-CPLX)
(:CREATOR |ptoole|)
(:CREATION-DATE 3145714090) )
((ACTIVATORS-UNKMECH ETOH CITATIONS "[97164349]")
(INHIBITORS-UNKMECH EDTA CITATIONS "[97164349]")
(INHIBITORS-UNKMECH |Nucleosides| CITATIONS "[97164349]")
(INHIBITORS-UNKMECH |Pi| CITATIONS "[97164349]")
(INHIBITORS-UNKMECH CA+2 CITATIONS "[97164349]")
(COFACTORS MG+2 COMMENT
"A metal cofactor is required for activity. |CITS: [97164349]| ")))
(APHA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT-INTERNAL "3/8/05 keseler removed NapA as synonym")
(COMMENT "AphA is found at high abundance in vivo |CITS: [9298646]|.")
(SYNONYMS "HobH" "B4055" "YjbP" "AphA")
(DBLINKS (MODBASE "P0AE22" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0AE22" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03767" IN-FAMILY |pkarp| 3346700432 NIL NIL)
(PDB "1N9K" NIL |pkarp| 3346695117 NIL NIL)
(UNIPROT "P0AE22" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_418479" NIL NIL NIL NIL NIL))
(COMMON-NAME "AphA")
(COMPONENT-OF APHA-CPLX)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 26.10350799999998d0)
(GENE EG11934)
(:CREATOR |ptoole|)
(:CREATION-DATE 3145713939) )
NIL)
(|apo-ACP| T (
(OCELOT-GFP::PARENTS |All-ACPs|)
(COMMON-NAME "apo-[acyl-carrier protein]")
(APPEARS-IN-RIGHT-SIDE-OF 3.1.4.14-RXN)
(DBLINKS (UNIPROT "P0A6A8" NIL |pkarp| 3354910689))
(APPEARS-IN-LEFT-SIDE-OF HOLO-ACP-SYNTH-RXN)
(SCHEMA? NIL)
(MODIFIED-FORM BETA-KETO-CIS-DELTA5-DODECENOYL-ACP CIS-DELTA5-DODECENOYL-ACP
TRANS-DELTA3-CIS-DELTA5-DODECENOYL-ACP
BETA-HYDROXY-CIS-DELTA5-DODECENOYL-ACP OCTANOYL-ACP LIPOYL-ACP
PALMITOLEOYL-ACP MYRISTOYL-ACP LAUROYL-ACP TRANS-D2-DECENOYL-ACP
CROTONYL-ACP SUCC-ACP MALONYL-ACP CITRYL-ACP CIS-DELTA3-DECENOYL-ACP
|cis-3,4-dehydrodecanoyl-acp| 3-OHMYRISTOYL-ACP ACETYL-ACP BUTYRYL-ACP
ACETOACETYL-S-ACP B-HYDROXYBUTYRYL-S-ACP BETA-HYDROXYDECANOYL-ACP ACP)
(:CREATOR |paley|)
(:CREATION-DATE 3347167210) )
NIL)
(APO-CITRATE-LYASE T (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(APPEARS-IN-LEFT-SIDE-OF 2.7.7.61-RXN)
(COMMON-NAME "an apo-citrate-lyase")
(:CREATOR |caspi|)
(:CREATION-DATE 3309809466) )
NIL)
(APO-ENTB NIL (
(OCELOT-GFP::PARENTS |Ent-B|)
(INHIBITORS-UNKMECH-OF ENTDB-ENZRXN)
(CITATIONS ":EV-EXP:3278872367:pkarp")
(:CREATION-DATE 3102766611)
(APPEARS-IN-LEFT-SIDE-OF ENTDB-RXN)
(COMMENT
"Recent gel filtration data suggest that EntB may be a trimer not a pentamer.
|CITS: [98153148]|")
(COMMON-NAME "apo-EntB")
(COMPONENTS ENTB-MONOMER)
(MODIFIED-FORM ENTB-CPLX) )
((COMPONENTS ENTB-MONOMER COEFFICIENT 5)))
(|Apo-GcvH| T (
(OCELOT-GFP::PARENTS |Gcv-H|)
(APPEARS-IN-LEFT-SIDE-OF RXN0-1138 RXN0-1141)
(DISPLAY-COORDS-2D (-1.0d0 -0.5938d0))
(CHEMICAL-FORMULA (|Apo-GcvH| 1))
(STRUCTURE-ATOMS |Apo-GcvH|)
(COMMON-NAME "an apo-GcvH protein")
(:CREATOR |kr|)
(:CREATION-DATE 3330289276) )
NIL)
(|Apo-Propionyl-CoA-CO2-ligases| T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMON-NAME "apo-[propionyl-CoA:carbon-dioxide ligase (ADP-forming)]")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(APOCAROTENOID-SYN T (
(OCELOT-GFP::PARENTS TETRATERPENOID-SYN)
(COMMON-NAME "Apocarotenoids")
(COMMENT
"Apocarotenoids are a class of natural products derived from the oxidative cleavage of carotenoids (tetraterpenoids). Some apocarotenoids have agronomic value as pigments and flavor/aroma components in a variety of foods.")
(:CREATOR |paley|)
(:CREATION-DATE 3324143236) )
NIL)
(|Apocytochromes-c| T (
(OCELOT-GFP::PARENTS |Cytochromes-c|)
(COMMON-NAME "an apocytochrome c")
(:CREATOR |paley|)
(:CREATION-DATE 3362411292) )
NIL)
(APORNAP-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |shearer|)
(CATALYZES ENZRXN0-6216)
(SPECIES ECOLI)
(COMPONENT-OF RNAPE-CPLX CPLX0-221 CPLX0-222 RNAPS-CPLX RNAP32-CPLX
RNAP54-CPLX RNAP70-CPLX)
(COMMENT
"RNA polymerase carries out DNA-dependent RNA synthesis, transcribing genes
into RNAs. The core polymerase, consisting of two alpha, one beta and one beta'
subunit, binds to one of several sigma factors to form an RNA polymerase
holoenzyme that can then initiate transcription at a target promoter. Following
initiation, the sigma factor is discarded and the core polymerase transcribes RNA in a step
called elongation, which ceases when it reaches a transcription termination site.
Initiation of RNA synthesis requires the RNA polymerase core enzyme, an associated
sigma factor and a promoter site. RNA polymerase moves along the DNA during
its promoter search, stopping to bind initially at one of a number of
possible positions in the -55 to -5
position relative to the transcription start site |CITS: [15469913][7844812][2693737][6285307][3308880][1651395][2192861][6344016]|.
When a -35 sequence is present, the sigma factor makes first contact
contact there |CITS: [9918716]|. Following initial contact, the binding interaction spreads to
the +20 position and involves the sigma, beta and beta' subunits |CITS: [2693737][3898021][1651395][2192861][8284224][2017366][2661827][7045809][7008032][387258]|.
Binding appears to involve contact between RNA polymerase and both helix
faces as the DNA is wrapped around the protein |CITS: [1651395][2192861][2671751][8503010][10079088][10449412]|. Mecsas91
Once binding is complete,
the DNA helix is opened starting at the -12 to -10 positions and proceeding
to around the +2 position |CITS: [3960716][6573669][2722774][450114][8420002][12484772]|.
Several factors modulate the strength of a promoter. Promoter sequence can
affect initiation time and the amount of transcript produced |CITS: [2259628][6098691]|.
Both the sequences of the -10 and -35 sites
and the distance between them play into activity at a given promoter |CITS: [3550697][8479900][2668539][6344016][3882710][6951162][2961367][16088348]|.
The -10 sequence alone
is important for helix unwinding |CITS: [16169843]|. Niedziela-Majka2005
In addition to the sequence near the start site, upstream promoter elements (UPs)
that occur from in the -40 to -60 region are very important for transcription
from some promoters and can stimulate transcription even in the absence of
sigma factors |CITS: [1870123][1651394][8107083][8248780][9922176][9144176]|.
The carboxy-terminus of the alpha subunit binds UPs in the minor groove,
though no conformational change occurs in the UP DNA |CITS: [8087855][8248780][11238372][11571305]|.
Generally, the effectiveness of a UP depends on its similarity to
the consensus UP sequence of alternating A and T tracts and on its
distance from the -35 site |CITS: [9765569][10377392]|.
The two alpha subunits of RNA polymerase bind in tandem to two helix
turns of a typical UP |CITS: [9050843]|. Modifications that alter
UP-promoter spacing by half a turn or one or two full turns abolish
transcription |CITS: [11600705]|. Finally, even for a promoter
without a UP, the simple presence of upstream DNA strongly enhances
transcription initiation |CITS: [15626761]|.
Targeting to a specific promoter depends on the appropriate sigma
factor |CITS: [4882047][4562312]|. For more information, see each
sigma factor holoenzyme complex.
Promoter clearance involves release of the promoter and loss of the sigma
subunit, both usually occuring after 7-12 nucleotides of RNA transcript
have been synthesized |CITS: [2409292][7000759][1593619][2439694][4896016]|.
There may be several abortive
attempts at elongation from a promoter before elongation proceeds |CITS: [6996702][6156091][2482070][6165380][2439694]|.
RNA polymerase can also slip when faced with an
initial AT tract, leading to an extended UA tract in the transcript |CITS: [1316869][7685823]|.
During elongation of the RNA transcript, one strand of DNA
is transcribed without permanent disruption of the double helix |CITS: [13704191]|.
Throughout elongation, about 18 bps
of double helix are unwound, with about 30-40 bps of
total DNA sequence in contact with the polymerase, rather than
the 75 bps or more of contact seen during initiation |CITS: [6286146][2722774][1281887][1593618][387258]|.
DNA continues to be bent
by RNA polymerase during transcription |CITS: [9790843][10471732]|.
Though one study indicates
as few as 3 bp of stable DNA-RNA hybrid may exist during
transcription, most results point to a hybrid of 8-10 bps
being required to keep RNA polymerase attached to substrate DNA |CITS: [9890901][1281887][9843952][9702191]|.
This may serve as a proofreading
mechanism for the polymerase, as a single mismatch forces
it to slide backwards from the point of the mismatch to
regain a stable hybrid |CITS: [9094712]|. Following
this slide, |FRAME: EG10415-MONOMER| and |FRAME: EG11578-MONOMER| induce cleavage near the 3'
end of the transcript to clear the mismatch |CITS: [1384037][8431948]|.
Transcription elongation is enhanced by |FRAME: EG10667-MONOMER|.
Measured elongation rates for individual RNA polymerases and for transcription
in general vary widely, from 0.5-50 nucleotides per second |CITS: [4986890][6223930][7514589][9012661][10741971]|. Mosteller70
rRNA can be synthesized at up to 90 nucleotides per second |CITS: [7514589]|.
At the molecular level, RNA polymerase progresses one bp per nucleotide
added to its transcript, though this movement appears to be by Brownian
ratchet rather than force generated by nucleotide addition itself |CITS: [9794753][16284617]|.
At larger scales, the
heterogeneity of translation rates appears to be due to variation in the
frequency and duration of transcriptional pausing, which can vary for
each polymerase |CITS: [12370445][14604986]|.
Notably, although many in vitro measurements of polymerase rate are done
with single molecules, when multiple polymerases are transcribing
the same DNA, the trailing proteins push the leader through pauses and
blocks, increasing the overall transcription rate |CITS: [12970184][12730602]|.
Though RNA polymerase generally proceeds as a unit, sometimes it appears
to undergo inchworm motion as it approaches pause and termination points, with
its carboxy-terminus advancing as the amino-terminus remains still |CITS: [8047884][7537637][7736587]|.
RNA polymerase appears to backtrack up to 5 bp at pause
sites, taking from 20 seconds to more than half an hour to restart transcription, though
at least one study suggests that no backtracking occurs |CITS: [9182561][14634670][14622598]|.
Transcriptional pause sites typically
occur shortly after a stretch of sequence that can generate an RNA hairpin once
it is transcribed |CITS: [2821285][9765211]|. Such hairpins may
stall RNA polymerase via electrostatic interaction with part of the polymerase, as well
as via the action of |FRAME: EG10665-MONOMER| |CITS: [8377190][11326100]|.
Transcription termination may depend on |FRAME: CPLX0-2441| or be Rho-independent.
Rho-independent termination appears to depend on a GC-rich stretch of
sequence that yields a stem-loop after transcription, followed by an A-rich
segment on the template strand |CITS: [3078109][1702475][1835546][3301003][6339503][2464590]|.
This A-rich tract may aid release by creating weak hybridization with
the U-tract generated in the transcript |CITS: [6159577]|. Rho-independent
termination has also been identified in the absence of stem-loop
formation |CITS: [10213678]|.
Termination can, in turn, be prevented by such proteins as |FRAME: CPLX0-2861|
and |FRAME: EG10666-MONOMER|, as well as the presence of a boxA element (TGCTCTTTAACA) downstream
from the promoter |CITS: [10200263][1698125][3301003][8430111][2479752][6091902]|.
The RNA polymerase core is assembled via dimerization of its alpha
subunit, followed by addition of beta and then beta' |CITS: [7015808]|.
Extensive examination of the core and holoenzymes via cryo-electron micrscopy
and small-angle X-ray scattering show that the enzyme is structurally flexible
amd undergoes conformational change on interacting with sigma and on binding
DNA |CITS: [2671751][10049799][11904365][11118218][16246367]|.")
(COMPONENTS EG10893-MONOMER RPOC-MONOMER RPOB-MONOMER)
(COMMON-NAME "RNA polymerase, core enzyme")
(:CREATOR |pkarp|)
(:CREATION-DATE 3128363327) )
((CREDITS SRI LAST-CURATED 3360939285)
(CREDITS |shearer| LAST-CURATED 3360939285)
(COMPONENTS RPOC-MONOMER COEFFICIENT 1)
(COMPONENTS EG10893-MONOMER COEFFICIENT 2)
(COMPONENTS RPOB-MONOMER COEFFICIENT 1)))
(APP-UBIOX-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(SYNONYMS "CbdAB" "AppCB")
(CATALYZES APP-UBIOX-ENZRXN)
(LOCATIONS CCO-PM-BAC-NEG)
(COMPONENTS APPC-MONOMER APPB-MONOMER)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/electrontransport/appCB.template")
(:CREATION-DATE 2995813777)
(:CREATOR |mriley|) )
((COMPONENTS APPB-MONOMER COEFFICIENT 1)
(COMPONENTS APPC-MONOMER COEFFICIENT 1)))
(APP-UBIOX-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS "8626304" "9079897" "1658595" "8626304:EV-EXP:3278430571:ingraham")
(COMMON-NAME "cytochrome bd-II terminal oxidase")
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT)
(REACTION CYT-UBIQUINOL-OXID-RXN)
(COMMENT
"Escherichia coli has three terminal oxidases: cytochrome bo encoded by the cyo operon,
cytochrome bd-I encoded by cyd, and cytochrome bd-II. The appC-encoded
subunit of cytochrome bd-II is 60% homologous with CydA and the appB-encoded subunit with CydB
|CITS: [1658595]|. However, under normal conditions of growth, cytochrome bd-II is apparently not expressed
because strains in which cytochrome bo and cytochrome bd-I have been mutationally inactivated are
unable to grow aerobically with succinate as a sole source of carbon and energy. However, if such a strain is
complemented with a chromosomal fragment from Bacillus firmus, cytochrome bd-II is expressed and
the strain can grow in a cytochrome bd-II-dependent manner, aerobically on succinate |CITS: [8626304]|.
The appCB-appA operon is under the control of the transcriptional activator AppY. It is induced upon entry
into the stationary phase, as well as starvation for carbon or phosphate |CITS: [9079897]|. The physiological role of
cytochrome bd-II terminal oxidase in wild-type strains of E. coli is obscure.
")
(ENZYME APP-UBIOX-CPLX)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/electrontransport/appCB.template")
(:CREATION-DATE 2995813777)
(:CREATOR |mriley|) )
NIL)
(APPA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0980" "AppA")
(COMPONENT-OF CPLX-722)
(COMMON-NAME "AppA")
(DBLINKS (MODBASE "P07102" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00328" IN-FAMILY |pkarp| 3346700326 NIL NIL)
(PDB "1DKL" NIL |pkarp| 3346695107 NIL NIL)
(REFSEQ "NP_415500" NIL NIL NIL NIL NIL)
(UNIPROT "P07102" NIL NIL |ouzounis| 3027899498))
(PI 6.67d0)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 47.0567859999999d0)
(GENE EG10049)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/appA.template")
(:CREATION-DATE 3016372603)
(:CREATOR |mriley|) )
NIL)
(APPB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (PFAM "PF02322" IN-FAMILY |pkarp| 3346700326 NIL NIL)
(UNIPROT "P26458" NIL |keseler| 3315846816 NIL NIL)
(ECOCYC "APPB-MONOMER" NIL |keseler| 3315846816 NIL NIL)
(ECOO157CYC "APPB-MONOMER" NIL |keseler| 3315846816 NIL NIL)
(REFSEQ "NP_415498" NIL |keseler| 3315846816 NIL NIL))
(SYNONYMS "B0979" "CyxB" "AppB" "CbdB")
(COMPONENT-OF APP-UBIOX-CPLX)
(PI 8.86d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 42.42377199999992d0)
(GENE EG11379)
(COMMON-NAME "cytochrome bd-II terminal oxidase subunit II")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/electrontransport/appCB.template")
(:CREATION-DATE 2995813777)
(:CREATOR |mriley|) )
NIL)
(APPC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(DBLINKS (PFAM "PF01654" IN-FAMILY |pkarp| 3346700326 NIL NIL)
(UNIPROT "P26459" NIL |keseler| 3315846709 NIL NIL)
(ECOCYC "APPC-MONOMER" NIL |keseler| 3315846709 NIL NIL)
(ECOO157CYC "APPC-MONOMER" NIL |keseler| 3315846709 NIL NIL)
(REFSEQ "NP_415497" NIL |keseler| 3315846709 NIL NIL))
(SYNONYMS "B0978" "CyxA" "CbdA" "AppC")
(COMPONENT-OF APP-UBIOX-CPLX)
(PI 7.28d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 57.91975899999978d0)
(GENE EG11380)
(COMMON-NAME "cytochrome bd-II terminal oxidase subunit I")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/electrontransport/appCB.template")
(:CREATION-DATE 2995813777)
(:CREATOR |mriley|) )
NIL)
(APPEARS-IN-BINDING-REACTIONS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3362338361)
(:DOMAIN |Polymer-Segments| |Chemicals|)
(:VALUE-TYPE |Binding-Reactions|)
(QUERYABLE? T)
(:DOCUMENTATION
"This slot is used to cross-reference a chemical to the one or more binding
reactions in which the chemical is a reactant. Binding reactions only
explicitly list their reactants, but not their products, so there is
no analog of this slot for products of binding reactions.
")
(:INVERSE REACTANTS) )
NIL)
(APPEARS-IN-LEFT-SIDE-OF NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION
"This slot lists all reactions in which this chemical appears in the
left side of the reaction (as a reactant).")
(:INVERSE LEFT)
(:INHERITANCE-TYPE :UNIQUE)
(QUERYABLE? T)
(:DOMAIN |Chemicals|)
(:VALUE-TYPE |Reactions|) )
NIL)
(APPEARS-IN-RIGHT-SIDE-OF NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:INVERSE RIGHT)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION
"This slot lists all reactions in which this chemical appears on
the right side (as a product).
")
(:INHERITANCE-TYPE :UNIQUE)
(QUERYABLE? T)
(:DOMAIN |Chemicals|)
(:VALUE-TYPE |Reactions|) )
NIL)
(APS NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER-2720)
(INHIBITORS-COMPETITIVE-OF ADENYLYLSULFKIN-ENZRXN)
(DBLINKS (LIGAND-CPD "C00224" NIL |keseler| 3342475894 NIL NIL)
(PUBCHEM "10238" NIL |keseler| 3342475894 NIL NIL) (CAS "485-84-7"))
(:CREATION-DATE 3073857204)
(MOLECULAR-WEIGHT 427.282d0)
(CHEMICAL-FORMULA (C 10) (H 14) (N 5) (O 10) (P 1) (S 1))
(DISPLAY-COORDS-2D (7.4515d0 -8.2792d0) (9.7667d0 -8.2792d0) (7.1474d0 0.0d0)
(4.258d0 -4.2914d0) (1.4703d0 -4.2914d0) (0.0d0 -5.7616d0)
(7.9079d0 -9.0396d0) (9.2425d0 -9.0396d0) (4.258d0 -7.2486d0)
(1.4703d0 -7.2486d0) (5.9645d0 -3.7171d0) (10.7467d0 -2.9228d0)
(6.8773d0 -5.7616d0) (5.9645d0 -2.2135d0) (7.2658d0 -4.4098d0)
(9.7156d0 -1.5881d0) (5.576d0 -5.7616d0) (8.6177d0 -6.725d0)
(2.8216d0 -5.7616d0) (7.1474d0 -1.4697d0) (8.4654d0 -2.1624d0)
(8.4654d0 -3.616d0) (7.9079d0 -8.2119d0) (9.2425d0 -8.2119d0)
(9.7667d0 -4.2914d0) (7.4515d0 -7.4004d0) (9.7667d0 -7.4004d0)
(4.258d0 -5.7616d0) (1.4703d0 -5.7616d0))
(STRUCTURE-BONDS (27 25 1 :UP) (24 27 1) (23 26 1) (23 24 1) (22 25 1)
(22 21 :AROMATIC) (21 20 :AROMATIC) (19 29 1) (19 28 1) (18 27 1) (18 26 1)
(17 28 1) (16 21 1) (15 22 :AROMATIC) (20 14 :AROMATIC) (26 13 1 :UP)
(13 17 1) (12 25 1) (12 16 2) (11 15 :AROMATIC) (14 11 :AROMATIC) (10 29 1)
(9 28 1) (24 8 1 :DOWN) (23 7 1 :DOWN) (6 29 2) (5 29 2) (4 28 2) (3 20 1)
(2 27 1) (1 26 1))
(STRUCTURE-ATOMS H H N O O O O O O O C C C N N N O O O C C C C C N C C P S)
(GIBBS-0 -156.3d0)
(APPEARS-IN-LEFT-SIDE-OF RXN-5077 ADENYLYLSULFKIN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF SULFATE-ADENYLYLTRANS-RXN)
(AROMATIC-RINGS (15 11 14 20 21 22))
(COMMON-NAME "APS")
(SYNONYMS "Adenosine 5'-phosphosulfate" "adenylyl-sulfate"
"adenosine phosphosulfate" "adenosine 5'-sulphatophosphate") )
NIL)
(AQPZ-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-53)
(MOLECULAR-WEIGHT-SEQ 23.702763999999977d0)
(:CREATION-DATE 3060112648)
(COMMENT
"AqpZ is a water channel, or aquaporin, that allows bi-directional passive diffusion
of water in E. coli. It is a member of the Major Intrinsic Protein (MIP) family,
which includes channel proteins such as aquaporins and glycerol facilitators. AqpZ
forms a tetramer of four channels |CITS:[14630323]|. Electron microscopic analysis
to a resolution of 8 angstroms of two-dimensional crystals of purified, solubilized
AqpZ shows the protein forms a homotetramer |CITS:[10518953]|. X-ray analysis of
purified AqpZ crystals has also been performed |CITS:[14993693]|. The crystal
structure of the tetrameric AqpZ has been determined to a resolution of 3.2 angstroms
and shows two conformations in the narrowest portion of the channels. One allows
passage of water through the channel, while the other blocks the channel. This allows
for regulation of diffusion of water through the pores |CITS:[16239219]|. AqpZ has an
important role in the osmoregulatory response since it allows E. coli to adapt to
osmotic variations by rapid diffusion of water molecules |CITS:[20392456]|. Water
channel activity has been demonstrated by expression of aqpZ in
Xenopus oocytes, which produced a marked increase in osmotic water
permeability |CITS:[96094287]|. In an aqpZ knockout strain, disruption of
aqpZ is not lethal for the organism, although it greatly reduces the growth
rate and size of the bacterial colonies |CITS:[98188253]|. In response to a
hypoosmotic downshock, a sudden influx of water into the bacterial cells through
AqpZ leads to an increase in intracellular pressure to within the range needed for
growth and survival. Northern analysis confirmed the monocistronic nature of the
aqpZ gene. Regulatory studies performed with an aqpZ-lacZ gene
fusion demonstrated that expression of the gene is dependent upon the extracellular
osmolality |CITS:[98188253]|.")
(SYNONYMS "B0875" "BniP" "AqpZ")
(DBLINKS (MODBASE "P60844" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P60844" NIL |pkarp| 3354911363)
(PFAM "PF00230" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(PDB "1RC2" NIL |keseler| 3314020165 NIL NIL)
(REFSEQ "NP_415396" NIL |keseler| 3314020165 NIL NIL))
(CATALYZES TRANS-ENZRXN-145)
(GENE EG13270)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AqpZ - water MIP channel") )
NIL)
(|Aquificae| T (
(OCELOT-GFP::PARENTS |Bacteria|)
(DBLINKS (NCBI-TAXONOMY-DB 200783))
(:CREATOR |paley|)
(:CREATION-DATE 3341087490) )
NIL)
(ARABCAT-PWY NIL (
(OCELOT-GFP::PARENTS |Sugars-And-Polysaccharides|)
(CREDITS O0-3 AU0-5)
(COMMENT
"Because L-arabinose enters E. coli either by a low-affinity proton-driven transporter (AraE) or a
high-affinity ATP-driven system (AraFGH) its first intracellar form is unphosphorylated. Then an isomerase
and a kinase convert it to L-ribose-5-phosphate, an intermediate of the pentose phosphate pathway.
Curiously, however, an ara-specific gene converts it to a second intermediate of the pathway,
D-xylulose-5-phosphate, which flows through the pathways of central metabolism to satisfy the cell's need
for precursor metabolites, reducing power, and metabolic energy.
Review: Mayer, C. and W. Boos, Hexose/Pentose and Hexitol/Pentitol Metabolism. EcoSal Module 3.4.1 |CITS: [ecosal]|
")
(PATHWAY-LINKS
(L-ARABINOSE (ABC-2-CPLX . :INCOMING) (ARAE-MONOMER . :INCOMING))
(XYLULOSE-5-PHOSPHATE NONOXIPENT-PWY))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(ENZYME-USE (RIBULPEPIM-RXN RIBULPEPIM-ENZRXN))
(SYNONYMS "L-arabinose catabolism")
(REACTION-LIST RXN0-5116 RIBULPEPIM-RXN ARABISOM-RXN)
(PREDECESSORS (RXN0-5116 ARABISOM-RXN) (RIBULPEPIM-RXN RXN0-5116))
(NET-REACTION-EQUATION "L-arabinose + ATP = D-xylulose 5-phosphate + ADP")
(COMMON-NAME "L-arabinose degradation")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/arabcat/arabpwy.template")
(:CREATION-DATE 2988132828)
(:CREATOR |mriley|) )
((CREDITS O0-3 REVISED 3356209337) (CREDITS AU0-5 REVISED 3356209337)))
(ARABINOSE NIL (
(OCELOT-GFP::PARENTS L-ARABINOSE)
(COMPONENT-OF CPLX-172)
(DBLINKS (LIGAND-CPD "C00259" NIL |kaipa| 3311532622 NIL NIL)
(CAS "147-81-9"))
(:CREATION-DATE 3073857204)
(APPEARS-IN-RIGHT-SIDE-OF ABC-2-RXN TRANS-RXN-40 TRANS-RXN-10)
(GIBBS-0 -178.6d0)
(APPEARS-IN-LEFT-SIDE-OF ABC-2-RXN TRANS-RXN-40 RXN0-295 TRANS-RXN-10)
(MOLECULAR-WEIGHT 150.131d0)
(CHEMICAL-FORMULA (C 5) (H 10) (O 5))
(DISPLAY-COORDS-2D (-0.8448d0 -0.676d0) (-0.8603d0 0.1489d0)
(-0.1537d0 0.5747d0) (0.5684d0 0.1757d0) (0.5839d0 -0.6491d0)
(-0.1227d0 -1.075d0) (1.306d0 -1.0481d0) (1.275d0 0.6016d0)
(-0.1692d0 1.3996d0) (-1.5824d0 0.5479d0))
(STRUCTURE-BONDS (1 2 1) (2 3 1) (3 4 1) (4 5 1) (5 6 1) (1 6 1) (5 7 1 :UP)
(8 4 1 :DOWN) (3 9 1 :UP) (2 10 1 :UP))
(STRUCTURE-ATOMS C C C C C O O O O O)
(COMMON-NAME "α-L-arabinose")
(SYNONYMS "arabinose") )
((GIBBS-0 -178.6d0 CITATIONS "GibbsGroups97")))
(ARABINOSE-5P NIL (
(OCELOT-GFP::PARENTS PENTOSE-5-PHOSPHATES)
(INHIBITORS-COMPETITIVE-OF TRANSKETOI-ENZRXN TRANSALDOLB-ENZRXN ENZRXN0-285)
(DBLINKS (LIGAND-CPD "C01112" NIL |kr| 3346617700 NIL NIL) (CAS "13137-52-5"))
(:CREATION-DATE 3073857204)
(MOLECULAR-WEIGHT 230.111d0)
(CHEMICAL-FORMULA (C 5) (H 11) (O 8) (P 1))
(DISPLAY-COORDS-2D (-0.5822454d0 0.59791124d0) (-0.17493469d0 0.59791124d0)
(-0.5822454d0 -0.5874673d0) (0.69712794d0 -0.5874673d0)
(0.28459537d0 -1.0d0) (-0.17493469d0 0.99477816d0)
(0.28459537d0 -0.5874673d0) (0.28459537d0 -0.17493469d0)
(-0.15404701d0 -0.5874673d0) (-0.5822454d0 0.20626628d0)
(-1.0d0 0.20626628d0) (-0.5822454d0 0.99477816d0)
(-0.5822454d0 -0.19060051d0) (-0.9947781d0 -0.19060051d0))
(STRUCTURE-BONDS (14 13 1) (13 3 1) (12 1 1) (11 10 1) (10 13 1) (9 7 1)
(8 7 2) (6 12 2) (5 7 1) (4 7 1) (3 9 1) (2 1 1) (1 10 1))
(STRUCTURE-ATOMS C O C O O O P O O C O C C O)
(APPEARS-IN-LEFT-SIDE-OF KDO-8PSYNTH-RXN DARAB5PISOM-RXN)
(COMMON-NAME "D-arabinose 5-phosphate")
(GIBBS-0 -189.4d0)
(OVERVIEW-NODE-SHAPE :SQUARE)
(SYNONYMS "D-arabinose-5-P" "arabinose-5P" "D-A-5-P" "arabinose 5-phosphate"
"arabinose-5-P")
(SYSTEMATIC-NAME "D-arabinose, 5-(dihydrogen phosphate)") )
NIL)
(|Arabinoses| T (
(OCELOT-GFP::PARENTS |Monosaccharides|)
(COMMON-NAME "D (or L)-arabinose")
(:CREATOR |paley|)
(:CREATION-DATE 3355681262) )
NIL)
(ARABISOM-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT "The subunits are arranged in a stack of two trimers. |CITS:
[78171523]|")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/arabcat2/araA2.template")
(CATALYZES ARABISOM-ENZRXN)
(:CREATION-DATE 3033845994)
(COMPONENTS ARABISOM-MONOMER) )
((COMPONENTS ARABISOM-MONOMER COEFFICIENT 6)))
(ARABISOM-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(COMMENT "The enzyme showed a dependence on Mn++ after
dialysis against EDTA. |CITS: [69004084]|"
"This enzyme was purified from E. coli B/r.")
(REACTION ARABISOM-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/arabcat2/araA2.template")
(ENZYME ARABISOM-CPLX)
(:CREATION-DATE 3033845994)
(COMMON-NAME "L-arabinose isomerase")
(SYNONYMS "L-arabinose ketol-isomerase")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE L-ARABITOL RIBITOL) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "The enzyme has a high substrate
specificity and shows only slight activity toward D-fucose, L-fucose
and D-xylose. |CITS: [69004084]|")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[69004084]")))
(ARABISOM-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMPONENT-OF ARABISOM-CPLX)
(DBLINKS (MODBASE "P08202" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02610" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414604" NIL NIL NIL NIL NIL) (UNIPROT "P08202"))
(PI 6.27d0)
(MOLECULAR-WEIGHT-SEQ 56.07392799999987d0)
(GENE EG10052)
(SYNONYMS "B0062" "AraA" "L-arabinose ketol-isomerase")
(COMMON-NAME "L-arabinose isomerase monomer")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/arabcat/araA.template")
(:CREATION-DATE 2988132822)
(:CREATOR |mriley|) )
NIL)
(ARABISOM-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-5.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ARABISOM-ENZRXN)
(IN-PATHWAY ARABCAT-PWY)
(RIGHT L-RIBULOSE)
(LEFT L-ARABINOSE)
(EC-NUMBER "5.3.1.4")
(COMMENT "The first step of L-arabinose catabolism after it is
transported into the cell.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/arabcat/araA.template")
(:CREATION-DATE 2988132822)
(:CREATOR |mriley|) )
NIL)
(ARAE-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 51.684328999999956d0)
(:CREATION-DATE 3060042779)
(COMMENT "AraE is an arabinose/proton symporter responsible for the uptake
of arabinose. Studies in membrane vesicles have shown that AraE
can transport L-arabinose with low affinity (140-320 μM) and
arabinose transport is coupled with proton transport
|CITS: [82205973]|. The AraE protein has been overproduced and
reconstituted in liposomes as a arabinose/proton symporter
|CITS: [86230078]|. AraE is a member of the major facilitator
superfamily (MFS) of transporters |CITS: [93040298]|.
Arabinose is the sole inducer of araE expression
|CITS: [82205973]|, which is controlled by the AraC regulator.
Imported arabinose is catabolised to xylulose-5-phosphate and
thence via the pentose phosphate pathway.")
(SYNONYMS "B2841" "AraE")
(DBLINKS (MODBASE "P0AE24" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700376 NIL NIL)
(UNIPROT "P0AE24" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_417318" NIL NIL NIL NIL NIL))
(CATALYZES TRANS-ENZRXN-10)
(GENE EG10056)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AraE arabinose MFS transporter") )
NIL)
(ARAF-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-5)
(MOLECULAR-WEIGHT-SEQ 35.54085699999994d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B1901" "AraF")
(DBLINKS (MODBASE "P02924" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00532" IN-FAMILY |pkarp| 3346700346 NIL NIL)
(REFSEQ "NP_416414" NIL NIL NIL NIL NIL) (PDB "9ABP") (PDB "8ABP")
(PDB "7ABP") (PDB "6ABP") (PDB "5ABP") (PDB "1BAP") (PDB "1APB")
(PDB "1ABF") (PDB "1ABE") (UNIPROT "P02924" NIL |pkarp| 3064869797))
(COMPONENT-OF ABC-2-CPLX)
(GENE EG10057)
(LOCATIONS CCO-PERI-BAC)
(COMMON-NAME "AraF") )
NIL)
(ARAG-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-3)
(MOLECULAR-WEIGHT-SEQ 55.01814999999982d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B1900" "AraG")
(DBLINKS (MODBASE "P0AAF3" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00005" IN-FAMILY |pkarp| 3346700345 NIL NIL)
(UNIPROT "P0AAF3" NIL |pkarp| 3343984387 NIL NIL)
(REFSEQ "NP_416413" NIL NIL NIL NIL NIL))
(COMPONENT-OF ABC-2-CPLX)
(GENE EG10058)
(LOCATIONS CCO-CYTOPLASM)
(COMMON-NAME "AraG") )
NIL)
(ARAH-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-4)
(MOLECULAR-WEIGHT-SEQ 34.34204699999993d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B4460" "AraH")
(DBLINKS (PFAM "PF02653" IN-FAMILY |pkarp| 3346700345 NIL NIL)
(UNIPROT "P0AE26" NIL |pkarp| 3343984411 NIL NIL))
(COMPONENT-OF ABC-2-CPLX)
(GENE EG10059)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME
"high-affinity L-arabinose transport protein (ABC superfamily, membrane)") )
NIL)
(ARAJ-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 41.926264999999916d0)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(:CREATION-DATE 3060042779)
(COMMENT "The AraJ protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Expression of araJ is under the control of an arabinose-inducible
promoter controlled by the AraC transcriptional regulator
|CITS: [82242076] [91039313]|. Disruption of araJ does not have an
apparent effect on arabinose uptake or utilisation |CITS: [92078081]|.
AraJ shares sequence similarity with drug efflux proteins of
the MFS, suggesting that it may function as a sugar efflux system.")
(SYNONYMS "B0396" "AraT" "AraJ")
(DBLINKS (MODBASE "P23910" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_414930" NIL NIL NIL NIL NIL)
(UNIPROT "P23910" NIL |pkarp| 3064869797))
(GENE EG10060)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AraJ MFS transporter") )
NIL)
(|Arc-A| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(|Arc-B| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(ARCA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Arc-A|)
(COMMON-NAME "ArcA transcriptional dual regulator")
(:CREATION-DATE 3079199701)
(HISTORY "Merged this frame with PD04423 from Regulon-DB, SMP 4/6/00.")
(DNA-FOOTPRINT-SIZE 61)
(DBLINKS (MODBASE "P0A9Q1" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P0A9Q1" NIL |pkarp| 3338704813 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF ALTARCA-RXN ARCA-RXN)
(PI 5.15702d0 5.4d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 27.291970999999986d0)
(MODIFIED-FORM PHOSPHO-ARCA)
(GENE EG10061)
(CITATIONS "[85157583]" "[95214091]" "[93128858]" "[90206041]" "[93272330]"
"12486057" ":EV-EXP:3278863360:pkarp")
(COMMENT
"This is a dual transcriptional regulator of aerobic respiration control. It functions as a transcriptional repressor for the
sdh, gltA lld, cyoABCDE, and sodA genes. It is an activator for cydAB, pfl, and traY genes in order to sustain
anaerobic growth. It belongs to the two-component (ArcB-ArcA) signal-transduction systems family.
In particular, ArcA works during microaerobic conditions to induce the expression of gene products
that allow the activity of central metabolism enzymes, sensibles to the oxigen lost |CITS: [12486057]|.
A microarray analysis for ArcA of Escherichia coli was done by |CITS: [15838044]|.
")
(SYNONYMS "B4401"
"negative response regulator of genes in aerobic pathways, (sensors, ArcB and CpxA)"
"CpxC" "Dye" "FexA" "Msp" "Seg" "SfrA" "arcB" "ArcA"
"respiration control protein ArcA"
"unphosphorylated respiration control protein ArcA"
"unmodified respiration control protein ArcA" "ArcA control protein"
"dye resistance protein" "aerobic respiration control protein ArcA") )
NIL)
(ARCA-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079199701)
(SPECIES ECOLI)
(CITATIONS "[98352006]" "[98348461]" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(DEPRESSORS
"unphosphorylated receiver module of sensor kinase-phosphotransferase ArcB")
(IN-PATHWAY ARCB-PWY)
(RIGHT PHOSPHO-ARCA ARCB-MONOMER)
(LEFT PHOSPHO-ARCB-HIS ARCA-MONOMER)
(COMMENT
"In this reaction the respiration control protein ArcA is phosphorylated by the
sensor kinase-phosphotransferase ArcB-his292-P protein. This is an alternative
route to ArcA activation."
"The respiration control protein ArcA can be phosphorylated by either the
phospho-ArcB-his292 protein or the phospho-ArcB-his717 protein depending upon
the cytosolic environment. In vitro studies indicated that the
phospho-ArcB-his717 protein was the more active phosphoryl donor. When activated
respiration control protein ArcA acts mainly as a negative regulator of aerobic
gene expression. However it can also function as a positive activator in a few
instances.
|CITS: [97431492] [94043221]
[Hoch&Silhavy] [95045412] [ColiSalII] [92380937] [95158706] [96422482]|") )
NIL)
(ARCB-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS ":EV-EXP:3278872019:pkarp")
(:CREATION-DATE 3079199701)
(COMMON-NAME "ArcB")
(SYNONYMS "aerobic respiration control sensor protein ArcB"
"aerobic respiration control sensor protein" "sensor protein ArcB"
"sensor kinase-phosphotransferase ArcB")
(COMPONENTS ARCB-MONOMER) )
((COMPONENTS ARCB-MONOMER COEFFICIENT 2)))
(ARCB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Arc-B|)
(CITATIONS ":EV-EXP:3309206544:keseler")
(COMMENT
"The ArcB protein is the sensor kinase component of the Arc two-component system which regulates the expression
of many genes in response to respiratory growth conditions |CITS: [14711822]|. D-lactate amplifies the kinase
activity of ArcB in vivo and in vitro |CITS: [15028693]|. Quinone electron carriers inhibit ArcB kinase
activity under aerobic conditions by oxidizing two redox-active cysteine residues that are involved in intermolecular
disulfide bond formation |CITS: [15326287]|.
The solution NMR structure of ArcB has been determined |CITS: [11148031]|, and crystal structures of parts of ArcB
have been solved |CITS: [9054511]|.")
(FEATURES FTR0-52 FTR0-51 FTR0-50)
(:CREATION-DATE 3079199701)
(DBLINKS (MODBASE "P0AEC3" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P0AEC3" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P0AEC3" NIL |pkarp| 3343984412 NIL NIL)
(PDB "2A0B" NIL |keseler| 3309206544 NIL NIL)
(PDB "1BDJ" NIL |keseler| 3309206014 NIL NIL)
(PDB "1A0B" NIL |keseler| 3309206014 NIL NIL)
(PDB "1FR0" NIL |keseler| 3298818287 NIL NIL))
(COMMON-NAME "ArcB sensory histidine kinase")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-312 ALTARCA-RXN ARCA-RXN)
(APPEARS-IN-LEFT-SIDE-OF ARCB-RXN)
(MODIFIED-FORM PHOSPHO-ARCB717 PHOSPHO-ARCB-ASP PHOSPHO-ARCB-HIS)
(PI 5.19d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 87.98277299999975d0)
(GENE EG10062)
(SYNONYMS "B3210" "ArcB" "sensor kinase-phosphotransferase ArcB"
"unphosphorylated sensor kinase-phosphotransferase ArcB"
"unmodified sensor kinase-phosphotransferase ArcB")
(COMPONENT-OF ARCB-CPLX) )
NIL)
(ARCB-PWY NIL (
(OCELOT-GFP::PARENTS |2Comp-Pathways|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3097513706)
(PRIMARIES (ALTARCA-RXN NIL (ARCB-MONOMER)))
(COMMENT "The ArcAB two-component signal transduction system is
involved in sensing certain aerobic and anaerobic growth
conditions. The phosphorylated ArcA protein acts as the
transcriptional repressor for the sdhCDAB operon. ArcA
can receive a phosphoryl group from either ArcB-His292
or ArcB-His717. The His717 transfer occurs primarily under
anoxic conditions and the His292 transfer can function under
fully aerobic conditions.
The SixA phosphatase, by removing the phosphoryl group
from His717, accelerates the derepression of the sdh operon
in response to the presence of anaerobic electron acceptors.
|CITS: [20200300]|")
(SYNONYMS "Arc system")
(COMMON-NAME "ArcAB Two-Component Signal Transduction System")
(LAYOUT-ADVICE (:CYCLE-TOP-CPD ARCB-MONOMER))
(REACTION-LIST RXN0-312 ARCA-RXN ARCB-RXN ARCB717-RXN ARCBTRANS-RXN
ALTARCA-RXN)
(PREDECESSORS (ALTARCA-RXN ARCB717-RXN) (ARCB-RXN ARCA-RXN)
(ARCA-RXN ARCB-RXN) (ARCB-RXN) (ARCB717-RXN ARCBTRANS-RXN)
(ARCBTRANS-RXN ARCB-RXN) (RXN0-312 ARCB717-RXN)) )
NIL)
(ARCB-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079199701)
(SPECIES ECOLI)
(SIGNAL "reduced oxygen")
(CITATIONS "[98352006]" "[98348461]" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(IN-PATHWAY ARCB-PWY)
(RIGHT ADP PHOSPHO-ARCB-HIS)
(LEFT ATP ARCB-MONOMER)
(COMMENT
"In this reaction the sensor kinase-phosphotransferase ArcB is autophosphorylated
on histidine residue H292."
"ArcB is a member of the two-component regulatory system, ArcB/ArcA. It is
unusual in that in addition to the conserved transmitter domain, it also
contains and a receiver and a C-terminal alternative transmitter domain.
Under anoxic or environmentally reducing conditions and in the presence of ATP,
the sensor kinase-phosphotransferase ArcB undergoes autophosphorylation at the
histidine residue H292 of the conserved transmitter domain. The phosphoryl group
is transferred to an aspartate residue, Asp576, in the receiver domain and
then to the alternative transmitter phosphorylation site, histidine H717. This
is achieved through intramolecular phosphorylation. The respiration control
protein ArcA can be phosphorylated by either the phospho-ArcB-his292 protein or
the phospho-ArcB-his717 protein depending upon the cytosolic environment. In
vitro studies indicated that the phospho-ArcB-his717 protein was the more
active phosphoryl donor.
The ArcB/ArcA system anaerobically represses expression of operons encoding
enzymes involved in aerobic metabolism. It is also known to activate several
operons under microaerobic growth conditions. |CITS: [97431492] [94043221]
[Hoch&Silhavy] [95045412] [ColiSalII] [92380937] [95158706] [96422482]|") )
NIL)
(ARCB717-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3087818959)
(SPECIES ECOLI)
(CITATIONS "[98352006]" "[98348461]" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(IN-PATHWAY ARCB-PWY)
(RIGHT PHOSPHO-ARCB717)
(LEFT PHOSPHO-ARCB-ASP)
(COMMENT
"In this reaction sensor kinase-phosphotransferase ArcB undergoes intramolecular
transphosphorylation. The phosphoryl group is transferred from the aspartate
residue to the histidine H717 residue in the C-terminal transmitter domain."
"Sensor kinase-phosphotransferase ArcB is
unusual in that in addition to the conserved transmitter domain, it also
contains and a receiver and a C-terminal alternative transmitter domain.
The phosphoryl group
is transferred from the aspartate residue, Asp576, in the receiver domain
to the alternative transmitter phosphorylation site, histidine H717. This
is achieved through intramolecular phosphorylation. |CITS: [97431492] [94043221]
[Hoch&Silhavy] [95045412] [ColiSalII] [92380937] [95158706] [96422482]|") )
NIL)
(ARCBTRANS-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079199701)
(SPECIES ECOLI)
(CITATIONS "[98348461]" "[98352006]" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(DEPRESSORS D-LACTATE PYRUVATE ACET NADH)
(IN-PATHWAY ARCB-PWY)
(RIGHT PHOSPHO-ARCB-ASP)
(LEFT PHOSPHO-ARCB-HIS)
(COMMENT
"In this reaction the sensor kinase-phosphotransferase ArcB undergoes
intramolecular transphosphorylation. The phosphoryl group is transferred from
the histidine residue H292 to an aspartate residue."
"Sensor kinase-phosphotransferase ArcB is
unusual in that in addition to the conserved transmitter domain, it also
contains and a receiver and a C-terminal alternative transmitter domain.
The autophosphorylation site, histidine residue H292, of the conserved
transmitter domain, transfers the phosphoryl group to the aspartate residue,
Asp576, in the receiver domain. This
is achieved through intramolecular phosphorylation.
|CITS: [97431492] [94043221]
[Hoch&Silhavy] [95045412] [ColiSalII] [92380937] [95158706] [96422482]|") )
((DEPRESSORS :FACET COMMENT
"All of these compounds inhibit the phosphatase activity. |CITS: [94043221]|")))
(ARCD-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 49.50137699999988d0)
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700338 NIL NIL)
(UNIPROT "P0AAE5" NIL |pkarp| 3343984392 NIL NIL)
(REFSEQ "NP_416122" NIL NIL NIL NIL NIL))
(GENE G6861)
(SYNONYMS "B1605" "YdgI" "ArcD")
(COMMENT "ArcD is an uncharacterised member of the APC family of
amino acid transporters. ArcD is highly similar to the
Pseudomonas aeruginosa ArcD arginine/ornithine
antiporter and probably has a similar function.")
(COMMON-NAME "ArcD APC transporter")
(:CREATION-DATE 3144104193) )
NIL)
(|Archaea| T (
(OCELOT-GFP::PARENTS |Organisms|)
(DBLINKS (NCBI-TAXONOMY-DB 2157))
(:CREATOR |paley|)
(:CREATION-DATE 3331579730) )
NIL)
(|Archaeoglobi| T (
(OCELOT-GFP::PARENTS |Archaea|)
(DBLINKS (NCBI-TAXONOMY-DB 183980))
(:CREATOR |paley|)
(:CREATION-DATE 3347159103) )
NIL)
(ARG NIL (
(OCELOT-GFP::PARENTS |L-Amino-Acids| |Positively-charged-polar-amino-acids|)
(COMPONENT-OF CPLX0-228)
(INHIBITORS-COMPETITIVE-OF AGMATIN-ENZRXN)
(INHIBITORS-UNKMECH-OF HOMOSERKIN-ENZRXN N-ACETYLTRANSFER-ENZRXN)
(DBLINKS (LIGAND-CPD "C00062" NIL |kr| 3346617700 NIL NIL) (CAS "74-79-3"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -67.7d0)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2162 ABC-4-RXN ARGSUCCINLYA-RXN)
(APPEARS-IN-LEFT-SIDE-OF RXN0-2162 RXN0-272
ARGININE-N-SUCCINYLTRANSFERASE-RXN ABC-4-RXN ARGDECARBOX-RXN
ARGININE--TRNA-LIGASE-RXN)
(COMMON-NAME "L-arginine")
(DISPLAY-COORDS-2D (6.5399d0 -3.3321d0) (0.0d0 -2.1009d0) (1.2086d0 0.0d0)
(7.9631d0 -0.8697d0) (9.6913d0 -2.1348d0) (8.4827d0 -4.2018d0)
(4.8343d0 -2.1009d0) (3.6258d0 -1.4119d0) (6.0429d0 -1.4119d0)
(2.4172d0 -2.1009d0) (1.2086d0 -1.4119d0) (8.4827d0 -2.8238d0)
(7.2515d0 -2.1009d0))
(STRUCTURE-BONDS (12 13 1) (10 11 1) (9 13 1) (8 10 1) (7 9 1) (7 8 1)
(6 12 1) (5 12 2) (4 13 1) (3 11 1) (2 11 2) (1 13 1))
(STRUCTURE-ATOMS H N N N O O C C C N C C C)
(CHEMICAL-FORMULA (C 6) (H 14) (N 4) (O 2))
(MOLECULAR-WEIGHT 174.202d0)
(PKA1 2.18d0)
(SYNONYMS "2-amino-5-guanidinovaleric acid" "R" "arginine" "arg") )
((GIBBS-0 -67.7d0 CITATIONS "GibbsGroups97")))
(ARG+POLYAMINE-SYN NIL (
(OCELOT-GFP::PARENTS |Super-Pathways|)
(:CREATION-DATE 3067198692)
(COMMON-NAME "superpathway of arginine and polyamine biosynthesis")
(SUB-PATHWAYS POLYAMSYN-PWY ARGSYN-PWY)
(PREDECESSORS POLYAMSYN-PWY ARGSYN-PWY (ARGDECARBOX-RXN ARGSUCCINLYA-RXN))
(REACTION-LIST ARGSYN-PWY POLYAMSYN-PWY) )
NIL)
(|ARG-tRNAs| T (
(OCELOT-GFP::PARENTS |tRNAs|)
(DBLINKS (LIGAND-CPD "C01636" NIL |kr| 3346617700 NIL NIL))
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF ARGININE--TRNA-LIGASE-RXN)
(SYNONYMS "TRNA(ARG)")
(COMMON-NAME "tRNAarg") )
NIL)
(ARGDECARBOX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY-40 ARGDEG-PWY PWY0-823)
(ENZYMATIC-REACTION ARGDECARBOXDEG-ENZRXN ARGDECARBOXBIO-ENZRXN)
(RIGHT CARBON-DIOXIDE AGMATHINE)
(LEFT ARG)
(EC-NUMBER "4.1.1.19")
(COMMENT "This is the first step in the biosynthesis of spermidine
from arginine.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speA.template")
(:CREATION-DATE 3000591045)
(:CREATOR |mriley|) )
NIL)
(ARGDECARBOXBIO-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ARGDECARBOXBIO-ENZRXN)
(COMPONENTS ARGDECARBOXBIO-MONOMER)
(LOCATIONS CCO-PERI-BAC)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speA.template")
(:CREATION-DATE 3000591045)
(:CREATOR |mriley|) )
((COMPONENTS ARGDECARBOXBIO-MONOMER COEFFICIENT 4)))
(ARGDECARBOXBIO-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "antizyme" "alpha-difluoromethylarginine" SPERMIDINE
PUTRESCINE "(E)-alpha-monofluoromethyl-3,4-dehydroarginine"
"alpha-monofluoromethylarginine" "alpha-monofluoromethylagmatine"
"alpha-ethynylagmatine" "alpha-allenylagmatine")
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(COFACTORS MG+2)
(ENZYME ARGDECARBOXBIO-CPLX)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ARGDECARBOX-RXN)
(COFACTOR-BINDING-COMMENT "The enzyme requires both Mg++ and pyridoxal
phosphate for activity. |CITS: [73149256]|")
(COMMENT "E. coli has two pathways by which it can synthesize
putrescine, leading to spermidine production. One pathway uses
ornithine decarboxylase to produce putrescine directly from ornithine.
The second uses biosynthetic arginine decarboxylase, coded for by the
speA gene, to begin a two reaction pathway to putrescine. The second
reaction is carried out by agmatine ureohydrolase, coded for by the
speB gene. This second pathway is necessary as E. coli lacks arginase
and so cannot convert arginine to ornithine. |CITS: [91267922]| In
addition, E. coli contains two forms of arginine decarboxylase, a
biosynthetic and a biodegradative or inducible form. The
biodegradative form is induced under conditions of acidic pH ,
anaerobiosis and rich growth medium. |CITS: [90330576] [93186686]|")
(SYNONYMS "ADC" "L-arginine carboxy-lyase")
(COMMON-NAME "arginine decarboxylase, biosynthetic")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speA.template")
(:CREATION-DATE 3000591045)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "antizyme" COMMENT "noncompetitive
inhibitor |CITS: [87260820]|")
(INHIBITORS-UNKMECH "alpha-difluoromethylarginine" COMMENT "irreversible
inhibitor |CITS: [85163236]|")
(INHIBITORS-UNKMECH SPERMIDINE COMMENT "feedback inhibitor |CITS:
[73149256]|")
(INHIBITORS-UNKMECH PUTRESCINE COMMENT "feedback inhibitor |CITS:
[73149256]|")
(INHIBITORS-UNKMECH "alpha-monofluoromethylarginine" COMMENT
"irreversible inhibitor |CITS: [87241320] [HandEnzInh]|")
(INHIBITORS-UNKMECH "alpha-monofluoromethylagmatine" COMMENT
"irreversible inhibitor |CITS: [87241320] [HandEnzInh]|")
(INHIBITORS-UNKMECH "alpha-ethynylagmatine" COMMENT
"The inhibition is partially reversible |CITS: [87241320] [HandEnzInh]| ")
(INHIBITORS-UNKMECH "alpha-allenylagmatine" COMMENT
"irreversible inhibitor |CITS: [87241320] [HandEnzInh]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "Has a high specificity for arginine,
and has no activity towards lysine or ornithine |CITS: [73149256] [85163236]|")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE COMMENT
"two moles of pyridoxal phosphate are bound per mole of enzyme |CITS: [85163236]|")))
(ARGDECARBOXBIO-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2938" "SpeA")
(COMMON-NAME "SpeA")
(COMPONENT-OF ARGDECARBOXBIO-CPLX)
(DBLINKS (MODBASE "P21170" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF02784" IN-FAMILY |pkarp| 3346700380 NIL NIL)
(REFSEQ "NP_417413" NIL NIL NIL NIL NIL) (UNIPROT "P21170"))
(ISOZYME-SEQUENCE-SIMILARITY (ARGDECARBOXDEG-MONOMER NO))
(PI 5.06d0)
(LOCATIONS CCO-PERI-BAC)
(MOLECULAR-WEIGHT-SEQ 73.89834999999991d0)
(GENE EG10959)
(COMMENT "Biosynthetic arginine decarboxylase undergoes reversible
association and dissociation depending on buffer conditions. |CITS:
[73149257]| The enzyme exists as a homotetramer in the presence of
Mg++ and pyridoxal phosphate. |CITS: [85163236]|
The monomeric form of the enzyme is found as a mixture of Mr
71,000 and Mr 75,500 polypeptides. The 75,500-Mr form is a precursor
to the 71,000-Mr form, which is found in the periplasmic space. This
may explain why exogenous arginine is more easily converted to
putrescine than arginine formed endogenously. |CITS: [85163236]|
")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/speA.template")
(:CREATION-DATE 3000591045)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"SpeA, coding for the biosynthetic decarboxylase and adi,
coding for the degradative form are only 10% homologous. |CITS:
[93186686]|")))
(ARGDECARBOXDEG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENTS ARGDECARBOXDEG-MONOMER)
(CATALYZES ARGDECARBOXDEG-ENZRXN)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/adi.template")
(:CREATION-DATE 3000591032)
(:CREATOR |mriley|) )
((COMPONENTS ARGDECARBOXDEG-MONOMER COEFFICIENT 10)))
(ARGDECARBOXDEG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(REACTION ARGDECARBOX-RXN)
(ENZYME ARGDECARBOXDEG-CPLX)
(ALTERNATIVE-COFACTORS (PYRIDOXAL_PHOSPHATE "2-norpyridoxal-P")
(PYRIDOXAL_PHOSPHATE "omega-methylpyridoxal-P")
(PYRIDOXAL_PHOSPHATE "6-methylpyridoxal-P"))
(ALTERNATIVE-SUBSTRATES (ARG CANAVANINE))
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE "guanido compounds" "ureido compounds" SPERMIDINE LYS
L-ORNITHINE)
(COMMENT "E. coli contains two types of arginine decarboxylase. The
biosynthetic form is expressed regardless of pH variations and is
involved in the synthesis of polyamines. Arginine decarboxylase,
degradative is induced in rich medium at a low pH in the presence of
excess substrate under anaerobic conditions. It appears to play a
role in pH homeostasis by consuming protons and neutralizing the
acidic by-products produced during carbohydrate fermentation. The
decarboxylase increases the surrounding pH by removing acidic carboxyl
groups and releasing CO2 from their substrates. |CITS: [93186686]|")
(SYNONYMS "ADC" "L-arginine carboxy-lyase")
(COMMON-NAME "arginine decarboxylase, degradative")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/adi.template")
(:CREATION-DATE 3000591032)
(:CREATOR |mriley|) )
((ALTERNATIVE-COFACTORS :FACET CITATIONS "[68243188]")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[68243188]")))
(ARGDECARBOXDEG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4117" "AdiA" "Adi")
(DBLINKS (MODBASE "P28629" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03709" IN-FAMILY |pkarp| 3346700435 NIL NIL)
(REFSEQ "NP_418541" NIL NIL NIL NIL NIL)
(UNIPROT "P28629" NIL NIL |ouzounis| 3027900167))
(COMMON-NAME "Adi")
(COMPONENT-OF ARGDECARBOXDEG-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (ARGDECARBOXBIO-MONOMER NO))
(PI 5.38d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 84.55632799999977d0)
(GENE EG11501)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/polyamines/adi.template")
(:CREATION-DATE 3000591032)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "SpeA, coding
for the biosynthetic decarboxylase and adi, coding for the degradative
form are only 10% homologous. |CITS: [93186686]|")))
(ARGDEG-PWY NIL (
(OCELOT-GFP::PARENTS ARGININE-DEG |Super-Pathways|)
(PRIMARIES (AGMATIN-RXN NIL (PUTRESCINE)))
(IN-PATHWAY ORNARGDEG-PWY)
(SYNONYMS "arginine utilization" "ADC pathway" "arginine degradation VII")
(SUPER-PATHWAYS ORNARGDEG-PWY)
(SUB-PATHWAYS PWY0-1221 PWY0-823 4AMINOBUTMETAB-PWY PUTDEG-PWY)
(REACTION-LIST PWY0-1221 PWY0-823 4AMINOBUTMETAB-PWY PUTDEG-PWY
ARGDECARBOX-RXN AGMATIN-RXN)
(ENZYME-USE (ARGDECARBOX-RXN ARGDECARBOXBIO-ENZRXN))
(PREDECESSORS (GABATRANSAM-RXN RXN0-3942) (RXN0-3901 AGMATIN-RXN) PWY0-1221
(GABATRANSAM-RXN AMINOBUTDEHYDROG-RXN)
(PUTTRANSAM-RXN AGMATIN-RXN) 4AMINOBUTMETAB-PWY PUTDEG-PWY
(AGMATIN-RXN ARGDECARBOX-RXN) (ARGDECARBOX-RXN) PWY0-823)
(COMMENT "Although E. coli does not generally use L-arginine as a sole
carbon source, it does have the capacity to degrade it to succinate.
|CITS: [ColiSalII]|")
(COMMON-NAME
"superpathway of arginine, putrescine, and 4-aminobutyrate degradation")
(TEMPLATE-FILE "~ecocyc/templates/new/aodeg/argdegpwy.template")
(:CREATION-DATE 3055885344)
(:CREATOR |mriley|) )
NIL)
(ARGININE--TRNA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS |tRNA-Charging-Reactions| EC-6.1.1)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY TRNA-CHARGING-PWY)
(ENZYMATIC-REACTION ARGS-ENZRXN)
(EC-NUMBER "6.1.1.19")
(COMMON-NAME "ARGININE--TRNA-LIGASE")
(RIGHT |Charged-ARG-tRNAs| PPI AMP)
(LEFT |ARG-tRNAs| ARG ATP)
(SYNONYMS "ARGINYL-TRNA SYNTHETASE") )
NIL)
(ARGININE-DEG T (
(OCELOT-GFP::PARENTS |Amino-Acid-Degradation|)
(COMMENT
"This class contains pathways by which the amino acid, arginine, and the structurally and metabolically related polyamines are degraded to serve as sources of nitrogen, carbon, and energy. Other amino acids, histidine and alanine, can be made from arginine by some of these pathways. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Arginine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104625) )
NIL)
(ARGININE-N-SUCCINYLTRANSFERASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY AST-PWY)
(ENZYMATIC-REACTION ARGSUCCTRAN-ENZRXN)
(EC-NUMBER "2.3.1.109")
(COMMON-NAME "ARGININE-N-SUCCINYLTRANSFERASE")
(RIGHT CPD-421 CO-A)
(LEFT ARG SUC-COA) )
NIL)
(ARGININE-SYN T (
(OCELOT-GFP::PARENTS IND-AMINO-ACID-SYN)
(COMMENT
"This class contains pathways of the various routes by which the amino acid, arginine, can be synthesized. Arginine is a constituent of proteins; it and its metabolic precursor, ornithine, are precursors of polyamines.")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Arginine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104632) )
NIL)
(|argQ-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argQ) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "ACG")
(MODIFIED-FORM |charged-argQ-tRNA|)
(COMMON-NAME "tRNAargQ")
(GENE EG30013) )
((CREDITS SRI LAST-CURATED 3355075742)
(CREDITS |shearer| LAST-CURATED 3355075742)))
(ARGS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(COFACTORS MG+2)
(COMMENT
"One molecule of ATP is utilized per aminoacylation reaction |CITS: [384995][37899]|.")
(CITATIONS "37899:EV-EXP-IDA-PURIFIED-PROTEIN:3293817429:keseler")
(INHIBITORS-COMPETITIVE CANAVANINE)
(ENZYME ARGS-MONOMER)
(REACTION ARGININE--TRNA-LIGASE-RXN)
(:CREATION-DATE 3067730803)
(:CREATOR |kr|)
(COMMON-NAME "arginyl-tRNA synthetase") )
((COFACTORS MG+2 CITATIONS "8797857")
(INHIBITORS-COMPETITIVE CANAVANINE CITATIONS "4890761")))
(ARGS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 64.68287399999973d0)
(COMMENT
"ArgS is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis.
ArgS belongs to the Class I aminoacyl tRNA synthetases; apart from sequence motifs within the active site, the different enzymes show little similarity in their primary amino acid sequences.
The argS gene has been cloned; the protein coding region uses the unusual initiation codon GUG and has a codon usage pattern which is typical for highly expressed genes |CITS: [2668891]|.
Several mutations in the argS gene have been described. The MA5002 mutant encodes a serine in place of arginine at position 134, close to the active site. The purified enzyme shows defects in enzymatic activity and Km value for ATP |CITS: [2183195]|.
The lov-1 mutation confers a slow growth phenotype as well as mecillinam resistance, which appears to be dependent on the RelA-mediated stringent response |CITS: [1563353]|. Similarly, an argS mutant conferring novobiocin resistance has been isolated |CITS: [10217798]|.
A mutant deleting the arginine residue at position 245 was constructed, and the resulting protein was purified by renaturation from inclusion bodies; the specific activity of the purified enzyme was 0.3 % of the native enzyme |CITS: [12167998]|.
The crystal structure of the ArgS enzyme has been determined at 2.8 Å and 3.1 Å resolutions |CITS: [9416614]|.
Conformational changes induced by interactions with tRNA substrates have been studied |CITS: [14672708][12860413][12232610]|, and specific interations with nucleotide residues in some tRNA species have been determined |CITS: [11733016]|.
")
(SYNONYMS "B1876" "Lov" "ArgS" "ArgRS")
(DBLINKS (MODBASE "P11875" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03485" IN-FAMILY |pkarp| 3346700345 NIL NIL)
(REFSEQ "NP_416390" NIL NIL NIL NIL NIL)
(UNIPROT "P11875" NIL |pkarp| 3102853742))
(GENE EG10071)
(CATALYZES ARGS-ENZRXN)
(:CREATION-DATE 3067730817)
(:CREATOR |kr|) )
NIL)
(ARGSUCCINLYA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH NI+2 CO+2)
(INHIBITORS-UNKMECH "sulfhydryl reagents" ZN+2)
(CITATIONS "6762207:EV-EXP-IDA-PART-PURIFIED-PROTEIN:3361562601:keseler")
(SYNONYMS "arginosuccinase" "N-(L-argininosuccinate)arginine-lyase")
(COMMON-NAME "argininosuccinate lyase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ARGSUCCINLYA-RXN)
(ENZYME ARGSUCCINLYA-MONOMER)
(:CREATION-DATE 2969204109)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH NI+2 CITATIONS "[74257921]")
(INHIBITORS-UNKMECH "sulfhydryl reagents" CITATIONS "[74257921]")
(INHIBITORS-UNKMECH ZN+2 CITATIONS "[74257921]")))
(ARGSUCCINLYA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CREDITS SRI |keseler|)
(COMMENT
"Argininosuccinate lyase catalyzes the final step in the L-arginine biosynthesis pathway.
A crystal structure of argininosuccinate lyase has been solved at 2.44 Å resolution; the enzyme appears to be
tetrameric, with a dimer as the asymmetric unit of this crystal form |CITS: [15502303]|.
ArgH expression is repressed by the addition of arginine or ornithine to the medium |CITS: [770426]|.")
(SYNONYMS "B3960" "ArgH")
(DBLINKS (PDB "1TJ7" NIL |keseler| 3361560438 NIL NIL)
(MODBASE "P11447" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00206" IN-FAMILY |pkarp| 3346700427 NIL NIL)
(REFSEQ "NP_418395" NIL |keseler| 3310235028 NIL NIL) (UNIPROT "P11447"))
(CATALYZES ARGSUCCINLYA-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 50.31816399999986d0)
(GENE EG11223)
(:CREATION-DATE 2969204109)
(:CREATOR |mriley|) )
((CREDITS SRI LAST-CURATED 3361562601)
(CREDITS |keseler| LAST-CURATED 3361562601)))
(ARGSUCCINLYA-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ARGSYN-PWY)
(ENZYMATIC-REACTION ARGSUCCINLYA-ENZRXN)
(RIGHT ARG FUM)
(LEFT L-ARGININO-SUCCINATE)
(EC-NUMBER "4.3.2.1")
(COMMENT "This is the eighth and final step in arginine biosynthesis.")
(:CREATION-DATE 2969204109)
(:CREATOR |mriley|) )
NIL)
(ARGSUCCINSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(COFACTORS MG+2)
(SYNONYMS "argininosuccinate synthetase" "citrulline-aspartate ligase"
"L-citrulline:L-aspartate ligase (AMP-forming)")
(COMMON-NAME "argininosuccinate synthase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ARGSUCCINSYN-RXN)
(COMMENT
"Very little is known about this enzyme in E. coli, although it has been
crystallized. |CITS: [20133106]|")
(ENZYME CPLX0-238)
(:CREATION-DATE 2969204106)
(:CREATOR |mriley|) )
NIL)
(ARGSUCCINSYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3172" "ArgG")
(COMPONENT-OF CPLX0-238)
(COMMON-NAME "ArgG")
(DBLINKS (PFAM "PF00764" IN-FAMILY |pkarp| 3346700389 NIL NIL)
(UNIPROT "P0A6E4" NIL |keseler| 3345578571 NIL NIL)
(REFSEQ "NP_417640" NIL |keseler| 3310234935 NIL NIL) (PDB "1KP3")
(PDB "1KP2") (PDB "1K97") (PDB "1K92"))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 49.898331999999876d0)
(GENE EG10068)
(COMMENT "The subunit structure is not known.")
(:CREATION-DATE 2969204106)
(:CREATOR |mriley|) )
NIL)
(ARGSUCCINSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.3.4)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ARGSYN-PWY)
(ENZYMATIC-REACTION ARGSUCCINSYN-ENZRXN)
(RIGHT L-ARGININO-SUCCINATE PPI AMP)
(LEFT L-ASPARTATE L-CITRULLINE ATP)
(EC-NUMBER "6.3.4.5")
(COMMENT "This is the seventh step in arginine biosynthesis. The
enzyme is also involved in the urea cycle.")
(:CREATION-DATE 2969204106)
(:CREATOR |mriley|) )
NIL)
(ARGSUCCTRAN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(:CREATION-DATE 3117798769)
(ALTERNATIVE-SUBSTRATES (L-ARGININE ORNITHINE))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ARGININE-N-SUCCINYLTRANSFERASE-RXN)
(COMMENT "Arginine succinyltransferase catalyzes the first reaction in the
ammonia-producing arginine catabolic pathway. |CITS: [98361920]|")
(ENZYME ARGSUCCTRAN-MONOMER)
(SYNONYMS "AST" "arginine N-succinyltransferase"
"succinyl-CoA:L-arginine N2-succinyltransferase")
(COMMON-NAME "arginine succinyltransferase") )
NIL)
(ARGSUCCTRAN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(MOLECULAR-WEIGHT-SEQ 38.4558139999999d0)
(:CREATION-DATE 3117798261)
(SYNONYMS "B1747" "YdjV" "AstA")
(DBLINKS (PFAM "PF04958" IN-FAMILY |pkarp| 3346700342 NIL NIL)
(UNIPROT "P0AE37" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_416261" NIL NIL NIL NIL NIL))
(CATALYZES ARGSUCCTRAN-ENZRXN)
(GENE G6943)
(COMMENT "The subunit structure has not been determined.") )
NIL)
(ARGSYN-PWY NIL (
(OCELOT-GFP::PARENTS ARGININE-SYN)
(SUB-PATHWAYS GLUTORN-PWY)
(PRIMARIES (ARGSUCCINLYA-RXN NIL (ARG)))
(CITATIONS ":EV-EXP:3277587223:pkarp")
(ENZYME-USE (ACETYLORNTRANSAM-RXN ACETYLORNTRANSAM-ENZRXN))
(IN-PATHWAY ARG+POLYAMINE-SYN)
(SUPER-PATHWAYS ARG+POLYAMINE-SYN)
(REACTION-LIST GLUTORN-PWY CARBPSYN-RXN ORNCARBAMTRANSFER-RXN
ARGSUCCINLYA-RXN ARGSUCCINSYN-RXN)
(PATHWAY-INTERACTIONS)
(PREDECESSORS (ORNCARBAMTRANSFER-RXN ACETYLORNDEACET-RXN) GLUTORN-PWY
(ARGSUCCINSYN-RXN ORNCARBAMTRANSFER-RXN)
(ARGSUCCINLYA-RXN ARGSUCCINSYN-RXN)
(ORNCARBAMTRANSFER-RXN CARBPSYN-RXN))
(NET-REACTION-EQUATION
"2 L-glutamate + acetyl-CoA + carbamoyl phosphate + aspartate + 2 ATP + NADPH + H+ + H2O = arginine + acetate + CoA + fumarate + 2-ketoglutarate + AMP + 3 Pi + NADP+ + ADP")
(COMMON-NAME "arginine biosynthesis I")
(:CREATION-DATE 2969204110)
(:CREATOR |mriley|) )
((PATHWAY-INTERACTIONS :FACET COMMENT "The pathway of synthesis of
arginine intersects with the urea cycle.")))
(ARGT-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-5)
(MOLECULAR-WEIGHT-SEQ 27.99163099999998d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B2310" "ArgP" "ArgT")
(DBLINKS (MODBASE "P09551" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00497" IN-FAMILY |pkarp| 3346700358 NIL NIL)
(PDB "1LAH" NIL |pkarp| 3346695110 NIL NIL)
(REFSEQ "NP_416813" NIL NIL NIL NIL NIL)
(SWISSMODEL "P09551" NIL |pkarp| 3064870651)
(UNIPROT "P09551" NIL |pkarp| 3064869797))
(COMPONENT-OF ABC-3-CPLX)
(GENE EG10072)
(LOCATIONS CCO-PERI-BAC)
(COMMON-NAME "ArgT") )
NIL)
(|argU-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argU) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNA(argU) translates a rare arginine codon. This rare codon appears
more frequently in the first 25 codons of many genes |CITS: [2109307]|.
Overexpression of argU allows increased expression of these
proteins and an argU ts mutation limits production of the
same proteins |CITS: [2515992][2139647]|. ts mutations
in argU also lead to growth inhibition caused by defective
translation |CITS: [15317795]|. A lack of tRNA(argU) can also
lead to frameshift defects when its cognate codon is encountered
during translation |CITS: [2205835]|.
Uridine 34 in tRNA(argU) is modified to 5-methylaminomethyluridine |CITS: [7690702]|.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|")
(:CREATION-DATE 3068309818)
(ANTICODON "UCU")
(MODIFIED-FORM |charged-argU-tRNA|)
(COMMON-NAME "tRNAargU")
(GENE EG30014) )
((CREDITS SRI LAST-CURATED 3355075756)
(CREDITS |shearer| LAST-CURATED 3355075756)))
(|argV-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argV) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(SYNONYMS "tRNA(Arg2)")
(:CREATION-DATE 3068309818)
(ANTICODON "ACG")
(MODIFIED-FORM |charged-argV-tRNA|)
(COMMON-NAME "tRNAargV")
(GENE EG30015) )
((CREDITS SRI LAST-CURATED 3355075765)
(CREDITS |shearer| LAST-CURATED 3355075765)))
(|argW-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argW) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "CCU")
(MODIFIED-FORM |charged-argW-tRNA|)
(COMMON-NAME "tRNAargW")
(GENE EG30016) )
((CREDITS SRI LAST-CURATED 3355075773)
(CREDITS |shearer| LAST-CURATED 3355075773)))
(|argX-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argX) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
RNase E processing of the argX operon is modulated by Hfq binding to the mRNA |CITS: [14622403]|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "CCG")
(MODIFIED-FORM |charged-argX-tRNA|)
(COMMON-NAME "tRNAargX")
(GENE EG30017) )
((CREDITS SRI LAST-CURATED 3355075781)
(CREDITS |shearer| LAST-CURATED 3355075781)))
(|argY-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argY) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "ACG")
(MODIFIED-FORM |charged-argY-tRNA|)
(COMMON-NAME "tRNAargY")
(GENE EG30018) )
((CREDITS SRI LAST-CURATED 3355075790)
(CREDITS |shearer| LAST-CURATED 3355075790)))
(|argZ-tRNA| NIL (
(OCELOT-GFP::PARENTS |ARG-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(argZ) is one of seven arginine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "ACG")
(MODIFIED-FORM |charged-argZ-tRNA|)
(COMMON-NAME "tRNAargZ")
(GENE EG30019) )
((CREDITS SRI LAST-CURATED 3355075800)
(CREDITS |shearer| LAST-CURATED 3355075800)))
(|arnaud| NIL (
(OCELOT-GFP::PARENTS |People|)
(CREDITED-FOR PWY0-501)
(LOGIN-ACCOUNT |arnaud|)
(LAST-NAME "Arnaud")
(FIRST-NAME "Martha")
(:CREATOR |pkarp|)
(:CREATION-DATE 3278260654) )
NIL)
(|arnaud-3250891812| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT "Added from Blattner ORF tables by M. Arnaud 1/6/03.
")
(REFERENT-FRAMES EG12281)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3250891812) )
NIL)
(|arnaud-3252192783| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT "This pathway supersedes the pathway formerly called \"purine
biosynthesis.\"")
(REFERENT-FRAMES DENOVOPURINE2-PWY)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252192783) )
NIL)
(|arnaud-3252192886| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"This pathway supersedes the pathway formerly called \"pyrimidine biosynthesis.\"")
(REFERENT-FRAMES PWY0-162)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252192886) )
NIL)
(|arnaud-3252192985| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"The pathways \"de novo biosynthesis of pyrimidine deoxyribonucleotides\" and \"salvage pathways of pyrimidine deoxyribonucleotides\" supersede the pathway formerly called \"deoxypyrimidine nucleotide/nucleoside metabolism.
")
(REFERENT-FRAMES PWY0-166)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252192985) )
NIL)
(|arnaud-3252193056| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"The pathways \"de novo biosynthesis of pyrimidine deoxyribonucleotides\" and \"salvage pathways of pyrimidine deoxyribonucleotides\" supersede the pathway formerly called \"deoxypyrimidine nucleotide/nucleoside metabolism.\"")
(REFERENT-FRAMES PWY0-181)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252193056) )
NIL)
(|arnaud-3252193153| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"This pathway supersedes the pathway formerly called \"pyrimidine ribonucleotide/ribonucleoside metabolism.\"
")
(REFERENT-FRAMES PWY0-163)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252193153) )
NIL)
(|arnaud-3252193461| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"The pathways \"salvage pathways of guanine, xanthine, and their nucleosides\" and \"salvage pathways of adenine, hypoxanthine, and their nucleotides\" supersede the pathway formerly called \"purine ribonucleotide/ribonucleoside metabolism.\"
")
(REFERENT-FRAMES SALVADEHYPOX-PWY)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252193461) )
NIL)
(|arnaud-3252193499| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"The pathways \"salvage pathways of guanine, xanthine, and their nucleosides\" and \"salvage pathways of adenine, hypoxanthine, and their nucleotides\" supersede the pathway formerly called \"purine ribonucleotide/ribonucleoside metabolism.\"")
(REFERENT-FRAMES SALVPURINE2-PWY)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3252193499) )
NIL)
(|arnaud-3280516363| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT
"This gene was mentioned in the reference of PMID: 12603745; the gene coordinates come from EcoGene.
")
(REFERENT-FRAMES G0-9121)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3280516363) )
NIL)
(|arnaud-3280614443| NIL (
(OCELOT-GFP::PARENTS |Notes|)
(TEXT "YdaE is mentioned in PMID=12207707; gene coordinates are from EcoGene.
")
(REFERENT-FRAMES G0-9081)
(SENDER |arnaud|)
(:CREATOR |arnaud|)
(:CREATION-DATE 3280614443) )
NIL)
(ARO-PWY NIL (
(OCELOT-GFP::PARENTS AMINO-ACID-FAMILY-SYN)
(CREDITS O0-3 AU0-5)
(PATHWAY-LINKS (ERYTHROSE-4P NONOXIPENT-PWY)
(CHORISMATE ENTBACSYN-PWY UBISYN-PWY FOLSYN-PWY MENAQUINONESYN-PWY TYRSYN
PHESYN TRPSYN-PWY))
(SUPER-PATHWAYS COMPLETE-ARO-PWY)
(IN-PATHWAY COMPLETE-ARO-PWY)
(PREDECESSORS (DAHPSYN-RXN) (3-DEHYDROQUINATE-SYNTHASE-RXN DAHPSYN-RXN)
(3-DEHYDROQUINATE-DEHYDRATASE-RXN
3-DEHYDROQUINATE-SYNTHASE-RXN)
(SHIKIMATE-5-DEHYDROGENASE-RXN
3-DEHYDROQUINATE-DEHYDRATASE-RXN)
(SHIKIMATE-KINASE-RXN SHIKIMATE-5-DEHYDROGENASE-RXN)
(2.5.1.19-RXN SHIKIMATE-KINASE-RXN)
(CHORISMATE-SYNTHASE-RXN 2.5.1.19-RXN))
(REACTION-LIST DAHPSYN-RXN 3-DEHYDROQUINATE-SYNTHASE-RXN
3-DEHYDROQUINATE-DEHYDRATASE-RXN SHIKIMATE-5-DEHYDROGENASE-RXN
SHIKIMATE-KINASE-RXN 2.5.1.19-RXN CHORISMATE-SYNTHASE-RXN)
(NET-REACTION-EQUATION
"D-erythrose-4-P + 2 phophoenolpyruvate + NADPH + H+ + ATP = chorismate + NADP+ + ADP + 4 Pi")
(CITATIONS ":EV-EXP:3339348537:keseler")
(COMMENT
"Chorismate is an intermediate in the synthesis of three amino acids: tyrosine, phenylalanine and
tryptophan. In addition it is a precursor of folic acid, ubiquinone, menaquinone, and enterochelin.
The first reaction in the pathway of synthesis of chorismate is catalyzed by three separate enzymes,
each of which is subject to feedback inhibition by one of the three amino acids. However, even in the
presence of all three amino acids, sufficient enzymatic activity is present to permit synthesis of the other
four metabolites synthesized from chorismate because the enzyme subject to regulation by tryptophan
cannot be inhibited more than 60 percent.
Review: Pittard, J. and J. Yang (2004) \"Biosynthesis of Phenylalanine and Tyrosine.\" EcoSal 3.6.1.8 |CITS: [ecosal]|
")
(SYNONYMS "aromatic amino acid biosynthesis")
(COMMON-NAME "chorismate biosynthesis")
(:CREATION-DATE 2956688290) )
((CREDITS O0-3 REVISED 3356193690) (CREDITS AU0-5 REVISED 3356193690)))
(AROA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0908" "AroA")
(DBLINKS (MODBASE "P0A6D3" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6D3" NIL |pkarp| 3354911363)
(PFAM "PF00275" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(REFSEQ "NP_415428" NIL NIL NIL NIL NIL) (PDB "1MI4") (PDB "1G6T")
(PDB "1G6S"))
(CATALYZES 3-P-SHIK-1-CARBOXYVINYLXFERASE-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 46.09572399999987d0)
(GENE EG10073)
(COMMENT "3-D structure has been studied |CITS:[PNAS88-5046-91]|")
(:CREATION-DATE 2955043943)
(:CREATOR |mriley|) )
NIL)
(AROB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3389" "AroB")
(DBLINKS (MODBASE "P07639" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P07639" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01761" IN-FAMILY |pkarp| 3346700399 NIL NIL)
(REFSEQ "NP_417848" NIL NIL NIL NIL NIL) (UNIPROT "P07639"))
(CATALYZES 3-DEHYDROQUINATE-SYNTHASE-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 38.880929999999914d0)
(GENE EG10074)
(CITATIONS "[86192828]")
(:CREATION-DATE 2955043970)
(:CREATOR |mriley|) )
NIL)
(AROC-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES CHORISMATE-SYNTHASE-ENZRXN)
(COMPONENTS AROC-MONOMER)
(:CREATION-DATE 2955044000)
(:CREATOR |mriley|) )
((COMPONENTS AROC-MONOMER COEFFICIENT 4)))
(AROC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Chorismate synthase acts in the shikimate pathway. It catalyses the conversion of
5-enolpyruvylshikimate 3-phosphate into chorismate, the key
branch-point intermediate in aromatic biosynthesis.
Chorismate synthase is an AroC tetramer |CITS: [2969724]|.
The enzymatic mechanism has been studied in detail |CITS: [2407239], [7978236], [7848266], [7559411], [8634296],
[8703965], [8824216], [10956653], [11034781], [11784161]|. The enzyme catalyzes phosphate elimination by a
1,4-elimination mechanism that proceeds with anti-stereochemistry |CITS: [4550759]|. The E. coli enzyme is
unable to generate reduced flavin via
the oxidation of reduced nicotinamide nucleotides; it can synthesize
chorismate only when supplied directly with either FMNH2 or FADH2, and the preferred
flavin is FMNH2 |CITS:[88293429]|. The reaction is oxygen sensitive and the enzyme
is inactive under aerobic conditions |CITS:[67082484]|. The enzyme remains tetrameric and undergoes significant
conformational changes during catalysis |CITS: [9761730]|.
A 36-residue C-terminal truncation does not eliminate enzyme activity |CITS: [2182772]|.
Chorismate synthase exhibits low abundance in wild-type
strains |CITS:[biosoctrans(87)15-144]|. Overproduction and purification has been described |CITS: [2969724]|.
Chorismate synthase has been studied in many different organisms. Phenotypes of an E. coli aroC mutant are
functionally complemented by production of Synechocystis PCC 6803 AroC |CITS: [7505271]|,
Vibrio anguillarum AroC |CITS: [8021209]|, or Brucella suis AroC |CITS: [11119550]|.
The shikimate pathway is of great interest as a drug target |CITS: [11865437]|. Salmonella typhimurium AroC
is required for wild-type virulence |CITS: [3058818]|, as is Brucella suis AroC |CITS: [11119550]|.
S. typhimurium |CITS: [3058818], [2187747], [1311488], [7483768], [12065485], [12531654]| and S. typhi
|CITS: [9916080], [11982332], [12065485], [12531654], [12555559]| aroC mutations have been used in vaccine
strains.
Reviews: |CITS: [8674765], [9951731], [11476485], [12521268]|.")
(SYNONYMS "B2329" "AroC")
(COMMON-NAME "AroC")
(DBLINKS (MODBASE "P12008" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P12008" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01264" IN-FAMILY |pkarp| 3346700359 NIL NIL)
(REFSEQ "NP_416832" NIL NIL NIL NIL NIL) (UNIPROT "P12008"))
(COMPONENT-OF AROC-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 39.13740099999994d0)
(GENE EG10075)
(:CREATION-DATE 2955044000)
(:CREATOR |mriley|) )
NIL)
(AROD-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES 3-DEHYDROQUINATE-DEHYDRATASE-ENZRXN)
(CITATIONS "[81261964]")
(COMPONENTS AROD-MONOMER)
(:CREATION-DATE 2955044017)
(:CREATOR |mriley|) )
((COMPONENTS AROD-MONOMER COEFFICIENT 2)))
(AROD-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1693" "AroD")
(COMMON-NAME "AroD")
(DBLINKS (MODBASE "P05194" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P05194" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01487" IN-FAMILY |pkarp| 3346700340 NIL NIL)
(REFSEQ "NP_416208" NIL NIL NIL NIL NIL) (UNIPROT "P05194"))
(COMPONENT-OF AROD-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 27.46661299999999d0)
(GENE EG10076)
(COMMENT "Comparisons of the coli
3-dehydroquinase sequence and with the partial sequence of arom gene
of aspergillus nidulans, which is known to include the
3-dehydroquinase domain, reveals significant homologies.")
(:CREATION-DATE 2955044017)
(:CREATOR |mriley|) )
NIL)
(AROE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3281" "AroE")
(DBLINKS (MODBASE "P15770" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01488" IN-FAMILY |pkarp| 3346700394 NIL NIL)
(PDB "1VI2" NIL |keseler| 3335296905 NIL NIL)
(PDB "1NYT" NIL |keseler| 3323189267 NIL NIL)
(REFSEQ "NP_417740" NIL NIL NIL NIL NIL) (UNIPROT "P15770"))
(CATALYZES SHIKIMATE-5-DEHYDROGENASE-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 29.413598999999945d0)
(GENE EG10077)
(CITATIONS "[85149271]" "[88134021]")
(:CREATION-DATE 2955044032)
(:CREATOR |mriley|) )
NIL)
(AROF-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES DAHPSYNTYR-ENZRXN)
(COMPONENTS AROF-MONOMER)
(:CREATION-DATE 2955044050)
(:CREATOR |mriley|) )
((COMPONENTS AROF-MONOMER COEFFICIENT 2)))
(AROF-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2601" "AroF")
(COMMON-NAME "AroF")
(DBLINKS (MODBASE "P00888" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00888" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00793" IN-FAMILY |pkarp| 3346700368 NIL NIL)
(REFSEQ "NP_417092" NIL NIL NIL NIL NIL) (UNIPROT "P00888"))
(COMPONENT-OF AROF-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 38.80391799999994d0)
(GENE EG10078)
(CITATIONS "[89053867]")
(COMMENT "aroF and tyrA encoding the bifunctional chorismate mutase
prephenate dehydrogenase form the tyrosine operon. The tyrosine operon
is repressed by tyrosine and phenylalanine. This repression is
mediated by the tyrR gene product postulated to bind at a regulatory
region preceding the aroF coding sequence.")
(:CREATION-DATE 2955044050)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"There are three DAHP synthase isoenzymes:
phenylalanine sensitive DAHP synthase, tyrosine sensitive DAHP
synthase, and tryptophan DHAP synthase.
The three isoenzymes probably arose by the duplication and
divergent evolution of a common ancestral gene. The aroF and
aroG genes have been found to be similar in size and sequence.
When optimally aligned, 58 of the nucleotides and 53 of the
amino acids of the derived polypeptide sequences are identical")))
(AROF-TYRA-TERMINATOR NIL (
(OCELOT-GFP::PARENTS |Rho-Independent-Terminators|)
(:CREATION-DATE 3188937346)
(COMPONENT-OF TU0-6653 TU00008)
(CITATIONS "85134883")
(RIGHT-END-POSITION 2736962)
(LEFT-END-POSITION 2736934)
(:CREATOR |sgama|) )
NIL)
(AROG-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES DAHPSYNPHE-ENZRXN)
(CITATIONS "[78194136]")
(COMPONENTS AROG-MONOMER)
(:CREATION-DATE 2955044079)
(:CREATOR |mriley|) )
((COMPONENTS AROG-MONOMER COEFFICIENT 4)))
(AROG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0754" "AroG")
(COMMON-NAME "AroG")
(DBLINKS (MODBASE "P0AB91" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00793" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(PDB "1QR7" NIL |pkarp| 3346695107 NIL NIL)
(UNIPROT "P0AB91" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_415275" NIL NIL NIL NIL NIL) (PDB "1KFL") (PDB "1GG1"))
(COMPONENT-OF AROG-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (AROF-MONOMER YES) (AROH-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 38.00947999999992d0)
(GENE EG10079)
(CITATIONS "[89053867]" "[78194136]")
(COMMENT "Expression of aroF and aroG is repressed by the tyrR protein
with tyrosine or phenylalanine plus tryptophan, respectively as corepressors
The three genes (aroF, aroG and aroH) are widely separated on the coli chromosome. In
wild-type cells grown in minimal mediuim, the AroG enzyme makes up
about 80% of the total DAHPS activity, the AroF isoenzyme makes up
20%, and the AroH isoenzyme makes up about 1% |CITS:[89053867]|.")
(:CREATION-DATE 2955044079)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "There are three DAHP synthase
isoenzymes, phenylalanine sensitive DAHP synthase, tyrosine sensitive
DAHP synthase and tryptophan sensitive DAHP synthase. AroG shows
substantial homology with that of aroH and aroF, indicating that these three
genes have arisen from a common ancestor by divergent evolution. The
three isoenzymes arose by the duplication
and divergent evolution of a common ancestral gene. Pairwise
comparisons of the three sequences reveal that AroH and AroG have 57%
amino acid residues in common, AroG and AroF have 53%, and AroH and
AroF have 48%. When all three polypeptides are compared, 41% residues
are identical.")
(ISOZYME-SEQUENCE-SIMILARITY (AROH-MONOMER YES) COMMENT)))
(AROH-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES DAHPSYNTRP-ENZRXN)
(COMPONENTS AROH-MONOMER)
(:CREATION-DATE 2955044173)
(:CREATOR |mriley|) )
((COMPONENTS AROH-MONOMER COEFFICIENT 2)))
(AROH-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1704" "AroH")
(COMMON-NAME "AroH")
(DBLINKS (MODBASE "P00887" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00887" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00793" IN-FAMILY |pkarp| 3346700341 NIL NIL)
(REFSEQ "NP_416219" NIL NIL NIL NIL NIL) (UNIPROT "P00887"))
(COMPONENT-OF AROH-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (AROG-MONOMER YES) (AROF-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 38.73500499999994d0)
(GENE EG10080)
(CITATIONS "[89053867]")
(COMMENT "The aroH gene has two promoters. One is regulated by the trp
repressor and is favored by growth on minimal media. The other
promoter is activated under conditions of growth in rich medium by an
unknown mechanism. The presence of a second promoter that is active
during growth in the presence of high levels of aromatic amino acid could allow
aroH to escape from repression and ensure a low level of metabolic flux
through the shikimate pathway for the biosynthesis of aromatic
vitamins not present in the growth medium. Of
the three isozymes, DAHP synthase (Trp) is only moderately
feedback-inhibited and will function despite high levels of
intracellular tryptophan |CITS:[91323737]|. In wild-type
cells grown in minimal medium,
the aroG isozyme makes up about 80% of the total DAHPS activity, the
aroF isozyme makes up 20%, and the aroH isozyme makes up
about 1%.")
(:CREATION-DATE 2955044173)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"The translated sequence of aroH shows substantial homology with that
of aroH and aroF, indicating that these three genes have arisen from a common
ancestor by divergent evolution. aroH and aroG have 57% identical
amino acids. aroH and aroF have 48% identical amino acids.
Although catalyzing the same
reaction, each isozyme is feedback regulated by a different amino acid.")
(ISOZYME-SEQUENCE-SIMILARITY (AROF-MONOMER YES) COMMENT)))
(AROK-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3390" "AroK")
(DBLINKS (MODBASE "P0A6D7" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6D7" NIL |pkarp| 3354911363)
(PFAM "PF01202" IN-FAMILY |pkarp| 3346700399 NIL NIL) (PDB "1KAG"))
(CATALYZES SHIKIMATE-KINASEI-ENZRXN)
(ISOZYME-SEQUENCE-SIMILARITY (AROL-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 19.538015000000016d0)
(GENE EG10081)
(CITATIONS "[92105021]")
(:CREATION-DATE 2955044220)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY (AROL-MONOMER YES) COMMENT
"the amino acids in shikimate kinase I and II are 34% similar|CITS:[92105021]|")))
(AROL-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0388" "AroL")
(DBLINKS (MODBASE "P0A6E1" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0A6E1" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A6E1" NIL |pkarp| 3354911363)
(PFAM "PF01202" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_414922" NIL NIL NIL NIL NIL))
(CATALYZES SHIKIMATE-KINASEII-ENZRXN)
(ISOZYME-SEQUENCE-SIMILARITY (AROK-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 19.15079500000002d0)
(GENE EG10082)
(CITATIONS "[86085676]" "[86085697]" "[87099857]" "[92105021]")
(COMMENT "Expression of the structural gene of one of the coli
shikimate kinase isoenzyme, the aroL gene product is regulated by the
tyrR gene product protein with tyrosine or tryptophan as co-repressor.
|CITS:[87099857]| A second gene, designated aroM, that encodes a
26-kilodalton gene product of unknown function was shown to be
cotranscribed with aroL. |CITS:[86085676]|")
(:CREATION-DATE 2955044220)
(:CREATOR |mriley|) )
NIL)
(|Aromatic-Acid| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(DISPLAY-COORDS-2D (-1.3082d0 0.225d0) (-0.5938d0 -0.1875d0)
(-0.5938d0 -1.0125d0) (0.2312d0 -0.1875d0))
(CHEMICAL-FORMULA (C 1) (H 1) (O 2) (R 1))
(STRUCTURE-BONDS (2 4 1) (2 3 2) (2 1 1))
(STRUCTURE-ATOMS R C O O)
(SYNONYMS "an aromatic acid")
(COMMON-NAME "an aromatic carboxylate")
(:CREATOR |paley|)
(:CREATION-DATE 3314378978) )
NIL)
(|Aromatic-Amino-Acids| T (
(OCELOT-GFP::PARENTS |Amino-Acids|)
(COMMENT "The R group in this compound contains an aromatic ring.")
(CHEMICAL-FORMULA (C 2) (H 4) (N 1) (O 2) (R 1))
(STRUCTURE-BONDS (5 6 1) (4 6 1) (3 5 1) (2 5 2) (1 6 1))
(DISPLAY-COORDS-2D (1.2124d0 0.0d0) (2.4248d0 -3.5d0) (3.6373d0 -1.4d0)
(0.0d0 -2.1d0) (2.4248d0 -2.1d0) (1.2124d0 -1.4d0))
(STRUCTURE-ATOMS N O O R C C)
(COMMON-NAME "an aromatic amino acid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(AROMATIC-COMPOUNDS-BIOSYN T (
(OCELOT-GFP::PARENTS |Biosynthesis|)
(COMMENT
"This class contains pathways of the biosynthesis of aromatic compounds, some of which play regulatory roles in cellular growth. Pathways of biosynthesis of hormones, secondary metabolites, and siderophores, some of which are aromatic, are found in other classes. ")
(COMMON-NAME "Aromatic Compounds")
(:CREATOR |paley|)
(:CREATION-DATE 3267465936) )
NIL)
(AROMATIC-COMPOUNDS-DEGRADATION T (
(OCELOT-GFP::PARENTS |Degradation|)
(COMMENT
"This class contains pathways of degradation of various aromatic compounds, including heterocyclic compounds and those that contain sulfur. The pathways provide a source of nutrients and energy.")
(COMMON-NAME "Aromatic compounds")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(|Aromatic-Oxoacids| T (
(OCELOT-GFP::PARENTS |All-Carboxy-Acids|)
(CHEMICAL-FORMULA (C 2) (H 3) (O 3) (R 1))
(STRUCTURE-BONDS (5 6 1) (4 6 1) (3 6 1) (2 5 1) (1 5 2))
(DISPLAY-COORDS-2D (2.4248d0 -3.5d0) (3.6373d0 -1.4d0) (0.0d0 -2.1d0)
(1.2125d0 0.0d0) (2.4248d0 -2.1d0) (1.2124d0 -1.4d0))
(STRUCTURE-ATOMS O O O R C C)
(COMMENT "The R group in this structure contains an aromatic ring.")
(COMMON-NAME "an aromatic oxo-acid")
(:CREATOR |paley|)
(:CREATION-DATE 3330790569) )
NIL)
(|Aromatic-Primary-Alcohols| T (
(OCELOT-GFP::PARENTS |Aryl-Alcohol|)
(CHEMICAL-FORMULA (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(DISPLAY-COORDS-2D (1.2124d0 0.0d0) (0.0d0 -0.7d0))
(STRUCTURE-ATOMS O R)
(COMMENT "The R group in this compounds structure contains an aromatic ring.")
(COMMON-NAME "an aromatic primary alcohol")
(:CREATOR |paley|)
(:CREATION-DATE 3330790568) )
NIL)
(AROMATIC-RINGS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3355687094)
(:VALUE-TYPE :LIST)
(:DOMAIN |Modified-Proteins| |Compounds|)
(:DOCUMENTATION
"Lists those atoms that participate in aromatic rings for this compound.")
(:INHERITANCE-TYPE :UNIQUE)
(:HIDE-SLOT? T)
(QUERYABLE? T) )
NIL)
(|Aromatics| T (
(OCELOT-GFP::PARENTS |Compounds|)
(SCHEMA? T)
(COMMENT
"This is a collection place for many aromatic compounds that can occur in toxic chemical waste, and are degraded by some microbes.")
(COMMON-NAME "an aromatic compound") )
NIL)
(AROP-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 49.69004299999982d0)
(:CREATION-DATE 3060042779)
(COMMENT
"AroP is an aromatic amino acid permease that is a member of the APC Superfamily of transporters |CITS: [99107637]|.
AroP is referred to as the general aromatic amino acid permease because it is responsible for the transport
of all three aromatic amino acids, phenylalanine, tyrosine, and tryptophan, across the inner membrane
|CITS: [97294474]|. Based on the hydrophobicity profile and distribution of charged amino acid residues,
AroP was shown to have 12 membrane-spanning regions connected by hydrophilic loops
|CITS: [97294474]|. This topographical model is very similar to that reported for the PheP permease,
a phenylalanine-specific transporter, which has 61% amino acid sequence identity with the AroP
permease |CITS: [20200359]|. However, despite their high degree of sequence similarity, their substrate
specificities and affinities differ. A series of AroP-PheP chimeric proteins were made using in vivo
recombination, and their respective substrate profiles and activities were analyzed |CITS: [20200359]|.
The AroP protein was found to transport each of the aromatic amino acids with a Km of
1 μM |CITS: [20200359]|. Wild-type AroP and chimeras that are predominantly AroP exhibited the
ability to transport both phenylalanine and tryptophan to the same steady-state levels, and transport
tyrosine to almost doubling steady-state levels |CITS: [20200359]|. Site directed mutagenisis of the chimera
and AroP has established that a key residue involved in tryptophan transport is tyrosine at position 103 in
AroP |CITS: [20200359]|. Studies with uncouplers of oxidative phosphorylation and with strains deficient in
F0F1-ATPase indicate that transport via the AroP system is driven by the proton
motive force |CITS: [20200359]|. Expression of aroP is subject to regulation involving the TyrR
protein |CITS: [20200359]|.")
(SYNONYMS "B0112" "TrpP" "AroT" "AroR" "AroP")
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414654" NIL NIL NIL NIL NIL)
(UNIPROT "P15993" NIL |pkarp| 3064869797))
(CATALYZES TRANS-ENZRXN-56B TRANS-ENZRXN-56A TRANS-ENZRXN-56)
(GENE EG10084)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AroP phenylalanine/tyrosine/tryptophan APC transporter") )
NIL)
(ARSENATE NIL (
(OCELOT-GFP::PARENTS |Anions|)
(ACTIVATORS-UNKMECH-OF GAPDH-A-ENZRXN GSDEADENYLATION-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ALKAPHOSPHA-ENZRXN)
(INHIBITORS-UNKMECH-OF LCYSDESULF-ENZRXN METHGLYSYN-ENZRXN)
(DBLINKS (CAS "7778-39-4" NIL |kr| 3346617699 NIL NIL)
(LIGAND-CPD "C01478" NIL |kr| 3346617699 NIL NIL))
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-7)
(APPEARS-IN-LEFT-SIDE-OF RXN-982 TRANS-RXN-7)
(MOLECULAR-WEIGHT 139.927d0)
(CHEMICAL-FORMULA (H 1) (O 4) (AS 1))
(DISPLAY-COORDS-2D (0.0d0 -1.3973d0) (1.4027d0 0.0d0) (1.4027d0 -2.8d0)
(2.8d0 -1.3973d0) (1.4027d0 -1.3973d0))
(STRUCTURE-BONDS (4 5 1) (3 5 1) (2 5 1) (1 5 2))
(STRUCTURE-ATOMS O O O O AS)
(ATOM-CHARGES (4 -1) (3 -1))
(CHARGE -3)
(COMMON-NAME "arsenate")
(SYNONYMS "inorganic arsenate" "orthoarsenate" "AsO43-")
(:CREATION-DATE 3155943641)
(:CREATOR |pkarp|) )
NIL)
(|arsenate detoxification| T (
(OCELOT-GFP::PARENTS |Detoxification|)
(COMMENT "This class contains pathways for arsenate detoxification")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3341087491) )
NIL)
(ARSF-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-20)
(MOLECULAR-WEIGHT-SEQ 45.49736399999993d0)
(COMMENT "Based on sequence similarity with
the R773-plasmid encoded arsenite resistance operon, ArsB is a transporter and ArsC is an arsenate reductase |CITS: [95164532]|.
The chromosomally encoded operon, however, is lacking arsA, which encodes a putative ATP-binding protein. Deletion mutants of the chromosomal arsRBC
operon exhibit 10-20 times more sensitivity to arsenite and 5-10 times more selectivity to antimonite and arsenate than the parent strain. Expression of the
cloned arsRBC conferred increased arsenite resistance compared with wild-type |CITS: [95164532]|
")
(GENE EG12236)
(SPECIES ECOLI)
(:CREATION-DATE 3060029818)
(SYNONYMS "B3502" "ArsF" "F172")
(DBLINKS (PFAM "PF02040" IN-FAMILY |pkarp| 3346700404 NIL NIL)
(UNIPROT "P0AB93" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_417959" NIL |keseler| 3309200185 NIL NIL))
(COMPONENT-OF CPLX-7)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "ArsB") )
NIL)
(ARTI-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-5)
(MOLECULAR-WEIGHT-SEQ 26.929529999999957d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B0863" "ArtI")
(DBLINKS (MODBASE "P30859" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00497" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(REFSEQ "NP_415384" NIL NIL NIL NIL NIL)
(UNIPROT "P30859" NIL |pkarp| 3064869797))
(COMPONENT-OF ABC-4-CPLX)
(GENE EG11625)
(LOCATIONS CCO-PERI-BAC)
(COMMON-NAME "ArtI") )
NIL)
(ARTJ-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-5)
(MOLECULAR-WEIGHT-SEQ 26.82945899999998d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B0860" "ArtJ")
(DBLINKS (MODBASE "P30860" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00497" IN-FAMILY |pkarp| 3346700324 NIL NIL)
(REFSEQ "NP_415381" NIL NIL NIL NIL NIL)
(UNIPROT "P30860" NIL |pkarp| 3064869797))
(COMPONENT-OF ABC-4-CPLX)
(GENE EG11628)
(LOCATIONS CCO-PERI-BAC)
(COMMON-NAME "ArtJ") )
NIL)
(ARTM-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-4)
(COMMENT "ArtM")
(MOLECULAR-WEIGHT-SEQ 24.91372799999998d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B0861" "ArtM")
(DBLINKS (PFAM "PF00528" IN-FAMILY |pkarp| 3346700324 NIL NIL)
(UNIPROT "P0AE30" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_415382" NIL NIL NIL NIL NIL))
(COMPONENT-OF ABC-4-CPLX)
(GENE EG11627)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "ArtM") )
NIL)
(ARTP-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-3)
(MOLECULAR-WEIGHT-SEQ 27.02201700000001d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B0864" "ArtP")
(DBLINKS (MODBASE "P0AAF6" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0AAF6" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00005" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(UNIPROT "P0AAF6" NIL |pkarp| 3343984387 NIL NIL)
(REFSEQ "NP_415385" NIL NIL NIL NIL NIL))
(COMPONENT-OF ABC-4-CPLX)
(GENE EG11624)
(LOCATIONS CCO-CYTOPLASM)
(COMMON-NAME "ArtP") )
NIL)
(ARTQ-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-4)
(MOLECULAR-WEIGHT-SEQ 26.217085d0)
(:CREATION-DATE 3059864719)
(SYNONYMS "B0862" "ArtQ")
(DBLINKS (PFAM "PF00528" IN-FAMILY |pkarp| 3346700324 NIL NIL)
(UNIPROT "P0AE34" NIL |pkarp| 3343984411 NIL NIL)
(REFSEQ "NP_415383" NIL NIL NIL NIL NIL))
(COMPONENT-OF ABC-4-CPLX)
(GENE EG11626)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "ArtQ") )
NIL)
(|Aryl-Alcohol| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(DISPLAY-COORDS-2D (1.2124d0 0.0d0) (0.0d0 -0.7d0))
(CHEMICAL-FORMULA (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(STRUCTURE-ATOMS O R)
(COMMENT "The R group in this structure contains an aromatic ring.")
(APPEARS-IN-RIGHT-SIDE-OF ARYLSULFAT-RXN)
(SYNONYMS "an aromatic alcohol" "aryl alcohol" "an aryl alcohol")
(COMMON-NAME "a phenol") )
NIL)
(|Aryl-Aldehyde| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(COMMON-NAME "an aryl aldehyde")
(DISPLAY-COORDS-2D (1.2124d0 -2.1d0) (0.0d0 0.0d0) (1.2124d0 -0.7d0))
(CHEMICAL-FORMULA (C 1) (H 1) (O 1) (R 1))
(STRUCTURE-BONDS (2 3 1) (1 3 2))
(STRUCTURE-ATOMS O R C)
(:CREATOR |suzannep|)
(:CREATION-DATE 3129396629)
(SYNONYMS "an aromatic aldehyde" "an aryl aldehyde")
(COMMENT "The R group in this structure contains an aromatic ring.") )
NIL)
(|Aryl-Amines| T (
(OCELOT-GFP::PARENTS |All-Amines| |Aromatics|)
(DISPLAY-COORDS-2D (0.03414631d0 0.6195122d0) (-0.39512193d0 -0.2878049d0)
(-0.39512193d0 0.9902439d0) (0.03414631d0 0.004878044d0)
(-0.39512193d0 -1.0d0) (-1.0d0 0.053658485d0) (-1.0d0 0.6097561d0))
(CHEMICAL-FORMULA (C 6) (H 7) (N 1))
(MOLECULAR-WEIGHT 93.128d0)
(STRUCTURE-BONDS (7 6 1) (6 2 2) (4 1 2) (3 7 2) (2 5 1) (2 4 1) (1 3 1))
(STRUCTURE-ATOMS C C C C N C C)
(COMMON-NAME "an arylamine")
(SYNONYMS "an aniline")
(COMMENT "This compound class collects various aryl amines.")
(:CREATOR |kr|)
(:CREATION-DATE 3265125796) )
NIL)
(|Aryl-beta-D-Glucosides| T (
(OCELOT-GFP::PARENTS |Aryl-Glucosides|)
(COMMON-NAME "an aryl β-D-glucoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Aryl-Dialkyl-Phosphate| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(COMMON-NAME "an aryl dialkyl phosphate") )
NIL)
(|Aryl-Glucosides| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(COMMON-NAME "an aryl glucoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Aryl-Sulfate| T (
(OCELOT-GFP::PARENTS |Aromatics|)
(APPEARS-IN-LEFT-SIDE-OF ARYLSULFAT-RXN)
(SYNONYMS "an aryl sulfate" "a phenol sulfate")
(COMMON-NAME "an aromatic sulfate")
(:CREATOR |kr|)
(:CREATION-DATE 3263152560) )
NIL)
(|Aryl-sulfates| T (
(OCELOT-GFP::PARENTS ORGANOSULFUR)
(AROMATIC-RINGS (2 5 8 7 3 12))
(COMMON-NAME "an aryl sulfate")
(CHEMICAL-FORMULA (C 6) (H 1) (O 4) (R1 1) (R2 1) (R3 1) (R 2) (S 1))
(STRUCTURE-BONDS (12 3 :AROMATIC) (10 11 2) (8 15 1) (8 5 :AROMATIC) (7 16 1)
(7 8 :AROMATIC) (6 12 1) (6 11 1) (5 14 1) (5 2 :AROMATIC) (4 11 1) (3 9 1)
(3 7 :AROMATIC) (2 13 1) (2 12 :AROMATIC) (1 11 2))
(DISPLAY-COORDS-2D (-0.1128d0 -1.5782d0) (-0.2254d0 0.476d0)
(-1.6535d0 0.476d0) (-0.9394d0 -2.4051d0) (-0.2254d0 1.3028d0)
(-0.9394d0 -0.7516d0) (-1.6535d0 1.3028d0) (-0.9394d0 1.716d0)
(-2.4051d0 -0.0125d0) (-1.7663d0 -1.5782d0) (-0.9394d0 -1.5782d0)
(-0.9394d0 0.075d0) (0.4307d0 -0.0242d0) (0.4009d0 1.8398d0)
(-0.9394d0 2.541d0) (-2.4105d0 1.6308d0))
(STRUCTURE-ATOMS O C C O C O C C R1 O S C R2 R3 R R)
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|Arylalkylamines| T (
(OCELOT-GFP::PARENTS |Aryl-Amines|)
(CHEMICAL-FORMULA (H 2) (N 1) (R 1))
(STRUCTURE-BONDS (1 2 1))
(DISPLAY-COORDS-2D (1.4d0 0.0d0) (0.0d0 0.0d0))
(STRUCTURE-ATOMS N R)
(COMMON-NAME "an arylalkylamine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(ARYLSULFAT-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ARYLSULFAT-RXN)
(COMMENT "The gene aslA codes for a latent arylsulfatase protein in
E. coli. It is expressed only when the adjacent tyramine oxidase gene
is induced and is not directly controlled by the sulfur supply.
|CITS: [79048295] [93163050]|")
(ENZYME ARYLSULFAT-MONOMER)
(SYNONYMS "sulfatase" "aryl-sulfate sulfohydrolase")
(COMMON-NAME "arylsulfatase")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/aslA.template")
(:CREATION-DATE 3016372616)
(:CREATOR |mriley|) )
NIL)
(ARYLSULFAT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3801" "GppB" "AtsA" "AslA")
(DBLINKS (MODBASE "P25549" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00884" IN-FAMILY |pkarp| 3346700419 NIL NIL)
(REFSEQ "NP_418245" NIL NIL NIL NIL NIL)
(UNIPROT "P25549" NIL NIL |ouzounis| 3027899498))
(CATALYZES ARYLSULFAT-ENZRXN)
(PI 6.32d0)
(MOLECULAR-WEIGHT-SEQ 60.717540999999855d0)
(GENE EG10089)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/aslA.template")
(:CREATION-DATE 3016372616)
(:CREATOR |mriley|) )
NIL)
(ARYLSULFAT-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.1.6)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ARYLSULFAT-ENZRXN)
(RIGHT SULFATE |Aryl-Alcohol|)
(LEFT WATER |Aryl-Sulfate|)
(EC-NUMBER "3.1.6.1")
(COMMENT "This reaction is part of central intermediary metabolism, a
mechanism for obtaining sulfur from arylsulfate compounds.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/loners/aslA.template")
(:CREATION-DATE 3016372616)
(:CREATOR |mriley|) )
NIL)
(AS NIL (
(OCELOT-GFP::PARENTS |Elements|)
(:CREATOR |paley|)
(:CREATION-DATE 3301322514)
(COMMON-NAME "As")
(VALENCE 3 5)
(ATOMIC-WEIGHT 74.9216d0)
(ATOMIC-NUMBER 33)
(SYNONYMS "arsenic") )
NIL)
(AS+5 NIL (
(OCELOT-GFP::PARENTS |Cations|)
(:CREATOR |shearer|)
(:CREATION-DATE 3347118527)
(COMMON-NAME "As+5")
(SYNONYMS "arsenic ion")
(STRUCTURE-ATOMS AS)
(DISPLAY-COORDS-2D (0.0313d0 -1.125d0))
(ATOM-CHARGES (1 5))
(CHEMICAL-FORMULA (AS 1))
(MOLECULAR-WEIGHT 74.922d0) )
NIL)
(ASCF-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(MOLECULAR-WEIGHT-SEQ 51.02587799999985d0)
(:CREATION-DATE 3060117329)
(COMMENT "contains PTS Enzyme IIA, IIB, and IIC domains")
(SYNONYMS "B2715" "Sac" "BglF" "AscF")
(DBLINKS (MODBASE "P24241" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00367" IN-FAMILY |pkarp| 3346700372 NIL NIL)
(REFSEQ "NP_417195" NIL NIL NIL NIL NIL)
(UNIPROT "P24241" NIL |pkarp| 3064869797))
(COMPONENT-OF CPLX-153)
(GENE EG10086)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "AscF") )
NIL)
(ASCORBATE NIL (
(OCELOT-GFP::PARENTS |Vitamins|)
(COMPONENT-OF MONOMER0-2162)
(INHIBITORS-UNKMECH-OF GTP-CYCLOHYDRO-I-ENZRXN)
(ACTIVATORS-UNKMECH-OF ENZRXN-203)
(APPEARS-IN-LEFT-SIDE-OF RXN0-4322 RXN0-2461 RXN0-707)
(DBLINKS (LIGAND-CPD "C00072" NIL |kr| 3346617701 NIL NIL) (CAS "50-81-7"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -192.4d0)
(MOLECULAR-WEIGHT 176.126d0)
(CHEMICAL-FORMULA (C 6) (H 8) (O 6))
(DISPLAY-COORDS-2D (-0.7002d0 -0.6033d0) (0.018d0 -0.1973d0)
(-0.2154d0 0.6418d0) (-1.1767d0 0.6407d0) (-1.4109d0 -0.1843d0)
(-2.2359d0 -0.1843d0) (-2.4494d0 -0.9812d0) (-3.1639d0 -1.3937d0)
(-2.6484d0 0.5302d0) (-1.5892d0 1.3551d0) (0.368d0 1.2252d0)
(0.8149d0 -0.4109d0) (-1.8101d0 -0.8952d0))
(STRUCTURE-BONDS (7 8 1) (6 7 1) (6 9 1 :UP) (13 5 1 :DOWN) (5 6 1) (4 10 2)
(3 11 1) (2 12 1) (4 5 1) (3 4 1) (2 3 2) (1 5 1) (1 2 1))
(STRUCTURE-ATOMS O C C C C C C O O O O O H)
(COMMON-NAME "L-ascorbate")
(SYSTEMATIC-NAME "L-ascorbate acid")
(SYNONYMS "vitamin C" "ascorbate" "L-ascorbate (vitamin C)" "ascorbic acid") )
((GIBBS-0 -192.4d0 CITATIONS "GibbsGroups97")))
(ASL-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B1131" "PurB")
(DBLINKS (MODBASE "P0AB89" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00206" IN-FAMILY |pkarp| 3346700328 NIL NIL)
(UNIPROT "P0AB89" NIL |pkarp| 3338704378 NIL NIL)
(REFSEQ "NP_415649" NIL NIL NIL NIL NIL))
(CATALYZES AICARSYN-ENZRXN AMPSYN-ENZRXN)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 51.54273299999985d0)
(GENE EG11314)
(:CREATION-DATE 2959814156)
(:CREATOR |mriley|) )
NIL)
(ASN NIL (
(OCELOT-GFP::PARENTS |Uncharged-polar-amino-acids| |L-Amino-Acids|)
(INHIBITORS-UNKMECH-OF ASPARAGHYDA-ENZRXN ASPARAGHYDB-ENZRXN ASNSYNA-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ASNSYNA-ENZRXN)
(DBLINKS (LIGAND-CPD "C00152" NIL |kaipa| 3311532638 NIL NIL) (CAS "70-47-3"))
(:CREATION-DATE 3072030649)
(GIBBS-0 -121.7d0)
(APPEARS-IN-LEFT-SIDE-OF TRANS-RXN-262 ASPARAGHYD-RXN
ASPARAGINE--TRNA-LIGASE-RXN)
(APPEARS-IN-RIGHT-SIDE-OF ASNSYNA-RXN ASNSYNB-RXN TRANS-RXN-262)
(MOLECULAR-WEIGHT 132.119d0)
(CHEMICAL-FORMULA (C 4) (H 8) (N 2) (O 3))
(DISPLAY-COORDS-2D (0.0d0 -2.7979d0) (4.8542d0 -2.7979d0)
(1.2095d0 -0.6853d0) (2.4433d0 0.0d0) (4.8461d0 -0.008d0) (2.427d0 -2.806d0)
(1.2095d0 -2.0883d0) (3.6447d0 -0.7257d0) (3.6447d0 -2.0883d0))
(STRUCTURE-BONDS (8 9 1) (6 9 1) (6 7 1) (5 8 1) (4 8 2) (3 7 2) (9 2 1 :UP)
(1 7 1))
(STRUCTURE-ATOMS N N O O O C C C C)
(COMMON-NAME "L-asparagine")
(PKA1 2.02d0)
(SYNONYMS "asparagine" "α-aminosuccinamic acid" "(-)-asparagine"
"(S)-2,4-diamino-4-oxobutanoic acid" "(S)-asparagine"
"2,4-diamino-4-oxobutanoic acid, (S)-" "2-aminosuccinamic acid, L-"
"agedoite" "altheine" "asparagine acid" "aspartic acid β-amide"
"butanoic acid, 2,4-diamino-4-oxo-, (S)-" "L-2,4-diamino-4-oxobutanoic acid"
"L-asparatamine" "L-β-asparagine") )
((GIBBS-0 -121.7d0 CITATIONS "GibbsGroups97")))
(|ASN-tRNAs| T (
(OCELOT-GFP::PARENTS |ASX-tRNAs|)
(DBLINKS (LIGAND-CPD "C01637" NIL |kr| 3346617700 NIL NIL))
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF ASPARAGINE--TRNA-LIGASE-RXN)
(SYNONYMS "TRNA(ASN)")
(COMMON-NAME "tRNAasn") )
NIL)
(ASNS-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(:CREATION-DATE 3067809728)
(COMPONENTS ASNS-MONOMER)
(CATALYZES ASNS-ENZRXN) )
((CREDITS SRI LAST-CURATED 3359736559)
(CREDITS |keseler| LAST-CURATED 3359736559)
(COMPONENTS ASNS-MONOMER CITATIONS "[ColiSalII]")
(COMPONENTS ASNS-MONOMER COEFFICIENT 2)))
(ASNS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (ATP 76) (ASN 32))
(SYNONYMS "AsnRS")
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT)
(CITATIONS "1544480:EV-EXP-IDA-PURIFIED-PROTEIN:3359734890:keseler")
(COMMENT
"Kinetic parameters of purified wild type and mutant enzymes were measured under various conditions
|CITS: [1544480]|. Reported below are the values measured for the aminoacylation reaction at 37° C.")
(ENZYME ASNS-CPLX)
(REACTION ASPARAGINE--TRNA-LIGASE-RXN)
(:CREATION-DATE 3067730804)
(:CREATOR |kr|)
(COMMON-NAME "asparaginyl-tRNA synthetase") )
((KM (ATP 76) CITATIONS "1544480") (KM (ASN 32) CITATIONS "1544480")))
(ASNS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Asparaginyl-tRNA synthetase (AsnRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AsnRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971]|.
AsnRS is a dimer in solution |CITS: [2693216][1425658]|. Analysis of mutants suggests that the Y426 residue is
involved in ATP binding |CITS: [2009959]|; a P231L mutation, which is located in the conserved motif 2 of class II
aminoacyl-tRNA synthetases, leads to increases in the Km for asparagine and ATP |CITS: [1544480]|.
Review: |CITS: [10966471]|")
(MOLECULAR-WEIGHT-EXP 54)
(MOLECULAR-WEIGHT-SEQ 52.57035899999977d0)
(SYNONYMS "B0930" "Tss" "Lcs" "AsnS")
(DBLINKS (UNIPROT "P0A8M0" NIL |pkarp| 3354911363)
(PFAM "PF01336" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(REFSEQ "NP_415450" NIL NIL NIL NIL NIL))
(COMPONENT-OF ASNS-CPLX)
(GENE EG10094)
(:CREATION-DATE 3067730817)
(:CREATOR |kr|)
(COMMON-NAME "asparaginyl-tRNA synthetase") )
((MOLECULAR-WEIGHT-EXP 54 CITATIONS "2693216")))
(ASNSYNA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CITATIONS "1369484")
(CATALYZES ASNSYNA-ENZRXN)
(COMPONENTS ASNSYNA-MONOMER)
(:CREATION-DATE 2963847600)
(:CREATOR |mriley|) )
((COMPONENTS ASNSYNA-MONOMER COEFFICIENT 2)))
(ASNSYNA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH NH4CL)
(INHIBITORS-UNKMECH SER "5-diazo-4-oxo-L-norvaline" ASN PPI)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "asparagine synthetase")
(COMMON-NAME "aspartate-ammonia ligase")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(REACTION ASNSYNA-RXN)
(INHIBITORS-COMPETITIVE NH4CL ASN AMP)
(COMMENT "Mechanism is proposed to be BiUniUniBiPingPong |CITS: [69257187]|")
(ENZYME ASNSYNA-CPLX)
(:CREATION-DATE 2963847600)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH SER COMMENT "partial inhibitor")
(INHIBITORS-UNKMECH ASN COMMENT "end product inhibition")
(INHIBITORS-UNKMECH ASN CITATIONS "[69257187]" "[69257186]")
(INHIBITORS-UNKMECH PPI COMMENT "with respect to aspartate and ATP")
(INHIBITORS-COMPETITIVE AMP COMMENT "with respect to ATP")
(INHIBITORS-COMPETITIVE ASN COMMENT "with respect to aspartate")))
(ASNSYNA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"The crystal structure of AsnA has been solved at 2.5 A resolution |CITS: [9437423]|.
Mutational studies in Klebsiella aerogenes show that in the absence of the
glutamine-hydrolyzing asparagine synthetase B enzyme, asparagine synthetase A is not sufficient for growth on poor
nitrogen sources. The asnA asnB double mutant is an asparagine auxotroph |CITS: [6125499]|.
Regulation has been described |CITS: [11814655]|.")
(SYNONYMS "B3744" "AsnA")
(COMMON-NAME "AsnA")
(DBLINKS (MODBASE "P00963" NIL |pkarp| 3355444116 NIL NIL)
(PFAM "PF03590" IN-FAMILY |pkarp| 3346700416 NIL NIL)
(REFSEQ "NP_418200" NIL NIL NIL NIL NIL) (PDB "12AS") (PDB "11AS")
(UNIPROT "P00963"))
(COMPONENT-OF ASNSYNA-CPLX)
(PI 5.6d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 36.65050699999997d0)
(GENE EG10091)
(:CREATION-DATE 2963847600)
(:CREATOR |mriley|) )
((PI 5.6d0 CITATIONS "[93315143]")))
(ASNSYNA-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ASPARAGINESYN-PWY)
(ENZYMATIC-REACTION ASNSYNA-ENZRXN)
(RIGHT ASN PPI AMP)
(LEFT AMMONIA L-ASPARTATE ATP)
(EC-NUMBER "6.3.1.1")
(COMMENT "This is one of two reactions in E. coli that synthesizes
asparagine from aspartate. The other reaction uses glutamine as the
preferred nitrogen donor.")
(:CREATION-DATE 2963847600)
(:CREATOR |mriley|) )
NIL)
(ASNSYNB-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASNSYNB-ENZRXN)
(COMPONENTS ASNSYNB-MONOMER)
(:CREATION-DATE 2963847631)
(:CREATOR |mriley|) )
((COMPONENTS ASNSYNB-MONOMER COEFFICIENT 4)
(COMPONENTS ASNSYNB-MONOMER CITATIONS "[20056034]")))
(ASNSYNB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "6-diazo-5-oxo-norvaline")
(CITATIONS ":EV-EXP:3277835750:pkarp" "[20056034]")
(COFACTORS MG+2)
(SYNONYMS "asparagine synthetase (glutamine-hydrolysing)"
"L-aspartate:L-glutamine amido-ligase (AMP-forming)")
(COMMON-NAME "asparagine synthetase B")
(ALTERNATIVE-SUBSTRATES (GLN AMMONIA))
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(REACTION ASNSYNB-RXN)
(COMMENT
"The enzyme has an unusual mode of nitrogen transfer compared to other
glutamine amido transferases. |CITS: [93050252][12706338]|
The asparagine synthetase B enzyme from Klebsiella aerogenes is a homotetramer |CITS: [6125499]|.")
(ENZYME ASNSYNB-CPLX)
(:CREATION-DATE 2963847631)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET COMMENT "glutamine is preferred")))
(ASNSYNB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"AsnB belongs to the family of glutamine amidotransferases |CITS: [9559052]|. The crystal structure of AsnB has
been determined at 2.0 A resolution |CITS: [10587437]|.
Mutational studies in Klebsiella aerogenes show that in the absence of asparagine synthetase B, the
ammonia-dependent asparagine synthetase A enzyme is not sufficient for growth on poor nitrogen sources. The
asnA asnB double mutant is an asparagine auxotroph |CITS: [6125499]|.
")
(SYNONYMS "B0674" "AsnB")
(COMMON-NAME "AsnB")
(DBLINKS (MODBASE "P22106" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00310" IN-FAMILY |pkarp| 3346700319 NIL NIL)
(PDB "1CT9" NIL |keseler| 3300470424 NIL NIL)
(REFSEQ "NP_415200" NIL NIL NIL NIL NIL) (UNIPROT "P22106"))
(COMPONENT-OF ASNSYNB-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 62.65893599999977d0)
(GENE EG10092)
(:CREATION-DATE 2963847631)
(:CREATOR |mriley|) )
NIL)
(ASNSYNB-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-6.3.5)
(BALANCE-STATE :BALANCED)
(LEFT GLN L-ASPARTATE ATP WATER)
(RIGHT GLT ASN PPI AMP)
(EC-NUMBER "6.3.5.4")
(OFFICIAL-EC? T)
(IN-PATHWAY ASPARAGINESYN-PWY)
(ENZYMATIC-REACTION ASNSYNB-ENZRXN)
(:CREATION-DATE 2963847631)
(:CREATOR |mriley|) )
NIL)
(|asnT-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASN-tRNAs|)
(CREDITS SRI |shearer|)
(CITATIONS "11946478")
(COMMENT "tRNA(asnT) is one of four asparagine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUU")
(MODIFIED-FORM |charged-asnT-tRNA|)
(COMMON-NAME "tRNAasnT")
(GENE EG30020) )
((CREDITS SRI LAST-CURATED 3355076010)
(CREDITS |shearer| LAST-CURATED 3355076010)))
(|asnU-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASN-tRNAs|)
(CREDITS SRI |shearer|)
(CITATIONS "11946478")
(COMMENT "tRNA(asnU) is one of four asparagine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUU")
(MODIFIED-FORM |charged-asnU-tRNA|)
(COMMON-NAME "tRNAasnU")
(GENE EG30021) )
((CREDITS SRI LAST-CURATED 3355076017)
(CREDITS |shearer| LAST-CURATED 3355076017)))
(|asnV-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASN-tRNAs|)
(CREDITS SRI |shearer|)
(CITATIONS "11946478")
(COMMENT "tRNA(asnV) is one of four asparagine tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUU")
(MODIFIED-FORM |charged-asnV-tRNA|)
(COMMON-NAME "tRNAasnV")
(GENE EG30022) )
((CREDITS SRI LAST-CURATED 3355076025)
(CREDITS |shearer| LAST-CURATED 3355076025)))
(ASOLECTIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(ACTIVATORS-ALLOSTERIC-OF MALOX-ENZRXN)
(:CREATOR |pkarp|)
(:CREATION-DATE 3352228510)
(COMMON-NAME "asolectin") )
NIL)
(|Asp-3| T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATOR |ptoole|)
(:CREATION-DATE 3200754469) )
NIL)
(ASP-SEMIALDEHYDE-DEHYDROGENASE-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASP-SEMIALDEHYDE-DEHYDROGENASE-ENZRXN)
(COMPONENTS ASP-SEMIALDEHYDE-DEHYDROGENASE-MONOMER)
(:CREATION-DATE 2963848014)
(:CREATOR |mriley|) )
((COMPONENTS ASP-SEMIALDEHYDE-DEHYDROGENASE-MONOMER COEFFICIENT 2)))
(ASP-SEMIALDEHYDE-DEHYDROGENASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH CYSTINE BORATE "Tris salts" AMMONIUM NA+ K+)
(INHIBITORS-NONCOMPETITIVE IODOACETATE N-ETHYLMALEIMIDE
P-HYDROXYMERCURIBENZOATE)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(SYNONYMS "L-Aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating)"
"Aspartate-β-semialdehyde dehydrogenase" "ASA-dehydrogenase")
(COMMON-NAME "aspartate semialdehyde dehydrogenase")
(REACTION ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN)
(REACTION-DIRECTION REVERSIBLE)
(COFACTOR-BINDING-COMMENT "Nucleotide cofactor is not bound.
|CITS: [80178689]|")
(COMMENT "The reaction is the reversible substrate-dependent
reduction of NADP in the presence of phosphate or arsenate. This
reaction is formally similar to that catalyzed by
glyceraldehyde-3-phosphate dehydrogenase. |CITS: [ColiSalII]| Formation
of an acyl-enzyme intermediate has been detected. The pro-S hydrogen of
NADPH is transferred, making the enzyme a class B dehydrogenase.
|CITS: [80178689]| Analogs of substrate and NADP,
2-amino-4-oxo-5-chloropentanoate and chloroacetyl-pyridine-ADP
respectively, inactivate the enzyme. |CITS: [80178690][80178691]|")
(ENZYME ASP-SEMIALDEHYDE-DEHYDROGENASE-CPLX)
(:CREATION-DATE 2963848014)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH CYSTINE CITATIONS "14726201")
(INHIBITORS-UNKMECH BORATE CITATIONS "[HandEnzInh]" "[MethEnz17A-708]")
(INHIBITORS-UNKMECH "Tris salts" CITATIONS "[HandEnzInh]"
"[MethEnz17A-708]")
(INHIBITORS-UNKMECH AMMONIUM CITATIONS "[HandEnzInh]" "[MethEnz17A-708]")
(INHIBITORS-UNKMECH NA+ CITATIONS "[HandEnzInh]" "[MethEnz17A-708]")
(INHIBITORS-UNKMECH K+ CITATIONS "[MethEnz17A-708]" "[HandEnzInh]")
(INHIBITORS-NONCOMPETITIVE IODOACETATE CITATIONS "MethEnz17A-708"
"HandEnzInh")
(INHIBITORS-NONCOMPETITIVE N-ETHYLMALEIMIDE CITATIONS "MethEnz17A-708"
"HandEnzInh")
(INHIBITORS-NONCOMPETITIVE P-HYDROXYMERCURIBENZOATE CITATIONS
"MethEnz17A-708" "HandEnzInh")))
(ASP-SEMIALDEHYDE-DEHYDROGENASE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Each subunit of aspartate semialdehyde dehydrogenase contains three cysteine residues; two are
reactive in the native enzyme, one is partially protected by the substrate |CITS: [80178689]|.
Crystal structures of aspartate semialdehyde dehydrogenase have been solved at high resolution
|CITS: [10369777][11724560][15288787][93078266]|.")
(SYNONYMS "B3433" "Dap" "Hom" "Asd")
(COMMON-NAME "Asd")
(DBLINKS (MODBASE "P0A9Q9" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01118" IN-FAMILY |pkarp| 3346700401 NIL NIL)
(UNIPROT "P0A9Q9" NIL |pkarp| 3338704373 NIL NIL)
(PDB "1GL3" NIL |keseler| 3308421435 NIL NIL)
(PDB "1T4D" NIL |keseler| 3308420886 NIL NIL)
(PDB "1T4B" NIL |keseler| 3308420886 NIL NIL)
(REFSEQ "NP_417891" NIL |keseler| 3308420886 NIL NIL) (PDB "1BRM"))
(COMPONENT-OF ASP-SEMIALDEHYDE-DEHYDROGENASE-CPLX)
(PI 4.3d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 40.0178279999999d0)
(GENE EG10088)
(:CREATION-DATE 2963848014)
(:CREATOR |mriley|) )
((PI 4.3d0 CITATIONS "80178689")))
(|ASP-tRNAs| T (
(OCELOT-GFP::PARENTS |ASX-tRNAs|)
(DBLINKS (LIGAND-CPD "C01638" NIL |kr| 3346617700 NIL NIL))
(SCHEMA? T)
(APPEARS-IN-LEFT-SIDE-OF ASPARTATE--TRNA-LIGASE-RXN)
(SYNONYMS "TRNA(ASP)")
(COMMON-NAME "tRNAasp") )
NIL)
(ASPAMINOTRANS-DIMER NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPAMINOTRANS-ENZRXN)
(LOCATIONS CCO-CYTOPLASM)
(COMPONENTS ASPAMINOTRANS-MONOMER)
(COMMENT "The enzyme is a dimeric form composed of two identical
subunits. Each subunit has two domains, a small and a large one.
In each subunit there exists a PLP molecule
forming a Schiff base with a lysine residue. The crystal structure has
been determined |CITS:[90105323],[91035344]| Aspartate 222 and
tyrosine 70 play important roles at the active site. |CITS: [92304971] [91329396]|")
(:CREATION-DATE 2963847713)
(:CREATOR |mriley|) )
((COMPONENTS ASPAMINOTRANS-MONOMER COEFFICIENT 2)))
(ASPAMINOTRANS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "2-methylaspartate" MALEATE)
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(SYNONYMS "aspartate aminotransferase" "transaminase A (sic)"
"glutamic-oxoaloacetic transaminase" "glutamic-aspartic transaminase"
"tyrosine non-repressible aspartate aminotransferase" "AspAT")
(COMMON-NAME "aspartate transaminase")
(ALTERNATIVE-SUBSTRATES (L-ASPARTATE TYR) (L-ASPARTATE PHE))
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPAMINOTRANS-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[87250482]" "[91035344]" "[91329346]"
"[91129283]" "[78214646]" "[73023347]" "[77165127]" "[91177849]"
"[92304971]")
(COFACTOR-BINDING-COMMENT "Aminotransferases almost without exception
require pyridoxal 5'phosphate as a cofactor, which is covalently bound
to the enzyme by the formation of a Schiff base with the E-amino group
of a lysine residue|CITS:[86242111]|")
(COMMENT "The aspC-gene product, the aspartate aminotransferase, is
active in the synthesis in vivo of aspartate, tyrosine, and
phenylalanine.|CITS:[86242111]| The reaction is catalyzed via a ping-pong
Bi-Bi mechanism in which the cofactor converts between the
pyridoxal phosphate and pyridoxamine phosphate form. |CITS:[91129283]|
When an amino acid subsrate binds to to the PLP form of AspAT, a new aldimine bond is formed between the subsrate and PLP. The next step is the withdrawal of the 2-hydrogen atom of
the substrate. The deprotonation leads to the formation of a quinonoid
intermediate, which should represent one transition-state structure.
The next reaction is the addition of a proton to the coenzyme,
leading to the formation of the ketimine intermediate. The
ketimine intermediate is then hydrolyzed to form a keto acid substrate
and the PMP form of the enzyme. |CITS:[90352297]| Kinetic
studies have been made |CITS:[91177849],[91329346], [90352297]|
Aspartate aminotransferase is capable of utilizing the aromatic amino acids
as substrates. The enzyme exhibits broad substrate specificity. Direct
transamination occurs between oxaloacetate and phenylalanine.
|CITS:[78214646] [86076977]| The enzyme has been crystallized. |CITS:
[91035344] [90105323]|")
(ENZYME ASPAMINOTRANS-DIMER)
(:CREATION-DATE 2963847713)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH MALEATE CITATIONS "[91129283]")))
(ASPAMINOTRANS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0928" "Aat" "AspC")
(COMMON-NAME "AspC")
(DBLINKS (MODBASE "P00509" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00155" IN-FAMILY |pkarp| 3346700325 NIL NIL)
(PDB "1CQ8" NIL |pkarp| 3346695107 NIL NIL)
(REFSEQ "NP_415448" NIL NIL NIL NIL NIL) (PDB "5EAA") (PDB "1YOO")
(PDB "1QIT") (PDB "1QIS") (PDB "1QIR") (PDB "1IX8") (PDB "1IX7")
(PDB "1IX6") (PDB "1G7X") (PDB "1G7W") (PDB "1G4X") (PDB "1G4V")
(PDB "1BQD") (PDB "1BQA") (PDB "1B4X") (PDB "1ARI") (PDB "1ARH")
(PDB "1ARG") (PDB "1AHY") (PDB "1AHX") (PDB "1AHG") (PDB "1AHF")
(PDB "1AHE") (PDB "3AAT") (PDB "2AAT") (PDB "1SPA") (PDB "1ASN")
(PDB "1ASM") (PDB "1ASL") (PDB "1ASG") (PDB "1ASF") (PDB "1ASE")
(PDB "1ASD") (PDB "1ASC") (PDB "1ASB") (PDB "1ASA") (PDB "1ART")
(PDB "1ARS") (PDB "1AMS") (PDB "1AMR") (PDB "1AMQ") (PDB "1AIC")
(PDB "1AIB") (PDB "1AIA") (PDB "1AAW") (PDB "1AAM") (UNIPROT "P00509"))
(COMPONENT-OF ASPAMINOTRANS-DIMER)
(PI 5.8d0)
(MOLECULAR-WEIGHT-SEQ 43.57330599999986d0)
(GENE EG10096)
(:CREATION-DATE 2963847713)
(:CREATOR |mriley|) )
NIL)
(ASPAMINOTRANS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ASPARTATESYN-PWY GLUTDEG-PWY)
(ENZYMATIC-REACTION ASPAMINOTRANS-ENZRXN)
(RIGHT OXALACETIC_ACID GLT)
(LEFT L-ASPARTATE 2-KETOGLUTARATE)
(EC-NUMBER "2.6.1.1")
(COMMENT
"The reversible reaction interconverts amino acids and their keto-derivatives.
The major biosynthetic pathway to aspartate is through
transamination between oxalacetate and glutamate.")
(:CREATION-DATE 2963847713)
(:CREATOR |mriley|) )
NIL)
(ASPARAGHYD-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY ASPASN-PWY)
(ENZYMATIC-REACTION ENZRXN0-302 ASPARAGHYDA-ENZRXN ASPARAGHYDB-ENZRXN)
(RIGHT L-ASPARTATE AMMONIA)
(LEFT ASN WATER)
(EC-NUMBER "3.5.1.1")
(:CREATION-DATE 2963847690)
(:CREATOR |mriley|) )
NIL)
(ASPARAGHYDA-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "5-diazo-4-oxo-norvaline" ASN DIACETYL)
(INHIBITORS-COMPETITIVE "L-2-amino-2-carboxy-ethane-sulfonamide")
(REACTION-DIRECTION REVERSIBLE)
(SYNONYMS "AnsI" "L-asparagine aminohydrolase I" "L-asparaginase I")
(COMMON-NAME "asparaginase I")
(REACTION ASPARAGHYD-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[69257186]" "[80182029]" "[89357501]")
(COMMENT "There are two asparaginases in E. coli, I and II. The two
enzymatic activities have different properties. Gel filtration of
cell extracts indicates that the active
form of the enzyme AnsI is a dimer. AnsII is regulated by oxygen levels in
the medium, with a high level of induction apparent under anaerobic
conditions. In contrast, no definite form of regulation has been
reported for AnsI, which is generally regarded as a constitutive
enzyme. Kinetic studies have been done. |CITS:[89357501]|")
(ENZYME ANSA-CPLX)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/old/aspasyn/tmp.template")
(:CREATION-DATE 3018692165) )
((INHIBITORS-UNKMECH DIACETYL CITATIONS "[HandEnzInh]" "[80105248]")
(INHIBITORS-COMPETITIVE "L-2-amino-2-carboxy-ethane-sulfonamide" CITATIONS
"[80105248]")))
(ASPARAGHYDB-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH ASN)
(REACTION-DIRECTION REVERSIBLE)
(COMMON-NAME "asparaginase II")
(SYNONYMS "AsnII" "L-asparaginase II" "L-asparagine aminohydrolase II")
(REACTION ASPARAGHYD-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[80182029]" "[89357501]")
(COMMENT "In contrast to the other asparaginase in E. coli, gel
filtration of cell extracts indicates that the active form of AnsII
is a tetramer. AnsII is regulated by oxygen levels in the medium,
with a high level of induction apparent under anaerobic conditions.
In contrast, no definite form of regulation has been reported for
AnsI, which is generally regarded as a constitutive enzyme. |CITS:[89357501]|")
(ENZYME ANSB-CPLX)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/old/aspasyn/tmp.template")
(:CREATION-DATE 3018692165) )
NIL)
(ASPARAGINE--TRNA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS |tRNA-Charging-Reactions| EC-6.1.1)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY TRNA-CHARGING-PWY)
(ENZYMATIC-REACTION ASNS-ENZRXN)
(EC-NUMBER "6.1.1.22")
(COMMON-NAME "ASPARAGINE--TRNA-LIGASE")
(RIGHT |Charged-ASN-tRNAs| PPI AMP)
(LEFT |ASN-tRNAs| ASN ATP)
(SYNONYMS "ASPARAGINYL-TRNA SYNTHETASE") )
NIL)
(ASPARAGINE-DEG T (
(OCELOT-GFP::PARENTS |Amino-Acid-Degradation|)
(COMMENT
"This class contains pathways of degradation of the amino acid, asparagine. The pathways provide a source of nutrients and energy.")
(SCHEMA? T)
(COMMON-NAME "Asparagine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104626) )
NIL)
(ASPARAGINE-SYN T (
(OCELOT-GFP::PARENTS IND-AMINO-ACID-SYN)
(COMMENT
"This class contains pathways of the biosynthesis of the amino acid, asparagine, which is a constituent of protein and a donor of amino groups. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Asparagine")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104633) )
NIL)
(ASPARAGINESYN-PWY NIL (
(OCELOT-GFP::PARENTS ASPARAGINE-SYN)
(CREDITS O0-3 AU0-5)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(IN-PATHWAY ASPASN-PWY)
(SYNONYMS "asparagine - aspartate pathway")
(SUPER-PATHWAYS ASPASN-PWY)
(REACTION-LIST ASNSYNA-RXN ASNSYNB-RXN)
(PREDECESSORS (ASNSYNA-RXN) (ASNSYNB-RXN))
(NET-REACTION-EQUATION
"N-donor + L-aspartate + ATP = L-asparagine + PP + AMP")
(COMMENT
"Asparagine is synthesized by either of the two reactions shown here. Each is ATP driven, yielding AMP
and pyrophosphate. Null mutations in both encoding genes, asnA and asnB, result in
asparagine auxotrophy, as does a null mutation only in asnB under conditions of ammonia-limited
growth. A null mutation only in asnA has no observable phenotype.
The only known role of asparagine in the metabolism of E. coli is as a constituent of protein.
Review: Reitzer, L. (2004) \"Biosynthesis of Glutamate, Aspartate, Asparagine, L-Alanine, and D-Alanine.\" EcoSal 3.6.1.3 |CITS: [ecosal]|
")
(COMMON-NAME "asparagine biosynthesis III")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/small-amino-acids/asparasynpwy.template")
(:CREATION-DATE 3016221689)
(:CREATOR |mriley|) )
((CREDITS O0-3 REVISED 3356191893) (CREDITS AU0-5 REVISED 3356191893)))
(ASPARTASE-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPARTASE-ENZRXN)
(COMPONENTS ASPARTASE-MONOMER)
(:CREATION-DATE 2963847642)
(:CREATOR |mriley|) )
((COMPONENTS ASPARTASE-MONOMER COEFFICIENT 4)))
(ASPARTASE-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH "ALPHA-METHYL-DL-ASPARTATE" CPD-302 L-ASPARTATE)
(INHIBITORS-UNKMECH DIETHYLPYROCARBONATE P-HYDROXYMERCURIBENZOATE
55-DITHIO-BIS2-NITROBENZOIC-ACID "S-2,3-dicarboxaziride")
(INHIBITORS-OTHER PPI EDTA CIT PROPANOL)
(ALTERNATIVE-COFACTORS (MG+2 MN+2 CO+2))
(COFACTORS MG+2)
(SYNONYMS "aspartase" "fumaric aminase")
(COMMON-NAME "aspartate ammonia-lyase")
(ALTERNATIVE-SUBSTRATES)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPARTASE-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[85215599]" "[89207495]" "[86187788]"
"[84291317]")
(INHIBITORS-COMPETITIVE CPD-3722 CPD-660 "DL-2-AMINO-3-PHOSPHONOPROPRIONATE")
(COFACTOR-BINDING-COMMENT "Alkali earth metals such as Mg+2 and
transition metals such as Mn+2 have been shown to provide some degree of
activation. |CITS:[89207495]|")
(COMMENT "This reaction is analagous to the reaction catalyzed by
fumarase except that ammonia rather than water is involved in the
trans-elimination reaction.")
(ENZYME ASPARTASE-CPLX)
(:CREATION-DATE 2963847642)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH "ALPHA-METHYL-DL-ASPARTATE" COMMENT
"The enzyme exists in a pH-dependent equilibrium between two forms. The higher pH form of L-aspartase is activated by divalent metal ions and substrate analogues"
"while the low-pH enzyme form does not require any effectors for catalytic activity")
(ACTIVATORS-UNKMECH CPD-302 COMMENT
"The enzyme exists in a pH-dependent equilibrium between two forms. The higher pH form of L-aspartase is activated by divalent metal ions and substrate analogues"
"while the low-pH enzyme form does not require any effectors for catalytic activity")
(ACTIVATORS-UNKMECH L-ASPARTATE COMMENT
"The enzyme exists in a pH-dependent equilibrium between two forms. The higher pH form of L-aspartase is activated by divalent metal ions and substrate analogues"
"while the low-pH enzyme form does not require any effectors for catalytic activity")
(INHIBITORS-UNKMECH DIETHYLPYROCARBONATE CITATIONS "[HandEnzInh]"
"[85130863]")
(INHIBITORS-UNKMECH P-HYDROXYMERCURIBENZOATE CITATIONS "[HandEnzInh]"
"[74026313]")
(INHIBITORS-UNKMECH 55-DITHIO-BIS2-NITROBENZOIC-ACID CITATIONS
"[HandEnzInh]" "[74026313]")
(INHIBITORS-UNKMECH "S-2,3-dicarboxaziride" CITATIONS "[HandEnzInh]")
(INHIBITORS-OTHER :FACET COMMENT
"inhibition has been found to be due to the ability of these compounds to chelate the divalent metal ion that is required for enzyme activity at higher pH.")
(INHIBITORS-COMPETITIVE :FACET CITATIONS "[89207495]")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT
"L-aspartase shows no activity with D-aspartic acid or crotonic acid. Binding of substrate analogues at the active site of L-aspartase requires the presence of a carboxylate or the functional equivalent of a carboxylate group in the 1- and 4-positions |CITS: [89207495]|")
(COFACTORS :FACET COMMENT
"The divalent metal ion binds with the activator at high pH where both
are required for activity at a site separate from the catalytic site")))
(ASPARTASE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4139" "AspA")
(COMMON-NAME "AspA")
(DBLINKS (MODBASE "P0AC38" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00206" IN-FAMILY |pkarp| 3346700437 NIL NIL)
(UNIPROT "P0AC38" NIL |pkarp| 3343984400 NIL NIL)
(REFSEQ "NP_418562" NIL NIL NIL NIL NIL) (PDB "1JSW"))
(COMPONENT-OF ASPARTASE-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 52.35605899999983d0)
(GENE EG10095)
(CITATIONS "[87099873]")
(:CREATION-DATE 2963847642)
(:CREATOR |mriley|) )
NIL)
(ASPARTASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.3.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY GLUTDEG-PWY ASPASN-PWY)
(ENZYMATIC-REACTION ASPARTASE-ENZRXN)
(RIGHT FUM AMMONIA)
(LEFT L-ASPARTATE)
(EC-NUMBER "4.3.1.1")
(COMMENT
"This reaction is the reversible deamination of L-aspartate to form fumarate and ammonia")
(:CREATION-DATE 2963847642)
(:CREATOR |mriley|) )
NIL)
(ASPARTATE--TRNA-LIGASE-RXN NIL (
(OCELOT-GFP::PARENTS |tRNA-Charging-Reactions| EC-6.1.1)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(IN-PATHWAY TRNA-CHARGING-PWY)
(ENZYMATIC-REACTION ASPS-ENZRXN)
(EC-NUMBER "6.1.1.12")
(COMMON-NAME "ASPARTATE--TRNA-LIGASE")
(RIGHT |Charged-ASP-tRNAs| PPI AMP)
(LEFT |ASP-tRNAs| L-ASPARTATE ATP)
(SYNONYMS "ASPARTYL-TRNA SYNTHETASE") )
NIL)
(ASPARTATE-DEG T (
(OCELOT-GFP::PARENTS |Amino-Acid-Degradation|)
(COMMENT
"This class contains pathways of degradation of the amino acid, aspartate. The pathways provide a source of nutrients and energy. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Aspartate")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104627) )
NIL)
(ASPARTATE-SEMIALDEHYDE-DEHYDROGENASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION ASP-SEMIALDEHYDE-DEHYDROGENASE-ENZRXN)
(IN-PATHWAY DAPLYSINESYN-PWY HOMOSERSYN-PWY)
(RIGHT NADPH L-BETA-ASPARTYL-P)
(LEFT NADP |Pi| L-ASPARTATE-SEMIALDEHYDE)
(EC-NUMBER "1.2.1.11")
(COMMENT
"An early reaction in the synthesis of lysine, methionine and threonine.")
(:CREATION-DATE 2963848014)
(:CREATOR |mriley|) )
NIL)
(ASPARTATE-SYN T (
(OCELOT-GFP::PARENTS IND-AMINO-ACID-SYN)
(COMMENT
"This class contains pathways of biosynthesis of the amino acid, aspartate, which is a constituent of proteins and an intermediate in various other biosyntheses. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Aspartate")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104633) )
NIL)
(ASPARTATEKIN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.7.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY DAPLYSINESYN-PWY HOMOSERSYN-PWY)
(ENZYMATIC-REACTION ASPARTATEKINIII-ENZRXN ASPARTATEKINII-ENZRXN
ASPARTATEKINI-ENZRXN)
(RIGHT L-BETA-ASPARTYL-P ADP)
(LEFT L-ASPARTATE ATP)
(EC-NUMBER "2.7.2.4")
(:CREATION-DATE 2963848189)
(:CREATOR |mriley|) )
NIL)
(ASPARTATEKINI-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT THR)
(INHIBITORS-UNKMECH "L-threo-3-hydroxyserine" THR)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(COMMON-NAME "aspartate kinase I")
(SYNONYMS "ATP:L-aspartate 4-phosphotransferase" "aspartokinase I")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPARTATEKIN-RXN)
(ENZYME ASPKINIHOMOSERDEHYDROGI-CPLX)
(:CREATION-DATE 2963848189)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH THR COMMENT "cooperative")
(INHIBITORS-UNKMECH THR CITATIONS "[79000361]" "[77157778]" "[84032511]"
"[89274327]")))
(ASPARTATEKINII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(SYNONYMS "aspartokinase II")
(COMMON-NAME "aspartate kinase II")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPARTATEKIN-RXN)
(ENZYME ASPKINIIHOMOSERDEHYDROGII-CPLX)
(:CREATION-DATE 2963848137)
(:CREATOR |mriley|) )
NIL)
(ASPARTATEKINIII-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT LYS)
(INHIBITORS-UNKMECH LYS)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(COMMON-NAME "aspartate kinase III")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPARTATEKIN-RXN)
(ENZYME ASPKINIII-CPLX)
(:CREATION-DATE 2963848103)
(:CREATOR |mriley|) )
NIL)
(ASPARTATESYN-PWY NIL (
(OCELOT-GFP::PARENTS ASPARTATE-DEG ASPARTATE-SYN)
(CREDITS O0-3 AU0-5)
(SYNONYMS "aspartate biosynthesis and degradation")
(CITATIONS ":EV-EXP:3277587223:pkarp")
(IN-PATHWAY PWY0-781 ASPASN-PWY)
(SUPER-PATHWAYS PWY0-781 ASPASN-PWY)
(COMMENT
"Aspartate is synthesized from and degraded to oxaloacetate, an intermediate of the TCA cycle, by a
transamination reaction with glutamate. As shown here, AspC is the principal transaminase that
catalyzes this reaction, but TryB also catalyzes it. Null mutations in aspC do not confer aspartate
auxotrophy; null mutations in both aspC and tryB do.
Aspartate is a constituent of proteins and participates in several other biosyntheses as shown here.
Approximately 27 percent of the cell's nitrogen flows through aspartate.
Review: Reitzer, L. (2004) \"Biosynthesis of Glutamate, Aspartate, Asparagine, L-Alanine, and D-Alanine.\" EcoSal 3.6.1.3 |CITS: [ecosal]|
")
(PATHWAY-LINKS (OXALACETIC_ACID TCA)
(L-ASPARTATE PWY0-162 DENOVOPURINE2-PWY PYRIDNUCSYN-PWY
|Amino-Acid-Biosynthesis| PANTO-PWY))
(PRIMARIES (ASPAMINOTRANS-RXN NIL (L-ASPARTATE)))
(REACTION-LIST ASPAMINOTRANS-RXN)
(PREDECESSORS (ASPAMINOTRANS-RXN))
(NET-REACTION-EQUATION
"oxaloacetate + L-glutamate = L-aspartate + 2-oxoglutarate")
(COMMON-NAME "aspartate biosynthesis I")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/small-amino-acids/aspsynpwy.template")
(:CREATION-DATE 3016221689)
(:CREATOR |mriley|) )
((CREDITS O0-3 REVISED 3356192412) (CREDITS AU0-5 REVISED 3356192412)))
(ASPARTYL-ASX-TRNAS T (
(OCELOT-GFP::PARENTS |Charged-tRNAs|)
(COMMON-NAME "aspartyl-tRNAAsx")
(:CREATOR |paley|)
(:CREATION-DATE 3314378977) )
NIL)
(ASPASN-PWY NIL (
(OCELOT-GFP::PARENTS AMINO-ACID-FAMILY-SYN)
(SUB-PATHWAYS ASPARAGINESYN-PWY ASPARTATESYN-PWY GLUTDEG-PWY)
(REACTION-LIST GLUTDEG-PWY ASPARTATESYN-PWY ASPARAGINESYN-PWY ASPARTASE-RXN
ASPARAGHYD-RXN)
(PATHWAY-INTERACTIONS "Aspartate is an important metabolite. In
addition to its role in synthesis of asparagine, aspartate serves as a
precursor in synthesis of lysine, methionine and threonine, plus the
pyrimidines. Also the intermediate argininosuccinate hydrolyses to
give citrulline and aspartate.")
(PREDECESSORS GLUTDEG-PWY ASPARTATESYN-PWY ASPARAGINESYN-PWY (ASPARTASE-RXN)
(ASPARAGHYD-RXN))
(COMMENT "Aspartate undergoes a number of reactions that are not in
any linear order. One reaction converts the TCA intermediate fumarate to
aspartate. Another reaction irreversibly converts aspartate to
asparagine. A third reaction facilitates reversible interconversion of
aspartate and asparargine.
In E. coli aspartase participates in at least
two metabolic processes: the regeneration of oxaloacetate as
amino-acceptor for enabling growth on glutamate, and the formation of
fumarate and succinate during anaerobic growth on glucose.
|CITS: [84291317] [89207495]|")
(COMMON-NAME
"superpathway of biosynthesis of aspartate and asparagine; interconversion of aspartate and asparagine.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/aspasnpwy.template")
(:CREATION-DATE 3001262159)
(:CREATOR |mriley|) )
NIL)
(ASPCARBCAT-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4245" "PyrB")
(COMMON-NAME "aspartate carbamoyltransferase, PyrB subunit")
(DBLINKS (UNIPROT "P0A786" NIL |pkarp| 3354911363)
(PFAM "PF02729" IN-FAMILY |pkarp| 3346700443 NIL NIL)
(PDB "1EKX" NIL |pkarp| 3346695118 NIL NIL)
(PDB "1TUG" NIL |keseler| 3308513447 NIL NIL)
(PDB "1TU0" NIL |keseler| 3308513447 NIL NIL)
(PDB "1TTH" NIL |keseler| 3308513368 NIL NIL)
(PDB "1SKU" NIL |keseler| 3308513368 NIL NIL)
(REFSEQ "NP_418666" NIL NIL NIL NIL NIL) (PDB "9ATC") (PDB "8ATC")
(PDB "8AT1") (PDB "7AT1") (PDB "6AT1") (PDB "5AT1") (PDB "4AT1")
(PDB "3AT1") (PDB "2ATC") (PDB "2AT1") (PDB "1NBE") (PDB "1I5O")
(PDB "1F1B") (PDB "1EZZ") (PDB "1AT1") (PDB "1ACM") (PDB "1RAI")
(PDB "1RAH") (PDB "1RAG") (PDB "1RAF") (PDB "1RAE") (PDB "1RAD")
(PDB "1RAC") (PDB "1RAB") (PDB "1RAA"))
(COMPONENT-OF ASPCARBCAT-TRIMER)
(PI 6.39d0)
(MOLECULAR-WEIGHT-SEQ 34.42731799999993d0)
(GENE EG10805)
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
NIL)
(ASPCARBCAT-TRIMER NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME "aspartatetranscarbamylase, catalytic subunit")
(COMPONENT-OF ASPCARBTRANS-CPLX)
(COMPONENTS ASPCARBCAT-MONOMER)
(COMMENT "The catalytic subunit is enzymatically active but lacks the
homotropic response to the substates, and is insensitive to inhibition
by CTP |CITS: [ColiSalII]|.")
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
((COMPONENTS ASPCARBCAT-MONOMER COEFFICIENT 3)))
(ASPCARBREG-DIMER NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMON-NAME "regulatory subunit")
(COMPONENT-OF ASPCARBTRANS-CPLX)
(COMPONENTS ASPCARBREG-MONOMER)
(COMMENT "The regulatory subunit is catalytically inactive but
contains the common binding site for the allosteric effectors CTP and
ATP |CITS: [ColiSalII]|.")
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
((COMPONENTS ASPCARBREG-MONOMER COEFFICIENT 2)))
(ASPCARBREG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4244" "PyrI")
(COMMON-NAME "aspartate carbamoyltransferase, PyrI subunit")
(DBLINKS (UNIPROT "P0A7F3" NIL |pkarp| 3354911363)
(PFAM "PF01948" IN-FAMILY |pkarp| 3346700443 NIL NIL)
(PDB "1TUG" NIL |pkarp| 3346695118 NIL NIL)
(REFSEQ "NP_418665" NIL NIL NIL NIL NIL) (PDB "9ATC") (PDB "2ATC")
(PDB "1NBE") (PDB "1I5O") (PDB "1F1B") (PDB "1EZZ") (PDB "8ATC")
(PDB "8AT1") (PDB "7AT1") (PDB "6AT1") (PDB "5AT1") (PDB "4AT1")
(PDB "3AT1") (PDB "2AT1") (PDB "1RAI") (PDB "1RAH") (PDB "1RAG")
(PDB "1RAF") (PDB "1RAE") (PDB "1RAD") (PDB "1RAC") (PDB "1RAB")
(PDB "1RAA") (PDB "1AT1") (PDB "1ACM"))
(COMPONENT-OF ASPCARBREG-DIMER)
(PI 7.44d0)
(MOLECULAR-WEIGHT-SEQ 17.12060900000001d0)
(GENE EG10811)
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
NIL)
(ASPCARBTRANS-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPCARBTRANS-ENZRXN)
(COMPONENTS ASPCARBCAT-TRIMER ASPCARBREG-DIMER)
(COMMENT "The enzyme is made up of two catalytic trimers (encoded by
the gene pyrB) and three regulatory dimers (encoded by the gene pyrI)
|CITS: [Prosite] [ColiSalII] [86033987]|.")
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
((COMPONENTS ASPCARBREG-DIMER COEFFICIENT 3)
(COMPONENTS ASPCARBCAT-TRIMER COEFFICIENT 2)))
(ASPCARBTRANS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT CTP ATP)
(INHIBITORS-COMPETITIVE "N-(phosphonacetyl)-L-aspartate" SUC)
(COFACTORS-OR-PROSTHETIC-GROUPS ZN+2)
(SYNONYMS "aspartate transcarbamylase" "carbamylaspartotranskinase" "ATCase"
"carbamoyl-phosphate:L-aspartate carbamoyltransferase"
"aspartate transcarbamoylase")
(COMMON-NAME "aspartate carbamoyltransferase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ASPCARBTRANS-RXN)
(CITATIONS ":EV-EXP:3277835750:pkarp" "[92042142]" "[83195078]" "[84248054]"
"[79074799]" "[91332902]" "[83294543]")
(INHIBITORS-ALLOSTERIC CTP)
(ACTIVATORS-ALLOSTERIC ATP)
(COFACTOR-BINDING-COMMENT
"Zinc binding domain interacts with the catalytic subunit; CTP binding domain interacts with an adjacent regulatory subunit. |CITS: [79074799]|")
(COMMENT
"UTP potentiates inhibition by CTP |CITS: [83195078]|. The inhibitor CTP and the activator ATP do not simply act in inverse ways on the same equilibrium |CITS: [91332902]|.")
(ENZYME ASPCARBTRANS-CPLX)
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
((INHIBITORS-ALLOSTERIC CTP CITATIONS "[92042142]" "[83195078]")
(INHIBITORS-COMPETITIVE "N-(phosphonacetyl)-L-aspartate" COMMENT
"Competitive with respect to carbamoyl-phosphate, non-competitive with
L-aspartate. |CITS: [72076852] [HandEnzInh]| ")
(INHIBITORS-COMPETITIVE SUC COMMENT
"competitive with respect to aspartate |CITS: [94339087]|")
(ACTIVATORS-ALLOSTERIC ATP CITATIONS "[84248054]")))
(ASPCARBTRANS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.1.3)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY0-162)
(ENZYMATIC-REACTION ASPCARBTRANS-ENZRXN)
(RIGHT CARBAMYUL-L-ASPARTATE |Pi|)
(LEFT L-ASPARTATE CARBAMOYL-P)
(EC-NUMBER "2.1.3.2")
(COMMENT "The first committed reaction, but the second step, in the
biosynthesis of pyrimidine.")
(:CREATION-DATE 2963848593)
(:CREATOR |mriley|) )
NIL)
(ASPDECARBOX-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"The PanD proenzyme (π protein) is processed at the serine residue at position 25, resulting in two subunits,
α and β, which form a complex that is enzymatically active. Autocatalytic processing of purified enzyme
preparations occurs slowly at room temperature or 37 degrees C, and at a higher rate at elevated temperatures
|CITS: [9169598]|. How processing occurs in vivo remains unclear.
An S25A mutation eliminates self-cleavage of the π protein and eliminates enzymatic activity. A strain containing
this mutant form of PanD absolutely requires exogenous β-alanine for growth |CITS: [15033515]|.")
(MODIFIED-FORM MONOMER0-1843 MONOMER0-1842)
(GENE EG11747)
(DBLINKS (MODBASE "P0A790" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0A790" NIL |pkarp| 3354911363)
(ECOO157CYC "PAND-MONOMER" NIL |keseler| 3315669749 NIL NIL)
(REFSEQ "NP_414673" NIL |keseler| 3315669749 NIL NIL)
(PDB "1AW8" NIL |keseler| 3315669749 NIL NIL))
(SYNONYMS "B0131" "PanD")
(COMMON-NAME "PanD proenzyme, π protein")
(PI 6.11d0)
(MOLECULAR-WEIGHT-SEQ 13.833713d0)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/panD.template")
(:CREATION-DATE 3000590672)
(:CREATOR |mriley|) )
NIL)
(ASPDECARBOX-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-4.1.1)
(BALANCE-STATE :BALANCED)
(ENZYMATIC-REACTION ENZRXN0-4281)
(OFFICIAL-EC? T)
(IN-PATHWAY PWY-5155)
(RIGHT B-ALANINE CARBON-DIOXIDE)
(LEFT L-ASPARTATE)
(EC-NUMBER "4.1.1.11")
(COMMENT "This reaction is responsible for the
biosynthesis of β-alanine, needed for pantothenate
biosynthesis.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/panto/panD.template")
(:CREATION-DATE 3000590672)
(:CREATOR |mriley|) )
NIL)
(ASPKINIHOMOSERDEHYDROGI-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPARTATEKINI-ENZRXN HOMOSERDEHYDROGI-ENZRXN)
(COMPONENTS ASPKINIHOMOSERDEHYDROGI-MONOMER)
(COMMENT
"This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).
The two activities of aspartate kinase I are located in two separate domains. The aspartate kinase domain is
associated with the amino-terminal part of the protein, while the homoserine dehydrogenase domain is on the
carboxy-terminal part |CITS: [73028842]|.")
(:CREATION-DATE 2963848189)
(:CREATOR |mriley|) )
((COMPONENTS ASPKINIHOMOSERDEHYDROGI-MONOMER COEFFICIENT 4)))
(ASPKINIHOMOSERDEHYDROGI-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0002" "ThrD" "ThrA")
(COMMON-NAME "ThrA")
(DBLINKS (MODBASE "P00561" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00696" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414543" NIL NIL NIL NIL NIL) (UNIPROT "P00561"))
(COMPONENT-OF ASPKINIHOMOSERDEHYDROGI-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 89.12011499999984d0)
(GENE EG10998)
(:CREATION-DATE 2963848189)
(:CREATOR |mriley|) )
((GENE :FACET COMMENT "gene is composed of two cistrons, thrA and thrA2
|CITS: [80077291]|")
(ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "Three different
isozymes which differ in sensitivity to repression and inhibition by
Lysine, Methionine and Threonine. AKI (gene thrA), AKII (gene metL),
are bifunctional enzymes which both consist of an N-terminal AK domain
and a C-terminal homoserine dehyratase domain. AKI is involved in the
biosynthesis of threonine, AKII of methionine. The third isozyme
AKIII (gene lysC), is monofunctional and involved in the synthesis of lysine.
|CITS: [prosite]|")))
(ASPKINIIHOMOSERDEHYDROGII-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ASPARTATEKINII-ENZRXN HOMOSERDEHYDROGII-ENZRXN)
(COMPONENTS ASPKINIIHOMOSERDEHYDROGII-MONOMER)
(COMMENT
"This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).
The two catalytic activities of aspartate kinase II are organized in two separate
domains |CITS: [78026516]|.
Synthesis of the enzyme is repressed by the MetJ protein and S-adenosylmethionine |CITS: [86103348]|.")
(:CREATION-DATE 2963848137)
(:CREATOR |mriley|) )
((COMPONENTS ASPKINIIHOMOSERDEHYDROGII-MONOMER COEFFICIENT 2)))
(ASPKINIIHOMOSERDEHYDROGII-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3940" "MetM" "MetL")
(COMMON-NAME "MetL")
(DBLINKS (MODBASE "P00562" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P00562" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00696" IN-FAMILY |pkarp| 3346700426 NIL NIL)
(REFSEQ "NP_418375" NIL NIL NIL NIL NIL) (UNIPROT "P00562"))
(COMPONENT-OF ASPKINIIHOMOSERDEHYDROGII-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 88.88757799999986d0)
(GENE EG10590)
(:CREATION-DATE 2963848137)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT "Three different
isozymes which differ in sensitivity to repression and inhibition by
lysine, methionine and threonine. AKI (gene thrA), AKII (gene metL),
are bifunctional enzymes which both consist of an N-terminal AK domain
and a C-terminal homoserine dehydratase domain. AKI is involved in
the biosynthesis of threonine, AKII of methionine. The third isozyme
AKIII (gene lysC), is monofunctional and involved in the synthesis of
lysine. |CITS: [Prosite]| The proteins are closely similar and derive
from a common ancestor. |CITS: [83135751]|")))
(ASPKINIII-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMMENT
"This reaction, the phosphorylation of aspartate, is the first step in the biosynthesis of 4 different amino acids,
namely lysine, methionine and threonine (through homoserine), and isoleucine (which is synthesized from threonine).
In E. coli there are three isozymes that catalyze this step, namely aspartate
kinase I, II and III. Each of the kinases is controlled by one of the end products of the different pathways
(threonine, methionine and lysine, respectively). Two of the three enzymes (aspartate kinase I and II) are
multifunctional proteins, also catalyzing the reaction of homoserine dehydrogenase |CITS: [4148765]|.
Aspartate kinase III does not have an associated homoserine dehydrogenase activity (it is not part of the lysine
biosynthesis pathway).")
(SYNONYMS "aspartate kinase III")
(CATALYZES ASPARTATEKINIII-ENZRXN)
(COMPONENTS ASPKINIII-MONOMER)
(:CREATION-DATE 2963848103)
(:CREATOR |mriley|) )
((COMPONENTS ASPKINIII-MONOMER COEFFICIENT 2)))
(ASPKINIII-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B4024" "Apk" "LysC")
(COMMON-NAME "LysC")
(DBLINKS (MODBASE "P08660" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00696" IN-FAMILY |pkarp| 3346700430 NIL NIL)
(REFSEQ "NP_418448" NIL NIL NIL NIL NIL) (UNIPROT "P08660"))
(COMPONENT-OF ASPKINIII-CPLX)
(ISOZYME-SEQUENCE-SIMILARITY (ASPKINIHOMOSERDEHYDROGI-MONOMER YES)
(ASPKINIIHOMOSERDEHYDROGII-MONOMER YES))
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 48.5316469999999d0)
(GENE EG10550)
(:CREATION-DATE 2963848103)
(:CREATOR |mriley|) )
((ISOZYME-SEQUENCE-SIMILARITY :FACET COMMENT
"Three different isozymes which differ in
sensitivity to repression and inhibition by lysine, methionine and
threonine. AKI (gene thrA) is involved in the biosynthesis of
threonine, AKII (gene metL) of methionine. The third isozyme AKIII
(gene lysC), is monofunctional and involved in the synthesis of
lysine. |CITS: [Prosite]| The proteins are closely similar and derive from a
common ancestor. |CITS: [83135751] [86111734]|")))
(ASPS-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(:CREATION-DATE 3067809728)
(COMPONENTS ASPS-MONOMER)
(CATALYZES ASPS-ENZRXN) )
((CREDITS SRI LAST-CURATED 3359752828)
(CREDITS |keseler| LAST-CURATED 3359752828)
(COMPONENTS ASPS-MONOMER CITATIONS "[ColiSalII]")
(COMPONENTS ASPS-MONOMER COEFFICIENT 2)))
(ASPS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (ATP 90) (L-ASPARTATE 60) (|ASP-tRNAs| 0.6d0))
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT)
(INHIBITORS-UNKMECH CPD0-916 CPD0-915)
(INHIBITORS-COMPETITIVE CPD0-914)
(SYNONYMS "AspRS")
(CITATIONS "9171418:EV-EXP-IDA-PURIFIED-PROTEIN:3359742342:keseler")
(COMMENT
"Kinetic parameters were also measured in crude extracts of a strain overexpressing aspS |CITS: [2129559]|.")
(ENZYME ASPS-CPLX)
(REACTION ASPARTATE--TRNA-LIGASE-RXN)
(:CREATION-DATE 3067730803)
(:CREATOR |kr|)
(COMMON-NAME "aspartyl-tRNA synthetase") )
((KM (ATP 90) CITATIONS "9171418") (KM (L-ASPARTATE 60) CITATIONS "9171418")
(KM (|ASP-tRNAs| 0.6d0) CITATIONS "9171418")
(INHIBITORS-UNKMECH CPD0-916 CITATIONS "15582453")
(INHIBITORS-UNKMECH CPD0-915 CITATIONS "15582453")
(INHIBITORS-COMPETITIVE CPD0-914 CITATIONS "15582453")))
(ASPS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Aspartyl-tRNA synthetase (AspRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the
genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP
hydrolysis. AspRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology
|CITS: [2203971]|.
The enzyme is a dimer in solution |CITS: [2129559]|. Crystal structures of AspRS have been determined and allow
modelling of specific interactions with the tRNA and the reaction mechanism |CITS: [10562565][10873442][11566892]|.
The tls-1 allele of aspS consists of a P555S mutation in the highly conserved proline residue of motif 3.
It has no significant effect on substrate binding, but may affect the active site |CITS: [9171418]|. Specific interactions
of AspRS with tRNA(Asp) were deduced from the crystal structures and by mutagenesis of the tRNA substrate
|CITS: [12649491]|. The L45 loop within the OB-fold domain of AspRS appears to be responsible for
anticodon recognition |CITS: [12766171]|. Mutations that allow charging of an amber tRNA(Asp) with aspartate mostly
localize to the anticodon binding domain of AspRS, although some are far from the anticodon binding domain
|CITS: [15289581]|.
Review: |CITS: [8955904][10966471]|")
(MOLECULAR-WEIGHT-EXP 65)
(CITATIONS "342244")
(MOLECULAR-WEIGHT-SEQ 65.91335899999974d0)
(SYNONYMS "B1866" "Tls" "AspS")
(DBLINKS (PDB "1C0A" NIL |keseler| 3359737260 NIL NIL)
(PDB "1EQR" NIL |keseler| 3359737260 NIL NIL)
(MODBASE "P21889" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01336" IN-FAMILY |pkarp| 3346700345 NIL NIL)
(REFSEQ "NP_416380" NIL NIL NIL NIL NIL) (PDB "1IL2")
(UNIPROT "P21889" NIL |pkarp| 3102853742))
(COMPONENT-OF ASPS-CPLX)
(GENE EG10097)
(:CREATION-DATE 3067730817)
(:CREATOR |kr|)
(COMMON-NAME "aspartyl-tRNA synthetase") )
((MOLECULAR-WEIGHT-EXP 65 CITATIONS "2129559")))
(|aspT-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASP-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(aspT) is one of three aspartate tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUC")
(MODIFIED-FORM |charged-aspT-tRNA|)
(COMMON-NAME "tRNAaspT")
(GENE EG30023) )
((CREDITS SRI LAST-CURATED 3355076671)
(CREDITS |shearer| LAST-CURATED 3355076671)))
(|aspU-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASP-tRNAs|)
(CREDITS SRI |shearer|)
(COMMENT "tRNA(aspU) is one of three aspartate tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUC")
(MODIFIED-FORM |charged-aspU-tRNA|)
(COMMON-NAME "tRNAaspU")
(GENE EG30024) )
((CREDITS SRI LAST-CURATED 3355076678)
(CREDITS |shearer| LAST-CURATED 3355076678)))
(|aspV-tRNA| NIL (
(OCELOT-GFP::PARENTS |ASP-tRNAs|)
(CREDITS SRI |shearer|)
(CITATIONS "3295485")
(COMMENT "tRNA(aspV) is one of three aspartate tRNAs.
tRNAs are the adapters that allow synthesis of proteins from mRNAs.
Each tRNA carries a specific amino acid to the ribosome for protein synthesis.
There, the tRNA recognizes an RNA codon with its own three-nucleotide
anticodon, thus allowing synthesis of a specific peptide based on an mRNA
template.
tRNAs are processed to their active, mature forms by RNA cleavage
and by modification of their bases. RNA cleavage consists of
removal of both 5' and 3' extensions in a multistep process involving
many RNases |CITS: [11252717]|. RNases taking part in tRNA processing include |FRAME: CPLX0-3461|,
|FRAME: CPLX0-3601|, |FRAME: EG10858-MONOMER|, |FRAME: EG11620-MONOMER|, |FRAME: EG11620-MONOMER|,
|FRAME: EG11620-MONOMER|, and |FRAME: CPLX0-3602|. tRNAs are also subject to a
wide variety of base modifications catalyzed by proteins such as
|FRAME: EG11932-MONOMER|, |FRAME: EG10595-MONOMER|, |FRAME: G6364-MONOMER|, |FRAME: EG11344-MONOMER|,
|FRAME: G7199-MONOMER|, |FRAME: CPLX0-1101|, |FRAME: EG11779-MONOMER|, |FRAME: G7422-MONOMER|,
|FRAME: G7449-MONOMER|, |FRAME: EG11177-MONOMER|, |FRAME: EG10454-MONOMER|, |FRAME: EG10967-MONOMER|,
and |FRAME: EG11022-MONOMER|.
Mature tRNAs are linked via a 3' CCA sequence to their cognate
amino acid in an ATP-dependent fashion by the appropriate
amino-acid-tRNA synthetase, as shown in the |FRAME: TRNA-CHARGING-PWY|.
Subsequently, these charged tRNAs interact with the ribosome
and template mRNA to generate polypeptides. The discovery of the
role of tRNA in protein synthesis is reviewed in detail in |CITS: [7033244]|.")
(:CREATION-DATE 3068309818)
(ANTICODON "GUC")
(MODIFIED-FORM |charged-aspV-tRNA|)
(COMMON-NAME "tRNAaspV")
(GENE EG30025) )
((CREDITS SRI LAST-CURATED 3355076687)
(CREDITS |shearer| LAST-CURATED 3355076687)))
(AST-PWY NIL (
(OCELOT-GFP::PARENTS ARGININE-DEG)
(PATHWAY-LINKS (SUC TCA))
(CREDITS O0-3 AU0-5)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3117814582)
(REACTION-LIST SUCCGLUDESUCC-RXN SUCCGLUALDDEHYD-RXN SUCCORNTRANSAM-RXN
SUCCARGDIHYDRO-RXN ARGININE-N-SUCCINYLTRANSFERASE-RXN)
(PREDECESSORS (SUCCGLUDESUCC-RXN SUCCGLUALDDEHYD-RXN)
(SUCCGLUALDDEHYD-RXN SUCCORNTRANSAM-RXN)
(SUCCORNTRANSAM-RXN SUCCARGDIHYDRO-RXN)
(SUCCARGDIHYDRO-RXN ARGININE-N-SUCCINYLTRANSFERASE-RXN))
(NET-REACTION-EQUATION
"arginine + succinyl-CoA + α-ketoglutarate + NAD = 2 glutamate + succinate + CoA + 2 NH3 + CO2 + NADH")
(COMMENT
"Although some prokaryotes possess several pathways that degrade arginine, this one (called the AST
pathway for its crucial enzyme, arginine succinyl transferase) is the only arginine-degrading pathway
found in E. coli. This pathway, which yields 2 molecules of ammonia and 2 of glutamate, can
satisfy E. coli's total nitrogen requirement, but not its total carbon requirement. It does, however,
permit other organisms, for example Klebsiella aerogenes, to utilize arginine as a total source of
carbon. With the exception of the third enzyme in the pathway, succinylornithine transaminase (encoded
by astC), enzymes of this pathway from E. coli have not been characterized beyond
assaying crude extracts. Succinylornithine transaminase gained special attention and was originally
designated as argM because is can substitute for acetylornithine transaminase (encoded by
argD) in the biosynthesis of arginine. The substrates of the two enzymes differ only in ornithine's
being acetylated in the biosynthetic pathway and succinylated in the degradative pathway.
Review: Reitzer, L. (2005) \"Catabolism of Amino Acids and Related Compounds.\" EcoSal 3.4.7 |CITS: [ecosal]|")
(SYNONYMS "arginine succinyltransferase pathway" "AST pathway"
"ammonia-producing arginine catabolic pathway" "arginine catabolism")
(COMMON-NAME "arginine degradation II") )
((CREDITS O0-3 REVISED 3356191209) (CREDITS AU0-5 REVISED 3356191209)))
(|ASX-tRNAs| T (
(OCELOT-GFP::PARENTS |tRNAs|)
(COMMON-NAME "tRNAAsx")
(:CREATOR |paley|)
(:CREATION-DATE 3314378977) )
NIL)
(ATABRINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN-153)
(DBLINKS (CAS "83-89-6"))
(:CREATOR |paley|)
(:CREATION-DATE 3194283553)
(MOLECULAR-WEIGHT 399.962d0)
(CHEMICAL-FORMULA (C 23) (H 30) (N 3) (O 1) (CL 1))
(DISPLAY-COORDS-2D (0.9971347d0 -0.22922635d0) (-0.43553007d0 -0.6733524d0)
(-0.81088823d0 -0.89111745d0) (-0.07163322d0 -0.23209167d0)
(0.67048717d0 -0.7106017d0) (-0.2464183d0 -0.56446993d0)
(0.12607455d0 -1.0d0) (0.6446992d0 -0.2464183d0)
(0.12607455d0 -0.56446993d0) (0.31518626d0 -0.89111745d0)
(0.46131814d0 -0.34957016d0) (0.45272207d0 0.057306647d0)
(-0.62177646d0 -0.56446993d0) (-0.07163322d0 -0.014326632d0)
(-0.060171902d0 -0.89111745d0) (-0.81088823d0 -0.6733524d0)
(0.8309456d0 -0.3724928d0) (0.31518626d0 -0.6733524d0)
(-0.43553007d0 -0.89111745d0) (0.2893983d0 -0.2464183d0)
(-0.060171902d0 -0.6733524d0) (-0.62177646d0 -1.0d0)
(0.6446992d0 -0.04584521d0) (-0.2464183d0 -1.0d0)
(-0.2464183d0 -0.34957016d0) (0.10601723d0 -0.36676216d0) (-1.0d0 -1.0d0)
(0.5042981d0 -0.56446993d0))
(STRUCTURE-BONDS (28 18 1) (27 3 1) (26 4 1) (25 6 1) (24 15 :AROMATIC)
(23 8 1) (22 19 :AROMATIC) (21 6 :AROMATIC) (20 26 1) (19 24 :AROMATIC)
(18 9 :AROMATIC) (17 8 1) (16 3 :AROMATIC) (15 21 :AROMATIC) (14 4 1)
(13 16 :AROMATIC) (12 23 1) (11 20 1) (10 7 :AROMATIC) (10 18 :AROMATIC)
(9 21 :AROMATIC) (8 11 1) (7 15 :AROMATIC) (6 2 :AROMATIC) (5 28 1) (4 25 1)
(3 22 :AROMATIC) (2 13 :AROMATIC) (2 19 :AROMATIC) (1 17 1))
(STRUCTURE-ATOMS C C C C C C C N C C C C C C C C C C C C C C C N N C CL O)
(AROMATIC-RINGS (22 3 16 13 2 19) (2 19 24 15 21 6) (9 18 10 7 15 21))
(COMMON-NAME "atabrine")
(SYNONYMS "quinacrine mustard" "mepacrine" "chinacrin" "atebrin" "acrichine"
"quinacrine" "atabrine") )
NIL)
(|Ato-C| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(ATO-PWY NIL (
(OCELOT-GFP::PARENTS |2Comp-Pathways|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3097616059)
(SYNONYMS "Ato system")
(COMMON-NAME "AtoSC Two-Component Signal Transduction System")
(PRIMARIES (ATOC-RXN (PHOSPHO-ATOS ATOC-MONOMER) (ATOS-MONOMER PHOSPHO-ATOC)))
(REACTION-LIST ATOC-RXN ATOS-RXN)
(PREDECESSORS (ATOC-RXN ATOS-RXN) (ATOS-RXN ATOC-RXN)) )
NIL)
(|Ato-S| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(ATOA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF ACETOACETYL-COA-TRANSFER-CPLX)
(COMPONENTS ATOA-MONOMER)
(COMMON-NAME "β complex")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
((COMPONENTS ATOA-MONOMER COEFFICIENT 2)))
(ATOA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CATALYZES ENZRXN0-2776)
(COMMENT
"Based on sequence similarity, AtoA is predicted to be an acetate CoA-transferase |CITS: [12952533]|.")
(SYNONYMS "B2222" "AtoA")
(DBLINKS (MODBASE "P76459" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01144" IN-FAMILY |pkarp| 3346700355 NIL NIL)
(REFSEQ "NP_416726" NIL NIL NIL NIL NIL)
(UNIPROT "P76459" NIL |pkarp| 3102853742))
(COMMON-NAME "AtoA")
(COMPONENT-OF ATOA-CPLX)
(MOLECULAR-WEIGHT-SEQ 22.959615999999976d0)
(GENE EG11670)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
NIL)
(ATOC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Ato-C|)
(SYMMETRY :INVERTED-REPEAT)
(COMMON-NAME "AtoC transcriptional activator")
(:CREATION-DATE 3080476870)
(PI 6.24051d0)
(HISTORY "This frame was merged w/ PD02480 from Regulon-DB on 4/5/00. SMP")
(DBLINKS (MODBASE "Q06065" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "Q06065" NIL |pkarp| 3355444108 NIL NIL) (UNIPROT "Q06065"))
(APPEARS-IN-LEFT-SIDE-OF ATOC-RXN)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 52.17630299999979d0)
(GENE EG11668)
(CITATIONS ":EV-EXP:3278863360:pkarp" "[93348226]" "[87194593]" "[95214091]"
"[93128858]" "[90206041]" "[93272330]")
(COMMENT
"The regulatory protein AtoC is part of the two-component AtoS/AtoC signal
transduction system. The AtoS/AtoC system is involved in the transcriptional
regulation of the genes for acetoacetate metabolism. The atoC gene also codes
for the ornithine decarboxylase antizyme. The antizyme is a noncompetitive
inhibitor of polyamine biosynthesis. |CITS: [93348226] [87194593] [87083402]|
The protein family is EBP.")
(SYNONYMS "B2220" "AtoC"
"response regulator of ato, ornithine decarboxylase antizyme (sensor ATOS)"
"regulatory protein AtoC" "unphosphorylated regulatory protein AtoC"
"unmodified regulatory protein AtoC" "ornithine decarboxylase antizyme"
"ornithine/arginine decarboxylase inhibitor"
"acetoacetate metabolism regulatory protein AtoC")
(MODIFIED-FORM PHOSPHO-ATOC) )
NIL)
(ATOC-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080477622)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY ATO-PWY)
(RIGHT ATOS-MONOMER PHOSPHO-ATOC)
(LEFT PHOSPHO-ATOS ATOC-MONOMER)
(COMMENT
"In this reaction the regulatory protein AtoC is phosphorylated by the
phospho-AtoS sensor protein. Based on analogy to other response regulators the
phosphorylation site of regulatory protein AtoC is shown as an aspartate
residue."
"The AtoS/AtoC system is involved in the transcriptional regulation of the genes
for acetoacetate metabolism. The regulatory protein AtoC is activated by the
phosphotransferase activity of the phospho-AtoS protein. The activated AtoC
protein then functions as a positive transcriptional regulator.
|CITS: [93348226] [87194593] [87083402]|") )
NIL)
(ATOD-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF ACETOACETYL-COA-TRANSFER-CPLX)
(COMPONENTS ATOD-MONOMER)
(COMMON-NAME "α complex")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
((COMPONENTS ATOD-MONOMER COEFFICIENT 2)))
(ATOD-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Based on sequence similarity, AtoD is predicted to be an acetate CoA-transferase |CITS: [12952533]|.")
(CATALYZES ENZRXN0-2777)
(SYNONYMS "B2221" "AtoD")
(DBLINKS (MODBASE "P76458" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF01144" IN-FAMILY |pkarp| 3346700355 NIL NIL)
(REFSEQ "NP_416725" NIL NIL NIL NIL NIL) (PDB "1K6D")
(UNIPROT "P76458" NIL |pkarp| 3102853742))
(COMMON-NAME "AtoD")
(COMPONENT-OF ATOD-CPLX)
(MOLECULAR-WEIGHT-SEQ 23.52616999999999d0)
(GENE EG11669)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/fadeg/atoAD.template")
(:CREATION-DATE 3001088656)
(:CREATOR |mriley|) )
NIL)
(ATOM-CHARGES NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3243015060)
(:DOCUMENTATION
"This slot lists the charges of specific atoms within the compound.
Each value of the slot is a list of the form (A C) where A is the
index of an atom in slot Structure-Atoms, and C is the charge
of that atom.
")
(:HIDE-SLOT? T)
(:INHERITANCE-TYPE :UNIQUE)
(:DOMAIN |Chemicals|)
(:VALUE-TYPE :LIST) )
NIL)
(ATOM-CHIRALITY NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3301322514)
(:DOCUMENTATION
"In analogy to the ATOM-CHARGES slot, this slot can contain multiple values, which are lists of two elements:
first the atom number, and second a description of the stereocenter. This slot was used for the \"atom stereo parity\",
as documented for the MDL molfile format, but it is currently not used.
Instead, this slot could be recycled later for describing stereocenters according to the CIP system.")
(:HIDE-SLOT? T)
(:INHERITANCE-TYPE :UNIQUE)
(:VALUE-TYPE :LIST)
(:DOMAIN |Chemicals|) )
NIL)
(ATOMIC-NUMBER NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION "This slot stores the atomic number of a chemical element.")
(:DOMAIN |Elements|)
(:VALUE-TYPE :NUMBER)
(:NUMERIC-MINIMUM 1)
(:MAXIMUM-CARDINALITY 1) )
NIL)
(ATOMIC-WEIGHT NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION "This slot stores the atomic weight of a chemical element.")
(:DOMAIN |Elements|)
(:VALUE-TYPE :NUMBER)
(:NUMERIC-MINIMUM 1)
(:MAXIMUM-CARDINALITY 1) )
NIL)
(ATOS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Ato-S|)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(:CREATION-DATE 3080477354)
(DBLINKS (MODBASE "Q06067" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "Q06067" NIL |pick| NIL NIL NIL))
(COMMON-NAME "AtoS")
(APPEARS-IN-RIGHT-SIDE-OF ATOC-RXN)
(APPEARS-IN-LEFT-SIDE-OF ATOS-RXN)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 67.78983499999968d0)
(GENE EG11667)
(SYNONYMS "B2219" "AtoS" "sensor protein AtoS"
"sensor kinase-phosphotransferase AtoS"
"unphosphorylated sensor kinase-phosphotransferase AtoS"
"unmodified sensor kinase-phosphotransferase AtoS")
(MODIFIED-FORM PHOSPHO-ATOS) )
NIL)
(ATOS-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080477622)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY ATO-PWY)
(RIGHT ADP PHOSPHO-ATOS)
(LEFT ATP ATOS-MONOMER)
(COMMENT "In this reaction the sensor kinase-phosphotransferase AtoS is
autophosphorylated. Based on analogy to other sensor proteins the
phosphorylation site is shown as a histidine residue."
"The sensor kinase-phosphotransferase AtoS is part of the two-component AtoS/AtoC
signal transduction system. The AtoS/AtoC system is involved in the
transcriptional regulation of the genes for acetoacetate metabolism.
|CITS: [93348226] [87194593] [87083402]|") )
NIL)
(ATP NIL (
(OCELOT-GFP::PARENTS |Purine-Triphosphates| |Purine-Related|)
(COMPONENT-OF MONOMER0-160 MONOMER0-158)
(INHIBITORS-NONCOMPETITIVE-OF PHOSACETYLTRANS-ENZRXN)
(ACTIVATORS-UNKMECH-OF BIOTINLIG-ENZRXN PHOSGLYCPHOS-ENZRXN
RIBONUCLEOSIDE-DIP-REDUCTI-ENZRXN PSII-ENZRXN GLYCEROL-KIN-ENZRXN)
(INHIBITORS-UNKMECH-OF PANTOATE-BETA-ALANINE-LIG-ENZRXN GUANOSINEKIN-ENZRXN
GLUTAMINB-ENZRXN GMP-REDUCT-ENZRXN PEPSYNTH-ENZRXN PEPDEPHOSI-ENZRXN
MANNONOXIDOREDUCT-ENZRXN THI-P-SYN-ENZRXN ENZRXN0-5803 LYXK-ENZRXN
PEPCARBOXYKIN-ENZRXN DLACTDEHYDROGNAD-ENZRXN PFRUCTPHOS-ENZRXN ENZRXN0-4101
ENZRXN0-402 DTMPKI-ENZRXN)
(INHIBITORS-COMPETITIVE-OF ENZRXN0-1627 ENZRXN0-6179 MALOX-ENZRXN
GTP-CYCLOHYDRO-I-ENZRXN PREPHENATEDEHYDROG-ENZRXN
METHYLENETHFDEHYDROG-NADP-ENZRXN MANNPDEHYDROG-ENZRXN
6PGLUCONDEHYDROG-ENZRXN CITSYN-ENZRXN)
(INHIBITORS-ALLOSTERIC-OF MALIC-NAD-ENZRXN ADENYLATECYC-ENZRXN)
(ACTIVATORS-ALLOSTERIC-OF RIBONUCLEOSIDE-TRIP-REDUCT-ENZRXN
ASPCARBTRANS-ENZRXN THYKI-ENZRXN URITRANS-ENZRXN ADENYLATECYC-ENZRXN)
(DBLINKS (LIGAND-CPD "C00002" NIL |kr| 3346617701 NIL NIL) (CAS "56-65-5"))
(:CREATION-DATE 3054395125)
(APPEARS-IN-LEFT-SIDE-OF RXN0-5123 RXN0-5121 RXN0-5116 RXN0-5098
GALACTOKIN-RXN GSADENYLATION-RXN POLYPHOSPHATE-KINASE-RXN PROPKIN-RXN
CARBPSYN-RXN CTPSYN-RXN RXN0-2921 FORMYLTHFGLUSYNTH-RXN
ACETYL-COA-CARBOXYLTRANSFER-RXN CITC-RXN PHOSICITDEHASE-RXN 3.6.3.39-RXN
RXN0-5023 RXN0-3 RXN0-21 RXN0-11 2.7.1.148-RXN RXN0-4621 RXN0-4522 RXN0-4342
RXN0-4341 N-ACETYLGLUCOSAMINE-KINASE-RXN RXN0-4261
FOLYLPOLYGLUTAMATESYNTH-RXN RXN0-3901 RIBOSYLNICOTINAMIDE-KINASE-RXN
RXN-5741 RXN0-2161 RXN0-948 RXN0-1402 NANK-RXN PHOSGLYPHOS-RXN ASNSYNA-RXN
ASNSYNB-RXN RXN0-2361 ALLOSE-KINASE-RXN FRUCTOKINASE-RXN RXN0-1961 RXN0-1139
RXN0-1140 RXN0-1141 DHBAMPLIG-RXN 4-COUMARATE--COA-LIGASE-RXN RXN0-2023
PROTEIN-TYROSINE-KINASE-RXN TRANS-RXN0-202 ABC-32-RXN RXN0-1401 R166-RXN
RXN0-962 BIOTINLIG-RXN TRANS-RXN0-162 PHENYLACETATE--COA-LIGASE-RXN
2.7.9.3-RXN GLUCOKIN-RXN RXN0-745 RXN0-742 LYXK-RXN RXN0-704 GDPKIN-RXN
DGDPKIN-RXN DADPKIN-RXN DUDPKIN-RXN CDPKIN-RXN UDPKIN-RXN DTDPKIN-RXN
DCDPKIN-RXN TRANS-RXN-224 ABC-2-RXN RXN0-382 TRANS-RXN-250 TRANS-RXN-34
ABC-42-RXN ABC-70-RXN ATPSYN-RXN PEPDEPHOS-RXN ENTMULTI-RXN TRANS-RXN-32
TRANS-RXN-37 ABC-64-RXN ABC-63-RXN RXN0-293 RXN0-309
PROPIONATE--COA-LIGASE-RXN THIFAMP-RXN GKI-RXN DCUS-RXN 2.7.7.1-RXN
TAGAKIN-RXN PYRAMKIN-RXN PROLINE-MULTI GUANOSINEKIN-RXN GSPSYN-RXN
GMKALT-RXN GDPPYPHOSKIN-RXN ENTF-RXN DURIDKI-RXN DARABKIN-RXN
COBINAMIDEKIN-RXN TRANS-RXN-7 TRANS-RXN-2 ABC-9-RXN ABC-8-RXN ABC-7-RXN
ABC-5-RXN ABC-4-RXN ABC-37-RXN ABC-36-RXN ABC-35-RXN ABC-34-RXN ABC-33-RXN
ABC-3-RXN ABC-29-RXN ABC-28-RXN ABC-27-RXN ABC-26-RXN ABC-25-RXN ABC-24-RXN
ABC-23-RXN ABC-22-RXN ABC-20-RXN ABC-19-RXN ABC-18-RXN ABC-16-RXN ABC-15-RXN
ABC-14-RXN ABC-13-RXN ABC-12-RXN ABC-11-RXN ABC-10-RXN
VALINE--TRNA-LIGASE-RXN TYROSINE--TRNA-LIGASE-RXN
TRYPTOPHAN--TRNA-LIGASE-RXN TRNA-ADENYLYLTRANSFERASE-RXN
THREONINE--TRNA-LIGASE-RXN SERINE--TRNA-LIGASE-RXN PROLINE--TRNA-LIGASE-RXN
PHENYLALANINE--TRNA-LIGASE-RXN METHIONINE--TRNA-LIGASE-RXN
LYSINE--TRNA-LIGASE-RXN LEUCINE--TRNA-LIGASE-RXN ISOLEUCINE--TRNA-LIGASE-RXN
HISTIDINE--TRNA-LIGASE-RXN GLYCINE--TRNA-LIGASE-RXN
GLUTAMINE--TRNA-LIGASE-RXN CYSTEINE--TRNA-LIGASE-RXN
ASPARTATE--TRNA-LIGASE-RXN ASPARAGINE--TRNA-LIGASE-RXN
ARGININE--TRNA-LIGASE-RXN ALANINE--TRNA-LIGASE-RXN
|RNA-3'-PHOSPHATE-CYCLASE-RXN| PROPIONYL-COA-CARBOXY-RXN NAD-SYNTH-GLN-RXN
GMP-SYN-GLUT-RXN FGAMSYN-RXN GMP-SYN-NH3-RXN GLYRIBONUCSYN-RXN
FORMATETHFLIG-RXN BIOTIN-CARBOXYL-RXN ARGSUCCINSYN-RXN DETHIOBIOTIN-SYN-RXN
AIRS-RXN UDP-NACMURALGLDAPLIG-RXN UDP-NACMURALGLDAPAALIG-RXN
UDP-NACMURALA-GLU-LIG-RXN UDP-NACMUR-ALA-LIG-RXN SAICARSYN-RXN
PANTOATE-BETA-ALANINE-LIG-RXN GLUTCYSLIG-RXN GLUTATHIONE-SYN-RXN
DIHYDROFOLATESYNTH-RXN DALADALALIG-RXN NAD-SYNTH-NH3-RXN GLUTAMINESYN-RXN
SUCCCOASYN-RXN O-SUCCINYLBENZOATE-COA-LIG-RXN ACYLCOASYN-RXN
ACYLACPSYNTH-RXN ACETATE--COA-LIGASE-RXN GLURS-RXN ADENYLATECYC-RXN
PEPCARBOXYKIN-RXN PEPSYNTH-RXN SULFATE-ADENYLYLTRANS-RXN
PANTEPADENYLYLTRAN-RXN NICONUCADENYLYLTRAN-RXN GLUC1PADENYLTRANS-RXN
FADSYN-RXN PRPPSYN-RXN H2PTERIDINEPYROPHOSPHOKIN-RXN GTPPYPHOSKIN-RXN
UMPKI-RXN THI-P-KIN-RXN PYRIMSYN3-RXN NUCLEOSIDE-DIP-KIN-RXN GUANYL-KIN-RXN
DTMPKI-RXN CMPKI-RXN ADENYL-KIN-RXN GLUTKIN-RXN ASPARTATEKIN-RXN
ACETYLGLUTKIN-RXN ACETATEKIN-RXN XYLULOKIN-RXN THYKI-RXN THIKIN-RXN
THIAZOLSYN3-RXN TETRAACYLDISACC4KIN-RXN SHIKIMATE-KINASE-RXN RIBOKIN-RXN
RIBOFLAVINKIN-RXN RHAMNULOKIN-RXN PYRIDOXKIN-RXN PNKIN-RXN
PANTOTHENATE-KIN-RXN OHMETPYRKIN-RXN NAD-KIN-RXN MANNKIN-RXN INOSINEKIN-RXN
HOMOSERKIN-RXN GLYCEROL-KIN-RXN GLY3KIN-RXN GLUCONOKIN-RXN FUCULOKIN-RXN
DIACYLGLYKIN-RXN DEPHOSPHOCOAKIN-RXN DEOXYGLUCONOKIN-RXN
DEHYDDEOXGALACTKIN-RXN ADENYLYLSULFKIN-RXN 6PFRUCTPHOS-RXN 1PFRUCTPHOSN-RXN
S-ADENMETSYN-RXN COBALADENOSYLTRANS-RXN BTUR2-RXN GARTRANSFORMYL2-RXN
UHPB-RXN TORS-RXN RSTB-RXN RCSF-RXN RCSC-RXN PHOR-RXN PHOQ-RXN NRIIPHOS-RXN
NARX-RXN NARQ-RXN KDPD-RXN HYDH-RXN EVGS-RXN ENVZ-RXN CREC-RXN CPXA-RXN
CHEA-RXN BASS-RXN BARA-RXN BAES-RXN ATOS-RXN ARCB-RXN)
(MOLECULAR-WEIGHT 507.183d0)
(CHEMICAL-FORMULA (C 10) (H 16) (N 5) (O 13) (P 3))
(DISPLAY-COORDS-2D (5.313d0 -3.3049d0) (7.2891d0 -1.3253d0)
(5.3105d0 -1.6639d0) (9.9778d0 -4.7867d0) (6.7454d0 -3.0291d0)
(9.4969d0 -5.4609d0) (7.9875d0 -3.9567d0) (6.1335d0 -2.4826d0)
(8.1839d0 -3.2502d0) (7.2769d0 -4.3761d0) (7.9875d0 -5.6161d0)
(8.7072d0 -5.2058d0) (8.7072d0 -4.3761d0) (7.5247d0 -2.7725d0)
(7.7737d0 -1.9874d0) (8.5987d0 -1.9874d0) (8.8524d0 -2.7725d0)
(7.2769d0 -5.2058d0) (9.4949d0 -4.1282d0) (5.3121d0 -2.4844d0)
(7.9852d0 -6.4411d0) (9.0842d0 -1.3204d0) (4.4916d0 -2.4844d0)
(3.6666d0 -3.3112d0) (3.6641d0 -1.6612d0) (3.6657d0 -2.4862d0)
(2.8407d0 -2.4862d0) (2.0157d0 -3.313d0) (2.0132d0 -1.663d0)
(1.1898d0 -2.488d0) (2.0148d0 -2.488d0))
(STRUCTURE-BONDS (30 31 1) (29 31 1) (28 31 2) (27 31 1) (27 26 1) (25 26 1)
(24 26 2) (23 26 1) (16 22 1 :DOWN) (21 11 1) (1 20 2) (15 2 1 :DOWN)
(3 20 1) (6 4 :AROMATIC) (4 19 :AROMATIC) (5 8 1) (14 5 1 :UP)
(12 6 :AROMATIC) (10 7 :AROMATIC) (7 13 :AROMATIC) (8 20 1) (9 14 1)
(9 17 1) (23 20 1) (18 10 :AROMATIC) (12 11 :AROMATIC) (11 18 :AROMATIC)
(13 12 :AROMATIC) (19 13 :AROMATIC) (14 15 1) (15 16 1) (16 17 1)
(17 19 1 :UP))
(STRUCTURE-ATOMS O O O C C N N O O C C C C C C C C N N P N O O O O P O O O O
P)
(GIBBS-0 -60.6d0)
(APPEARS-IN-RIGHT-SIDE-OF ATPPHOSPHORIBOSYLTRANS-RXN)
(AROMATIC-RINGS (4 6 12 13 19) (7 10 18 11 12 13))
(CHARGE -4)
(COMMON-NAME "ATP")
(SYNONYMS "adenylpyrophosphate" "adenosine-triphosphate"
"adenosine-5'-triphosphate") )
NIL)
(ATPA-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3065819321)
(COMPONENTS ATPA-MONOMER)
(COMMENT
"The alpha subunit plays an essential role in the catalytic mechanism of the
enzyme and in the binding and coupling between the F-1 and F-O complexes. The
alpha-subunit also contains an adenine-specific binding site which is
noncatalytic, nonregulatory and not essential for enzyme assembly in vitro. Its
function has not yet been determined. The alpha subunit complex is a homotrimer.
|CITS: [89034048]|")
(COMMON-NAME "α subunit complex")
(COMPONENT-OF F-1-CPLX) )
((COMPONENTS ATPA-MONOMER COEFFICIENT 3)))
(ATPA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(SYNONYMS "B3734" "Unc" "UncA" "PapA" "AtpA")
(DBLINKS (MODBASE "P0ABB0" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P0ABB0" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02874" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(UNIPROT "P0ABB0" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418190" NIL NIL NIL NIL NIL))
(GENE EG10098)
(LOCATIONS CCO-CYTOPLASM CCO-PM-BAC-NEG)
(PI 6.16d0)
(MOLECULAR-WEIGHT-SEQ 55.222007999999796d0)
(COMMON-NAME "ATP synthase, F1 complex, α subunit")
(COMPONENT-OF ATPA-CPLX) )
NIL)
(ATPASE-1-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES TRANS-ENZRXN-2)
(SPECIES ECOLI)
(COMMON-NAME "potassium ion P-type ATPase transporter")
(COMMENT
"The kdpFABC genes encode an ATP-dependent high affinity P-Type ATPase potassium ion
transporter |CITS: [89078396] [89174642]|. The transporter has a high affinity and substrate specificity for
potassium ion (Km= 10 μM). It is activated by magnesium ion with an affinity constant of
80 μM |CITS: [89078396]|. ATP-driven potassium ion transport has been observed when the Kdp
complex is reconstituted in vesicles |CITS: [95204461]|. Kdp is unusual among P- type ATPases in
having three subunits: one for energy coupling (KdpB), one for substrate binding and transport (KdpA),
and one for associating the first two subunits together (KdpC) |CITS: [95204461]|. The largest subunit,
KdpB, is the homologue of other P-type ATPases. Neither of the other two subunits, KdpA or KdpC, has
homologues in other P-type ATPases. Mutation experiments have shown that all three subunits are
required for normal Kdp activity |CITS: [95204461]|. KdpA is highly hydrophobic with many predicted
membrane-spanning segments |CITS:[95204461]|. The fact that most mutants displaying lower affinity for
potassium ion had mutations that altered KdpA implies that KdpA has a major role in determining affinity for
potassium ion |CITS: [95204461]|. A truncated version of KdpA with only the N-terminal 135 amino acids
(which contains two transmembrane segments) is able to rescue a K+ transporter mutant in
media with low K+ concentration even without KdpA and KdpB. This is predicted to occur in
response to the membrane potential |CITS:[11344160]|. KdpC is predicted to have only a single
membrane-spanning segment |CITS:[95204461]|. Complementation experiments with complete and
truncated KdpC proteins and hybrids as well as sequence analysis of KdpC proteins have identified 4
major parts to the protein. There are two highly conserved regions (regions 2 and 4) and two highly
variable regions (1 and 3). Region 1, the N-terminal region, is predicted to be the membrane spanning
segment |CITS:[11248697]|. Mutational analysis also showed that KdpC is involved in linking KdpA and
KdpB together, serving to assemble and stabilize the KdpFABC complex |CITS: [99077600]|. A fourth gene
on the same operon, kdpF, encodes a small non-essential polypeptide, which was shown by
SDS-polyacrylamide gel analysis of the transporter complex to be associated with and stabilize the
KdpFABC complex in vivo |CITS: [99005984] [20076462]|. The kdp genes are expressed
when growth is limited by the availability of potassium ion |CITS:[89078396]|. Two other important
potassium ion uptake systems in E. coli include Trk and Kup |CITS: [95204461]|.")
(COMPONENTS MONOMER0-12 EG10513-MONOMER KDPB-MONOMER EG10515-MONOMER)
(:CREATOR |jchen|)
(:CREATION-DATE 3200911910) )
NIL)
(ATPB-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(DBLINKS (MODBASE "P0AB98" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00119" IN-FAMILY |pkarp| 3346700416 NIL NIL)
(UNIPROT "P0AB98" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418194" NIL NIL NIL NIL NIL))
(PI 6.8d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 30.303199999999965d0)
(GENE EG10099)
(COMMENT "The a subunit of the F0 complex plays a critical role in the proton
translocation mechanism. |CITS: [89123453] [93147708]|")
(SYNONYMS "B3738" "UncB" "PapD" "AtpB" "protein 6" "chain A")
(COMMON-NAME "ATP synthase, F0 complex, a subunit")
(COMPONENT-OF F-O-CPLX) )
NIL)
(ATPC-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(SYNONYMS "B3731" "Unc" "UncC" "PapG" "AtpC")
(DBLINKS (UNIPROT "P0A6E6" NIL |pkarp| 3354911363)
(PFAM "PF02823" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(REFSEQ "NP_418187" NIL NIL NIL NIL NIL) (PDB "1QO1") (PDB "1FS0")
(PDB "1AQT"))
(PI 5.73d0)
(LOCATIONS CCO-CYTOPLASM CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 15.068242999999992d0)
(GENE EG10100)
(COMMENT
"The epsilon subunit appears to play an important role in coupling the catalytic
site events with proton translocation in association with the gamma subunit.
The coupling involves conformational changes and probable translocations of one
or both subunits. This subunit is also required for binding of the F-1 complex
to the F-O complex. |CITS: [96216373] [90303438]|")
(COMMON-NAME "ATP synthase, F1 complex, ε subunit")
(COMPONENT-OF F-1-CPLX) )
NIL)
(ATPD-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3065819321)
(COMMENT
"The beta subunit contains the catalytic site. The complex is a homotrimer.
|CITS: [91358411] [90303438]|")
(COMMON-NAME "β subunit complex")
(COMPONENTS ATPD-MONOMER)
(COMPONENT-OF F-1-CPLX) )
((COMPONENTS ATPD-MONOMER COEFFICIENT 3)))
(ATPD-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(SYNONYMS "B3732" "Unc" "UncD" "PapB" "AtpD")
(DBLINKS (SWISSMODEL "P0ABB4" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02874" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(UNIPROT "P0ABB4" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418188" NIL NIL NIL NIL NIL))
(PI 5.1d0)
(LOCATIONS CCO-CYTOPLASM CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 50.32534299999982d0)
(GENE EG10101)
(COMMON-NAME "ATP synthase, F1 complex, β subunit")
(COMPONENT-OF ATPD-CPLX) )
NIL)
(ATPE-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3065819321)
(COMPONENT-COEFFICIENTS 10)
(COMMON-NAME "c subunit complex")
(COMPONENTS ATPE-MONOMER)
(COMPONENT-OF F-O-CPLX) )
((COMPONENT-COEFFICIENTS 10 COMMENT
"The stoichiometry of the subunits has not been fully resolved. Values have been
obtained ranging from 10 to 18. |CITS: [90303438]|")
(COMPONENTS ATPE-MONOMER COEFFICIENT 10)))
(ATPE-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"The c subunit of the F0 complex of ATP synthase is absolutely required for proton translocation and is also
necessary for binding of the F-1 complex. This is the subunit affected by the
inhibitor dicyclohexylcarbodiimide. The stoichiometry of the subunits has not
been fully resolved. Values have been obtained ranging from 10 to 18.
|CITS: [93147708] [92329454] [92041957] [90303438]|
The initiating methionine is cleaved |CITS: [9868784]|.")
(:CREATION-DATE 3065819321)
(DBLINKS (MODBASE "P68699" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P68699" NIL |pkarp| 3354911363)
(PFAM "PF00137" IN-FAMILY |pkarp| 3346700416 NIL NIL)
(REFSEQ "NP_418193" NIL NIL NIL NIL NIL) (PDB "1QO1") (PDB "1L6T")
(PDB "1J7F") (PDB "1IJP") (PDB "1ATY") (PDB "1A91"))
(PI 4.69d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 8.256097000000002d0)
(GENE EG10102)
(SYNONYMS "B3737" "UncE" "PapH" "AtpE"
"dicyclohexylcarbodiimide-binding protein" "lipid-binding protein" "c chain")
(COMMON-NAME "ATP synthase, F0 complex, c subunit")
(COMPONENT-OF ATPE-CPLX) )
NIL)
(ATPF-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3065819321)
(COMMENT
"The b subunit complex is involved in binding the F-1 complex to the F-O complex
and is necessary for the assembly of the F-O complex. Most of the subunit
complex is exposed to the cytoplasm with only the short hydrophobic amino
terminus embedded in the membrane. |CITS: [85234519] [93147708]|")
(COMMON-NAME "b subunit complex")
(COMPONENTS ATPF-MONOMER)
(COMPONENT-OF F-O-CPLX) )
((COMPONENTS ATPF-MONOMER COEFFICIENT 2)))
(ATPF-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(DBLINKS (MODBASE "P0ABA0" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00430" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(UNIPROT "P0ABA0" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418192" NIL NIL NIL NIL NIL) (PDB "1L2P"))
(PI 6.26d0)
(MOLECULAR-WEIGHT-SEQ 17.263932999999998d0)
(GENE EG10103)
(SYNONYMS "B3736" "Unc" "UncF" "PapF" "AtpF" "B chain")
(COMMON-NAME "ATP synthase, F0 complex, b subunit")
(COMPONENT-OF ATPF-CPLX) )
((LOCATIONS :FACET COMMENT
"Most of the subunit complex is exposed to the cytoplasm with only the short
hydrophobic amino terminus embedded in the membrane. |CITS: [85234519]|")))
(ATPG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(SYNONYMS "B3733" "Unc" "UncG" "PapC" "AtpG")
(DBLINKS (MODBASE "P0ABA6" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00231" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(UNIPROT "P0ABA6" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418189" NIL NIL NIL NIL NIL) (PDB "1FS0"))
(PI 8.96d0)
(LOCATIONS CCO-CYTOPLASM CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 31.577378999999958d0)
(GENE EG10104)
(COMMENT
"The gamma subunit appears to play an important role in coupling the catalytic
site events with proton translocation in association with the epsilon subunit.
The coupling involves conformational changes and probable translocations of
one or both subunits. |CITS: [96216373]|")
(COMMON-NAME "ATP synthase, F1 complex, γ subunit")
(COMPONENT-OF F-1-CPLX) )
NIL)
(ATPH-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3065819321)
(SYNONYMS "B3735" "Unc" "UncH" "PapE" "AtpH")
(DBLINKS (MODBASE "P0ABA4" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00213" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(UNIPROT "P0ABA4" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418191" NIL NIL NIL NIL NIL) (PDB "1ABV"))
(PI 5.11d0)
(LOCATIONS CCO-CYTOPLASM CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 19.332192d0)
(GENE EG10105)
(COMMENT
"The delta subunit is required for binding the F-1 complex to the F-O complex.
It may also block proton conduction through the F-O complex. |CITS: [90148989] [94308197]|")
(COMMON-NAME "ATP synthase, F1 complex, δ subunit")
(COMPONENT-OF F-1-CPLX) )
NIL)
(ATPPHOSPHORIBOSYLTRANS-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH PHOSPHORIBOSYL-ATP "AMP + HISTIDINE > AMP"
GUANOSINE-5DP-3DP)
(PHYSIOLOGICALLY-RELEVANT GUANOSINE-5DP-3DP AMP ADP HIS)
(COFACTORS MG+2)
(SYNONYMS "phosphoribosyl ATP pyrophosphorylase"
"adenosine triphosphate phosphoribosyl-transferase"
"1-(5'-phosphoribosyl)-ATP:pyrophosphate phosphoribosyltransferase"
"phosphoribosyladenosine triphosphate synthetase"
"phosphoribosyl-ATP synthetase")
(COMMON-NAME "ATP phosphoribosyltransferase")
(REACTION-DIRECTION REVERSIBLE)
(REACTION ATPPHOSPHORIBOSYLTRANS-RXN)
(CITATIONS "[ColiSalII]")
(INHIBITORS-ALLOSTERIC "2-THIAZOLE-ALANINE" HIS)
(INHIBITORS-COMPETITIVE ADP AMP)
(COFACTOR-BINDING-COMMENT "It is probably the magnesium-complexed
forms of both substrates which are catalytically active. It is
possible that the enzyme itself at least weakly binds magnesium. It
is possible that Mg could have an effect on the conformation of the
enzyme|CITS:[76267506]|")
(COMMENT "The synthesis of phosphoribosyl-ATP involves a displacement
on C-1 of PRPP (5-phospho-α-D-ribose-1-diphosphate)
by N-1 of the purine ring of ATP. Mg ion dependent condensation
releases a pyrophosphate molecule, inverts the ribose moiety derived
from PRPP from the α to the β configuration, and is
reversible.The flow of intermediates through the histidine
biosynthetic pathway can be adjusted by varying the enzymatic
activity of the hisG protein. Although hisG protein is a hexamer
under near-physiological conditions, the aggregation state of the
protein is influenced in complex ways by temperature, ionic strength, pH
and the presence of ligands. The Km of the enzyme for ATP is much
lower than the intracellular ATP concentration whereas the Km for PRPP
is probably closer to the intracellular PRPP concentration; therefore,
the rate of histidine biosynthesis most likely is directly affected by
variations in the intracellular PRPP pool size.|CITS:[ColiSalII]| Substrate
and product kinetics were studied by Morton and Parsons and for the S. typhimurium
enzyme by Martin |CITS:[76267506],[martinjbc238257-268]|")
(ENZYME ATPPHOSRIBOSTRANS)
(:CREATION-DATE 2956698897)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH "AMP + HISTIDINE > AMP" COMMENT
"In this enzyme the presence of the end product histidine" "is
necessary for the enzyme to exhibit sensitivity to energy charge. This behavior has been shown to result from synergistic interaction between histidine and AMP. Histidine affected the synthetase reaction weakly and AMP had almost no effect but the two compounds were strongly inhibitory when added together")
(INHIBITORS-UNKMECH GUANOSINE-5DP-3DP COMMENT
"In the presence of partially inhibiting concentrations of histidine"
"the alarmone which is a positive effector of his operon transcription does not inhibit hisG enzyme activity by itself"
"however in the presence of moderate histidine concentration"
"physiologically sigificant concentrations of ppGpp strongly inhibit hisG enzyme activity in a positively cooperative manner")
(INHIBITORS-COMPETITIVE :FACET COMMENT
"inhibition of histidine biosynthesis in response to a decrease in energy charge is greater when histidine is present than when its supply is restricted")
(INHIBITORS-COMPETITIVE AMP COMMENT "In the absence of histidine")
(INHIBITORS-ALLOSTERIC HIS COMMENT
"an example of feedback inhibition histine inhibits the synthetic
reaction much more strongly than the reverse reaction")
(REACTION-DIRECTION :FACET COMMENT
"although the reaction equilibrium in isolation favors phosphorolysis"
"in the cell the synthetic direction is favored because the PRPP is utilized in a subsequent irreversible reaction")))
(ATPPHOSPHORIBOSYLTRANS-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.4.2)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY HISTSYN-PWY)
(ENZYMATIC-REACTION ATPPHOSPHORIBOSYLTRANS-ENZRXN)
(RIGHT ATP PRPP)
(LEFT PHOSPHORIBOSYL-ATP PPI)
(EC-NUMBER "2.4.2.17")
(COMMENT "This is the first reaction of histidine biosynthesis")
(:CREATION-DATE 2956698897)
(:CREATOR |mriley|) )
NIL)
(ATPPHOSRIBOSTRANS NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES ATPPHOSPHORIBOSYLTRANS-ENZRXN)
(COMPONENTS ATPPHOSRIBOSTRANS-MONOMER)
(COMMENT "Each subunit of the hisG protein hexamer contains one
allosteric site for histidine binding, which does not seem to overlap
the subunit's active site.")
(:CREATION-DATE 2956698897)
(:CREATOR |mriley|) )
((COMPONENTS ATPPHOSRIBOSTRANS-MONOMER COEFFICIENT 6)))
(ATPPHOSRIBOSTRANS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2019" "HisG")
(DBLINKS (MODBASE "P60757" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P60757" NIL |pkarp| 3354911363)
(PFAM "PF01634" IN-FAMILY |pkarp| 3346700349 NIL NIL)
(REFSEQ "NP_416523" NIL NIL NIL NIL NIL))
(COMPONENT-OF ATPPHOSRIBOSTRANS)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 33.36666299999997d0)
(GENE EG10449)
(COMMON-NAME "ATP phosphoribosyltransferase monomer")
(:CREATION-DATE 2956698897)
(:CREATOR |mriley|) )
NIL)
(ATPSYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATION-DATE 3064091736)
(COMPONENTS F-O-CPLX F-1-CPLX)
(COMMENT
"The enzyme is made up of two subcomplexes, the F-1 complex and the F-O complex.
There are eight total subunits all required for activity. The F-1 complex is
the catalytic unit. The F-O complex anchors the F-1 complex to the membrane
and also forms the proton channel. |CITS: [89123355] [90303438] [93252965]|")
(CATALYZES ATPSYN-ENZRXN) )
((COMPONENTS F-1-CPLX COEFFICIENT 1) (COMPONENTS F-O-CPLX COEFFICIENT 1)))
(ATPSYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "aurovertin" "citreoviridin" "efrapeptin" "venturicidin"
"oligomycin" "dicyclohexylcarbodiimide" "4-chloro-7-nitrobenzofurazan"
"fluoroaluminate")
(CITATIONS "89123355:EV-EXP-IMP-REACTION-BLOCKED:3277662343:ipaulsen"
"89123355:EV-EXP-IDA-PURIFIED-PROTEIN:3277662343:ipaulsen")
(:CREATION-DATE 3064091736)
(REACTION-DIRECTION REVERSIBLE)
(REACTION ATPSYN-RXN)
(ALTERNATIVE-SUBSTRATES (ATP ITP) (ATP GTP) (ADP IDP) (ADP GDP) (ADP GDP IDP)
(ATP GTP ITP))
(COFACTORS MG+2)
(COMMENT
"ATP synthase catalyzes the synthesis of ATP under aerobic cell growth. The
energy derived from oxygen respiration is coupled to ATP synthesis by a process
known as electron transport-linked phosphorylation. Under anaerobic growth
conditions an electrochemical proton gradient can also be generated using a
number of alternative electron acceptors and ATP synthase can also synthesize
ATP under these conditions. During fermentation however, ATP is synthesized
only by substrate-level phosphorylation reactions. ATP synthase catalyzes the
hydrolysis of ATP under these conditions to generate the electrochemical proton
gradient needed for other membrane functions. |CITS: [96421980]| The enzyme is
comprised of two subcomplexes known as F-1 and F-O. The F-1 complex contains the
catalytic sites and consists of five subunits in a stoichiometry of 3:3:1:1:1.
The F-O complex is membrane-embedded and forms the proton channel through the
membrane. This complex consists of three subunits in a stoichiometry of
1:2:10-18. |CITS: [89123453] [91294204]|")
(ENZYME ATPSYN-CPLX)
(SYNONYMS "F-1F-0-type ATPase" "adenosinetriphosphatase" "ATPase"
"ATP phosphohydrolase (H+-transporting)" "H+-transporting ATPase"
"H+-transporting ATP synthase")
(COMMON-NAME "ATP synthase") )
((INHIBITORS-UNKMECH "aurovertin" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "citreoviridin" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "efrapeptin" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "venturicidin" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "oligomycin" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "dicyclohexylcarbodiimide" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "4-chloro-7-nitrobenzofurazan" CITATIONS "[90303438]")
(INHIBITORS-UNKMECH "fluoroaluminate" CITATIONS "[90303438]")
(ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[90303438]")
(COFACTORS MG+2 COMMENT
"Co++ and Mn++ can also substitute for Mg++ in vivo. Ca++ can substitute in
vitro. |CITS: [86026307] [90303438]|")))
(ATPSYN-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| TR-13 EC-3.6.1)
(OFFICIAL-EC? T)
(:CREATION-DATE 3064091736)
(ENZYMATIC-REACTION ATPSYN-ENZRXN)
(COMMENT
"Under conditions where respiration produces a proton gradient across the plasma
membrane, this reaction synthesizes ATP. The energy of electron transport and
proton extrusion is in this way captured in the form of ATP. Under low proton
gradient conditions the reaction is reversible, hydrolyzing ATP and pumping
protons into the periplasmic space, thereby increasing the proton gradient.
Pi + H+(periplasm) + ADP = ATP + H+(cytoplasm) + H2O |CITS: [90303438]|")
(EC-NUMBER "3.6.1.34")
(RIGHT PROTON |Pi| ADP)
(LEFT PROTON WATER ATP)
(SYNONYMS "H(+)-TRANSPORTING ATPASE" "MITOCHONDRIAL ATPASE"
"CHLOROPLAST ATPASE" "COUPLING FACTORS (F(O), F(1) AND CF(1))") )
((RIGHT PROTON COMPARTMENT CCO-PERI-BAC)))
(|Atrazine-Degradation| T (
(OCELOT-GFP::PARENTS |s-Triazine-Degradation|)
(COMMON-NAME "Atrazine degradation")
(COMMENT "This class holds pathways for the degradation of atrazine")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(ATTACHED-GROUP NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3273339786)
(:VALUE-TYPE (:OR |Chemicals| |Protein-Binding-Features| :STRING))
(:DOCUMENTATION "The entity that binds to the protein feature")
(:DOMAIN |Protein-Binding-Features|) )
NIL)
(AU0-1 NIL (
(OCELOT-GFP::PARENTS |People|)
(CREDITED-FOR RPOS-MONOMER)
(LOGIN-ACCOUNT ||)
(EMAIL "mmandel@wisc.edu")
(LAST-NAME "Mandel")
(MIDDLE-NAME "J")
(FIRST-NAME "Mark")
(:CREATOR |keseler|)
(:CREATION-DATE 3341092078) )
NIL)
(AU0-5 NIL (
(OCELOT-GFP::PARENTS |People|)
(CREDITED-FOR PENTOSE-P-PWY PWY0-181 PWY0-163 PYRUVDEHYD-PWY PROUT-PWY
OXIDATIVEPENT-PWY NONOXIPENT-PWY GLYOXDEG-PWY GLYCOLATEMET-PWY PWY0-1280
ACETOACETATE-DEG-PWY ACETATEUTIL-PWY XYLCAT-PWY SORBDEG-PWY RIBOKIN-PWY
RHAMCAT-PWY MANNIDEG-PWY ARABCAT-PWY GLUAMCAT-PWY GALACTITOLCAT-PWY
FUCCAT-PWY TYRSYN POLYAMSYN-PWY PHESYN GLUTSYNIII-PWY GLUTSYN-PWY
ENTNER-DOUDOROFF-PWY ARO-PWY ASPARTATESYN-PWY ASPARAGINESYN-PWY AST-PWY)
(LOGIN-ACCOUNT |jingraham|)
(EMAIL "jingrah1@earthlink.net")
(LAST-NAME "Ingraham")
(MIDDLE-NAME "L")
(FIRST-NAME "John")
(:CREATOR |keseler|)
(:CREATION-DATE 3356191060) )
NIL)
(AURONE-SYN T (
(OCELOT-GFP::PARENTS FLAVONOID-SYN)
(COMMENT
"This class contains pathways of biosynthesis of aurones, which are a class of plant flavonoids with the basic skeletal structure of two benzene rings joined by a linear C3 chain (C6-C3-C6). Aurones confer yellow color to flowers and exist mostly as 6-O-glucosides. ")
(COMMON-NAME "Aurones")
(:CREATOR |paley|)
(:CREATION-DATE 3324143236) )
NIL)
(AUTHORS NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3253300280)
(:DOCUMENTATION
"This slot lists the authors of a publication. Each value of this
slot lists a single author.
")
(:DOMAIN |Publications|)
(:VALUE-TYPE :STRING) )
NIL)
(AUXIN-BIOSYNTHESIS T (
(OCELOT-GFP::PARENTS |Plant-Hormone-Biosynthesis|)
(COMMENT
"This class contains pathways of the biosynthesis of auxins, which are commonly found in plants, and promote or inhibit cell growth. Auxins are involved in phototropism, gravitropism, apical dominance and leaf abscission.")
(COMMON-NAME "Auxins")
(:CREATOR |paley|)
(:CREATION-DATE 3324143237) )
NIL)
(AUXINS-DEGRADATION T (
(OCELOT-GFP::PARENTS PLANT-HORMONE-DEG)
(COMMENT
"This class contains pathways of the degradation of auxins, which are commonly found in plants, and promote or inhibit cell growth. Auxins are involved in phototropism, gravitropism, apical dominance and leaf abscission.")
(COMMON-NAME "Auxins")
(:CREATOR |paley|)
(:CREATION-DATE 3324143236) )
NIL)
(|Azurins| T (
(OCELOT-GFP::PARENTS |Glutaredoxins|)
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(B-ALANINE NIL (
(OCELOT-GFP::PARENTS |Amino-Acid-Derivatives|)
(INHIBITORS-COMPETITIVE-OF GLYRIBONUCSYN-ENZRXN)
(DBLINKS (LIGAND-CPD "C00099" NIL |kaipa| 3311532641 NIL NIL)
(CAS "107-95-9"))
(:CREATION-DATE 3073857204)
(GIBBS-0 -87.9d0)
(COMMON-NAME "β-alanine")
(APPEARS-IN-RIGHT-SIDE-OF ASPDECARBOX-RXN)
(APPEARS-IN-LEFT-SIDE-OF PANTOATE-BETA-ALANINE-LIG-RXN)
(MOLECULAR-WEIGHT 89.094d0)
(CHEMICAL-FORMULA (C 3) (H 7) (N 1) (O 2))
(DISPLAY-COORDS-2D (0.49664d0 -0.70805d0) (-0.5d0 -0.70805d0)
(0.99664d0 -0.98658d0) (-0.00671d0 -1.0d0) (0.49664d0 -0.13423d0)
(-1.0d0 -0.99329d0))
(STRUCTURE-BONDS (6 2 1) (5 1 2) (4 1 1) (3 1 1) (2 4 1))
(STRUCTURE-ATOMS C C O C O N)
(SYNONYMS "β-alanine" "3-aminopropanoate") )
((GIBBS-0 -87.9d0 CITATIONS "GibbsGroups97")))
(|b-D-mannosyl-R| T (
(OCELOT-GFP::PARENTS |Modified-Proteins|)
(COMMENT
"R represents the remainder of the N-linked oligosaccharide in the glycoprotein acceptor.")
(SYNONYMS "b-D-mannosyl-R")
(COMMON-NAME "β-D-mannosyl-R")
(CHEMICAL-FORMULA (C 6) (H 11) (O 6) (|Protein| 1) (R1 1))
(STRUCTURE-BONDS (14 13 1) (9 12 1) (9 11 1) (8 12 1) (8 10 1) (12 7 1 :UP)
(14 6 1 :DOWN) (11 6 1 :UP) (5 11 1) (5 10 1) (10 3 1 :UP) (3 4 1)
(9 2 1 :UP) (8 1 1 :DOWN))
(DISPLAY-COORDS-2D (6.5494d0 -6.8785d0) (4.9658d0 -4.5684d0)
(7.9687d0 -5.9049d0) (8.7766d0 -5.707d0) (7.2094d0 -4.7498d0)
(6.3023d0 -3.5948d0) (5.1308d0 -6.202d0) (6.5494d0 -6.0534d0)
(5.7909d0 -4.8984d0) (7.2094d0 -5.5749d0) (6.5494d0 -4.4198d0)
(5.7909d0 -5.7234d0) (6.3023d0 -1.9455d0) (6.3023d0 -2.7705d0))
(STRUCTURE-ATOMS O O C O O O O C C C C C |Protein| R1)
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(B-HYDROXYBUTYRYL-S-ACP NIL (
(OCELOT-GFP::PARENTS OH-ACYL-ACP)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(:CREATION-DATE 3054565679)
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(SYNONYMS "B1094" "AcpP" "3-hydroxybutyryl-S-ACP" "3-OH-butyryl-ACP"
"3-hydroxybutyryl-ACP")
(CHEMICAL-FORMULA (C 4) (H 7) (O 2) (ACP 1))
(DISPLAY-COORDS-2D (0.525d0 -2.2261d0) (0.525d0 -1.4011d0)
(-0.1895d0 -0.9886d0) (-0.904d0 -1.4011d0) (-1.6184d0 -0.9886d0)
(-0.904d0 -2.2261d0) (1.2395d0 -0.9886d0))
(STRUCTURE-BONDS (3 2 1) (2 1 1 :DOWN) (2 7 1) (3 4 1) (4 6 2) (4 5 1))
(STRUCTURE-ATOMS O C C C ACP O C)
(COMMON-NAME "β-3-hydroxybutyryl-S-ACP") )
NIL)
(B-KETOACYL-ACP T (
(OCELOT-GFP::PARENTS |Modified-Proteins| |All-ACPs|)
(DISPLAY-COORDS-2D (0.525d0 -2.2261d0) (0.525d0 -1.4011d0)
(1.2394d0 -0.9886d0) (-0.1895d0 -0.9886d0) (-0.904d0 -1.4011d0)
(-1.6184d0 -0.9886d0) (-0.904d0 -2.2261d0))
(CHEMICAL-FORMULA (C 3) (H 2) (O 2) (R 1) (ACP 1))
(STRUCTURE-BONDS (4 2 1) (2 1 2) (2 3 1) (4 5 1) (5 7 2) (5 6 1))
(STRUCTURE-ATOMS O C R C C ACP O)
(SCHEMA? T)
(APPEARS-IN-RIGHT-SIDE-OF 3-OXOACYL-ACP-REDUCT-RXN 3-OXOACYL-ACP-SYNTH-RXN)
(SYNONYMS "3-oxoacyl-[acyl-carrier protein]" "acetoacyl-ACP"
"CH3(CH2)xCOCH2CO-S-ACP")
(COMMON-NAME "a β-ketoacyl-ACP") )
NIL)
(B0070-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 42.71309699999992d0)
(DBLINKS (MODBASE "P31675" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700315 NIL NIL)
(REFSEQ "NP_414612" NIL NIL NIL NIL NIL)
(UNIPROT "P31675" NIL |paley| 3169408120))
(SYNONYMS "B0070" "SetA" "YabM")
(CATALYZES TRANS-ENZRXN-204)
(COMMON-NAME "YabM MFS transporter")
(COMMENT
"YabM is a probable efflux transporter for sugars such as lactose and IPTG.
Cells overexpressing yabM show decreased accumulation of lactose and IPTG |CITS: [99226230]|.
Everted membrane vesicles prepared from cells overexpressing yabM exhibit
lactose transport activity which is abolished by uncouplers |CITS: [99226230]|. YabM is a member
of the major facilitator superfamily (MFS) of transporters, and it probably
functions as a proton/sugar antiporter. The physiological significance and
regulation of yabM remain unclear. The yabM gene probably constitutes a
monocistronic operon.")
(GENE EG11754)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160738) )
NIL)
(B0260-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 50.5257239999998d0)
(CITATIONS "9882684:EV-EXP-IMP:3310740033:keseler")
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(REFSEQ "NP_414794" NIL |keseler| 3310740033 NIL NIL)
(UNIPROT "Q47689" NIL |paley| 3169408120))
(SYNONYMS "B0260" "MmuP" "YkfD")
(COMMON-NAME "MmuP APC transporter")
(COMMENT
"MmuP belongs to the APC superfamily of amino acid transporters and is a putative S-methylmethionine transporter
|CITS: [9882684]|.
A mutant with a non-polar in-frame deletion in mmuP is unable to utilize S-methylmethionine as a source of
methionine in a metE metH mutant background |CITS: [9882684]|.
mmuP : \"S-methylmethionine utilization\" |CITS: [9882684]|")
(COMMENT-INTERNAL "Substrate: histidine?")
(GENE G6135)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160739) )
NIL)
(B0270-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-27)
(MOLECULAR-WEIGHT-SEQ 50.63174199999985d0)
(DBLINKS (MODBASE "P75683" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(ECOO157CYC "Z5001-MONOMER" |Homolog| |pick| 3278712116 NIL NIL)
(REFSEQ "NP_414804" NIL NIL NIL NIL NIL)
(UNIPROT "P75683" NIL |paley| 3169408120))
(COMMENT "The YagG protein is an uncharacterized member of the
GPH family of galactose-pentose-hexuronide transporters
|CITS: [96249685]|. Based on sequence similarity, it
may function as a proton or other ion-driven sugar
uptake system.")
(SYNONYMS "B0270" "YagG")
(COMMON-NAME "YagG GPH Transporter")
(GENE G6142)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160745) )
NIL)
(B0427-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 48.809860999999806d0)
(DBLINKS (MODBASE "P77726" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_414961" NIL NIL NIL NIL NIL)
(UNIPROT "P77726" NIL |paley| 3169408120))
(COMMON-NAME "YajR MFS transporter")
(SYNONYMS "B0427" "YajR")
(COMMENT "The YajR protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, YajR may function as a proton-driven
drug efflux system.")
(GENE G6241)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160731) )
NIL)
(B0486-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 45.65854499999988d0)
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(REFSEQ "NP_415019" NIL NIL NIL NIL NIL)
(UNIPROT "P77400" NIL |paley| 3169408120))
(SYNONYMS "B0486" "YbaT")
(COMMON-NAME "YbaT APC transporter")
(COMMENT "The YbaT protein is an uncharacterised member of the
APC superfamily of amino acid transporters.
Based on sequence similarity, YbaT may function as a proton-driven
amino acid uptake system.")
(GENE G6262)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160740) )
NIL)
(B0511-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-38)
(MOLECULAR-WEIGHT-SEQ 52.45599499999984d0)
(COMMENT "The YbbW protein is an uncharacterized member of the
NCS1 family of purine and pyrimidine transporters
|CITS: [99184734]|. Based on sequence similarity,
YbbW may function as a proton-driven allantoin uptake
system. Supporting this notion, the downstream gene
from ybbW encodes a putative allantoinase enzyme.")
(DBLINKS (PFAM "PF02133" IN-FAMILY |pkarp| 3346700318 NIL NIL)
(REFSEQ "NP_415044" NIL NIL NIL NIL NIL)
(UNIPROT "P75712" NIL |paley| 3169408120))
(SYNONYMS "B0511" "AllP" "YbbW")
(COMMON-NAME "YbbW NCS1 Transporter")
(COMMENT-INTERNAL
"moved comment out of \"comment, internal\" slot to \"comment\" slot -March04")
(GENE G6280)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160748) )
NIL)
(B0612-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-45)
(MOLECULAR-WEIGHT-SEQ 53.0924649999999d0)
(DBLINKS (PFAM "PF00939" IN-FAMILY |pkarp| 3346700319 NIL NIL)
(UNIPROT "P0AE74" NIL |pkarp| 3343984412 NIL NIL)
(REFSEQ "NP_415145" NIL NIL NIL NIL NIL))
(CATALYZES TRANS-ENZRXN-208)
(SYNONYMS "B0612" "YbdS" "CitT")
(COMMON-NAME "CitT citrate DASS Transporter")
(COMMENT "CitT is a probable citrate/succinate antiporter, responsible for
the uptake of citrate. In aerobic conditions, most E. coli strains do not utilise citrate
due to lack of citrate transport, although some strains carry a plasmid-encoded
citrate transporter |CITS: [86059247]|. Under anaerobic conditions, citrate
can be utilised if an oxidizable cosubstrate is present suchas glycerol or
glucose. Expression of the cloned citT gene conferred the ability to
utilise citrate in aerobic conditions. Whole cell transport assays indicated
that CitT mediated exchange of citrate with citrate, succinate, tartrate or
fumarate |CITS: [98361905]|. Since succinate is the end product of citrate
fermentation, it seems probable that CitT functions physiologically as a
citrate/succinate exchanger in anaerobic conditions |CITS: [98361905]|.
Consistent with this supposition, CitT is a member of the DASS family of
di- and tri-carboxylic acid transporters. The citT gene is located in
an operon including the genes for citrate lyase.")
(GENE G6338)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160751) )
NIL)
(B0709-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-29)
(MOLECULAR-WEIGHT-SEQ 54.15887399999986d0)
(DBLINKS (MODBASE "P75742" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700319 NIL NIL)
(REFSEQ "NP_415237" NIL NIL NIL NIL NIL)
(UNIPROT "P75742" NIL |paley| 3169408120))
(SYNONYMS "B0709" "YbgH")
(COMMENT "The YbgH protein is an uncharacterised member of the POT family
of peptide transporters |CITS: [95117128]|. Based on sequence similarity,
YbgH may function as a proton-dependent peptide transporter. The
ybgH probably constitutes a moncistronic operon.")
(COMMON-NAME "YbgH peptide POT Transporter")
(GENE G6378)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160746) )
NIL)
(B0752-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-31)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 34.678357d0)
(CATALYZES TRANS-ENZRXN-300)
(DBLINKS (PFAM "PF01545" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(REFSEQ "NP_415273" NIL NIL NIL NIL NIL)
(UNIPROT "P75757" NIL |paley| 3169408120))
(SYNONYMS "B0752" "ZitB" "YbgR")
(COMMON-NAME "ZitB zinc CDF transporter")
(COMMENT
"ZitB (formerly known as YbgR) is a probable Zn2+ transporter.
It is a member of the cation diffusion facilitator family of metal ion efflux proteins |CITS: [97232493]|.
Studies have shown that disruption of zntA and zitB results in a greater
degree of Zn2+ sensitivity than disruption of zntA alone |CITS: [21336524]|.
Furthermore, overexpression of zitB results in a significant increase in Zn2+
resistance and a decrease in Zn2+ accumulation. Thus, ZitB probably functions as a
Zn2+ efflux system possibly playing a role in zinc homeostasis at low Zn2+ levels.
Transcription is Zn2+ inducible, based on zitB-lacZ gene fusion studies |CITS: [21336524]|.
Membrane topology predictions using experimentally determined C terminus
locations indicate that ZitB has 6 transmembrane helices and the C-terminus is
located in the cytoplasm |CITS:[15044727]|.")
(GENE G6393)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160747) )
((LOCATIONS CCO-PM-BAC-NEG CITATIONS "15044727")))
(B0770-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-45)
(MOLECULAR-WEIGHT-SEQ 51.350611999999906d0)
(DBLINKS (PFAM "PF00939" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(REFSEQ "NP_415291" NIL NIL NIL NIL NIL)
(UNIPROT "P75763" NIL |paley| 3169408120))
(SYNONYMS "B0770" "YbhI")
(COMMON-NAME "YbhI DASS Transporter")
(COMMENT "The YbhI protein is an uncharacterised member of the
DASS family of di- and tri-carboxylate transporters.
Based on sequence similarity, YbhI may function as a
tricarboxylate transporter.")
(GENE G6400)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160750) )
NIL)
(B0899-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 12.287756d0)
(CITATIONS "15716429:EV-EXP-IEP:3350642767:djohnson")
(DBLINKS (PFAM "PF05957" IN-FAMILY |pkarp| 3346700370 NIL NIL)
(UNIPROT "P0ADQ7" NIL |pkarp| 3343984409 NIL NIL)
(REFSEQ "NP_417158" NIL NIL NIL NIL NIL))
(SYNONYMS "B2672" "YgaM")
(COMMON-NAME "predicted protein")
(COMMENT
"ygaM is upregulated by sodium salicylate, which is also known to cause the induction
of the marRAB regulon resulting in resistance to oxidative agents and antibiotics
|CITS:[11395452]|. ygaM was also shown to be induced at the transition to stationary
phase, upon NaCl shock, and upon acid shock in a rpoS+ strain
compared to a rpoS mutant, and is therefore believed to be controlled by the general
stress response master regulator, σS |CITS:[15716429]|. ygaM
was shown to cluster with osmoprotectant genes having supercoiling-dependent transcription
|CITS:[12566398]|. ygaM is among the 25 genes most susceptible to phage μ
insertion at mid-log phase growth, which was shown to prefer regions of low transcription
|CITS:[15210965]|.")
(GENE G7400)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160740) )
NIL)
(B1-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF RIBONUCLEOSIDE-DIP-REDUCTI-CPLX)
(COMPONENTS NRDA-MONOMER)
(SYNONYMS "R1 protein")
(COMMON-NAME "B1 protein")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/pyrnusal/nrdAB.template")
(:CREATION-DATE 3010324856)
(:CREATOR |mriley|) )
((COMPONENTS NRDA-MONOMER COEFFICIENT 2)))
(B1006-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-54)
(CITATIONS "11121068:EV-EXP-IEP:3355580988:keseler"
":EV-COMP-HINF-FN-FROM-SEQ:3355580988:keseler")
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-SEQ 45.5572989999999d0)
(DBLINKS (PFAM "PF00860" IN-FAMILY |pkarp| 3346700326 NIL NIL)
(REFSEQ "NP_415526" NIL NIL NIL NIL NIL)
(UNIPROT "P75892" NIL |paley| 3169408120))
(SYNONYMS "B1006" "YcdG" "RutG")
(COMMON-NAME "predicted xanthine/uracil transporter")
(COMMENT
"E. coli K-12 contains a previously undescribed pathway for pyrimidine degradation. The enzymes of the
pathway are encoded by the rutABCDEFG operon. The rutG gene product is an uncharacterized
member of the NCS2 family of nucleobase transporters. Based on sequence similarity, RutG may function as a
proton-driven uracil uptake system.
RutG contains 11 predicted transmembrane helices; the C terminus of the protein is located on the cytoplasmic side
of the inner membrane |CITS: [15919996]|.
The rutG gene is the last gene in an operon together with genes involved in the utilization of
pyrimidines as nitrogen sources. Expression of the rutABCDEFG operon is under the control of nitrogen
regulatory protein C (NtrC) |CITS: [11121068]|.
RutG: \"pyrimidine utilization\" |CITS: [16540542]|
")
(COMMENT-INTERNAL "Substrate: uracil?")
(GENE G6517)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160748) )
((CREDITS SRI LAST-CURATED 3348593581)
(CREDITS |keseler| LAST-CURATED 3348593581)))
(B1065-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 44.36310899999993d0)
(DBLINKS (MODBASE "P69367" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P69367" NIL |pkarp| 3354911363)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700327 NIL NIL)
(REFSEQ "NP_415583" NIL NIL NIL NIL NIL))
(SYNONYMS "B1065" "MdtH" "YceL")
(COMMON-NAME "YceL MFS transporter")
(COMMENT
"The YceL protein is, based on sequence similarity and hydropathy analysis, a member of the majosr facilitator
superfamily (MFS) |CITS: [20384838]|. Overexpression of the cloned yceL gene in a drug-sensitive background
strain resulted in a two-fold increase in resistance to norfloxacin and enoxacin |CITS: [21450803]|.")
(GENE G6559)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160732) )
NIL)
(B1296-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 50.85295899999987d0)
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700332 NIL NIL)
(REFSEQ "NP_415812" NIL NIL NIL NIL NIL)
(UNIPROT "P76037" NIL |paley| 3169408120))
(SYNONYMS "B1296" "YcjJ" "PuuP")
(COMMON-NAME "putrescine importer")
(COMMENT "The YcjJ protein is a member of the
APC superfamily of amino acid transporters.
Based on sequence similarity, YcjJ may function as a proton-driven
amino acid uptake system.
PuuP is a putrescine importer |CITS: [15590624]|.")
(COMMENT-INTERNAL "Substrate: lysine?")
(GENE G6643)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160741) )
NIL)
(B1433-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 40.583308999999936d0)
(DBLINKS (PFAM "PF00860" IN-FAMILY |pkarp| 3346700335 NIL NIL)
(REFSEQ "NP_415950" NIL NIL NIL NIL NIL)
(UNIPROT "P76103" NIL |paley| 3169408120))
(SYNONYMS "B1433" "YdcO")
(COMMON-NAME "YdcO")
(COMMENT "The B1433 protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
It shares a very high level of sequence similarity to a benzoate
transporter, suggesting that it may function as a benzoate/proton
symporter. The b1433 gene probably constitutes a monocistronic
operon.")
(COMMENT-INTERNAL "Substrate: benzoate?")
(GENE G6744)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160732) )
NIL)
(B1543-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-SEQ 46.26705999999988d0)
(SYNONYMS "B1543" "YdfJ")
(DBLINKS (MODBASE "P77228" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700337 NIL NIL)
(REFSEQ "NP_416061" NIL NIL NIL NIL NIL)
(UNIPROT "P77228" NIL |paley| 3169408120))
(COMMON-NAME "predicted transporter")
(COMMENT "The YdfJ protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G6817)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160733) )
((CREDITS SRI LAST-CURATED 3350330752)
(CREDITS |keseler| LAST-CURATED 3350330752)))
(B1596-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 45.25741899999996d0)
(DBLINKS (MODBASE "P43531" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700338 NIL NIL)
(REFSEQ "NP_416113" NIL NIL NIL NIL NIL)
(UNIPROT "P43531" NIL |paley| 3169408120))
(SYNONYMS "B1596" "YzyC" "YnfM")
(COMMON-NAME "YnfM MFS transporter")
(COMMENT "The B1596 protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
drug efflux system.")
(COMMENT-INTERNAL "Substrate: multidrug efflux?")
(GENE G6854)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160733) )
NIL)
(B1599-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-26)
(MOLECULAR-WEIGHT-SEQ 11.720136d0)
(LOCATIONS CCO-PM-BAC-NEG)
(COMPONENT-OF YDGEF-CPLX)
(DBLINKS (MODBASE "P69210" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P69210" NIL |pkarp| 3354911363)
(PFAM "PF00893" IN-FAMILY |pkarp| 3346700338 NIL NIL)
(REFSEQ "NP_416116" NIL NIL NIL NIL NIL))
(SYNONYMS "MdtI" "B1599" "YdgE")
(COMMON-NAME "YdgE SMR Protein")
(COMMENT "YdgE is a member of the SMR family of proton-dependent drug efflux
transporters |CITS: [96332653]|. Drug resistance studies indicate that
ydgEF products form a dimeric two-component SMR complex which
may function in drug efflux |CITS:[21450803]|.
Protein topology in the inner membrane has been determined |CITS: [11867724]|.")
(COMMENT-INTERNAL "Substrate: multidrug efflux")
(GENE G6857)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160744) )
NIL)
(B1600-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-26)
(MOLECULAR-WEIGHT-SEQ 13.114813000000012d0)
(COMPONENT-OF YDGEF-CPLX)
(DBLINKS (MODBASE "P69212" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P69212" NIL |pkarp| 3354911363)
(PFAM "PF00893" IN-FAMILY |pkarp| 3346700338 NIL NIL)
(REFSEQ "NP_416117" NIL NIL NIL NIL NIL))
(SYNONYMS "B1600" "MdtJ" "YdgF")
(COMMON-NAME "YdgF SMR protein; toxin of a putative toxin-antitoxin pair")
(COMMENT "YdgF is a member of the SMR family of proton-dependent drug efflux
transporters |CITS: [96332653]|. Together with YdgE, YdgF forms a two-component
SMR transporter which may function in drug efflux |CITS:[21450803]|.
Episomal expression causes inhibition of cell growth, compared to wild type |CITS: [14594833]|.")
(COMMENT-INTERNAL "Substrate: multidrug efflux")
(GENE G6858)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160744) )
NIL)
(B1634-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-29)
(MOLECULAR-WEIGHT-SEQ 53.99104999999983d0)
(CITATIONS ":EV-COMP:3303150910:keseler")
(DBLINKS (MODBASE "P77304" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700339 NIL NIL)
(REFSEQ "NP_416151" NIL NIL NIL NIL NIL)
(UNIPROT "P77304" NIL |paley| 3169408120))
(SYNONYMS "B1634" "YdgR" "TppB")
(COMMON-NAME "YdgR putative peptide POT Transporter")
(COMMENT "The YdgR protein is an uncharacterised member of the POT family
of peptide transporters |CITS: [95117128]|. Based on sequence similarity,
YdgR may function as a proton-dependent peptide transporter.
ydgR is similar to tppB in Salmonella enterica serovar Thyphimurium |CITS: [15175316]|.
ydgR was identified as a member of the OmpR regulon in a DNA microarray experiment |CITS: [12366850]|.
Like tppB in Salmonella, ydgR expression is transcriptionally regulated by OmpR, but is not sensitive to
changes in medium osmolarity |CITS: [15175316]|.
")
(GENE G6877)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160746) )
NIL)
(B1657-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 40.063994999999885d0)
(DBLINKS (MODBASE "P77389" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700340 NIL NIL)
(REFSEQ "NP_416174" NIL NIL NIL NIL NIL)
(UNIPROT "P77389" NIL |paley| 3169408120))
(SYNONYMS "B1657" "YdhP")
(COMMON-NAME "YdhP")
(COMMENT "The YdhP protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
drug or sugar efflux system. The ydhP gene probably constitutes
a monocistronic operon.")
(COMMENT-INTERNAL "Substrate: AraJ homologue")
(GENE G6893)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160734) )
NIL)
(B1690-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 44.6080159999999d0)
(DBLINKS (MODBASE "P76197" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700340 NIL NIL)
(REFSEQ "NP_416205" NIL NIL NIL NIL NIL)
(UNIPROT "P76197" NIL |paley| 3169408120))
(SYNONYMS "B1690" "YdiM")
(COMMON-NAME "YdiM")
(COMMENT "The B1690 protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G6916)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160733) )
NIL)
(B1691-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 46.08019699999986d0)
(DBLINKS (MODBASE "P76198" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700340 NIL NIL)
(REFSEQ "NP_416206" NIL NIL NIL NIL NIL)
(UNIPROT "P76198" NIL |paley| 3169408120))
(SYNONYMS "B1691" "YdiN")
(COMMON-NAME "YdiN MFS transporter")
(COMMENT "The YdiN protein is an uncharacterised member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G6917)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160738) )
NIL)
(B1775-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 49.601859999999895d0)
(DBLINKS (MODBASE "P76230" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700342 NIL NIL)
(REFSEQ "NP_416289" NIL NIL NIL NIL NIL)
(UNIPROT "P76230" NIL |paley| 3169408120))
(SYNONYMS "B1775" "YdjK")
(COMMON-NAME "predicted transporter")
(COMMENT "The YdjK protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G6962)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160734) )
NIL)
(B1791-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 41.208172999999945d0)
(DBLINKS (MODBASE "P76242" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700343 NIL NIL)
(REFSEQ "NP_416305" NIL NIL NIL NIL NIL)
(UNIPROT "P76242" NIL |paley| 3169408120))
(SYNONYMS "B1791" "YeaN")
(COMMON-NAME "predicted transporter")
(COMMENT "The YeaN protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(COMMENT-INTERNAL "Substrate: cyanate?")
(GENE G6977)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160735) )
NIL)
(B1828-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 48.15160299999993d0)
(DBLINKS (MODBASE "P76269" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700344 NIL NIL)
(REFSEQ "NP_416342" NIL NIL NIL NIL NIL)
(UNIPROT "P76269" NIL |paley| 3169408120))
(SYNONYMS "B1828" "YebQ")
(COMMON-NAME "predicted transporter")
(COMMENT "The YebQ protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
drug efflux system. The yebQ gene probably constitutes a monocistronic
operon.")
(COMMENT-INTERNAL "Substrate: drug efflux?")
(GENE G7004)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160736) )
NIL)
(B2-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(COMPONENT-OF RIBONUCLEOSIDE-DIP-REDUCTI-CPLX)
(COMPONENTS NRDB-MONOMER)
(SYNONYMS "R2 protein")
(COMMON-NAME "B2 protein")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/pyrnusal/nrdAB.template")
(:CREATION-DATE 3010324856)
(:CREATOR |mriley|) )
((COMPONENTS NRDB-MONOMER COEFFICIENT 2)))
(B2075-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-25)
(MOLECULAR-WEIGHT-SEQ 112.07737999999925d0)
(COMPONENT-OF TRANS-CPLX-202)
(COMMON-NAME "MdtB")
(DBLINKS (MODBASE "P76398" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00873" IN-FAMILY |pkarp| 3346700350 NIL NIL)
(REFSEQ "NP_416579" NIL NIL NIL NIL NIL)
(UNIPROT "P76398" NIL |paley| 3169408120))
(SYNONYMS "B2075" "MdtB" "YegN")
(COMMENT-INTERNAL
"MdtB is a component of the MdtABC RND-type Drug Exporter |CITS:[12107133]|. Based on sequence similarity, MdtB/C are thought to comprise a heteromultimeric transmembrane complex.")
(GENE G7114)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160743) )
NIL)
(B2076-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-25)
(MOLECULAR-WEIGHT-SEQ 111.01024199999931d0)
(COMPONENT-OF TRANS-CPLX-202)
(COMMON-NAME "MdtC")
(DBLINKS (MODBASE "P76399" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00873" IN-FAMILY |pkarp| 3346700351 NIL NIL)
(REFSEQ "NP_416580" NIL NIL NIL NIL NIL)
(UNIPROT "P76399" NIL |paley| 3169408120))
(SYNONYMS "B2076" "MdtC" "YegO")
(COMMENT-INTERNAL
"MdtC is a component of the MdtABC RND-type Drug Exporter |CITS:[12107133]|. Based on sequence similarity, MdtB/C are
thought to comprise a heteromultimeric transmembrane complex.")
(GENE G7115)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160743) )
NIL)
(B2077-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 50.90079299999992d0)
(DBLINKS (MODBASE "P36554" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700351 NIL NIL)
(REFSEQ "NP_416581" NIL NIL NIL NIL NIL)
(UNIPROT "P36554" NIL |paley| 3169408120))
(COMMON-NAME "YegB")
(SYNONYMS "B2077" "MdtD" "YegB")
(COMMENT "The YegB protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, YegB may function as a proton-driven
drug efflux system.")
(GENE EG12136)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160736) )
NIL)
(B2098-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 47.359074999999876d0)
(DBLINKS (MODBASE "P76417" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF03825" IN-FAMILY |pkarp| 3346700351 NIL NIL)
(REFSEQ "NP_416601" NIL NIL NIL NIL NIL)
(UNIPROT "P76417" NIL |paley| 3169408120))
(SYNONYMS "B2098" "YegT")
(COMMON-NAME "YegT MFS transporter")
(COMMENT "The YegT protein is an uncharacterised member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
nucleoside uptake system.")
(COMMENT-INTERNAL "Substrate: nucleosides?")
(GENE G7130)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160737) )
NIL)
(B2170-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(CITATIONS "14617174:EV-EXP-IMP:3343471169:djohnson")
(MOLECULAR-WEIGHT-SEQ 42.745977999999944d0)
(DBLINKS (MODBASE "P33026" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700353 NIL NIL)
(REFSEQ "NP_416675" NIL NIL NIL NIL NIL)
(UNIPROT "P33026" NIL |paley| 3169408120))
(SYNONYMS "B2170" "YeiO" "SetB")
(COMMON-NAME "SetB MFS transporter")
(CATALYZES TRANS-ENZRXN-205)
(COMMENT
"SetB is a probable efflux transporter for sugars such as lactose and IPTG.
Everted membrane vesicles prepared from cells overexpressing setB
exhibit lactose transport activity which is abolished by uncouplers |CITS:[99226230]|.
SetB is a member of the major facilitator superfamily (MFS) of transporters,
and it probably functions as a proton/sugar antiporter.
SetB also appears to play a role in chromosome segregation. Deletion of
setB resulted in smaller cells with a minor defect in chromosome
segregation increasing the time required for segregation to occur.
Overexpression of setB resulted in cell elongation, filamentation,
and stretched or fragmented nucleoids. At high copy number, setB
suppresses a mutation in the ParC subunit of topoisomerase IV. Deletion of
setB combined with mutation of ftsK, responsible for segregation
of dimeric chromosomes, resulted in reduced growth rates, increased
filamentation, and increased the incidence of large nucleoids and
condensed DNA in the middle of the cell. SetB-GFP fusions showed
a helical localization pattern similar to MreB. Co-expression of SetB-GFP
and Myc-MreB showed that the two proteins co-localized. Yeast
two-hybrid experiments revealed that SetB and MreB interact. SetB is
involved in protein segregation and likely acts somewhere in the linkage
of chromosomes to the force required to separate them |CITS:[14617174]|.
")
(GENE EG12034)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160738) )
NIL)
(B2246-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 46.29367599999986d0)
(DBLINKS (MODBASE "P76470" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700356 NIL NIL)
(REFSEQ "NP_416749" NIL NIL NIL NIL NIL)
(UNIPROT "P76470" NIL |paley| 3169408120))
(SYNONYMS "B2246" "YfaV")
(COMMON-NAME "YfaV")
(COMMENT "The YfaV protein is an uncharacterised member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G7159)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160736) )
NIL)
(B2322-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 40.4651389999999d0)
(DBLINKS (MODBASE "P77549" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700358 NIL NIL)
(REFSEQ "NP_416825" NIL NIL NIL NIL NIL)
(UNIPROT "P77549" NIL |paley| 3169408120))
(SYNONYMS "B2322" "YfcJ")
(COMMON-NAME "YfcJ MFS transporter")
(COMMENT "The YfcJ protein is an uncharacterised member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system.")
(GENE G7198)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160737) )
NIL)
(B2372-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-75)
(MOLECULAR-WEIGHT-SEQ 33.61592899999994d0)
(:CREATION-DATE 3143230962)
(DBLINKS (PFAM "PF03547" IN-FAMILY |pkarp| 3346700360 NIL NIL)
(UNIPROT "P0AA49" NIL |pkarp| 3338704376 NIL NIL)
(REFSEQ "NP_416873" NIL NIL NIL NIL NIL))
(SYNONYMS "B2372" "YfdV")
(COMMON-NAME "YfdV AEC Transporter")
(COMMENT "The YfdV protein is an uncharacterised member of the AEC family of
auxin efflux transporters. Its closest functionally characterised
homologue is a malonate transporter from Klebsiella pneumoniae
|CITS: [97352552]|.")
(GENE G7235) )
NIL)
(B2740-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-24)
(MOLECULAR-WEIGHT-SEQ 46.769524999999945d0)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(DBLINKS (PFAM "PF02447" IN-FAMILY |pkarp| 3346700372 NIL NIL)
(REFSEQ "NP_417220" NIL NIL NIL NIL NIL)
(UNIPROT "Q46892" NIL |paley| 3169408120))
(SYNONYMS "B2740" "YgbN")
(COMMON-NAME "YgbN Gnt transporter")
(COMMENT
"YgbN is a transporter of unknown function belonging to the Gnt family of
gluconate transporters |CITS: [97212001]|. Based on sequence similarity,
YgbN may function as a proton-driven metabolite uptake system. The cloned
ygbN gene did not confer gluconate transport |CITS: [97212001]|.")
(GENE G7421)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160742) )
NIL)
(B2771-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 48.234063999999925d0)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(DBLINKS (MODBASE "Q46909" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700374 NIL NIL)
(REFSEQ "NP_417251" NIL NIL NIL NIL NIL)
(UNIPROT "Q46909" NIL |paley| 3169408120))
(COMMON-NAME "YgcS MFS transporter")
(SYNONYMS "B2771" "YgcS")
(COMMENT "The YgcS protein is an uncharacterised member of the
major facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, YgcS may function as a proton-driven
metabolite uptake system.")
(GENE G7437)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160730) )
NIL)
(B2775-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 46.83060399999991d0)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(DBLINKS (MODBASE "P77031" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700374 NIL NIL)
(REFSEQ "NP_417255" NIL NIL NIL NIL NIL)
(UNIPROT "P77031" NIL |paley| 3169408120))
(SYNONYMS "B2775" "YqcF" "YqcE")
(COMMON-NAME "YqcE MFS transporter")
(COMMENT "The YqcE protein is an uncharacterised member of the major
facilitator superfamily (MFS) of transporters |CITS: [98190790]|.
Based on sequence similarity, it may function as a proton-driven
metabolite uptake system. The yqcE gene probably forms part
of a dicistronic operon with a putative kinase gene.")
(COMMENT-INTERNAL "Substrate: YihN homologue")
(GENE EG13174)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160737) )
NIL)
(B2789-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(CITATIONS ":EV-COMP-HINF-FN-FROM-SEQ:3343057790:keseler")
(MOLECULAR-WEIGHT-SEQ 49.14199799999992d0)
(DBLINKS (MODBASE "Q46916" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00083" IN-FAMILY |pkarp| 3346700374 NIL NIL)
(REFSEQ "NP_417269" NIL NIL NIL NIL NIL)
(UNIPROT "Q46916" NIL |paley| 3169408120))
(COMMON-NAME "YgcZ MFS transporter")
(COMMENT "The YgcZ protein may function as a glucarate transporter. The
ygcZ gene is encoded in a probable operon with genes
encoding two subunits of a putative glucarate dehydratase. YgcZ
is a member of the major facilitator superfamily (MFS) of
transporters |CITS: [98190790]| and shares a high level of sequence
similarity with probable glucarate transporters from various
organisms. YgcZ probably functions as a glucarate/proton transporter.")
(SYNONYMS "B2789" "GudP" "GudT" "YgcZ")
(GENE G7447)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160729) )
NIL)
(B2845-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-22)
(MOLECULAR-WEIGHT-SEQ 45.099165999999876d0)
(DBLINKS (UNIPROT "P63340" NIL |pkarp| 3354911363)
(REFSEQ "NP_417322" NIL NIL NIL NIL NIL))
(SYNONYMS "B2845" "YqeG")
(COMMON-NAME "YqeG STP transporter")
(COMMENT "The YqeG protein is an uncharacterised member of the
STP family of transporters. Based on sequence similarity
YqeG may function as an amino acid/proton symporter.")
(COMMENT-INTERNAL "Substrate: ?")
(GENE G7465)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160742) )
NIL)
(B2975-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-30)
(MOLECULAR-WEIGHT-SEQ 58.92005999999984d0)
(CATALYZES TRANS-ENZRXN-105)
(DBLINKS (PFAM "PF02652" IN-FAMILY |pkarp| 3346700381 NIL NIL)
(REFSEQ "NP_417449" NIL NIL NIL NIL NIL)
(UNIPROT "Q46839" NIL |paley| 3169408120))
(SYNONYMS "B2975" "GlcA" "YghK")
(COMMON-NAME "YghK glycolate transporter")
(COMMENT
"YghK, also named GlcA, is a glycolate transporter that belongs to the Lactate Permease Family (LctP) |CITS:
[20156664]|, due to its strong sequence similarity with the L-lactate permease, LldP. The yghK gene is
located in the glc operon. Expression studies using Northern blot analysis and lacZ fusion
experiments have shown that the yghK gene is transcribed from the same promoter as the other
glc structural genes |CITS: [21178909]|. Expression of this operon is induced by growth on glycolate and
is under the control of an activator protein, GlcC |CITS: [21178909]|. Growth of a yghK::cat mutant
on glycolate was not totally abolished, but its rate was much lower than that of the parental strain, indicating
that YghK probably functions as a glycolate transporter, although glycolate can also enter the cell through
another transport system |CITS: [21178909]|. The lactate permease LldP was also found to be capable of
glycolate transport. Growth on glycolate was abolished in a double mutant of the paralogous genes
yghK and lldP, and restored with plasmids expressing either YghK or LldP |CITS:
[21178909]|. Characterization of the putative substrates for these two related permeases showed, in both cases,
specificity for the 2-hydroxy-monocarboxylates glycolate, L-lactate, and D-lactate |CITS: [21178909]|.
")
(GENE G7542)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160747) )
NIL)
(B3659-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 43.49326799999995d0)
(DBLINKS (MODBASE "P31436" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700411 NIL NIL)
(REFSEQ "NP_418115" NIL NIL NIL NIL NIL)
(UNIPROT "P31436" NIL |paley| 3169408120))
(SYNONYMS "B3659" "SetC" "YicK")
(COMMON-NAME "YicK MFS Transporter")
(COMMENT "YicK may be a sugar efflux transporter. It shares a high degree
of similarity with the lactose efflux transporters YabM and YeiO
from the major facilitator superfamily. However, YicK-mediated
lactose transport activity was not observed in everted
membrane vesicles prepared from cells overexpressing yicK.
")
(COMMENT-INTERNAL "Substrate: ?")
(GENE EG11687)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160738) )
NIL)
(B4141-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-7)
(MOLECULAR-WEIGHT-SEQ 44.7775029999999d0)
(COMMON-NAME "YjeH APC transporter")
(COMMENT
"YjeH is an uncharacterized member of the APC superfamily of amino acid
transporters |CITS:[20391827]|. Sequence similarity suggests that it may function
as a solute/solute antiporter.")
(DBLINKS (PFAM "PF00324" IN-FAMILY |pkarp| 3346700437 NIL NIL)
(REFSEQ "NP_418565" NIL NIL NIL NIL NIL)
(UNIPROT "P39277" NIL |paley| 3169408120))
(SYNONYMS "B4141" "YjeH")
(COMMENT-INTERNAL "Substrate: antiporter")
(GENE G7833)
(:CREATOR |pkarp|)
(:CREATION-DATE 3130160738) )
NIL)
(BA NIL (
(OCELOT-GFP::PARENTS |Elements|)
(COMMON-NAME "Ba")
(SYNONYMS "barium")
(ATOMIC-NUMBER 56)
(ATOMIC-WEIGHT 137.34d0) )
NIL)
(BA+2 NIL (
(OCELOT-GFP::PARENTS |Cations|)
(INHIBITORS-UNKMECH-OF PANTOATE-BETA-ALANINE-LIG-ENZRXN
ADENPRIBOSYLTRAN-ENZRXN HYPOXANPRIBOSYLTRAN-ENZRXN)
(:CREATION-DATE 3101477439)
(COMMON-NAME "Ba2+")
(SYNONYMS "Ba+2" "Ba++")
(CHARGE 2) )
NIL)
(BACIMETHRIN NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-1882 TRANSKETOI-ENZRXN)
(DISPLAY-COORDS-2D (0.0d0 -5.6d0) (4.8497d0 -4.2d0) (4.8497d0 0.0d0)
(2.4249d0 -1.4d0) (4.8497d0 -1.4d0) (1.2124d0 -2.1d0) (2.4249d0 -4.2d0)
(0.0d0 -4.2d0) (3.6373d0 -3.5d0) (3.6373d0 -2.1d0) (1.2124d0 -3.5d0))
(AROMATIC-RINGS (6 4 10 9 7 11))
(CHEMICAL-FORMULA (C 6) (H 9) (N 3) (O 2))
(MOLECULAR-WEIGHT 155.156d0)
(STRUCTURE-BONDS (9 10 :AROMATIC) (8 11 1) (11 7 :AROMATIC) (7 9 :AROMATIC)
(6 11 :AROMATIC) (5 10 1) (10 4 :AROMATIC) (4 6 :AROMATIC) (3 5 1) (2 9 1)
(1 8 1))
(STRUCTURE-ATOMS C N O C C N N O C C C)
(SYNONYMS "2-methoxy-4-amino-5-hydroxymethylpyrimidine"
"4-amino-2-methoxy-5-pyrimidinemethanol"
"4-amino-5-hydroxymethyl-2-methoxypyrimidine" "bacimethrine"
"5-pyrimidinemethanol, 4-amino-2-methoxy-")
(CITATIONS "11527707")
(COMMON-NAME "bacimethrin")
(:CREATOR |arnaud|)
(:CREATION-DATE 3270318138) )
NIL)
(|Bacteria| T (
(OCELOT-GFP::PARENTS |Organisms|)
(DBLINKS (NCBI-TAXONOMY-DB 2))
(:CREATOR |paley|)
(:CREATION-DATE 3331579730) )
NIL)
(|Bacterial-Endotoxins| T (
(OCELOT-GFP::PARENTS |Lipids|)
(COMMON-NAME "a bacterial endotoxin")
(SYNONYMS "a bacterial endotoxin" "bacterial endotoxin")
(COMMENT
"This compound class stands for generic and unspecified bacterial endotoxins. These are components from the outer membrane and cell wall of bacteria, which are toxic to humans and can cause sepsis. The Gram negative bacteria produce lipopolysaccharide, whereas the Gram positive bacteria produce the less active lipoteichoic acids and muramyl peptides.")
(:CREATOR |kr|)
(:CREATION-DATE 3267308629) )
NIL)
(|Bacteroidetes-Chlorobi| T (
(OCELOT-GFP::PARENTS OCELOT-GFP::FRAMES)
(COMMON-NAME "Bacteroidetes/Chlorobi group")
(DBLINKS (NCBI-TAXONOMY-DB 68336))
(:CREATOR |paley|)
(:CREATION-DATE 3331579734) )
NIL)
(BADH-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES BADH-ENZRXN)
(COMPONENTS BADH-MONOMER)
(TEMPLATE-FILE "~ecocyc/templates/new/betaine/betB.template")
(:CREATION-DATE 3053887812)
(:CREATOR |mriley|) )
((COMPONENTS BADH-MONOMER COEFFICIENT 4)))
(BADH-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH IODOACETAMIDE IODOACETATE CPD-29 ZNCL2 CPD-2501 NADP
BETAINE_ALDEHYDE)
(CITATIONS ":EV-EXP:3277835751:pkarp")
(REACTION-DIRECTION IRREVERSIBLE-LEFT-TO-RIGHT)
(REACTION BADH-RXN)
(INHIBITORS-COMPETITIVE "aldehydes" "N-methylated compounds")
(COMMENT "Betaine acts as an osmoprotectant in E. coli. E.coli can
take up betaine from the environment or synthesize it from externally
supplied choline. Betaine aldehyde dehydrogenase (BADH) catalyzes the
second reaction in the two-step pathway. |CITS: [90304165]
[86139897]|")
(ENZYME BADH-CPLX)
(SYNONYMS "BADH" "betaine aldehyde:NAD+ oxidoreductase")
(COMMON-NAME "betaine aldehyde dehydrogenase")
(TEMPLATE-FILE "~ecocyc/templates/new/betaine/betB.template")
(:CREATION-DATE 3053887812)
(:CREATOR |mriley|) )
((INHIBITORS-UNKMECH IODOACETAMIDE CITATIONS "[90304165]")
(INHIBITORS-UNKMECH IODOACETATE CITATIONS "[90304165]")
(INHIBITORS-UNKMECH CPD-29 CITATIONS "[90304165]")
(INHIBITORS-UNKMECH ZNCL2 CITATIONS "[90304165]")
(INHIBITORS-UNKMECH CPD-2501 CITATIONS "[90304165]")
(INHIBITORS-UNKMECH NADP COMMENT
"Although not the preferred substrate, at concentrations above 10mM
NADP was inhibitory. |CITS: [90304165]|")
(INHIBITORS-UNKMECH BETAINE_ALDEHYDE COMMENT "The enzyme
was subject to substrate inhibition by betaine aldehyde at
concentrations above 0.5mM. |CITS: [90304165]|")
(ALTERNATIVE-SUBSTRATES :FACET COMMENT "Although the enzyme could utilize
NADP in the reaction, NAD is the probable substrate in the cell.
|CITS: [90304165]|")
(INHIBITORS-COMPETITIVE "aldehydes" COMMENT "Among those tested were,
acetaldehyde, trimethylacetaldehyde, glyceraldehyde, isovaleraldehyde,
benzaldehyde and phenylacetaldehyde. |CITS: [90304165]|")
(INHIBITORS-COMPETITIVE "N-methylated compounds" COMMENT
"Among those tested were,
N-methylglycine, N,N-dimethylglycine, ethanolamine,
N-methylethanolamine, N,N-dimethylethanolamine, choline,
butyrylcholine and tetramethylammonium hydroxide. |CITS:[90304165]|")
(INHIBITORS-COMPETITIVE :FACET COMMENT
"In general, aldehydes with apolar groups were the most
effective inhibitors. Within the N-methylated compounds group the
alcohols were more inhibitory than the acids. |CITS: [90304165]|")))
(BADH-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B0312" "BetB")
(COMMON-NAME "BetB")
(DBLINKS (MODBASE "P17445" NIL |pkarp| 3355444109 NIL NIL)
(SWISSMODEL "P17445" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00171" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(REFSEQ "NP_414846" NIL NIL NIL NIL NIL)
(UNIPROT "P17445" NIL |pkarp| 3064869797))
(COMPONENT-OF BADH-CPLX)
(PI 5.4d0)
(MOLECULAR-WEIGHT-SEQ 52.911060999999854d0)
(GENE EG10110)
(TEMPLATE-FILE "~ecocyc/templates/new/betaine/betB.template")
(:CREATION-DATE 3053887812)
(:CREATOR |mriley|) )
NIL)
(BADH-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-1.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(IN-PATHWAY BETSYN-PWY)
(ENZYMATIC-REACTION BADH-ENZRXN)
(RIGHT BETAINE NADH)
(LEFT BETAINE_ALDEHYDE NAD WATER)
(EC-NUMBER "1.2.1.8")
(COMMENT "This is the second reaction in the betaine biosynthetic
pathway.")
(TEMPLATE-FILE "~ecocyc/templates/new/betaine/betB.template")
(:CREATION-DATE 3053887812)
(:CREATOR |mriley|) )
NIL)
(BAE-PWY NIL (
(OCELOT-GFP::PARENTS |2Comp-Pathways|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3097616059)
(SYNONYMS "Bae system")
(COMMON-NAME "BaeSR Two-Component Signal Transduction System")
(PRIMARIES (BAER-RXN (PHOSPHO-BAES BAER-MONOMER) (BAES-MONOMER PHOSPHO-BAER)))
(REACTION-LIST BAES-RXN BAER-RXN)
(PREDECESSORS (BAER-RXN BAES-RXN) (BAES-RXN BAER-RXN)) )
NIL)
(|Bae-R| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(|Bae-S| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(BAER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Bae-R|)
(COMMON-NAME "BaeR transcriptional regulator")
(:CREATION-DATE 3080316899)
(DBLINKS (MODBASE "P69228" NIL |pkarp| 3355444108 NIL NIL)
(SWISSMODEL "P69228" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P69228" NIL |pkarp| 3354911363))
(APPEARS-IN-LEFT-SIDE-OF BAER-RXN)
(PI 5.8d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 27.655893999999996d0)
(GENE EG11618)
(CITATIONS ":EV-EXP:3278863360:pkarp" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(COMMENT
"The transcriptional regulatory protein BaeR is part of the two-component
BaeS/BaeR signal transduction system |CITS: [94110256]|. BaeR is a positive response regulator of RNA
synthesis. Overproduction of BaeR increases resistance to novobiocin, deoxycholate, bile salts, SDS,
and a number of β-lactam antibiotics by stimulating expression of the mdtABCD and
acrDmultidrug transporter genes |CITS:[12107133], [12107134], [12618449], [12951338]|. BaeR was
also shown to regulate gene clusters involved in flagellar biosynthesis, chemotaxis, multidrug transport,
maltose transport, signal transduction, and unknown functions |CITS:[12107134], [12354228], [15716448]|.
Expression of a number of these genes is induced by indole via BaeSR and CpxAR signal transduction
systems |CITS:[15686558]|. The BaeSR, PhoBR, and CreBC two-component systems have been shown to
interact in the regulation of gene expression |CITS:[15716448]|.
BaeR suppresses envZ and phoR/creC mutations |CITS:[8282725]|.")
(MODIFIED-FORM PHOSPHO-BAER)
(SYNONYMS "B2079" "BaeR" "transcriptional regulatory protein BaeR"
"unphosphorylated transcriptional regulatory protein BaeR"
"unmodified transcriptional regulatory protein BaeR") )
NIL)
(BAER-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080316899)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY BAE-PWY)
(RIGHT BAES-MONOMER PHOSPHO-BAER)
(LEFT PHOSPHO-BAES BAER-MONOMER)
(COMMENT
"In this reaction the transcriptional regulatory protein BaeR is phosphorylated
by the phospho-BaeS sensor protein. Based on analogy to other response regulators
the BaeR phosphorylation site is shown as an aspartate residue.") )
NIL)
(BAES-MONOMER NIL (
(OCELOT-GFP::PARENTS |Bae-S|)
(COMMENT
"BaeS is the sensor kinase protein of the two-component BaeSR signal transduction system
|CITS:[8282725]|. Overproduction of BaeR increases resistance to novobiocin, deoxycholate, bile salts,
SDS, and a number of β-lactam antibiotics by stimulating expression of the mdtABCD and
acrD multidrug transporter genes |CITS:[12107133], [12107134], [12618449], [12951338]|. BaeR
was also shown to regulate gene clusters involved in flagellar biosynthesis, chemotaxis, multidrug
transport, maltose transport, signal transduction, and unknown functions |CITS:[12107134],[12354228],
[15716448]|. Expression of a number of these genes is induced by indole via BaeSR and
CpxAR signal transduction systems |CITS:[15686558]|. The BaeSR, PhoBR, and CreBC two-component
systems have been shown to interact in the regulation of gene expression |CITS:[15716448]|.")
(CITATIONS "8282725:EV-EXP-IGI:3343138470:djohnson")
(:CREATION-DATE 3080316899)
(DBLINKS (MODBASE "P30847" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P30847" NIL |pick| NIL NIL NIL))
(COMMON-NAME "BaeS")
(APPEARS-IN-RIGHT-SIDE-OF BAER-RXN)
(APPEARS-IN-LEFT-SIDE-OF BAES-RXN)
(PI 7.01d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 51.99126199999985d0)
(GENE EG11617)
(MODIFIED-FORM PHOSPHO-BAES)
(SYNONYMS "B2078" "BaeS" "sensor protein BaeS"
"sensor kinase-phosphotransferase BaeS"
"unphosphorylated sensor kinase-phosphotransferase BaeS"
"unmodified sensor kinase-phosphotransferase BaeS") )
NIL)
(BAES-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080316899)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY BAE-PWY)
(RIGHT ADP PHOSPHO-BAES)
(LEFT ATP BAES-MONOMER)
(COMMENT
"In this reaction the sensor kinase-phosphotransferase BaeS is autophosphorylated.
Based on analogy to other sensor proteins the phosphorylation site is shown as
a histidine residue."
"The sensor kinase-phosphotransferase BaeS is part of the two-component BaeS/BaeR
signal transduction system. The physiological role of the BaeS/BaeR system is
not yet known. |CITS: [94110256]|") )
NIL)
(BALANCE-STATE NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:VALUE-TYPE
(:ONE-OF :BALANCED :UNBALANCED-UNKNOWN :UNBALANCED-INCOMPLETE
:UNBALANCED-DIFFERING-R-GROUPS))
(:CREATOR |paley|)
(:CREATION-DATE 3314378976)
(:DOMAIN |Reactions|)
(:MAXIMUM-CARDINALITY 1)
(:DOCUMENTATION
"This slot describes what is known about the element balance state of this
reaction. Its possible values are:
NIL -- The balance state is unknown
:BALANCED -- The last time the reaction-balancing code checked
this reaction, it was balanced.
:UNBALANCED-UNKNOWN -- The reaction is unbalanced, and the curation team cannot
determine how to balance it.
:UNBALANCED-INCOMPLETE -- The reaction is unbalanced because the complete
reaction equation is not known.
:UNBALANCED-DIFFERING-R-GROUPS -- The reaction is unbalanced because it
contains substrates with R-groups where the structures of the two R-groups differ.
") )
NIL)
(|Bar-A| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(BARA-MONOMER NIL (
(OCELOT-GFP::PARENTS |Bar-A|)
(CITATIONS "12193630" ":EV-EXP:3278863360:pkarp")
(:CREATION-DATE 3079972550)
(DBLINKS (MODBASE "P0AEC5" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P0AEC5" NIL |pkarp| 3343984412 NIL NIL))
(COMMON-NAME "BarA")
(APPEARS-IN-RIGHT-SIDE-OF RXN0-321 BAROMP-RXN)
(APPEARS-IN-LEFT-SIDE-OF BARA-RXN)
(PI 5.68d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 102.4530099999995d0)
(GENE EG11367)
(COMMENT
"The BarA protein contains both a sensory kinase and a response regulator domain as well as a second
phosphorylated histidine site in the C-terminal region |CITS: [7957084]|. UvrY has been shown to be the cognate
response regulator for the BarA sensor protein |CITS: [11022030]|.
barA is maximally expressed during early exponential phase, and the BarA protein is required for the induction of
expression of RpoS during exponential phase |CITS: [10931332]|, but not stationary phase |CITS: [12193624]|.
A barA mutant is hypersensitive to hydrogen peroxide. In uropathogenic E. coli, mutations in barA and uvrY lower
survival in long-term competition cultures; the BarA/UvrY two-component system appears to be important for
adaptation between metabolic pathways |CITS: [12533459]|.
Downstream genes regulated by BarA have been identified by preliminary microarray studies |CITS: [14619967]|.
barA = \"bacterial adaptive responses\" |CITS: [1574005]|")
(MODIFIED-FORM PHOSPHO-BARA-ASP PHOSPHO-BARA-HIS)
(SYNONYMS "B2786" "sensor protein BarA"
"sensor kinase-phosphotransferase BarA") )
NIL)
(BARA-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079972550)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY PWY0-21 OMP-PWY)
(RIGHT ADP PHOSPHO-BARA-HIS)
(LEFT ATP BARA-MONOMER)
(COMMENT
"In this reaction the sensor kinase-phosphotransferase BarA is autophosphorylated."
"The sensor kinase-phosphotransferase BarA has been shown to autophosphorylate
in the presence of ATP. The BarA protein has both a sensor and a response
regulator domain. The sensor domain is similar in sequence to the sensor protein
EnvZ and the regulator domain is similar to the regulator protein OmpR. In
addition, the BarA protein contains a second phospho-donor histidine site in
the C-terminal region. By `cross-talk' phosphorylation of OmpR, BarA seems to
affect ompC and ompF expression. |CITS: [92244050] [95045412] [96422482]|") )
NIL)
(BARASP-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079972550)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY OMP-PWY)
(RIGHT PHOSPHO-BARA-ASP)
(LEFT PHOSPHO-BARA-HIS)
(COMMENT
"In this reaction the phosphoryl group is transferred from the histidine residue
to the aspartate residue in sensor kinase-phosphotransferase BarA."
"As a member of the same sensory kinase family as ArcB, it is likely that BarA
is also capable of intermolecular transfer of a phosphoryl group from its
histidine residue in the sensor domain to its aspartate residue in its regulator
domain.") )
NIL)
(BAROMP-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3079972550)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY OMP-PWY)
(RIGHT PHOSPHO-OMPR BARA-MONOMER)
(LEFT PC00029 PHOSPHO-BARA-HIS)
(COMMENT
"In this reaction the trancriptional regulatory protein OmpR is phosphorylated
by transphosphorylation from the phospho-BarA protein."
"By `cross-talk' phosphorylation of OmpR, BarA seems to affect ompC and ompF
expression. |CITS: [92244050] [95045412] [96422482]|") )
NIL)
(BAS-PWY NIL (
(OCELOT-GFP::PARENTS |2Comp-Pathways|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(:CREATION-DATE 3097616059)
(SYNONYMS "Bas system")
(COMMON-NAME "BasSR Two-Component Signal Transduction System")
(PRIMARIES (BASR-RXN (PHOSPHO-BASS BASR-MONOMER) (BASS-MONOMER PHOSPHO-BASR)))
(REACTION-LIST BASS-RXN BASR-RXN)
(PREDECESSORS (BASR-RXN BASS-RXN) (BASS-RXN BASR-RXN)) )
NIL)
(|Bas-R| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(|Bas-S| T (
(OCELOT-GFP::PARENTS |Polypeptides|) )
NIL)
(BASAL-TRANSCRIPTION-VALUE NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |pkarp|)
(:CREATION-DATE 3199046812)
(:VALUE-TYPE :NUMBER)
(:DOCUMENTATION
"A number indicating the transcription of the promoter in the absence of any regulator.")
(:DOMAIN |RNA-Polymerase-Binding-Reactions|) )
NIL)
(|Base-Derivatives| T (
(OCELOT-GFP::PARENTS |All-Nucleosides|)
(COMMON-NAME "a base derivative")
(SCHEMA? T) )
NIL)
(BASE-EXCISION-REPAIR T (
(OCELOT-GFP::PARENTS INDIRECT-REPAIR)
(COMMON-NAME "Base excision DNA repair proteins")
(:CREATOR |paley|)
(:CREATION-DATE 3314378978) )
NIL)
(BASE-URL NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |paley|)
(:CREATION-DATE 3324392159)
(:DOMAIN |Databases|)
(:VALUE-TYPE :STRING)
(:DOCUMENTATION "Stores URL for Database home page") )
NIL)
(|Bases| T (
(OCELOT-GFP::PARENTS |All-Nucleosides|)
(COMMON-NAME "a base")
(COMMENT
"Probably this class of aromatic bases should not be under the nucleosides, as this is not strictly correct.")
(SCHEMA? T) )
NIL)
(BASIS-FOR-ASSIGNMENT NIL (
(OCELOT-GFP::PARENTS OCELOT-GFP::DOMAIN-SLOTS)
(:CREATOR |kr|)
(:CREATION-DATE 3339519670)
(:VALUE-TYPE
(:ONE-OF :EC-NUMBER :AUTOMATED-NAME-MATCH :MANUAL
:MANUAL-AMBIGUOUS-NAME-MATCH :MANUAL-NAME-TUPLE-MATCH
:INFERRED-TRANSPORT-RXN))
(:DOCUMENTATION
"Records the basis for assignment of the protein to the reaction, whether manually by a curator (the default), or automatically by various means.")
(:DOMAIN |Enzymatic-Reactions|) )
NIL)
(BASR-MONOMER NIL (
(OCELOT-GFP::PARENTS |Bas-R|)
(COMMON-NAME "BasR transcriptional regulator")
(:CREATION-DATE 3080311848)
(DBLINKS (MODBASE "P30843" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P30843" NIL |pick| NIL NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF BASR-RXN)
(PI 5.99d0)
(LOCATIONS CCO-CYTOPLASM)
(MOLECULAR-WEIGHT-SEQ 25.03077099999998d0)
(GENE EG11615)
(CITATIONS ":EV-EXP:3278863360:pkarp" "[95214091]" "[93128858]" "[90206041]"
"[93272330]")
(COMMENT
"The transcriptional regulatory protein BasR is part of the two-component
BasS/BasR signal transduction system. The physiological role of the BasS/BasR
system is not yet known. |CITS: [94110256]|
A microarray analysis for BasR of Escherichia coli was done by |CITS: [15322361]|.
")
(MODIFIED-FORM PHOSPHO-BASR)
(SYNONYMS "B4113" "PmrA" "BasR" "transcriptional regulatory protein BasR"
"unphosphorylated transcriptional regulatory protein BasR"
"unmodified transcriptional regulatory protein BasR") )
NIL)
(BASR-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080313680)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY BAS-PWY)
(RIGHT BASS-MONOMER PHOSPHO-BASR)
(LEFT PHOSPHO-BASS BASR-MONOMER)
(COMMENT
"In this reaction the transcriptional regulatory protein BasR is phosphorylated
by phospho-BasS. Based on analogy to other response regulators the
phosphorylation site of BasR is shown as an aspartate residue.") )
NIL)
(BASS-MONOMER NIL (
(OCELOT-GFP::PARENTS |Bas-S|)
(CITATIONS ":EV-EXP:3278863360:pkarp")
(:CREATION-DATE 3080312453)
(DBLINKS (MODBASE "P30844" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P30844" NIL |pick| NIL NIL NIL))
(COMMON-NAME "BasS")
(APPEARS-IN-RIGHT-SIDE-OF BASR-RXN)
(APPEARS-IN-LEFT-SIDE-OF BASS-RXN)
(PI 6.34d0)
(LOCATIONS CCO-PM-BAC-NEG)
(MOLECULAR-WEIGHT-SEQ 41.02916999999996d0)
(GENE EG11614)
(MODIFIED-FORM PHOSPHO-BASS)
(SYNONYMS "B4112" "PmrB" "BasS" "sensor protein BasS"
"sensor kinase-phosphotransferase BasS"
"unphosphorylated sensor kinase-phosphotransferase BasS"
"unmodified sensor kinase-phosphotransferase BasS") )
NIL)
(BASS-RXN NIL (
(OCELOT-GFP::PARENTS |Protein-Modification-Reactions|)
(OFFICIAL-EC? T)
(:CREATION-DATE 3080313680)
(SPECIES ECOLI)
(CITATIONS "[95214091]" "[93128858]" "[90206041]" "[93272330]")
(IN-PATHWAY BAS-PWY)
(RIGHT ADP PHOSPHO-BASS)
(LEFT ATP BASS-MONOMER)
(COMMENT
"In this reaction the sensor kinase-phosphotransferase BasS is autophosphorylated.
Based on analogy to other sensor proteins the phosphorylation site is shown as
a histidine residue."
"Sensor kinase-phosphotransferase BasS is part of the two-component BasS/BasR
signal transduction system. The physiological role of the BasS/BasR system is
not yet known. |CITS: [94110256]|") )
NIL)
(BC-1 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "carbon utilization")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1.1 T (
(OCELOT-GFP::PARENTS BC-1.1)
(COMMON-NAME "carbon compounds")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1.2 T (
(OCELOT-GFP::PARENTS BC-1.1)
(COMMON-NAME "fatty acids")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1.3 T (
(OCELOT-GFP::PARENTS BC-1.1)
(COMMON-NAME "amino acids")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1.4 T (
(OCELOT-GFP::PARENTS BC-1.1)
(COMMON-NAME "amines")
(:CREATOR |pkarp|) )
NIL)
(BC-1.1.5 T (
(OCELOT-GFP::PARENTS BC-1.1)
(COMMON-NAME "other compounds")
(:CREATOR |pkarp|) )
NIL)
(BC-1.2 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "degradation of macromolecules")
(:CREATOR |pkarp|) )
NIL)
(BC-1.2.1 T (
(OCELOT-GFP::PARENTS BC-1.2)
(COMMON-NAME "RNA")
(:CREATOR |pkarp|) )
NIL)
(BC-1.2.2 T (
(OCELOT-GFP::PARENTS BC-1.2)
(COMMON-NAME "DNA")
(:CREATOR |pkarp|) )
NIL)
(BC-1.2.3 T (
(OCELOT-GFP::PARENTS BC-1.2)
(COMMON-NAME "proteins/peptides/glycopeptides")
(:CREATOR |pkarp|) )
NIL)
(BC-1.2.4 T (
(OCELOT-GFP::PARENTS BC-1.2)
(COMMON-NAME "polysaccharides")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "energy metabolism, carbon")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.1 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "glycolysis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.2 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "pentose pwy, oxidative branch")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.3 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "pyruvate dehydrogenase")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.4 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "TCA cycle")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.5 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "fermentation")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.6 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "aerobic respiration")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.7 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "anaerobic respiration")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.8 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "ATP proton motive force interconversion")
(:CREATOR |pkarp|) )
NIL)
(BC-1.3.9 T (
(OCELOT-GFP::PARENTS BC-1.3)
(COMMON-NAME "Entner-Doudoroff")
(:CREATOR |pkarp|) )
NIL)
(BC-1.4 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "energy production/transport")
(:CREATOR |pkarp|) )
NIL)
(BC-1.4.1 T (
(OCELOT-GFP::PARENTS BC-1.4)
(COMMON-NAME "electron donors")
(:CREATOR |pkarp|) )
NIL)
(BC-1.4.2 T (
(OCELOT-GFP::PARENTS BC-1.4)
(COMMON-NAME "electron acceptors")
(:CREATOR |pkarp|) )
NIL)
(BC-1.4.3 T (
(OCELOT-GFP::PARENTS BC-1.4)
(COMMON-NAME "electron carriers")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "biosynthesis of building blocks")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1 T (
(OCELOT-GFP::PARENTS BC-1.5)
(COMMON-NAME "amino acids")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.1 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "glutamate")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.10 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "glycine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.11 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "serine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.12 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "cysteine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.13 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "phenylalanine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.14 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "tyrosine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.15 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "tryptophan")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.16 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "histidine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.17 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "alanine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.18 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "isoleucine/valine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.19 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "leucine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.2 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "glutamine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.20 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "chorismate")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.21 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "homoserine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.3 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "arginine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.4 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "proline")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.5 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "aspartate")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.6 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "asparagine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.7 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "lysine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.8 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "threonine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.1.9 T (
(OCELOT-GFP::PARENTS BC-1.5.1)
(COMMON-NAME "methionine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.2 T (
(OCELOT-GFP::PARENTS BC-1.5)
(COMMON-NAME "nucleotides")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.2.1 T (
(OCELOT-GFP::PARENTS BC-1.5.2)
(COMMON-NAME "purine biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.2.2 T (
(OCELOT-GFP::PARENTS BC-1.5.2)
(COMMON-NAME "pyrimidine biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.2.3 T (
(OCELOT-GFP::PARENTS BC-1.5.2)
(COMMON-NAME "purine ribonucleotide biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.2.4 T (
(OCELOT-GFP::PARENTS BC-1.5.2)
(COMMON-NAME "pyrimidine ribonucleotide biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3 T (
(OCELOT-GFP::PARENTS BC-1.5)
(COMMON-NAME "cofactors, small molecule carriers")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.1 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "biotin")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.10 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "glutathione")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.11 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "menaquinone, ubiquinone")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.12 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "heme, porphyrine")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.13 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "cobalamin")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.14 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "enterochelin (enterobactin)")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.2 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "folic acid")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.3 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "lipoate")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.4 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "molybdenum")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.5 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "Coenzyme A and its modification")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.6 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "pyridoxal 5'phosphate")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.7 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "nicotinamide adenine dinucleotide")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.8 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "thiamin")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.3.9 T (
(OCELOT-GFP::PARENTS BC-1.5.3)
(COMMON-NAME "riboflavin")
(:CREATOR |pkarp|) )
NIL)
(BC-1.5.4 T (
(OCELOT-GFP::PARENTS BC-1.5)
(COMMON-NAME "fatty acids and phosphatidic acid")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMENT
"The cell structure category contains both genes encoding components of the structure and genes encoding products involved in the biosynthesis of the structure.")
(COMMON-NAME "biosynthesis of macromolecules (cellular constituents)")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.1 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "phospholipid")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.10 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "lipoprotein")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.11 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "glycoprotein")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.12 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "flagellum")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.13 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "fimbri, pili")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.15 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "large molecule carriers")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.15.1 T (
(OCELOT-GFP::PARENTS BC-1.6.15)
(COMMON-NAME "cytochromes")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.15.2 T (
(OCELOT-GFP::PARENTS BC-1.6.15)
(COMMON-NAME "thioredoxin, glutaredoxin")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.15.3 T (
(OCELOT-GFP::PARENTS BC-1.6.15)
(COMMON-NAME "biotin carboxyl carrier protein")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.15.4 T (
(OCELOT-GFP::PARENTS BC-1.6.15)
(COMMON-NAME "acyl carrier protein")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.2 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "colanic acid (M antigen)")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.3 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "lipopolysaccharide")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.3.1 T (
(OCELOT-GFP::PARENTS BC-1.6.3)
(COMMON-NAME "O antigen")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.3.2 T (
(OCELOT-GFP::PARENTS BC-1.6.3)
(COMMON-NAME "core region")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.3.3 T (
(OCELOT-GFP::PARENTS BC-1.6.3)
(COMMON-NAME "lipid A")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.4 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "enterobacterial common antigen (surface glycolipid)")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.5 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "K antigen")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.6 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "osmoregulated periplasmic glucan")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.7 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "murein (peptidoglycan)")
(:CREATOR |pkarp|) )
NIL)
(BC-1.6.9 T (
(OCELOT-GFP::PARENTS BC-1.6)
(COMMON-NAME "cytoplasmic polysaccharides")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "central intermediary metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.1 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "unassigned reversible reactions")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.10 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "sugar nucleotide biosynthesis, conversions")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.12 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "amino sugar conversions")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.13 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "amino acid conversion")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.14 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "polyamine biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.15 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "2'-deoxyribonucleotide metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.17 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "formyl-THF biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.18 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "betaine biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.19 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "incorporation of metal ions")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.2 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "glyoxylate bypass")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.20 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "S-adenosyl methionine biosynthesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.21 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "glyoxylate degradation")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.22 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "carnitine metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.23 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "methylglyoxal metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.24 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "cyanate catabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.25 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "glycolate metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.26 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "allantoin assimilation")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.27 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "pyridoxal 5'-phosphate salvage")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.28 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "pyruvate oxidation")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.29 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "acetate catabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.3 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "non-oxidative branch, pentose pathway")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.30 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "threonine catabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.31 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "aminobutyrate catabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.32 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "putrescine catabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.33 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "nucleotide and nucleoside conversions")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.34 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "murein turnover, recycling")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.6 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "misc. glycerol metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.7 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "galactose metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.8 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "gluconeogenesis")
(:CREATOR |pkarp|) )
NIL)
(BC-1.7.9 T (
(OCELOT-GFP::PARENTS BC-1.7)
(COMMON-NAME "misc. glucose metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.8 T (
(OCELOT-GFP::PARENTS BC-1)
(COMMON-NAME "metabolism of other compounds")
(:CREATOR |pkarp|) )
NIL)
(BC-1.8.1 T (
(OCELOT-GFP::PARENTS BC-1.8)
(COMMON-NAME "phosphorous metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.8.2 T (
(OCELOT-GFP::PARENTS BC-1.8)
(COMMON-NAME "sulfur metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-1.8.3 T (
(OCELOT-GFP::PARENTS BC-1.8)
(COMMON-NAME "nitrogen metabolism")
(:CREATOR |pkarp|) )
NIL)
(BC-2 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "information transfer")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1 T (
(OCELOT-GFP::PARENTS BC-2)
(COMMON-NAME "DNA related")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1.1 T (
(OCELOT-GFP::PARENTS BC-2.1)
(COMMON-NAME "DNA replication")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1.2 T (
(OCELOT-GFP::PARENTS BC-2.1)
(COMMON-NAME "DNA restriction/modification")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1.3 T (
(OCELOT-GFP::PARENTS BC-2.1)
(COMMON-NAME "DNA recombination")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1.4 T (
(OCELOT-GFP::PARENTS BC-2.1)
(COMMON-NAME "DNA repair")
(:CREATOR |pkarp|) )
NIL)
(BC-2.1.5 T (
(OCELOT-GFP::PARENTS BC-2.1)
(COMMON-NAME "DNA degradation")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2 T (
(OCELOT-GFP::PARENTS BC-2)
(COMMON-NAME "RNA related")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.2 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "Transcription related")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.3 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "RNA modification")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.4 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "RNA degradation")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.5 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "tRNA")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.6 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "rRNA, stable RNA")
(:CREATOR |pkarp|) )
NIL)
(BC-2.2.7 T (
(OCELOT-GFP::PARENTS BC-2.2)
(COMMON-NAME "antisense RNA")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3 T (
(OCELOT-GFP::PARENTS BC-2)
(COMMON-NAME "protein related")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.1 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "amino acid -activation")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.2 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "translation")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.3 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "posttranslational modification")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.4 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "chaperoning, repair (refolding)")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.5 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "export, signal peptide cleavage")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.6 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "turnover, degradation")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.7 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "nucleoproteins, basic proteins")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.8 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "ribosomal proteins")
(:CREATOR |pkarp|) )
NIL)
(BC-2.3.9 T (
(OCELOT-GFP::PARENTS BC-2.3)
(COMMON-NAME "Non-ribosomal peptide synthetase")
(:CREATOR |pkarp|) )
NIL)
(BC-3 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "regulation")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1 T (
(OCELOT-GFP::PARENTS BC-3)
(COMMON-NAME "type of regulation")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.1 T (
(OCELOT-GFP::PARENTS BC-3.1)
(COMMON-NAME "DNA structure level")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.1.1 T (
(OCELOT-GFP::PARENTS BC-3.1.1)
(COMMON-NAME "bent DNA or supercoiling, inversion")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.1.2 T (
(OCELOT-GFP::PARENTS BC-3.1.1)
(COMMON-NAME "methylation")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2 T (
(OCELOT-GFP::PARENTS BC-3.1)
(COMMON-NAME "transcriptional level")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.1 T (
(OCELOT-GFP::PARENTS BC-3.1.2)
(COMMON-NAME "sigma factors, anti-sigmafactors")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.2 T (
(OCELOT-GFP::PARENTS BC-3.1.2)
(COMMON-NAME "activator")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.3 T (
(OCELOT-GFP::PARENTS BC-3.1.2)
(COMMON-NAME "repressor")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.4 T (
(OCELOT-GFP::PARENTS BC-3.1.2)
(COMMON-NAME "complex regulation")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.4.1 T (
(OCELOT-GFP::PARENTS BC-3.1.2.4)
(COMMON-NAME "more than one signal needed")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.4.2 T (
(OCELOT-GFP::PARENTS BC-3.1.2.4)
(COMMON-NAME "regulons or multilayer component regulatory systems")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.4.3 T (
(OCELOT-GFP::PARENTS BC-3.1.2.4)
(COMMON-NAME "two component regulatory systems (external signal)")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.4.4 T (
(OCELOT-GFP::PARENTS BC-3.1.2.4)
(COMMON-NAME "quorum sensing")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.2.5 T (
(OCELOT-GFP::PARENTS BC-3.1.2)
(COMMON-NAME "action unknown")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3 T (
(OCELOT-GFP::PARENTS BC-3.1)
(COMMON-NAME "posttranscriptional")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.1 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "translation attenuation and efficiency")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.2 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "covalent modification, demodification, maturation")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.3 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "inhibition / activation of enzymes")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.4 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "proteases, cleavage of compounds")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.5 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "multilayer regulatory system")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.3.6 T (
(OCELOT-GFP::PARENTS BC-3.1.3)
(COMMON-NAME "antisense RNA")
(:CREATOR |pkarp|) )
NIL)
(BC-3.1.4 T (
(OCELOT-GFP::PARENTS BC-3.1)
(COMMON-NAME "unknown")
(:CREATOR |pkarp|) )
NIL)
(BC-3.3 T (
(OCELOT-GFP::PARENTS BC-3)
(COMMON-NAME "genetic unit regulated")
(:CREATOR |pkarp|) )
NIL)
(BC-3.3.1 T (
(OCELOT-GFP::PARENTS BC-3.3)
(COMMON-NAME "operon")
(:CREATOR |pkarp|) )
NIL)
(BC-3.3.2 T (
(OCELOT-GFP::PARENTS BC-3.3)
(COMMON-NAME "regulon")
(:CREATOR |pkarp|) )
NIL)
(BC-3.3.3 T (
(OCELOT-GFP::PARENTS BC-3.3)
(COMMON-NAME "stimulon")
(:CREATOR |pkarp|) )
NIL)
(BC-3.3.4 T (
(OCELOT-GFP::PARENTS BC-3.3)
(COMMON-NAME "global")
(:CREATOR |pkarp|) )
NIL)
(BC-3.4 T (
(OCELOT-GFP::PARENTS BC-3)
(COMMENT
"The terms trigger (3.4) and modulator (3.5) were meant to specify specific compounds/proteins either triggering a response or modulating a response. Ie for lacI, lactose is the trigger and CRP a modulator of the regulation. The activator or repressor would be specified by 3.1.2.2 or 3.1.2.3 respectively.")
(COMMON-NAME "trigger (some information added)")
(:CREATOR |pkarp|) )
NIL)
(BC-3.5 T (
(OCELOT-GFP::PARENTS BC-3)
(COMMENT
"The terms trigger (3.4) and modulator (3.5) were meant to specify specific compounds/proteins either triggering a response or modulating a response. Ie for lacI, lactose is the trigger and CRP a modulator of the regulation. The activator or repressor would be specified by 3.1.2.2 or 3.1.2.3 respectively.")
(COMMON-NAME "trigger modulation (some information added)")
(:CREATOR |pkarp|) )
NIL)
(BC-4 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "transport")
(:CREATOR |pkarp|) )
NIL)
(BC-4.1 T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Channel-type Transporters")
(:CREATOR |pkarp|) )
NIL)
(BC-4.1.A T (
(OCELOT-GFP::PARENTS BC-4.1)
(COMMON-NAME "alpha-type channels")
(:CREATOR |pkarp|) )
NIL)
(BC-4.1.B T (
(OCELOT-GFP::PARENTS BC-4.1)
(COMMON-NAME
"Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)")
(:CREATOR |pkarp|) )
NIL)
(BC-4.2 T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Electrochemical potential driven transporters")
(:CREATOR |pkarp|) )
NIL)
(BC-4.2.A T (
(OCELOT-GFP::PARENTS BC-4.2)
(COMMON-NAME "Porters (Uni-, Sym- and Antiporters)")
(:CREATOR |pkarp|) )
NIL)
(BC-4.2.C T (
(OCELOT-GFP::PARENTS BC-4.2)
(COMMON-NAME "Ion-gradient-driven energizers")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3 T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Primary Active Transporters")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A T (
(OCELOT-GFP::PARENTS BC-4.1)
(COMMON-NAME
"Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A.1 T (
(OCELOT-GFP::PARENTS BC-4.3.A)
(COMMON-NAME
"The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases")
(:CREATOR |pkarp|) )
NIL)
(|BC-4.3.A.1.a| T (
(OCELOT-GFP::PARENTS BC-4.3.A.1)
(COMMON-NAME "ABC superfamily ATP binding cytoplasmic component")
(:CREATOR |pkarp|) )
NIL)
(|BC-4.3.A.1.am| T (
(OCELOT-GFP::PARENTS BC-4.3.A.1)
(COMMON-NAME "ABC superfamily, ATP binding and membrane component")
(:CREATOR |pkarp|) )
NIL)
(|BC-4.3.A.1.m| T (
(OCELOT-GFP::PARENTS BC-4.3.A.1)
(COMMON-NAME "ABC superfamily, membrane component")
(:CREATOR |pkarp|) )
NIL)
(|BC-4.3.A.1.p| T (
(OCELOT-GFP::PARENTS BC-4.3.A.1)
(COMMON-NAME "ABC superfamily, periplasmic binding component")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A.2 T (
(OCELOT-GFP::PARENTS BC-4.3.A)
(COMMON-NAME
"The H+- or Na+-translocating F-type, V-type and A-type ATPase (F-ATPase) Su")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A.3 T (
(OCELOT-GFP::PARENTS BC-4.3.A)
(COMMON-NAME "The P-type ATPase (P-ATPase) Superfamily")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A.4 T (
(OCELOT-GFP::PARENTS BC-4.3.A)
(COMMON-NAME "The Arsenite-Antimonite (Ars) Efflux Family")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.A.5 T (
(OCELOT-GFP::PARENTS BC-4.3.A)
(COMMON-NAME "The Type II (General) Secretory Pathway (IISP) Family")
(:CREATOR |pkarp|) )
NIL)
(BC-4.3.D T (
(OCELOT-GFP::PARENTS BC-4.3)
(COMMON-NAME "Oxidoreduction-driven Active Transporters")
(:CREATOR |pkarp|) )
NIL)
(BC-4.4 T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Group Translocators")
(:CREATOR |pkarp|) )
NIL)
(BC-4.4.A T (
(OCELOT-GFP::PARENTS BC-4.4)
(COMMON-NAME "Phosphotransferase Systems (PEP-dependent PTS)")
(:CREATOR |pkarp|) )
NIL)
(BC-4.8.A T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Accessory Factors Involved in Transport")
(:CREATOR |pkarp|) )
NIL)
(BC-4.9.A T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Transporters of Unknown Classification")
(:CREATOR |pkarp|) )
NIL)
(BC-4.9.B T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "Putative uncharacterized transport protein")
(:CREATOR |pkarp|) )
NIL)
(BC-4.S T (
(OCELOT-GFP::PARENTS BC-4)
(COMMON-NAME "substrate")
(:CREATOR |pkarp|) )
NIL)
(BC-5 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "cell processes")
(:CREATOR |pkarp|) )
NIL)
(BC-5.1 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "cell division")
(:CREATOR |pkarp|) )
NIL)
(BC-5.10 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMENT
"The adaptation to stress was meant to cover the classical stress inducers such as osmotic pressure, temperature, starvation.
The protection category was meant to cover those related to compound / chemical induced killing or stress.
The defense/survival category was meant to cover virulence factors (although K-12 does not have many).")
(COMMON-NAME "defense/survivial")
(:CREATOR |pkarp|) )
NIL)
(BC-5.11 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "DNA uptake")
(:CREATOR |pkarp|) )
NIL)
(BC-5.2 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "cell cycle physiology")
(:CREATOR |pkarp|) )
NIL)
(BC-5.3 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)")
(:CREATOR |pkarp|) )
NIL)
(BC-5.4 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "genetic exchange, recombination (for future)")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMENT
"The adaptation to stress was meant to cover the classical stress inducers such as osmotic pressure, temperature, starvation.
The protection category was meant to cover those related to compound / chemical induced killing or stress.
The defense/survival category was meant to cover virulence factors (although K-12 does not have many).")
(COMMON-NAME "adaptations")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.1 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "osmotic pressure")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.2 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "temperature extremes")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.3 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "starvation")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.4 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "pH")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.5 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "dessication")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.6 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "other (mechanical, nutritional, oxidative stress)")
(:CREATOR |pkarp|) )
NIL)
(BC-5.5.7 T (
(OCELOT-GFP::PARENTS BC-5.5)
(COMMON-NAME "Fe aquisition")
(:CREATOR |pkarp|) )
NIL)
(BC-5.6 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMENT
"The adaptation to stress was meant to cover the classical stress inducers such as osmotic pressure, temperature, starvation.
The protection category was meant to cover those related to compound / chemical induced killing or stress.
The defense/survival category was meant to cover virulence factors (although K-12 does not have many).")
(COMMON-NAME "protection")
(:CREATOR |pkarp|) )
NIL)
(BC-5.6.1 T (
(OCELOT-GFP::PARENTS BC-5.6)
(COMMON-NAME "radiation")
(:CREATOR |pkarp|) )
NIL)
(BC-5.6.2 T (
(OCELOT-GFP::PARENTS BC-5.6)
(COMMON-NAME "detoxification")
(:CREATOR |pkarp|) )
NIL)
(BC-5.6.3 T (
(OCELOT-GFP::PARENTS BC-5.6)
(COMMON-NAME "cell killing")
(:CREATOR |pkarp|) )
NIL)
(BC-5.6.4 T (
(OCELOT-GFP::PARENTS BC-5.6)
(COMMON-NAME "drug resistance/sensitivity")
(:CREATOR |pkarp|) )
NIL)
(BC-5.8 T (
(OCELOT-GFP::PARENTS BC-5)
(COMMON-NAME "SOS response")
(:CREATOR |pkarp|) )
NIL)
(BC-6 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "cell structure")
(:CREATOR |pkarp|) )
NIL)
(BC-6.1 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "membrane")
(:CREATOR |kr|)
(:CREATION-DATE 3333904171) )
NIL)
(BC-6.2 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "murein")
(:CREATOR |pkarp|) )
NIL)
(BC-6.3 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "surface antigens (ECA, O antigen of LPS)")
(:CREATOR |pkarp|) )
NIL)
(BC-6.4 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "flagella")
(:CREATOR |pkarp|) )
NIL)
(BC-6.5 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "pilus")
(:CREATOR |pkarp|) )
NIL)
(BC-6.6 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "ribosomes")
(:CREATOR |pkarp|) )
NIL)
(BC-6.7 T (
(OCELOT-GFP::PARENTS BC-6)
(COMMON-NAME "capsule (M and K antigens)")
(:CREATOR |pkarp|) )
NIL)
(BC-7 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "location of gene products")
(:CREATOR |pkarp|) )
NIL)
(BC-7.1 T (
(OCELOT-GFP::PARENTS BC-7)
(COMMON-NAME "cytoplasm")
(:CREATOR |pkarp|) )
NIL)
(BC-7.2 T (
(OCELOT-GFP::PARENTS BC-7)
(COMMON-NAME "periplasm")
(:CREATOR |pkarp|) )
NIL)
(BC-7.3 T (
(OCELOT-GFP::PARENTS BC-7)
(COMMON-NAME "inner membrane")
(:CREATOR |kr|)
(:CREATION-DATE 3333901403) )
NIL)
(BC-7.4 T (
(OCELOT-GFP::PARENTS BC-7)
(COMMON-NAME "outer membrane")
(:CREATOR |pkarp|) )
NIL)
(BC-7.5 T (
(OCELOT-GFP::PARENTS BC-7)
(COMMON-NAME "extracellular")
(:CREATOR |pkarp|) )
NIL)
(BC-8 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMENT
"Extrachromosomal origin should include chromosomal genes affecting functions of genes of extrachromosomal origin.
")
(COMMON-NAME "extrachromosomal")
(:CREATOR |pkarp|) )
NIL)
(BC-8.1 T (
(OCELOT-GFP::PARENTS BC-8)
(COMMON-NAME "prophage genes and phage related functions")
(:CREATOR |pkarp|) )
NIL)
(BC-8.2 T (
(OCELOT-GFP::PARENTS BC-8)
(COMMON-NAME "plasmid related")
(:CREATOR |pkarp|) )
NIL)
(BC-8.3 T (
(OCELOT-GFP::PARENTS BC-8)
(COMMON-NAME "transposon related")
(:CREATOR |pkarp|) )
NIL)
(BC-8.4 T (
(OCELOT-GFP::PARENTS BC-8)
(COMMON-NAME "colicin related")
(:CREATOR |pkarp|) )
NIL)
(BC-9 T (
(OCELOT-GFP::PARENTS |Physiological-Roles|)
(COMMON-NAME "DNA sites")
(:CREATOR |pkarp|) )
NIL)
(|BCAA-dehydrogenase-2MB-DH-lipoyl| T (
(OCELOT-GFP::PARENTS |Branched-ketoacid-E2|)
(COMMON-NAME
"enzyme N6-(S-[2-methylbutanoyl]dihydrolipoyl)lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(|BCAA-dehydrogenase-2MP-DH-lipoyl| T (
(OCELOT-GFP::PARENTS |Branched-ketoacid-E2|)
(COMMON-NAME
"enzyme N6-(S-[2-methylpropanoyl]dihydrolipoyl)lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(|BCAA-dehydrogenase-3MB-DH-lipoyl| T (
(OCELOT-GFP::PARENTS |Branched-ketoacid-E2|)
(COMMON-NAME
"enzyme N6-(S-[3-methylbutanoyl]dihydrolipoyl)lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(|BCAA-dehydrogenase-DH-lipoyl| T (
(OCELOT-GFP::PARENTS |Branched-ketoacid-E2|)
(COMMON-NAME "enzyme N6-(dihydrolipoyl)lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(|BCAA-dehydrogenase-lipoyl| T (
(OCELOT-GFP::PARENTS |Branched-ketoacid-E2|)
(COMMON-NAME "enzyme N6-(lipoyl)lysine")
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(BCCP T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(:CREATION-DATE 3064789704)
(:CREATOR |kr|)
(COMMON-NAME "BCCP family") )
NIL)
(BCCP-BIOTIN NIL (
(OCELOT-GFP::PARENTS |BCCP-biotin-monomers|)
(CITATIONS "14594796")
(MOLECULAR-WEIGHT-SEQ 16.687185000000007d0)
(:CREATION-DATE 3064793438)
(DBLINKS (MODBASE "P0ABD8" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00364" IN-FAMILY |pkarp| 3346700393 NIL NIL)
(UNIPROT "P0ABD8" NIL |pkarp| 3338704821 NIL NIL)
(REFSEQ "NP_417721" NIL NIL NIL NIL NIL))
(GENE EG10275)
(COMPONENT-OF BCCP-CPLX)
(UNMODIFIED-FORM BCCP-MONOMER)
(SYNONYMS "B3255" "FabE" "AccB"
"[acetyl-CoA:carbon-dioxide ligase (ADP forming)]" "BCCP-biotin (monomer)"
"biotin-BCCP (monomer)")
(COMMON-NAME "biotinylated biotin-carboxyl carrier protein") )
NIL)
(BCCP-BIOTIN-CO2 NIL (
(OCELOT-GFP::PARENTS |Carboxybiotin-BCCP|)
(DBLINKS (MODBASE "P0ABD8" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0ABD8" NIL |pkarp| 3338704821 NIL NIL))
(MOLECULAR-WEIGHT-SEQ 16.687185000000007d0)
(:CREATION-DATE 3064793438)
(GENE EG10275)
(UNMODIFIED-FORM BCCP-CPLX)
(SYNONYMS "B3255" "FabE" "AccB" "BCCP-biotin-CO2")
(COMMON-NAME "carboxybiotin-carboxyl-carrier protein") )
NIL)
(|BCCP-biotin-monomers| T (
(OCELOT-GFP::PARENTS |BCCP-monomers|)
(APPEARS-IN-LEFT-SIDE-OF RXN-7101)
(APPEARS-IN-RIGHT-SIDE-OF BIOTINLIG-RXN)
(COMMON-NAME "biotin-BCCP (monomer)")
(:CREATOR |caspi|)
(:CREATION-DATE 3347812974) )
NIL)
(BCCP-CPLX NIL (
(OCELOT-GFP::PARENTS |BCCP-dimers| |Protein-Complexes|)
(APPEARS-IN-LEFT-SIDE-OF BR0-10390)
(SYMMETRY :INVERTED-REPEAT)
(MODIFIED-FORM BCCP-BIOTIN-CO2)
(CITATIONS "[20011362]" "14594796")
(COMPONENT-OF CPLX0-5535 ACETYL-COA-CARBOXYLMULTI-CPLX)
(COMPONENTS BCCP-BIOTIN)
(COMMENT "Biotin carboxyl carrier protein (BCCP) plays a central role
in the acetyl-CoA carboxylase complex. The overall carboxylase
reaction takes place in two distinct half-reactions. BCCP, which
contains a biotinyl prosthetic group covalently attached to a specific
lysyl residue, is carboxylated in the first partial reaction. In the
second partial reaction the carboxyl group is transferred to an
acceptor and BCCP is regenerated for further carboxylation. |CITS:
[77187896]|.
On the other hand, BCCP amino terminal is able to bind to DNA; this means, BCCP autoregulates its coding
gene expression (the accBD operon) |CITS:[14594796]|.")
(SYNONYMS "BCCP" "AccB")
(COMMON-NAME
"AccB transcriptional repressor; biotin carboxyl carrier protein (dimer)")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/carriers/accB.template")
(:CREATION-DATE 2995810365)
(:CREATOR |mriley|) )
((COMPONENTS BCCP-BIOTIN COEFFICIENT 2)))
(|BCCP-dimers| T (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(APPEARS-IN-LEFT-SIDE-OF BIOTIN-CARBOXYL-RXN)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-5055 RXN-7101)
(SYNONYMS "BCCP dimer" "biotin carboxy carrier protein (dimer)")
(COMMON-NAME "a biotin-BCCP (dimer)")
(:CREATOR |caspi|)
(:CREATION-DATE 3347813035) )
NIL)
(BCCP-MONOMER NIL (
(OCELOT-GFP::PARENTS |BCCP-monomers|)
(CITATIONS ":EV-EXP:3278863360:pkarp" "[2822655]" "[2660106]" "[2575489]"
"[7945216]")
(COMMENT
"The accB gene encodes the biotin carboxyl carrier protein (BCCP), a component of acetyl CoA carboxylase |CITS: [2575489]|. AccB is active as a dimer |CITS: [11495922]|.
The kinetics of the biotinylation reaction have been determined, and the N terminus does not appear to have any role in the modification |CITS: [8631788]|. Biotinylation causes a large structural change in the C-terminal region of the protein |CITS: [9325338]|. Biotinylation results in loss of conformational flexibility of the biotin interaction region |CITS: [10048324]|; a \"thumb\" domain comprising amino acids 94-101 fastens the biotin moiety to the surface of the protein |CITS: [10213607]| and this interaction results in increased protein stability |CITS: [11943781]|. This thumb domain is important for acetyl CoA carboxylase activity |CITS: [11495922], [10213607]|. Unbiotinylated AccB C-terminal domain dimerizes, and biotinylated AccB C-terminal domain is monomeric |CITS: [9325338]|.
AccB appears to interact with the C terminus of the BirA biotin ligase |CITS: [11714929]|. The interaction of BirA with AccB BirA-BCCP binding may preclude BirA dimerization and therefore DNA binding and transcriptional repressor activity of BirA |CITS: [11714930]|.
A crystal structure of the biotinyl domain is presented at 1.8 angstrom resolution |CITS: [8747466]|. An NMR structure of the C-terminal domain has also been determined |CITS: [9398236], [10213607]| and implications with respect to specificity of protein-protein interactions are discussed |CITS: [9398236]|. Structural characterization of biotin carboxyl carrier protein (BCCP) by circular dichroism indicates that the biotin moiety may be partly engulfed within the protein rather than fully exposed in solution |CITS: [5438]|. Secondary structure predictions have been made |CITS: [8102604]|.
Mutation of the MKM biotinylation sequence reveals substrate requirements; the position of the lysine is critical and the flanking methionines are not |CITS: [9445386]|. Production of a protein with a mutation of the biotinylated lysine residue partially complements the heat sensitivity of another accB mutant, probably due to formation of mutant heterodimers |CITS: [11495922]|. A fabE/accB mutation is shown to disrupt biotinylation |CITS: [1370469]|. E119K and E147K mutant proteins exhibit defects in biotinylation that are due to defects in interaction with BirA, the biotin ligase |CITS: [9880519]|. Mutation of residue G133, G143, or V146 causes structural disruption of the protein |CITS: [9880519]|. A linker region N-terminal to the biotinoyl domain is also essential for function (but not required for biotinylation) |CITS: [11956202]|. Mutations in accB or accC suppress the inviability of an htrB mutant at 42 deg, which is due to accumulation of excess phospholipids |CITS: [1358874]|.
AccB has 57% identity to Anabaena sp. strain PCC 7120 biotin carboxyl carrier protein |CITS: [8102363]| and has similarity to biotin carboxyl carrier proteins from Pseudomonas aeruginosa |CITS: [7693652]|, Mycobacterium leprae |CITS: [7909542]|, Mycobacterium tuberculosis |CITS: [7909542]|, Bacillus subtilis |CITS: [7592499]|, Glycine max (soybean) |CITS: [10069834]|, Sulfolobus metallicus |CITS: [10591844]|, Lactobacillus plantarum |CITS: [11133475]|, Arabidopsis thaliana |CITS: [11299381]|, and Aquifex aeolicus |CITS: [12631286]|. AccB has similarity to the putative protein encoded by ORF2 of Lactobacillus sanfranciscensis DSM20451T |CITS: [9851037]|. AccB also has similarity to Streptomyces venezuelae ISP5230 JadJ protein, which is involved in biosynthesis of the polyketide antibiotic jadomycin B |CITS: [10784049]|. Pseudomonas aeruginosa AccB functionally complements conditional lethality of an accB mutation in E. coli|CITS: [7693652]|.
AccB exhibits an abnormally large apparent molecular weight of 22.5 kDa, compared to the predicted molecular weight of about 16.7 kDa |CITS: [1370469]|.
Purification of AccB is described |CITS: [8631788]|.
AccB peptides have been fused to exogenous proteins for use as biotinylation signals that facilitate purification |CITS: [7827508], [10357213]|.
Reviews: |CITS: [12121720], [10470036]|.
")
(MOLECULAR-WEIGHT-EXP 22.5d0)
(SYNONYMS "B3255" "FabE" "AccB"
"apo-[acetyl-CoA:carbon-dioxide ligase (ADP forming)]"
"biotin carboxyl carrier protein monomer" "BCCP (monomer)")
(MODIFIED-FORM BCCP-BIOTIN)
(COMMON-NAME "biotin carboxyl carrier protein")
(DBLINKS (MODBASE "P0ABD8" NIL |pkarp| 3355444109 NIL NIL)
(UNIPROT "P0ABD8" NIL |pkarp| 3338704821 NIL NIL) (PDB "1K69") (PDB "1K67")
(PDB "1BDO") (PDB "1A6X"))
(PI 4.74d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 16.687185000000007d0)
(GENE EG10275)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/carriers/accB.template")
(:CREATION-DATE 2995810365)
(:CREATOR |mriley|) )
NIL)
(|BCCP-monomers| T (
(OCELOT-GFP::PARENTS |Polypeptides|)
(APPEARS-IN-LEFT-SIDE-OF BIOTINLIG-RXN)
(SCHEMA? T)
(SYNONYMS "biotin-carboxyl-carrier protein" "BCCP"
"biotin-carboxyl-carrier protein monomer")
(:CREATION-DATE 3347812973)
(:CREATOR |caspi|)
(COMMON-NAME "BCCP (monomer)") )
NIL)
(BCR-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-6)
(MOLECULAR-WEIGHT-SEQ 43.3527889999999d0)
(:CREATION-DATE 3060042779)
(SYNONYMS "B2182" "Sur" "SuxA" "BicR" "BicA" "Bcr")
(DBLINKS (MODBASE "P28246" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF07690" IN-FAMILY |pkarp| 3346700354 NIL NIL)
(REFSEQ "NP_416687" NIL NIL NIL NIL NIL)
(UNIPROT "P28246" NIL |pkarp| 3064869797))
(CATALYZES TRANS-ENZRXN-11)
(COMMENT
"Bcr is a probable multidrug efflux protein, expression of which has been shown
to confer resistance to bicyclomycin |CITS: [93252267 ]| and sulfathiazole
|CITS: [98109320 ]|. Bcr is a member of the major facilitator superfamily
and has been proposed to function as a drug/proton antiporter |CITS: [93178956]|.")
(GENE EG11419)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "Bcr multidrug MFS transporter") )
NIL)
(BE NIL (
(OCELOT-GFP::PARENTS |Elements|)
(VALENCE 2)
(SYNONYMS "beryllium")
(COMMON-NAME "Be")
(ATOMIC-WEIGHT 9.012d0)
(ATOMIC-NUMBER 4)
(:CREATOR |paley|)
(:CREATION-DATE 3301322514) )
NIL)
(BENZALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Aryl-Aldehyde|)
(INHIBITORS-COMPETITIVE-OF ACETALD-DEHYDROG-ENZRXN)
(DBLINKS (CAS "100-52-7"))
(:CREATION-DATE 3073857204)
(GIBBS-0 2.1d0)
(SYNONYMS "benzanoaldehyde")
(COMMON-NAME "benzaldehyde")
(STRUCTURE-ATOMS C H O C C C C C C)
(STRUCTURE-BONDS (9 8 :AROMATIC) (8 6 1) (7 9 :AROMATIC) (6 3 2)
(8 5 :AROMATIC) (5 4 :AROMATIC) (2 6 1) (4 1 :AROMATIC) (1 7 :AROMATIC))
(DISPLAY-COORDS-2D (-1.0d0 -0.50083d0) (0.99669d0 -0.08099d0)
(0.96694d0 -1.0d0) (-0.73223d0 -0.98678d0) (-0.17025d0 -0.98678d0)
(0.66612d0 -0.53058d0) (-0.70909d0 -0.0314d0) (0.12727d0 -0.53058d0)
(-0.1405d0 -0.0314d0))
(CHEMICAL-FORMULA (C 7) (H 6) (O 1))
(MOLECULAR-WEIGHT 106.124d0)
(AROMATIC-RINGS (4 5 8 9 7 1)) )
((GIBBS-0 2.1d0 CITATIONS "GibbsGroups97")))
(BENZENE NIL (
(OCELOT-GFP::PARENTS |Rings|)
(DBLINKS (CAS "71-43-2"))
(:CREATION-DATE 3073857204)
(GIBBS-0 30.8d0)
(COMMON-NAME "benzene")
(DISPLAY-COORDS-2D (-1.38d0 -0.67d0) (-0.1d0 -1.53d0) (-1.27d0 0.85d0)
(1.27d0 -0.85d0) (0.1d0 1.53d0) (1.38d0 0.67d0))
(STRUCTURE-BONDS (2 1 :AROMATIC) (1 3 :AROMATIC) (4 2 :AROMATIC)
(3 5 :AROMATIC) (5 6 :AROMATIC) (6 4 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C)
(CHEMICAL-FORMULA (C 6) (H 6))
(MOLECULAR-WEIGHT 78.113d0)
(SYNONYMS "benzol" "benzole")
(AROMATIC-RINGS (2 4 6 5 3 1)) )
((GIBBS-0 30.8d0 CITATIONS "GibbsGroups97")))
(BENZENOID-SYN T (
(OCELOT-GFP::PARENTS PHENYLPROPANOID-SYN)
(COMMENT
"This class contains pathways of biosynthesis of benzoic acid and their derivatives characterized by a C6-C1 skeleton. Benzenoids are involved in many biological activities such as plant-plant interactions and defensive mechanisms. ")
(COMMON-NAME "Benzenoids")
(:CREATOR |paley|)
(:CREATION-DATE 3324143236) )
NIL)
(BENZOATE NIL (
(OCELOT-GFP::PARENTS |Aromatic-Acid|)
(INHIBITORS-COMPETITIVE-OF SARCOX-ENZRXN)
(DBLINKS (CAS "65-85-0"))
(:CREATION-DATE 3194283551)
(GIBBS-0 -52.1d0)
(:CREATOR |paley|)
(COMMON-NAME "benzoate")
(SYNONYMS "benzoic acid" "benzenecarboxylic acid" "phenylformic acid")
(STRUCTURE-ATOMS C C C C C C O O C)
(STRUCTURE-BONDS (6 7 2) (6 8 1) (5 6 1) (9 4 :AROMATIC) (4 3 :AROMATIC)
(3 2 :AROMATIC) (2 1 :AROMATIC) (5 9 :AROMATIC) (1 5 :AROMATIC))
(DISPLAY-COORDS-2D (-1.3707d0 -0.2563d0) (-1.3707d0 0.5688d0)
(-0.6563d0 0.9813d0) (0.0582d0 0.5688d0) (-0.6563d0 -0.6688d0)
(-0.6563d0 -1.4938d0) (0.0582d0 -1.9063d0) (-1.3707d0 -1.9063d0)
(0.0582d0 -0.2563d0))
(CHEMICAL-FORMULA (C 7) (H 6) (O 2))
(MOLECULAR-WEIGHT 122.123d0)
(AROMATIC-RINGS (2 3 4 9 5 1)) )
((GIBBS-0 -52.1d0 CITATIONS "GibbsGroups97")))
(|Benzoate-Degradation| T (
(OCELOT-GFP::PARENTS AROMATIC-COMPOUNDS-DEGRADATION)
(COMMON-NAME "benzoate degradation")
(COMMENT "This class holds pathways for the degradation of benzoate.")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(|Benzoyl-CoA-Degradation| T (
(OCELOT-GFP::PARENTS AROMATIC-COMPOUNDS-DEGRADATION)
(COMMON-NAME "benzoyl-coA degradation")
(COMMENT "This class holds pathways for the degradation of benzoyl-coA.")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3362411293) )
NIL)
(BENZYL-ALCOHOL NIL (
(OCELOT-GFP::PARENTS |Aromatics|)
(INHIBITORS-COMPETITIVE-OF PHES-ENZRXN)
(:CREATOR |keseler|)
(:CREATION-DATE 3360345092)
(SYNONYMS "α-hydroxytoluene" "benzenemethanol" "phenylmethanol"
"phenylcarbinol" "hydroxymethylbenzene")
(STRUCTURE-ATOMS C C C C C C C O)
(DISPLAY-COORDS-2D (2.0083d0 -0.4583d0) (2.0083d0 0.3d0) (2.6579d0 0.6833d0)
(3.3157d0 0.3d0) (3.3157d0 -0.4583d0) (2.6579d0 -0.8333d0)
(2.6558d0 -1.5833d0) (3.3043d0 -1.9601d0))
(STRUCTURE-BONDS (7 8 1) (6 7 1) (6 5 :AROMATIC) (5 4 :AROMATIC)
(4 3 :AROMATIC) (3 2 :AROMATIC) (2 1 :AROMATIC) (1 6 :AROMATIC))
(CHEMICAL-FORMULA (C 7) (H 8) (O 1))
(MOLECULAR-WEIGHT 108.14d0)
(AROMATIC-RINGS (2 3 4 5 6 1))
(COMMON-NAME "benzyl alcohol")
(DBLINKS (CAS "100-51-6")) )
NIL)
(BETA-ACIDS T (
(OCELOT-GFP::PARENTS BITTER-ACIDS)
(COMMON-NAME "a β-acid")
(:CREATOR |paley|)
(:CREATION-DATE 3355681268) )
NIL)
(|Beta-Alanine-Biosynthesis| T (
(OCELOT-GFP::PARENTS IND-AMINO-ACID-SYN)
(COMMON-NAME "β alanine biosynthesis")
(VARIANTS? T)
(:CREATOR |paley|)
(:CREATION-DATE 3347159103) )
NIL)
(|Beta-b-L-arabinosides| T (
(OCELOT-GFP::PARENTS |L-Arabinosides|)
(COMMON-NAME "a β-L-arabinoside")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(|Beta-D-Galactosides| T (
(OCELOT-GFP::PARENTS |Galactosides|)
(APPEARS-IN-LEFT-SIDE-OF GALACTOACETYLTRAN-RXN)
(SYNONYMS "a β-D-galactoside" "β-D-galactoside")
(COMMENT
"This compound class stands for generic and unspecified β-D-galactosides.")
(:CREATOR |kr|)
(:CREATION-DATE 3265036151) )
NIL)
(|Beta-D-Glucans| T (
(OCELOT-GFP::PARENTS |Glycogens|)
(COMMON-NAME "a β-D glucan")
(:CREATOR |paley|)
(:CREATION-DATE 3355681261) )
NIL)
(|Beta-D-Glucuronides| T (
(OCELOT-GFP::PARENTS |Glucuronides|)
(DISPLAY-COORDS-2D (0.0d0 -3.5d0) (1.2124d0 -5.6d0) (3.6373d0 0.0d0)
(6.0622d0 -1.4d0) (1.2124d0 -1.4d0) (7.2746d0 -3.5d0) (6.0622d0 -4.2d0)
(3.6373d0 -4.2d0) (1.2124d0 -4.2d0) (3.6373d0 -1.4d0) (4.8497d0 -2.1d0)
(2.4249d0 -2.1d0) (4.8497d0 -3.5d0) (2.4249d0 -3.5d0))
(CHEMICAL-FORMULA (C 6) (H 9) (O 7) (R 1))
(STRUCTURE-BONDS (12 14 1) (11 13 1) (10 12 1) (10 11 1) (14 9 1 :UP)
(8 14 1) (8 13 1) (13 7 1 :UP) (6 7 1) (12 5 1 :DOWN) (11 4 1 :DOWN)
(10 3 1 :UP) (2 9 1) (1 9 2))
(STRUCTURE-ATOMS O O O O O R O O C C C C C C)
(SYNONYMS "an acceptor-β-D-glucuronoside" "a β-D-glucuronide"
"an acceptor β-D-glucuronoside" "a glucuronide")
(APPEARS-IN-LEFT-SIDE-OF BETA-GLUCURONID-RXN)
(COMMON-NAME "a β-D-glucuronoside")
(:CREATOR |pkarp|)
(:CREATION-DATE 3139670155) )
NIL)
(BETA-GLUCURONID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(COMMENT "β-glucuronidase catalyzes the cleavage of a wide variety
of β-glucuronides. The substrates are generally water-soluble.
|CITS: [87041472]|")
(REACTION BETA-GLUCURONID-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/glugalcat2/uidA2.template")
(ENZYME BETA-GLUCURONID-MONOMER)
(:CREATION-DATE 3037378158)
(COMMON-NAME "β-glucuronidase")
(SYNONYMS "β-D-glucuronoside glucuronosohydrolase" "GUS" "GUD")
(REACTION-DIRECTION REVERSIBLE) )
NIL)
(BETA-GLUCURONID-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CATALYZES BETA-GLUCURONID-ENZRXN)
(DBLINKS (MODBASE "P05804" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02837" IN-FAMILY |pkarp| 3346700339 NIL NIL)
(REFSEQ "NP_416134" NIL NIL NIL NIL NIL) (UNIPROT "P05804"))
(PI 5.55d0)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 68.44692299999976d0)
(GENE EG11055)
(SYNONYMS "B1617" "VidA" "GusA" "GurA" "BglR" "UidA"
"β-D-glucuronoside glucuronosohydrolase")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uidA.template")
(:CREATION-DATE 2988132855)
(:CREATOR |mriley|) )
NIL)
(BETA-GLUCURONID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(ENZYMATIC-REACTION BETA-GLUCURONID-ENZRXN)
(IN-PATHWAY GLUCUROCAT-PWY)
(RIGHT |Alcohols| GLUCURONATE)
(LEFT WATER |Beta-D-Glucuronides|)
(EC-NUMBER "3.2.1.31")
(COMMENT "Part of the glucuronate pathway.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/degradation/glugalcat/uidA.template")
(:CREATION-DATE 2988132855)
(:CREATOR |mriley|) )
NIL)
(BETA-HYDROXY-CIS-DELTA5-DODECENOYL-ACP NIL (
(OCELOT-GFP::PARENTS |All-ACPs|)
(UNMODIFIED-FORM |apo-ACP|)
(SYNONYMS "β-hydroxy-cis-δ5-dodecenoyl-ACP")
(APPEARS-IN-LEFT-SIDE-OF RXN0-2144)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2142)
(COMMON-NAME "β-hydroxy-cis-Δ5-dodecenoyl-ACP")
(:CREATOR |ingraham|)
(:CREATION-DATE 3284396381) )
NIL)
(BETA-HYDROXY-DL-ASPARTATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-COMPETITIVE-OF ENZRXN0-4281)
(:CREATOR |shearer|)
(:CREATION-DATE 3329668552)
(COMMON-NAME "β-hydroxy-D,L-aspartate") )
NIL)
(BETA-HYDROXYDECANOYL-ACP NIL (
(OCELOT-GFP::PARENTS OH-ACYL-ACP)
(MOLECULAR-WEIGHT-SEQ 8.639505000000005d0)
(DBLINKS (MODBASE "P02901" NIL |pkarp| 3355444108 NIL NIL)
(UNIPROT "P02901" NIL |pick| NIL NIL NIL))
(GENE EG50003)
(SYNONYMS "B1094" "AcpP")
(UNMODIFIED-FORM |apo-ACP| ACP-MONOMER)
(APPEARS-IN-LEFT-SIDE-OF FABAUNSATDEHYDR-RXN)
(:CREATION-DATE 3054567319)
(:CREATOR |kr|)
(COMMON-NAME "β-hydroxydecanoyl-ACP") )
NIL)
(BETA-KETO-CIS-DELTA5-DODECENOYL-ACP NIL (
(OCELOT-GFP::PARENTS |All-ACPs|)
(UNMODIFIED-FORM |apo-ACP|)
(SYNONYMS "β-keto-cis-δ5-dodecenoyl-ACP")
(APPEARS-IN-LEFT-SIDE-OF RXN0-2142)
(APPEARS-IN-RIGHT-SIDE-OF RXN0-2141)
(COMMON-NAME "β-keto-cis-Δ5-dodecenoyl-ACP")
(:CREATOR |paley|)
(:CREATION-DATE 3284397786) )
NIL)
(BETA-LACTAMASE-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.5.2)
(ENZYMATIC-REACTION ENZRXN0-2709)
(OFFICIAL-EC? T)
(:CREATION-DATE 3053895482)
(SPECIES ECOLI)
(EC-NUMBER "3.5.2.6")
(COMMON-NAME "β-LACTAMASE")
(COMMENT
"A GROUP OF ENZYMES OF VARYING SPECIFICITY HYDROLYSING β-LACTAMS; SOME ACT MORE RAPIDLY ON PENICILLINS, SOME MORE RAPIDLY ON CEPHALOSPORINS.")
(RIGHT "A SUBSTITUTED BETA-AMINO ACID")
(LEFT WATER |Beta-Lactams|)
(SYNONYMS "PENICILLINASE" "CEPHALOSPORINASE") )
NIL)
(|Beta-Lactams| T (
(OCELOT-GFP::PARENTS |Antibiotics|)
(APPEARS-IN-LEFT-SIDE-OF BETA-LACTAMASE-RXN)
(COMMENT
"This compound class stands for generic and unspecified β-lactam antibiotics, such as the penicillins and cephalosporins.")
(COMMON-NAME "a β-lactam")
(:CREATOR |kr|)
(:CREATION-DATE 3264891209) )
NIL)
(BETACOMP-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B2763" "CysI")
(DBLINKS (MODBASE "P17846" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF03460" IN-FAMILY |pkarp| 3346700373 NIL NIL)
(REFSEQ "NP_417243" NIL NIL NIL NIL NIL) (PDB "8GEP") (PDB "7GEP")
(PDB "6GEP") (PDB "5GEP") (PDB "5AOP") (PDB "4GEP") (PDB "4AOP")
(PDB "3GEO") (PDB "3AOP") (PDB "2GEP") (PDB "2AOP") (PDB "1AOP")
(UNIPROT "P17846"))
(COMPONENT-OF SULFITE-REDUCT-CPLX)
(NEIDHARDT-SPOT-NUMBER)
(MOLECULAR-WEIGHT-SEQ 63.99803699999983d0)
(GENE EG10190)
(COMMENT "Contains one siroheme and one 4-Fe-4S iron-sulfur center per
chain. The heme is an octacarboxylic iron-tetrahydroporphyrin.
|CITS: [74127023] [74127024] [74127025]|")
(COMMON-NAME "sulfite reductase hemoprotein subunit")
(:CREATION-DATE 2974150781)
(:CREATOR |mriley|) )
NIL)
(BETAGALACTOSID-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/galactocat2/lacZ2.template")
(CATALYZES BETAGALACTOSID-ENZRXN)
(:CREATION-DATE 3037559203)
(COMPONENTS BETAGALACTOSID-MONOMER) )
((COMPONENTS BETAGALACTOSID-MONOMER COEFFICIENT 4)))
(BETAGALACTOSID-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(INHIBITORS-UNKMECH "mercaptoethylamine" CPD-3682 ETHANOL-AMINE PROPANOL
2-MERCAPTOETHANOL "metal chelators" "organomercuric compounds"
"heavy metal ions" 5-AMINO-5-DEOXY-D-GALACTOPYRANOSIDE
"(1/2,5,6)-2-(3-azibutylthio)-5,6-epoxy-3-cyclohexen-1-ol"
"2-deoxy-2-fluoro-beta-D-galactopyranosyl fluoride"
15-DIDEOXY-15-IMINO-D-GALACTITOL
"1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide" D-GALACTOSYLAMINE
"isopropyl-beta-D-galactopyranoside")
(CITATIONS ":EV-EXP:3277835751:pkarp" "12776212")
(COMMENT "β-galacotsidase is a metalloenzyme exhibiting broad
substrate specificity. The specificity of the enzyme is confined to
the sugar moiety and the anomeric character of the linkage but not to
a particular aglycon. |CITS: [WallenfelsTheEnzymes7-617] [79025019]|
The enzyme has been crystallized. |CITS: [94277211]|
Activation by cations seems to be substrate
dependent. K+, Na+, NH4+, Rb+, Cs+ and Mn++ all activate enzyme
activity based upon the substrate used. |CITS:
[WallenfelsTheEnzymes7-617]|
Review: |CITS: [15950161]|")
(REACTION BETAGALACTOSID-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/galactocat2/lacZ2.template")
(ENZYME BETAGALACTOSID-CPLX)
(PROSTHETIC-GROUPS MG+2)
(:CREATION-DATE 3037559203)
(COMMON-NAME "β-galactosidase")
(SYNONYMS "β-D-galactosidase" "lactase"
"β-D-galactosidase galactohydrolase")
(REACTION-DIRECTION REVERSIBLE)
(INHIBITORS-COMPETITIVE GALACTOSE "2-aminogalactopyranose" "D-galactal"
"phenyl-1-thio-beta-D-galactopyranoside"
"o-nitrophenyl 1-thio-beta-D-galactopyranoside"
"beta-D-galactopyranosyl trimethylammonium bromide"
"conduritol C cis-epoxide") )
((INHIBITORS-UNKMECH "mercaptoethylamine" CITATIONS
"[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH CPD-3682 CITATIONS "[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH ETHANOL-AMINE CITATIONS "[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH PROPANOL CITATIONS "[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH 2-MERCAPTOETHANOL CITATIONS
"[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH "metal chelators" CITATIONS
"[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH "organomercuric compounds" CITATIONS
"[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH "heavy metal ions" CITATIONS
"[WallenfelsTheEnzymes7-617]")
(INHIBITORS-UNKMECH 5-AMINO-5-DEOXY-D-GALACTOPYRANOSIDE CITATIONS
"[HandEnzInh]")
(INHIBITORS-UNKMECH
"(1/2,5,6)-2-(3-azibutylthio)-5,6-epoxy-3-cyclohexen-1-ol" CITATIONS
"[HandEnzInh]")
(INHIBITORS-UNKMECH "2-deoxy-2-fluoro-beta-D-galactopyranosyl fluoride"
CITATIONS "[88228003]" "[HandEnzInh]")
(INHIBITORS-UNKMECH 15-DIDEOXY-15-IMINO-D-GALACTITOL CITATIONS
"[HandEnzInh]")
(INHIBITORS-UNKMECH "1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide"
CITATIONS "[HandEnzInh]")
(INHIBITORS-UNKMECH D-GALACTOSYLAMINE CITATIONS "[HandEnzInh]")
(INHIBITORS-UNKMECH "isopropyl-beta-D-galactopyranoside" CITATIONS
"[HandEnzInh]")
(INHIBITORS-COMPETITIVE "2-aminogalactopyranose" CITATIONS "[83001455]"
"[HandEnzInh]")
(INHIBITORS-COMPETITIVE GALACTOSE CITATIONS "[83001455]" "[HandEnzInh]")
(INHIBITORS-COMPETITIVE "D-galactal" COMMENT "D-galactal is also a
substrate of beta-galacosidase. |CITS:
[WallenfelsTheEnzymes7-617]|")
(INHIBITORS-COMPETITIVE "phenyl-1-thio-beta-D-galactopyranoside" CITATIONS
"[72159495]")
(INHIBITORS-COMPETITIVE "o-nitrophenyl 1-thio-beta-D-galactopyranoside"
CITATIONS "[72159495]")
(INHIBITORS-COMPETITIVE "beta-D-galactopyranosyl trimethylammonium bromide"
CITATIONS "[73227161]")
(INHIBITORS-COMPETITIVE "conduritol C cis-epoxide" COMMENT "Also known as
1,2-anhydro-epi-inositol |CITS: [84108409]|")
(PROSTHETIC-GROUPS MG+2 COMMENT "The enzyme binds 1 Mg++/monomer
|CITS: [72233224] [79025019] [73227161]|")))
(BETAGALACTOSID-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(CITATIONS "12776212" "12853150")
(COMPONENT-OF BETAGALACTOSID-CPLX)
(DBLINKS (MODBASE "P00722" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF02837" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(REFSEQ "NP_414878" NIL NIL NIL NIL NIL) (PDB "1JZ8") (PDB "1JZ7")
(PDB "1JZ6") (PDB "1JZ5") (PDB "1JZ4") (PDB "1JZ3") (PDB "1JZ2")
(PDB "1JZ1") (PDB "1JZ0") (PDB "1JYZ") (PDB "1JYY") (PDB "1JYX")
(PDB "1JYW") (PDB "1JYV") (PDB "1JYN") (PDB "1HN1") (PDB "1GHO")
(PDB "1F4H") (PDB "1F4A") (PDB "1F49") (PDB "1DP0") (PDB "1BGM")
(PDB "1BGL") (UNIPROT "P00722" NIL NIL |ouzounis| 3027899498))
(PI 5.55d0)
(MOLECULAR-WEIGHT-SEQ 116.48272799999963d0)
(GENE EG10527)
(SYNONYMS "B0344" "LacZ" "β-D-galactosidase" "lactase"
"β-D-galactoside galactohydrolase")
(COMMON-NAME "β-galactosidase monomer")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/lacZ.template")
(:CREATION-DATE 3016309394)
(:CREATOR |mriley|) )
NIL)
(BETAGALACTOSID-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-3.2.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? YES)
(ENZYMATIC-REACTION BETAGALACTOSID-ENZRXN)
(IN-PATHWAY BGALACT-PWY)
(RIGHT GALACTOSE GLC)
(LEFT WATER LACTOSE)
(EC-NUMBER "3.2.1.23")
(COMMENT "Part of galactose, galactoside and glucose catabolism.")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/lacZ.template")
(:CREATION-DATE 3016309394)
(:CREATOR |mriley|) )
NIL)
(BETAINE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C00719" NIL |kr| 3346617699 NIL NIL) (CAS "107-43-7"))
(:CREATION-DATE 3053888749)
(APPEARS-IN-LEFT-SIDE-OF TRANS-RXN-29A)
(GIBBS-0 -61.6d0)
(APPEARS-IN-RIGHT-SIDE-OF TRANS-RXN-29A BADH-RXN)
(COMMON-NAME "glycine betaine")
(MOLECULAR-WEIGHT 117.147d0)
(CHEMICAL-FORMULA (C 5) (H 11) (N 1) (O 2))
(DISPLAY-COORDS-2D (-1.0d0 -0.03618d0) (0.51974d0 -0.60855d0)
(-0.13158d0 0.04276d0) (-0.05263d0 -0.82237d0) (-0.52632d0 -0.43092d0)
(-0.92105d0 -0.90461d0) (0.99671d0 -1.0d0) (0.625d0 -0.00329d0))
(STRUCTURE-BONDS (8 2 2) (7 2 1) (6 5 1) (5 4 1) (4 2 1) (3 5 1) (1 5 1))
(STRUCTURE-ATOMS C C C C N C O O)
(SYNONYMS "oxyneurine" "lycine" "acidin-pepsin" "betaine"
"trimethylammonioacetate" "N,N,N-trimethylglycine")
(ATOM-CHARGES (7 -1) (5 1)) )
((GIBBS-0 -61.6d0 CITATIONS "GibbsGroups97")))
(|Betaine-Biosynthesis| T (
(OCELOT-GFP::PARENTS |Polyamine-Biosynthesis|)
(COMMENT
"This class contains pathways of synthesis of betaine, an osmoprotectant that allows organisms to grow in high-osmolarity environments. Some organism can synthesize betaine de novo from intermediates of central metabolism; other can synthesize it only from exogenously supplied choline.")
(COMMON-NAME "Betaine")
(:CREATOR |paley|)
(:CREATION-DATE 3267465937) )
NIL)
(BETAINE_ALDEHYDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF BADH-ENZRXN)
(DBLINKS (LIGAND-CPD "C00576" NIL |kr| 3346617700 NIL NIL) (CAS "7418-61-3"))
(:CREATION-DATE 3053888749)
(GIBBS-0 -7.4d0)
(MOLECULAR-WEIGHT 102.156d0)
(CHEMICAL-FORMULA (C 5) (H 12) (N 1) (O 1))
(DISPLAY-COORDS-2D (0.4819944d0 -0.4155125d0) (0.54016614d0 -1.0d0)
(0.9972298d0 -0.698061d0) (-1.0d0 -0.7036011d0) (-0.48753464d0 -0.4155125d0)
(-0.008310258d0 -0.69529086d0) (0.8171744d0 0.06648195d0))
(STRUCTURE-BONDS (7 1 1) (6 1 1) (5 6 1) (4 5 2) (3 1 1) (2 1 1))
(STRUCTURE-ATOMS N C C O C C C)
(APPEARS-IN-LEFT-SIDE-OF BADH-RXN)
(APPEARS-IN-RIGHT-SIDE-OF CHD-RXN)
(COMMON-NAME "betaine aldehyde")
(SYNONYMS "glycine betaine aldehyde") )
((GIBBS-0 -7.4d0 CITATIONS "GibbsGroups97")))
(BETALAIN-ALKALOIDS T (
(OCELOT-GFP::PARENTS ALKALOIDS-SYN)
(COMMENT
"Betalain alkaloids are derived biosynthetically from the amino acid 3,4-dihydroxyphenylalanine (DOPA) via the intermediate betalamic acid representing the common chromphore of betalains. The water soluble betalain alkaloids split up into two major groups, the betacyanins and betaxanthins. Betacyanins, for instance amaranthin and betaxanthins such as indicaxanthin are often found in fruits, flowers and leaves of higher plants. Betalaines replace other biological important plant pigments such as anthocyanine in most of the plant families of the order Centrospermae.")
(COMMON-NAME "Betalaine alkaloids")
(:CREATOR |paley|)
(:CREATION-DATE 3347159103) )
NIL)
(BETSYN-PWY NIL (
(OCELOT-GFP::PARENTS |Betaine-Biosynthesis|)
(CITATIONS ":EV-EXP:3277587223:pkarp")
(COMMENT
"E. coli can synthesize betaine from externally supplied choline. The conversion
to betaine takes place in two steps and requires a terminal electron acceptor.
|CITS: [ColiSalII]|")
(REACTION-LIST BADH-RXN CHD-RXN)
(PREDECESSORS (CHD-RXN) (BADH-RXN CHD-RXN))
(NET-REACTION-EQUATION
"choline + acceptor + NAD+ + H2O = betaine + NADH + reduced acceptor")
(COMMON-NAME "glycine betaine biosynthesis I (Gram-negative bacteria)")
(TEMPLATE-FILE "~ecocyc/templates/new/betaine/betsynpwy.template")
(:CREATION-DATE 3053887820)
(:CREATOR |mriley|) )
NIL)
(BETT-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-28)
(MOLECULAR-WEIGHT-SEQ 75.84205899999982d0)
(:CREATION-DATE 3060042779)
(COMMENT
"BetT is a proton-motive-force-driven choline transporter that belongs to the Betaine
Carnitine Choline Transport (BCCT) family of proteins. Deletion mutants of betT
displayed essentially no choline uptake activity, but could be complemented with a
betT-encoding plasmid, restoring rapid choline uptake |CITS: [92065800]|. Choline uptake
activity was completely inhibited by the protonophore carbonylcyanide
p-trifluoromethoxyphenyl hydrazone, suggesting that choline transport by BetT is
driven by the proton-motive force |CITS: [92065800]|. Choline is used to synthesize glycine
betaine, which is used by E. coli to overcome growth inhibition caused by
osmotic stress |CITS: [89124888]|. The betTIAB genes are expressed only under aerobic
conditions, and are induced by osmotic stress |CITS: [92065800]|. Analysis of betT-lacZ
fusions showed that betT transcription increased 7-10 fold in response to
increases in medium osmolarity. The presence of choline further increases this response
|CITS: [89033906]|.")
(SYNONYMS "B0314" "BetT")
(DBLINKS (PFAM "PF02028" IN-FAMILY |pkarp| 3346700316 NIL NIL)
(UNIPROT "P0ABC9" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_414848" NIL NIL NIL NIL NIL))
(CATALYZES TRANS-ENZRXN-99)
(GENE EG10112)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "BetT choline BCCT transporter") )
NIL)
(BGALACT-PWY NIL (
(OCELOT-GFP::PARENTS LACTOSE-DEG)
(COMMENT-INTERNAL "C. Fulcher 9/30/04
The EcoCyc lactose degradation III pathway (BGALACT-PWY) was enhanced by adding pathway comments, gene comments, and references.")
(COMMENT
"In E. coli the disaccharide lactose is degraded by hydrolysis of the β-1,4 glycosidic bond by
β-galactosidase, producing β-D-glucose and β-D-galactose. The enzyme can also catalyze
conversion of lactose to allolactose (β-D-galactopyranosyl-(1-6)-D-glucopyranose) by transglycosylation,
and can hydrolyze allolactose (in |CITS: [6767683]|). Allolactose is the physiological inducer of this pathway.
Further metabolism of glucose and galactose inside the cell is thought to proceed by their initial transport out of the
cell, followed by reentry. It has been shown that when lactose is added to a growing culture of E. coli,
galactose, glucose and allolactose reach high levels inside the cells and are rapidly effluxed into the medium
|CITS: [6767683]|. It has also been shown that an E. coli mutant defective in the uptake of glucose and
galactose grew poorly with lactose as a sole carbon source. Additional transport rate and radiotracer studies
supported the efflux mechanism |CITS: [6426769]|. No E. coli genes specifically involved in sugar efflux during
lactose metabolism have been conclusively identified. However, SetA and SetB, members of the SET
(sugar efflux transporter) family may have a role |CITS: [10438463] [10209755]|.
It has been suggested that as glucose reenters the cell it could be phosphorylated to glucose-1-phosphate by the
phosphoenolpyruvate-phosphotransferase system (in |CITS: [6767683]|). Glucose-1-phosphate could then be
converted to glucose-6-phosphate by phosphoglucomutase and enter glycolysis. Galactose could reenter the cell
by facilitated diffusion (in |CITS: [6767683]|), or active transport systems galP, or mgl
(Lin in |CITS: [ColiSalII]|). Galactose can also be converted to glucose-1-phosphate
(Fraenkel in |CITS: [ColiSalII]|). (See EcoCyc pathways: glucose and glucose-1-phosphate degradation;
galactose degradation I; and superpathway of glycolysis and Entner-Doudoroff).
The E. coli lacZ gene coding for β-galactosidase is the first of three structural genes of the historically
significant lac operon. The study of this operon provided the primary basis for the original operon concept
|CITS: [13718526]|. Lactose and other galactosides are transported into the cell by lactose permease, the product of
the second structural gene of the operon |CITS: [12893935]|. The third structural gene codes for galactoside
acetyltransferase (thiogalactoside transacetylase). The proposed function of this enzyme is acetylation of potentially
toxic pyranosides that are exported from the cell, thereby preventing their reentry |CITS: [11937062]|. A review of
biochemical studies of the three lac enzymes by Zabin and Fowler can be found in |CITS: [Operon78]|.")
(CITATIONS "6767683" "6426769" "10438463" "10209755" "ColiSalII" "13718526"
"12893935" "11937062" "OPERON78" "Operon78:EV-EXP:3305563912:fulcher")
(SYNONYMS "lactose degradation 3")
(COMMON-NAME "lactose degradation III")
(PRIMARIES (BETAGALACTOSID-RXN NIL (GALACTOSE GLC)))
(REACTION-LIST BETAGALACTOSID-RXN)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/gala/Bgalapwy.template")
(:CREATION-DATE 3016310126)
(:CREATOR |mriley|) )
NIL)
(BGLF-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-9)
(COMMENT-INTERNAL "1/24/05 keseler removed BglC as synonym")
(MOLECULAR-WEIGHT-SEQ 66.48287099999982d0)
(:CREATION-DATE 3060117329)
(COMMENT "contains PTS Enzyme IIA, IIB and IIC domains")
(SYNONYMS "B3722" "BglS" "AscF" "BglF")
(DBLINKS (MODBASE "P08722" NIL |pkarp| 3355444108 NIL NIL)
(PFAM "PF00367" IN-FAMILY |pkarp| 3346700415 NIL NIL)
(REFSEQ "NP_418178" NIL NIL NIL NIL NIL)
(SWISSMODEL "P08722" NIL |pkarp| 3064870651)
(UNIPROT "P08722" NIL |pkarp| 3064869797))
(COMPONENT-OF CPLX-154)
(GENE EG10115)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "BglF") )
NIL)
(BH4NA NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ENZRXN0-4281 OHMETHYLBILANESYN-ENZRXN)
(SYNONYMS "sodium borohydride" "BH4Na")
(COMMON-NAME "NaBH4")
(:CREATOR |paley|)
(:CREATION-DATE 3277498322) )
NIL)
(|Binding-Reactions| T (
(OCELOT-GFP::PARENTS |Simple-Reactions|)
(COMMENT
"This class consists of reactions in which no covalent modification of the substrates takes place, but in which the net effect is that one substrate
noncovalently binds to or unbinds from another molecule via weak bonds (e.g. hydrogen bonds). This class includes protein complex assembly
and dissociation reactions. In reactions of this class, each of the substrates maintains its original molecular identity, meaning reactions of this class
affect intermolecular bonds, not intramolecular bonds.")
(SCHEMA? T) )
((INHIBITORS :FACET :VALUE-TYPE :SEXPR)
(ACTIVATORS :FACET :VALUE-TYPE :SEXPR)))
(BIO-5-AMP NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(COMPONENT-OF MONOMER-48)
(AROMATIC-RINGS (22 10 9 11 23 1))
(CHEMICAL-FORMULA (C 20) (H 28) (N 7) (O 9) (P 1) (S 1))
(MOLECULAR-WEIGHT 573.516d0)
(DISPLAY-COORDS-2D (8.2459d0 4.4109d0) (11.5078d0 4.9109d0)
(5.4878d0 -6.6198d0) (6.7674d0 -3.8491d0) (7.0748d0 -2.8975d0)
(5.7896d0 -4.0587d0) (8.0526d0 -2.6879d0) (10.9303d0 0.5861d0)
(9.9779d0 5.4109d0) (9.1119d0 5.9109d0) (9.9779d0 4.4109d0)
(4.5406d0 -6.3183d0) (5.4823d0 -5.0103d0) (11.2376d0 1.5376d0)
(4.5371d0 -5.3183d0) (12.1881d0 1.8483d0) (12.1864d0 2.8483d0)
(11.2348d0 3.1557d0) (3.0d0 -5.8236d0) (8.3599d0 -1.7363d0)
(9.1119d0 6.9109d0) (8.2459d0 5.4109d0) (9.1119d0 3.9109d0)
(10.9242d0 5.7157d0) (3.5906d0 -6.6306d0) (3.585d0 -5.0126d0)
(10.9242d0 4.1062d0) (12.9982d0 1.2619d0) (12.9944d0 3.4375d0)
(8.6935d0 -0.2678d0) (2.0d0 -5.8271d0) (7.6895d0 -0.9943d0)
(10.5967d0 -0.8825d0) (10.6484d0 2.3456d0) (9.9525d0 0.3765d0)
(9.3377d0 -1.5267d0) (9.6451d0 -0.5751d0) (6.0686d0 -5.813d0)
(7.709d0 4.1009d0) (12.1278d0 4.9109d0) (6.0263d0 -6.9271d0)
(5.2388d0 -7.1875d0) (7.3815d0 -3.9343d0) (6.7901d0 -4.4687d0)
(6.4607d0 -2.8123d0) (7.0521d0 -2.2779d0) (5.1755d0 -3.9735d0)
(5.7669d0 -3.4391d0) (8.6667d0 -2.7731d0) (8.0753d0 -3.3075d0)
(11.5444d0 0.5008d0) (10.953d0 -0.0335d0) (4.5435d0 -6.9383d0)
(6.0944d0 -4.912d0) (10.6254d0 1.4396d0) (4.5358d0 -4.6983d0)
(12.0922d0 1.2358d0) (12.7393d0 2.5678d0) (10.6223d0 3.2516d0)
(8.575d0 7.2209d0) (9.6489d0 7.2209d0) (3.401d0 -7.2209d0)
(3.3913d0 -4.4236d0) (12.9344d0 0.6452d0) (13.5612d0 3.1863d0)
(8.5636d0 0.3385d0))
(STRUCTURE-BONDS (30 66 1) (29 65 1) (28 64 1) (26 63 1) (25 62 1) (21 61 1)
(21 60 1) (18 59 1) (17 58 1) (16 57 1) (15 56 1) (14 55 1) (13 54 1)
(12 53 1) (8 52 1) (8 51 1) (7 50 1) (7 49 1) (6 48 1) (6 47 1) (5 46 1)
(5 45 1) (4 44 1) (4 43 1) (3 42 1) (3 41 1) (2 40 1) (1 39 1) (36 37 1)
(35 37 1) (33 37 2) (30 37 1) (20 36 1) (20 32 2) (19 31 2) (19 26 1)
(19 25 1) (18 34 1) (18 27 1 :DOWN) (17 29 1 :UP) (17 18 1) (16 28 1 :UP)
(16 17 1) (15 26 1) (14 34 1) (14 16 1) (13 38 1) (13 15 1) (12 25 1)
(12 15 1) (11 27 1) (23 11 :AROMATIC) (10 22 :AROMATIC) (10 21 1) (9 24 1)
(11 9 :AROMATIC) (9 10 :AROMATIC) (8 35 1) (14 8 1 :DOWN) (7 20 1)
(13 6 1 :UP) (5 7 1) (4 6 1) (4 5 1) (3 38 1) (3 12 1) (2 27 1) (2 24 2)
(1 23 :AROMATIC) (22 1 :AROMATIC))
(STRUCTURE-ATOMS C C C C C C C C C C C C C C C C C C C C N N N N N N N O O O
O O O O O O P S H H H H H H H H H H H H H H H H H H H H H H H H H H H H)
(DBLINKS (PUBCHEM "440839" NIL |hopkinso| 3317145317 NIL NIL))
(APPEARS-IN-LEFT-SIDE-OF R131-RXN)
(SYNONYMS "biotinyl-5'-adenylate")
(COMMON-NAME "bio-5'-AMP")
(:CREATOR |paley|)
(:CREATION-DATE 3189435679) )
NIL)
(|Biosynthesis| T (
(OCELOT-GFP::PARENTS |Pathways|)
(COMMENT
"This class contains pathways that constitute a cell's complete spectrum of biosynthetic capacities, including the routes of synthesis of small molecules, macromolecules and organelles. ")
(SCHEMA? T)
(COMMON-NAME "Biosynthesis") )
NIL)
(BIOTIN NIL (
(OCELOT-GFP::PARENTS |Vitamins|)
(INHIBITORS-NONCOMPETITIVE-OF BIOTIN-CARBOXYL-ENZRXN)
(PROSTHETIC-GROUPS-OF PROPIONYL-COA-CARBOXY-ENZRXN
ACETYL-COA-CARBOXYLMULTI-ENZRXN)
(APPEARS-IN-LEFT-SIDE-OF BIOTINLIG-RXN)
(DBLINKS (LIGAND-CPD "C00120" NIL |kaipa| 3311532642 NIL NIL) (CAS "58-85-5"))
(:CREATION-DATE 3067881497)
(COMMON-NAME "biotin")
(SYNONYMS "vitamin H" "coenzyme R" "d-biotin")
(APPEARS-IN-RIGHT-SIDE-OF R401-RXN 2.8.1.6-RXN)
(DISPLAY-COORDS-2D (0.0d0 -3.415d0) (4.2d0 -3.415d0) (9.3005d0 0.0d0)
(2.1d0 -6.9694d0) (10.5072d0 -2.1033d0) (6.8718d0 -1.3934d0)
(5.6575d0 -2.0901d0) (8.0823d0 -2.0967d0) (4.447d0 -1.3868d0)
(0.9674d0 -2.0835d0) (0.9674d0 -4.7465d0) (3.2326d0 -4.7465d0)
(2.1d0 -1.2606d0) (9.2967d0 -1.4d0) (2.1d0 -5.5694d0) (3.2326d0 -2.0835d0)
(1.4d0 -3.415d0) (2.8d0 -3.415d0))
(STRUCTURE-BONDS (17 18 1) (16 18 1) (13 16 1) (12 18 1) (12 15 1) (11 17 1)
(11 15 1) (10 17 1) (10 13 1) (16 9 1 :DOWN) (8 14 1) (7 9 1) (6 8 1)
(6 7 1) (5 14 1) (4 15 2) (3 14 2) (18 2 1 :UP) (17 1 1 :UP))
(STRUCTURE-ATOMS H H O O O C C C C C N N S C C C C C)
(CHEMICAL-FORMULA (C 10) (H 16) (N 2) (O 3) (S 1))
(MOLECULAR-WEIGHT 244.308d0) )
NIL)
(BIOTIN-CARBOXYL-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES BIOTIN-CARBOXYL-ENZRXN)
(COMPONENT-OF ACETYL-COA-CARBOXYLMULTI-CPLX)
(COMPONENTS BIOTIN-CARBOXYL-MONOMER)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accC.template")
(:CREATION-DATE 3001089016)
(:CREATOR |mriley|) )
((COMPONENTS BIOTIN-CARBOXYL-MONOMER CITATIONS "[84288087]")
(COMPONENTS BIOTIN-CARBOXYL-MONOMER COEFFICIENT 2)))
(BIOTIN-CARBOXYL-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(PHYSIOLOGICALLY-RELEVANT BIOTIN)
(INHIBITORS-NONCOMPETITIVE CPD-764 BIOTIN)
(CITATIONS ":EV-EXP:3277835750:pkarp")
(INHIBITORS-COMPETITIVE CPD-764)
(SYNONYMS
"biotin carboxyl carrier protein:carbon dioxide ligase (ADP-forming)")
(COMMON-NAME "biotin carboxylase")
(ALTERNATIVE-SUBSTRATES (BCCP BIOTIN))
(REACTION-DIRECTION REVERSIBLE)
(REACTION BIOTIN-CARBOXYL-RXN)
(COMMENT "The acetyl-CoA carboxylase complex is composed of four
different subunits. One of which, biotin carboxylase, mediates the
first step of the acetyl-CoA carboxylase reaction. The overall
reaction takes place in two distinct half-reactions, with a
carboxyltransferase carrying out the second half. |CITS: [92052166]
[94066913]|")
(ENZYME BIOTIN-CARBOXYL-CPLX)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accC.template")
(:CREATION-DATE 3001089016)
(:CREATOR |mriley|) )
((INHIBITORS-NONCOMPETITIVE BIOTIN COMMENT
"Biotin exhibits noncompetitive substrate inhibition.")
(INHIBITORS-NONCOMPETITIVE CPD-764 COMMENT
"Noncompetitive with respect to bicarbonate.")
(INHIBITORS-NONCOMPETITIVE CPD-764 CITATIONS "20068789")
(INHIBITORS-NONCOMPETITIVE BIOTIN CITATIONS "20068789")
(INHIBITORS-COMPETITIVE CPD-764 CITATIONS "20068789")
(INHIBITORS-COMPETITIVE CPD-764 COMMENT
"Competitive with respect to ATP. |CITS: [20068789]| ")
(ALTERNATIVE-SUBSTRATES (BCCP BIOTIN) CITATIONS "[84288087]")))
(BIOTIN-CARBOXYL-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Mutations in the homologous and functionally identical subunit in mammalian proprionyl-CoA carboxylase and
3-methylcrotonyl-CoA carboxylase result in the metabolic deficiency diseases of propionic acidemia or
methylcrotonylglycinuria. Kinetic analysis of mutants analogous to the disease-causing mutants has been
performed to determine the function of those residues |CITS: [14960587]|.")
(SYNONYMS "B3256" "FabG" "AccC")
(COMMON-NAME "AccC")
(DBLINKS (MODBASE "P24182" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00289" IN-FAMILY |pkarp| 3346700393 NIL NIL)
(PDB "1DV1" NIL |pkarp| 3346695112 NIL NIL)
(REFSEQ "NP_417722" NIL NIL NIL NIL NIL) (PDB "1K69") (PDB "1BNC")
(UNIPROT "P24182"))
(COMPONENT-OF BIOTIN-CARBOXYL-CPLX)
(PI 7.08d0)
(MOLECULAR-WEIGHT-SEQ 49.320672999999886d0)
(GENE EG10276)
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accC.template")
(:CREATION-DATE 3001089016)
(:CREATOR |mriley|) )
NIL)
(BIOTIN-CARBOXYL-RXN NIL (
(OCELOT-GFP::PARENTS EC-6.3.4 |Protein-Modification-Reactions|)
(IN-PATHWAY PWY0-1264)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION BIOTIN-CARBOXYL-ENZRXN)
(RIGHT |Carboxybiotin-BCCP| |Pi| ADP)
(LEFT |BCCP-dimers| CARBON-DIOXIDE ATP)
(EC-NUMBER "6.3.4.14")
(COMMENT "This is a subreaction of the overall acetyl-CoA carboxylase
reaction, which is the first committed step in fatty acid synthesis.")
(TEMPLATE-FILE
"/home/bolinas2/ecocyc/templates/new/fattyacidsyn/accC.template")
(:CREATION-DATE 3001089016)
(:CREATOR |mriley|) )
NIL)
(BIOTIN-SYN T (
(OCELOT-GFP::PARENTS |Vitamin-Biosynthesis|)
(COMMENT
"This class contains slightly differing pathways by which various organisms synthesize the vitamin, biotin, which is required as a cofactor for various enzymatic reactions, including carboxylations. ")
(SCHEMA? T)
(VARIANTS? T)
(COMMON-NAME "Biotin")
(:CREATOR |pkarp|)
(:CREATION-DATE 3243104634) )
NIL)
(BIOTIN-SYN-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CREDITS SRI |keseler|)
(MOLECULAR-WEIGHT-EXP 82)
(SPECIES ECOLI)
(SYNONYMS "BioB")
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin2/bioB2.template")
(CATALYZES BIOTIN-SYN-ENZRXN)
(:CREATION-DATE 3033846056)
(COMPONENTS BIOTIN-SYN-MONOMER) )
((MOLECULAR-WEIGHT-EXP 82 CITATIONS "8142361")
(CREDITS SRI LAST-CURATED 3343565935)
(CREDITS |keseler| LAST-CURATED 3343565935)
(COMPONENTS BIOTIN-SYN-MONOMER COEFFICIENT 2)))
(BIOTIN-SYN-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(KM (DETHIOBIOTIN 2))
(PHYSIOLOGICALLY-RELEVANT CH33ADO)
(INHIBITORS-UNKMECH CH33ADO)
(COFACTORS S-ADENOSYLMETHIONINE)
(CITATIONS ":EV-EXP-IDA-PURIFIED-PROTEIN:3337457645:keseler")
(REACTION 2.8.1.6-RXN)
(:CREATOR |mriley|)
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin2/bioB2.template")
(ENZYME BIOTIN-SYN-CPLX)
(:CREATION-DATE 3033846056)
(COMMON-NAME "biotin synthase")
(SYNONYMS "dethiobiotin:sulfur sulfurtransferase")
(REACTION-DIRECTION PHYSIOL-LEFT-TO-RIGHT) )
((KM (DETHIOBIOTIN 2) CITATIONS "8142361")
(INHIBITORS-UNKMECH CH33ADO CITATIONS "15911379")))
(BIOTIN-SYN-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMMENT
"Biotin synthase catalyzes the final reaction of biotin biosynthesis by inserting a sulfur atom between C6 and C9 of
dethiobiotin in a S-adenosylmethoinine (SAM)-dependent reaction. It has not been possible to reconstitute
a catalytic reaction in vitro, and considerable uncertainty regarding the reaction mechanism, cofactor
requirements, and the source of the sulfur atom still remains |CITS: [15850974]|.
BioB belongs to the family of \"radical SAM\" enzymes |CITS: [15581586]|. The enzyme purifies as a homodimer
|CITS: [8142361]|. It contains two distinct iron-sulfur binding sites; one carries a [2Fe-2S] cluster, and the other a
[4Fe-4S] cluster that binds SAM and facilitates its reductive cleavage to generate a 5'-deoxyadenosyl radical
which activates dethiobiotin |CITS: [11834738][12614166][14704425][14967042]|. One of the reaction products,
5'-deoxyadenosine, inhibits BioB function |CITS: [15911379]|.
A crystal structure of biotin synthase has been solved at 3.4 Å resolution |CITS: [14704425]|. Reaction mechanisms
involving either the [2Fe-2S] cluster |CITS: [9862460][11444982]| or the cofactor PLP |CITS: [12119030][12482614]|
have been proposed; however, the crystal structure of BioB |CITS: [14704425]| and the cofactor composition of the
enzyme |CITS: [14967041]| do not support involvement of PLP.
Consistent with a proposed role as the sulfur donor, degradation of the [2Fe-2S] cluster is observed during turnover
of the enzyme |CITS: [14967042]|. The enzyme does not appear to be able to function catalytically in vitro
|CITS: [15610037]|; BioB is catalytically active in vivo, but it is thought that reconstitution of the [2Fe-2S]
cluster makes the enzyme susceptible to proteolytic degradation |CITS: [15850983]|.
Reviews: |CITS: [15581586][16042606]|")
(GENE EG10118)
(SPECIES ECOLI)
(SYNONYMS "B0775" "BioH" "BioB")
(COMPONENT-OF BIOTIN-SYN-CPLX)
(DBLINKS (MODBASE "P12996" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF04055" IN-FAMILY |pkarp| 3346700320 NIL NIL)
(PDB "1R30" NIL |keseler| 3337448908 NIL NIL)
(REFSEQ "NP_415296" NIL NIL NIL NIL NIL) (UNIPROT "P12996"))
(PI 5.55d0)
(MOLECULAR-WEIGHT-SEQ 38.64804699999991d0)
(COMMON-NAME "biotin synthase monomer")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin/bioB.template")
(:CREATION-DATE 3000588742)
(:CREATOR |mriley|) )
NIL)
(BIOTIN-SYNTHESIS-PWY NIL (
(OCELOT-GFP::PARENTS BIOTIN-SYN)
(PRIMARIES (2.8.1.6-RXN (DETHIOBIOTIN) (BIOTIN)))
(COMMENT
"The biotin biosynthetic pathway has not been fully elucidated. The early steps leading up to pimeloyl-CoA synthesis
are still unknown, and the origin of the sulfur atom in the final biotin synthase reaction has not been fully determined.
To begin to determine the sources for carbon atoms in biotin biosynthesis, feeding experiments with various
13C-labelled compounds have suggested a possible pathway for the biosynthesis of pimeloyl-CoA
|CITS: [8125118]|.
Biotin enzymes function as carboxyl group transfer enzymes. |CITS: [ColiSalII]|
")
(CITATIONS ":EV-EXP:3277587223:pkarp" "[74169143]" "[ColiSalII]")
(REACTION-LIST 7KAPSYN-RXN DAPASYN-RXN 2.8.1.6-RXN DETHIOBIOTIN-SYN-RXN)
(PREDECESSORS (2.8.1.6-RXN DETHIOBIOTIN-SYN-RXN)
(DETHIOBIOTIN-SYN-RXN DAPASYN-RXN) (DAPASYN-RXN 7KAPSYN-RXN))
(COMMON-NAME "biotin biosynthesis I")
(TEMPLATE-FILE "/home/bolinas2/ecocyc/templates/new/biotin/biopwy.template")
(:CREATION-DATE 3000588790)
(:CREATOR |mriley|) )
NIL)
(BIOTINLIG-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(ACTIVATORS-UNKMECH ATP)
(CITATIONS ":EV-EXP:3277835749:pkarp")
(REACTION-DIRECTION REVERSIBLE)
(REACTION BIOTINLIG-RXN)
(COFACTORS MG+2)
(COMMENT "The birA gene codes for a multifunctional protein,
possessing both enzymatic and regulatory activities. The enzymatic
functions include the synthesis of the enzyme-bound
biotinyl-5'-adenylate (bio-5'-AMP), and the transfer of the biotin
from the adenylate to a lysine residue of the biotin carboxyl carrier
protein (BCCP) of the acetyl-CoA-carboxylase. The transfer reaction
results in the active form of acetyl-CoA-carboxylase.
Alternatively,
as a regulator, the enzyme-bound to bio-5'-AMP represses transcription of
the biotin biosynthetic operon by binding to the biotin operator
sequence.
|CITS: [6129246]
[3275654] [2667763] [1409631] [8611542] [8527435]|")
(ENZYME BIOTINLIG-MONOMER)
(SYNONYMS
"biotin operon repressor/biotin acetyl coenzyme A carboxylase synthetase"
"biotin-[acetyl-CoA carboxylase] synthetase"
"birA bifunctional protein (biotin operon repressor)"
"biotin:apo-[acetyl-CoA:carbon-dioxide ligase(ADP-forming)] ligase (AMP-forming)")
(COMMON-NAME "biotin-[acetyl-CoA-carboxylase] ligase")
(TEMPLATE-FILE "~ecocyc/templates/new/bir/birA.template")
(:CREATION-DATE 3064793208)
(:CREATOR |mriley|) )
((ACTIVATORS-UNKMECH ATP CITATIONS "[82010688]")
(COFACTORS MG+2 COMMENT "The synthetase reaction requires a
divalent cation. |CITS: [82010688]|")))
(BIOTINLIG-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(COMPONENT-OF MONOMER-48)
(LOCATIONS CCO-CYTOPLASM)
(APPEARS-IN-LEFT-SIDE-OF R131-RXN)
(COMMENT
"BirA is a bifunctional protein that exhibits biotin ligase activity and also acts as the DNA binding transcriptional repressor of the biotin operon |CITS: [6129246]|. The effector of BirA transcriptional repression activity, biotinyl-5'-adenylate (bio-5'-AMP), is also a substrate in the BirA-mediated biotinylation of the biotin carboxyl carrier protein monomer (apoBCCP), and this relationship results in repression of the biotin operon when the abundance of apoBCCP (and therefore the cellular demand for biotin) is reduced |CITS: [9750231]|.
BirA is observed to be predominantly monomeric in solution |CITS: [6129246], [8373769], [9485476]|, with some minor multimeric species observed |CITS: [6129246]|. BirA binds as a dimer to its 40 bp DNA site, the biotin operator |CITS: [1659455]|. An additional, low-affinity BirA DNA binding site has been identified |CITS: [9931500]|. Initial models suggested that monomeric BirA-bio-5'-AMP shows cooperative binding to its DNA site |CITS: [8373769]|, whereas more recent studies indicate that dimerization occurs before DNA binding |CITS: [12527300]|. BirA-BCCP binding may preclude dimerization and therefore DNA binding and repressor activity |CITS: [11714930]|. Biotinyl-5'-adenylate (bio-5'-AMP, the physiological effector) |CITS: [10529178]| and biotin |CITS: [11353844], [350835]| stimulate dimerization and DNA binding.
Crystal structures at 2.3 angstrom resolution |CITS: [1409631]| and of a BirA-biotin complex |CITS: [11353844]| are presented. Crystallization has been described |CITS: [2642476]|. The implications of the structure with respect to the binding of biotin and ATP are discussed |CITS: [1409631]|. ApoBirA, the BirA-bio-5'-AMP complex, and the BirA-biotin complex have distinct structural characteristics |CITS: [8527435], [10497026]|. DNA binding affects the structure of the C terminus as well as the structure of the N terminus |CITS: [10497026]|. Disordered loop structures on the protein surface appear to be involved in binding to biotin, bio-5'-AMP, and/or DNA |CITS: [10497026]| and in protein dimerization |CITS: [11124029], [11353844]|. A model of binding and reaction progression is presented |CITS: [11847279]|.
The enzymatic reaction of bio-5'-AMP formation has been kinetically characterized |CITS: [8003500]| and the kinetics of biotinylation of biotin carboxyl carrier protein monomer have been determined |CITS: [8631788]|. The thermodynamics of association between BirA and biotin and between BirA and bio-5'-AMP have been characterized |CITS: [8611542], [11847279]|, as well as the thermodynamics of dimerization and DNA binding by BirA, the BirA-biotin complex, and the BirA-bio-5'-AMP complex |CITS: [12450391]|. Substrate characteristics have been examined |CITS: [7764094], [2113052], [10211839], [10981714], [11042165], [3040718], [8554526]|.
Some birA mutations cause heat sensitivity |CITS: [3899863]|. Mutants also show defects in transcriptional repression at the biotin operon promoter |CITS: [6782078]| and an increased requirement for biotin |CITS: [6991489]|. Mutants exhibit resistance to alpha-dehydrobiotin, defects in repression of the production of the enzymes of biotin synthesis, and increased secretion of biotin vitamers |CITS: [1091631]|. Deletion of the N-terminal DNA binding domain eliminates DNA binding activity and reduces binding to biotin and bio-5'-AMP, but does not affect the production of bio-5'-AMP or the BCCP biotinylation activity |CITS: [8639659]|. The DNA binding region is distinct from the regions in which mutations lead to heat sensitivity |CITS: [3536662]|. G115S, R118G, and R119W mutations cause defects in binding to biotin and bio-5'-AMP |CITS: [10975574]|. Mutations in the region that binds bio-5'-AMP also cause defects in dimerization and DNA binding |CITS: [11124029]|. An R317E mutation affects binding to ATP, and a K277E mutation affects substrate recognition |CITS: [11714929]|.
BirA overproduction and purification is described |CITS: [3275654]|. BirA fusion proteins with affinity tags have been purified |CITS: [9815166], [11922751]|.
Structural similarity between lipoylating and biotinylating enzymes, and implications with respect to the catalytic site, are discussed |CITS: [11106165]|. BirA has similarity to human holocarboxylase synthetase (HCS), mutations in which cause the biotin-responsive multiple carboxylase deficiency |CITS: [7842009], [7753853]|. BirA has 27% identity to Bacillus subtilis BirA protein |CITS: [7730294]| and has similarity to Streptomyces peucetius ATCC 29050 DnrO protein |CITS: [7868594]| and Saccharomyces cerevisiae Bpl1 |CITS: [7649444]|. BirA has structural similarity to Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) |CITS: [8563641]|. Human HCS |CITS: [7753853], [10068510]|, Arabidopsis thaliana biotin holocarboxylase synthetase |CITS: [9173880]|, or Saccharomyces cerevisiae Bpl1 |CITS: [7649444]| functionally complements an E. coli birA mutation. Arabidopsis thaliana biotin holocarboxylase synthetase does not show transcriptional repression activity in E. coli |CITS: [11019362]|.
BirA has been used as a reagent for biotinylation of exogenous proteins |CITS: [9750126], [9490786], [11237761], [8655479], [11399324], [11779110], [12137785], [2113052]|.
Reviews: |CITS: [10470036], [10796994], [2667763]|.")
(SYNONYMS "B3973" "BirA" "BioR" "DhbB"
"biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor"
"biotin ligase" "BirA transcriptional repressor")
(HISTORY "Merged w/ PD04060 from Regulon-DB -- SMP 4/10/00")
(CITATIONS "[87055242]" "[9750231]" "[6456358]" "[7024555]" "[3325774]"
"[1097077]" "[11106165]" "[7945216]")
(DNA-FOOTPRINT-SIZE 40)
(DBLINKS (MODBASE "P06709" NIL |pkarp| 3355444109 NIL NIL) (PDB "1K67")
(PDB "1HXD") (PDB "1BIB") (PDB "1BIA")
(UNIPROT "P06709" NIL |pkarp| 3064869797))
(CATALYZES BIOTINLIG-ENZRXN)
(PI 8.0479d0 8.21d0)
(MOLECULAR-WEIGHT-SEQ 35.31194799999994d0)
(GENE EG10123)
(TEMPLATE-FILE "~ecocyc/templates/new/bir/birA.template")
(:CREATION-DATE 3064793208)
(:CREATOR |mriley|) )
NIL)
(BIOTINLIG-RXN NIL (
(OCELOT-GFP::PARENTS EC-6.3.4 |Protein-Modification-Reactions|)
(IN-PATHWAY PWY0-1264)
(CITATIONS "[8631788]")
(COMMENT
"The kinetics of the BirA-mediated ligation of biotin (from BirA-biotinyl-5'-AMP) to biotin carboxyl carrier protein monomer have been determined |CITS: [8631788]|.")
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION BIOTINLIG-ENZRXN)
(RIGHT |BCCP-biotin-monomers| PPI AMP)
(LEFT |BCCP-monomers| BIOTIN ATP)
(EC-NUMBER "6.3.4.15")
(TEMPLATE-FILE "~ecocyc/templates/new/bir/birA.template")
(:CREATION-DATE 3064793208)
(:CREATOR |mriley|) )
NIL)
(|Bis-NAC-GLC-Man-Man-R| T (
(OCELOT-GFP::PARENTS |Modified-Proteins|)
(SYNONYMS
"3-(2,4-bis[N-acetyl-b-D-glucosaminyl]-a-D-mannosyl)-b-D-mannosyl-R")
(COMMON-NAME
"3-(2,4-bis[N-acetyl-β-D-glucosaminyl]-α-D-mannosyl)-β-D-mannosyl-R")
(COMMENT
"R represents the remainder of the N-linked oligosaccharide in the glycoprotein acceptor.")
(CHEMICAL-FORMULA (C 28) (H 47) (N 2) (O 21) (R1 1) (|Protein| 1))
(STRUCTURE-BONDS (52 53 1) (46 51 1) (45 48 1) (44 47 1) (42 50 1) (38 51 1)
(38 50 1) (37 49 1) (37 43 1) (36 49 1) (36 41 1) (35 48 1) (34 47 1)
(33 40 1) (33 35 1) (32 39 1) (32 34 1) (49 29 1 :UP) (46 29 1 :DOWN)
(51 28 1 :UP) (45 28 1 :UP) (50 27 1 :DOWN) (44 27 1 :UP) (26 46 1)
(26 42 1) (25 45 1) (25 40 1) (24 44 1) (24 39 1) (23 43 1) (23 41 1)
(43 21 1 :UP) (48 20 1 :DOWN) (20 31 1) (47 19 1 :DOWN) (19 30 1)
(41 18 1 :UP) (18 22 1) (42 17 1 :UP) (40 16 1 :UP) (39 15 1 :UP) (52 21 1)
(38 14 1 :UP) (37 13 1 :UP) (36 12 1 :DOWN) (35 11 1 :UP) (34 10 1 :UP)
(33 9 1 :DOWN) (32 8 1 :DOWN) (7 17 1) (6 16 1) (5 15 1) (4 31 2) (3 30 2)
(2 31 1) (1 30 1))
(DISPLAY-COORDS-2D (4.1221d0 0.0d0) (8.7528d0 -4.7829d0) (5.2535d0 -0.769d0)
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(8.3349d0 -7.7195d0) (9.1599d0 -7.7195d0))
(STRUCTURE-ATOMS C C O O O O O O O O O O O O C C C C N N O O O O O O O O O C
C C C C C C C C C C C C C C C C C C C C C R1 |Protein|)
(:CREATOR |paley|)
(:CREATION-DATE 3355681260) )
NIL)
(BIS-P-NITROPHENOLPHOSPHATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(AROMATIC-RINGS (4 16 3 11 14 18) (7 1 19 20 5 9))
(DISPLAY-COORDS-2D (0.6066667d0 -1.0d0) (0.87666667d0 -0.83d0)
(-0.25d0 -0.83d0) (-0.58666664d0 -0.6166667d0) (0.39999998d0 -0.6166667d0)
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(0.0033333302d0 -1.0d0) (-0.66999996d0 -0.83d0) (0.6833334d0 -0.83d0)
(0.6066667d0 -0.6166667d0) (0.97333336d0 -1.0d0) (-1.0d0 -1.0d0)
(0.0033333302d0 -0.83d0))
(CHEMICAL-FORMULA (C 12) (H 11) (N 2) (O 8) (P 1))
(MOLECULAR-WEIGHT 342.201d0)
(STRUCTURE-BONDS (23 15 1) (23 17 2) (23 13 1) (20 19 :AROMATIC) (19 2 1)
(18 14 :AROMATIC) (18 6 1) (16 3 :AROMATIC) (16 4 :AROMATIC) (15 9 1)
(11 14 :AROMATIC) (10 23 1) (9 7 :AROMATIC) (9 5 :AROMATIC) (7 1 :AROMATIC)
(6 22 1) (6 8 2) (5 20 :AROMATIC) (4 18 :AROMATIC) (3 11 :AROMATIC) (3 10 1)
(2 21 2) (2 12 1) (1 19 :AROMATIC))
(STRUCTURE-ATOMS C N C C C N C O C O C O O C O C O C C C O O P)
(SYNONYMS "BNPP" "di-p-nitrophenyl phosphate" "bis(4-nitrophenyl) phosphate")
(COMMON-NAME "bis(p-nitrophenyl) phosphate")
(:CREATOR |arnaud|)
(:CREATION-DATE 3264197760) )
NIL)
(|Bisdiphospho-myo-inositol-polyphosphates| T (
(OCELOT-GFP::PARENTS |Inositols|)
(COMMON-NAME "a bis(diphospho)-1D-myo-inositol tetrakisphosphate")
(:CREATOR |paley|)
(:CREATION-DATE 3341087492) )
NIL)
(BISOHMYR-GLC NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04932" NIL |kr| 3346617701 NIL NIL))
(DISPLAY-COORDS-2D (6.8638d0 6.8403d0) (5.0956d0 7.6179d0)
(5.7383d0 -2.3476d0) (3.7162d0 -1.6401d0) (7.4653d0 -6.0499d0)
(5.71d0 -0.9361d0) (3.7383d0 -0.2214d0) (3.5682d0 -3.308d0)
(7.4653d0 -4.4d0) (6.4451d0 6.1294d0) (4.6723d0 6.9098d0)
(6.8515d0 5.4113d0) (5.0738d0 6.1892d0) (6.4328d0 4.7005d0)
(4.6504d0 5.4811d0) (6.8392d0 3.9825d0) (5.052d0 4.7604d0)
(6.4205d0 3.2716d0) (4.6286d0 4.0523d0) (6.8087d0 2.6218d0)
(5.0302d0 3.3316d0) (6.3901d0 1.911d0) (4.6068d0 2.6235d0)
(6.7964d0 1.1929d0) (5.0084d0 1.9028d0) (6.3778d0 0.4821d0)
(4.585d0 1.1947d0) (3.5701d0 -4.9637d0) (6.7841d0 -0.236d0)
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(6.6541d0 -3.2153d0) (4.9762d0 -2.314d0) (4.9991d0 -4.9637d0)
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(6.3655d0 -0.9468d0) (4.5632d0 -0.234d0) (4.2847d0 -3.7171d0)
(4.2847d0 -4.5512d0) (5.7226d0 -4.5512d0) (5.7226d0 -3.7171d0)
(4.9991d0 -3.2954d0) (7.4653d0 -5.2249d0) (8.2903d0 -5.2249d0)
(3.0817d0 7.516d0) (1.3135d0 8.2937d0) (1.9562d0 -1.6719d0)
(-0.0659d0 -0.9643d0) (-0.212d0 -5.1129d0) (1.9279d0 -0.2603d0)
(-0.0438d0 0.4543d0) (-0.2139d0 -2.6322d0) (2.663d0 6.8052d0)
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(1.2699d0 5.4361d0) (2.6384d0 3.9474d0) (0.8465d0 4.7281d0)
(3.0266d0 3.2976d0) (1.2481d0 4.0074d0) (2.608d0 2.5867d0)
(0.8247d0 3.2993d0) (3.0143d0 1.8687d0) (1.2263d0 2.5786d0)
(2.5957d0 1.1579d0) (0.8029d0 1.8705d0) (-0.212d0 -4.2879d0)
(3.002d0 0.4398d0) (1.2045d0 1.1498d0) (2.9897d0 -0.9891d0)
(1.1477d0 -0.2101d0) (2.872d0 -2.5396d0) (1.1941d0 -1.6383d0)
(1.217d0 -4.2879d0) (2.8556d0 -4.5511d0) (2.5829d0 -1.6623d0)
(0.7586d0 -0.9376d0) (2.5834d0 -0.2711d0) (0.7811d0 0.4417d0)
(0.5026d0 -3.0413d0) (0.5026d0 -3.8754d0) (1.9405d0 -3.8754d0)
(1.9405d0 -3.0413d0) (1.217d0 -2.6197d0))
(CHEMICAL-FORMULA (C 68) (H 129) (N 2) (O 20) (P 1))
(MOLECULAR-WEIGHT 1325.742d0)
(STRUCTURE-BONDS (28 82 1) (90 91 1) (89 90 1) (87 88 1) (87 91 1)
(89 82 1 :UP) (81 88 1) (81 89 1) (80 84 1) (91 80 1 :UP) (79 83 1)
(90 79 1 :DOWN) (78 84 1) (78 86 1) (77 83 1) (77 85 1) (76 86 1) (75 85 1)
(88 74 1 :UP) (73 76 1) (72 75 1) (71 73 1) (70 72 1) (69 71 1) (68 70 1)
(67 69 1) (66 68 1) (65 67 1) (64 66 1) (63 65 1) (62 64 1) (61 63 1)
(60 62 1) (59 61 1) (58 60 1) (57 59 1) (56 58 1) (87 55 1 :DOWN)
(86 54 1 :UP) (85 53 1 :UP) (52 74 1) (51 84 2) (83 50 2) (49 57 1)
(48 56 1) (46 47 1) (37 3 2) (1 10 1) (2 11 1) (4 38 2) (5 46 2)
(39 6 1 :UP) (40 7 1 :UP) (41 8 1 :DOWN) (9 46 1) (10 12 1) (11 13 1)
(12 14 1) (13 15 1) (14 16 1) (15 17 1) (16 18 1) (17 19 1) (18 20 1)
(19 21 1) (20 22 1) (21 23 1) (22 24 1) (23 25 1) (24 26 1) (25 27 1)
(26 29 1) (27 30 1) (42 28 1 :UP) (29 39 1) (30 40 1) (31 37 1) (31 39 1)
(32 38 1) (32 40 1) (33 37 1) (44 33 1 :DOWN) (34 38 1) (45 34 1 :UP)
(35 42 1) (35 43 1) (43 36 1 :DOWN) (36 46 1) (41 42 1) (41 45 1) (43 44 1)
(44 45 1))
(STRUCTURE-ATOMS C C O O O O O O O C C C C C C C C C C C C C C C C C C C C C
C C N O O O C C C C C C C C C P O C C O O O O O O C C C C C C C C C C C C C
C C C C C C C C C C N O O O C C C C C C C C C)
(APPEARS-IN-LEFT-SIDE-OF TETRAACYLDISACC4KIN-RXN)
(APPEARS-IN-RIGHT-SIDE-OF LIPIDADISACCHARIDESYNTH-RXN)
(COMMON-NAME "lipid A disaccharide")
(SYNONYMS
"2,3-bis-(3-hydroxytetradecanoyl)-D-glucosaminyl-(β-D-1,6)-2,3-bis-(3-hydroxytetradecanoyl)-D-glucosaminyl-β-phosphate"
"2,3-bis(3-hydroxymyristoyl)-D-glucosaminyl-1,6-β-D-2,3-bis(3-hydroxymyristoyl)-β-D-glucosaminyl 1-phosphate"
"2'-3'-diacyl-GlcN(β-1'-6)2,3-diacyl-GlcN-1-P"
"2,3,2',3'-tetrakis(3-hydroxymyristoyl)-D-glucosaminyl-1,6-β-D-glucosamine 1-phosphate"
"2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6-β-D-2,3-bis(3-hydroxytetradecanoyl)-β-D-glucosaminyl 1-phosphate"
"[2-N,3-O-bis(3-hydroxytetradecanoyl)-β-D-glucosaminyl]-(1 => 6)-[2-N,3-O-bis(3-hydroxytetradecanoyl)-β-D-glucosaminyl phosphate]") )
NIL)
(BISOHMYR-GLUCOSAMINYL-1P NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(DBLINKS (LIGAND-CPD "C04824" NIL |sreddy| 3299606423 NIL NIL))
(HISTORY |kr-3290870141|)
(:CREATION-DATE 3115390701)
(DISPLAY-COORDS-2D (5.5511d0 -1.3098d0) (2.5728d0 0.0d0) (3.6553d0 -16.786d0)
(0.2493d0 -15.5943d0) (6.5643d0 -23.0222d0) (0.0032d0 -22.582d0)
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(1.8598d0 -1.1927d0) (5.5304d0 -3.7168d0) (2.536d0 -2.4065d0)
(4.8252d0 -4.9141d0) (1.8229d0 -3.5992d0) (5.5097d0 -6.1235d0)
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(4.7325d0 -12.0196d0) (1.7127d0 -10.8193d0) (0.0032d0 -21.1926d0)
(5.4169d0 -13.2292d0) (2.3892d0 -12.0331d0) (5.3962d0 -15.6359d0)
(2.2935d0 -14.3237d0) (5.1979d0 -18.2475d0) (2.3716d0 -16.7294d0)
(2.4102d0 -21.1926d0) (5.1703d0 -21.6359d0) (4.711d0 -16.7698d0)
(1.6381d0 -15.5491d0) (4.7118d0 -14.4265d0) (1.676d0 -13.2258d0)
(1.2069d0 -20.4977d0) (1.2069d0 -19.0928d0) (3.6289d0 -20.4977d0)
(3.6289d0 -19.0928d0) (2.4102d0 -18.3825d0) (6.5643d0 -21.6325d0))
(CHEMICAL-FORMULA (C 34) (H 66) (N 1) (O 12) (P 1))
(MOLECULAR-WEIGHT 711.869d0)
(STRUCTURE-BONDS (46 47 1) (45 46 1) (44 47 1) (43 44 1) (38 48 1)
(45 38 1 :DOWN) (37 45 1) (37 43 1) (47 36 1 :UP) (36 40 1) (46 35 1 :DOWN)
(35 39 1) (34 42 1) (34 40 1) (33 41 1) (33 39 1) (32 42 1) (31 41 1)
(43 30 1 :UP) (29 32 1) (28 31 1) (27 29 1) (26 28 1) (25 27 1) (24 26 1)
(23 25 1) (22 24 1) (21 23 1) (20 22 1) (19 21 1) (18 20 1) (17 19 1)
(16 18 1) (15 17 1) (14 16 1) (13 15 1) (12 14 1) (11 48 1) (10 48 1)
(44 9 1 :DOWN) (42 8 1 :UP) (41 7 1 :UP) (6 30 1) (5 48 2) (4 40 2) (3 39 2)
(2 13 1) (1 12 1))
(STRUCTURE-ATOMS C C O O O O O O O O O C C C C C C C C C C C C C C C C C C C
C C C C N O O O C C C C C C C C C P)
(APPEARS-IN-LEFT-SIDE-OF LIPIDADISACCHARIDESYNTH-RXN)
(APPEARS-IN-RIGHT-SIDE-OF LIPIDXSYNTHESIS-RXN)
(SYNONYMS "2,3-diacyl-glucosamine 1-phosphate"
"2,3-bis(3-hydroxytetradecanoyl)-β-D-glucosaminyl 1-phosphate"
"2,3-bis(β-hydroxymyristoyl)-β-D-glucosaminyl 1-phosphate"
"lipid X")
(COMMON-NAME "2,3-bis(3-hydroxymyristoyl)-β-D-glucosaminyl 1-phosphate") )
NIL)
(BITTER-ACIDS T (
(OCELOT-GFP::PARENTS |Terpenophenolics|)
(SYNONYMS "a prenylated acylphloroglucinol")
(COMMON-NAME "a bitter acid")
(:CREATOR |paley|)
(:CREATION-DATE 3355681267) )
NIL)
(|Blocking-Modifications| T (
(OCELOT-GFP::PARENTS |Modified-Residues|)
(SCHEMA? T)
(COMMENT "Undetermined N- or C-terminal blocking group.")
(:CREATOR |paley|)
(:CREATION-DATE 3273414656) )
NIL)
(BORATE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF ASP-SEMIALDEHYDE-DEHYDROGENASE-ENZRXN)
(:CREATOR |paley|)
(:CREATION-DATE 3340979855)
(COMMON-NAME "borate") )
NIL)
(BOROHYDRIDE NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(INHIBITORS-UNKMECH-OF PHOSPHASERDECARB-ENZRXN SAMDECARB-ENZRXN
F16ALDOLASE-ENZRXN-CLASSI)
(:CREATOR |paley|)
(:CREATION-DATE 3340979762)
(COMMON-NAME "borohydride") )
NIL)
(BOUND-TORT NIL (
(OCELOT-GFP::PARENTS |Tor-T|)
(MOLECULAR-WEIGHT-SEQ 37.86463199999994d0)
(FEATURES FTR0-341)
(:CREATION-DATE 3087649046)
(DBLINKS (MODBASE "P38683" NIL |pkarp| 3355444109 NIL NIL)
(PFAM "PF00532" IN-FAMILY |pkarp| 3346700326 NIL NIL)
(REFSEQ "NP_415514" NIL NIL NIL NIL NIL)
(UNIPROT "P38683" NIL |pkarp| 3102853742))
(COMMON-NAME "TorT-unknown inducer")
(GENE G6515)
(APPEARS-IN-RIGHT-SIDE-OF TORT-RXN)
(SYNONYMS "B0994" "YccH" "TorT"
"inducer-binding protein TorT-unknown inducer"
"bound inducer-binding protein TorT")
(UNMODIFIED-FORM TORT-MONOMER) )
NIL)
(BR NIL (
(OCELOT-GFP::PARENTS |Elements|)
(ACTIVATORS-UNKMECH-OF GLUTDECARBOXB-ENZRXN GLUTDECARBOXA-ENZRXN)
(COMMON-NAME "Br")
(VALENCE 1)
(ATOMIC-WEIGHT 79.904d0)
(ATOMIC-NUMBER 35)
(SYNONYMS "bromine") )
NIL)
(BR- NIL (
(OCELOT-GFP::PARENTS |Anions|)
(INHIBITORS-UNKMECH-OF KDGALDOL-ENZRXN)
(INHIBITORS-COMPETITIVE-OF CYANLY-ENZRXN)
(:CREATION-DATE 3101477439)
(ATOM-CHARGES (1 -1))
(DISPLAY-COORDS-2D (-1.0d0 -1.0d0))
(CHEMICAL-FORMULA (BR 1))
(MOLECULAR-WEIGHT 79.904d0)
(STRUCTURE-ATOMS BR)
(COMMON-NAME "Br-")
(SYNONYMS "bromide" "bromide ion")
(CHARGE -1)
(:CREATOR |paley|) )
NIL)
(BR-10175 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8764)
(RIGHT CPLX0-7026)
(ACTIVATORS CPLX0-5571)
(:CREATOR |martin|)
(:CREATION-DATE 3347903084) )
((ACTIVATORS CPLX0-5571 COMMENT) (ACTIVATORS CPLX0-5571 CITATIONS "15716448")))
(BR-10176 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-BAER BS-7046)
(RIGHT CPLX0-5571)
(:CREATOR |martin|)
(:CREATION-DATE 3347903184) )
NIL)
(BR-10177 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8765)
(RIGHT CPLX0-7025)
(INHIBITORS CPLX0-5748)
(ACTIVATORS CPLX0-5570)
(:CREATOR |martin|)
(:CREATION-DATE 3347903708) )
((INHIBITORS CPLX0-5748 CITATIONS "16377617")
(INHIBITORS CPLX0-5748 COMMENT
"By making use of micro arrays analysis, Constantinidou et al |CITS: [16377617]| concluded that FNR represses ycaC gene expression. They also identified a putative FNR binding site upstream of the gene, but the sequence was not shown.
")
(ACTIVATORS CPLX0-5570 CITATIONS "15716448") (ACTIVATORS CPLX0-5570 COMMENT)))
(BR-10178 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-BAER BS-7047)
(RIGHT CPLX0-5570)
(:CREATOR |martin|)
(:CREATION-DATE 3347903952) )
NIL)
(BR-10179 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8766)
(RIGHT CPLX0-7023)
(:CREATOR |asantos|)
(:CREATION-DATE 3347912585) )
NIL)
(BR-10180 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8767)
(RIGHT CPLX0-7022)
(:CREATOR |asantos|)
(:CREATION-DATE 3347913592) )
NIL)
(BR-10181 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8768)
(RIGHT CPLX0-7021)
(:CREATOR |asantos|)
(:CREATION-DATE 3347985146) )
NIL)
(BR-10182 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM00638)
(RIGHT CPLX0-6964)
(:CREATOR |asantos|)
(:CREATION-DATE 3348001365) )
NIL)
(BR-10183 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8770)
(RIGHT CPLX0-7019)
(ACTIVATORS CPLX0-5568 CPLX0-5569)
(:CREATOR |martin|)
(:CREATION-DATE 3348405718) )
((ACTIVATORS CPLX0-5568 CITATIONS "16194231")
(ACTIVATORS CPLX0-5569 CITATIONS "16194231")))
(BR-10184 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7575-MONOMER BS-7048)
(RIGHT CPLX0-5569)
(:CREATOR |martin|)
(:CREATION-DATE 3348408855) )
NIL)
(BR-10185 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8771)
(RIGHT CPLX0-7018)
(:CREATOR |sgama|)
(:CREATION-DATE 3348414021) )
NIL)
(BR-10186 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8772)
(RIGHT CPLX0-7017)
(:CREATOR |sgama|)
(:CREATION-DATE 3348510512) )
NIL)
(BR-10187 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8773)
(RIGHT CPLX0-7016)
(:CREATOR |sgama|)
(:CREATION-DATE 3348510758) )
NIL)
(BR-10188 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8774)
(RIGHT CPLX0-7014)
(:CREATOR |asantos|)
(:CREATION-DATE 3348606937) )
NIL)
(BR-10189 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8775)
(RIGHT CPLX0-7013)
(:CREATOR |asantos|)
(:CREATION-DATE 3348607644) )
NIL)
(BR-10190 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8776)
(RIGHT CPLX0-7012)
(:CREATOR |asantos|)
(:CREATION-DATE 3348858705) )
NIL)
(BR-10191 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8777)
(RIGHT CPLX0-7011)
(:CREATOR |martin|)
(:CREATION-DATE 3348859803) )
NIL)
(BR-10192 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8779)
(RIGHT CPLX0-7010)
(:CREATOR |asantos|)
(:CREATION-DATE 3348860818) )
NIL)
(BR-10193 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8780)
(RIGHT CPLX0-7009)
(:CREATOR |asantos|)
(:CREATION-DATE 3348862078) )
NIL)
(BR-10194 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8781)
(RIGHT CPLX0-7008)
(:CREATOR |asantos|)
(:CREATION-DATE 3348863369) )
NIL)
(BR-10195 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7575-MONOMER BS-7049)
(RIGHT CPLX0-5568)
(:CREATOR |martin|)
(:CREATION-DATE 3348884019) )
NIL)
(BR-10196 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8782)
(RIGHT CPLX0-7007)
(ACTIVATORS CPLX0-5566 CPLX0-5567)
(:CREATOR |martin|)
(:CREATION-DATE 3349037583) )
((ACTIVATORS CPLX0-5567 CITATIONS "15941987") (ACTIVATORS CPLX0-5567 COMMENT)
(ACTIVATORS CPLX0-5566 CITATIONS "15941987") (ACTIVATORS CPLX0-5566 COMMENT)))
(BR-10197 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8783)
(RIGHT CPLX0-7006)
(ACTIVATORS CPLX0-5564 CPLX0-5565)
(:CREATOR |martin|)
(:CREATION-DATE 3349040429) )
((ACTIVATORS CPLX0-5564 CITATIONS "15941987") (ACTIVATORS CPLX0-5564 COMMENT)
(ACTIVATORS CPLX0-5565 CITATIONS "15941987") (ACTIVATORS CPLX0-5565 COMMENT)))
(BR-10198 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7050)
(RIGHT CPLX0-5567)
(:CREATOR |martin|)
(:CREATION-DATE 3349040924) )
NIL)
(BR-10199 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7051)
(RIGHT CPLX0-5566)
(:CREATOR |martin|)
(:CREATION-DATE 3349041273) )
NIL)
(BR-10200 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7052)
(RIGHT CPLX0-5565)
(:CREATOR |martin|)
(:CREATION-DATE 3349041501) )
NIL)
(BR-10201 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7053)
(RIGHT CPLX0-5564)
(:CREATOR |martin|)
(:CREATION-DATE 3349041683) )
NIL)
(BR-10202 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8784)
(RIGHT CPLX0-7005)
(ACTIVATORS CPLX0-5741 CPLX0-5562 CPLX0-5563)
(:CREATOR |martin|)
(:CREATION-DATE 3349043300) )
((ACTIVATORS CPLX0-5741 CITATIONS "16377617")
(ACTIVATORS CPLX0-5741 COMMENT
"By making use of micro arrays analysis, Constantinidou et al |CITS: [16377617]| concluded that FNR activates yecRp gene expression. They also identified a putative FNR binding site upstream of the gene, but the sequence was not shown.")
(ACTIVATORS CPLX0-5562 CITATIONS "15941987")
(ACTIVATORS CPLX0-5563 CITATIONS "15941987")))
(BR-10203 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7054)
(RIGHT CPLX0-5563)
(:CREATOR |martin|)
(:CREATION-DATE 3349043361) )
NIL)
(BR-10204 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7055)
(RIGHT CPLX0-5562)
(:CREATOR |martin|)
(:CREATION-DATE 3349043397) )
NIL)
(BR-10205 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7056)
(RIGHT CPLX0-5561)
(:CREATOR |martin|)
(:CREATION-DATE 3349049450) )
NIL)
(BR-10206 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7057)
(RIGHT CPLX0-5560)
(:CREATOR |martin|)
(:CREATION-DATE 3349051767) )
NIL)
(BR-10207 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7058)
(RIGHT CPLX0-5559)
(:CREATOR |martin|)
(:CREATION-DATE 3349051820) )
NIL)
(BR-10208 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7059)
(RIGHT CPLX0-5558)
(:CREATOR |martin|)
(:CREATION-DATE 3349055235) )
NIL)
(BR-10209 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7060)
(RIGHT CPLX0-5557)
(:CREATOR |martin|)
(:CREATION-DATE 3349055340) )
NIL)
(BR-10210 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7061)
(RIGHT CPLX0-5556)
(:CREATOR |martin|)
(:CREATION-DATE 3349055431) )
NIL)
(BR-10212 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7063)
(RIGHT CPLX0-5555)
(:CREATOR |martin|)
(:CREATION-DATE 3349097120) )
NIL)
(BR-10213 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7064)
(RIGHT CPLX0-5554)
(:CREATOR |martin|)
(:CREATION-DATE 3349097181) )
NIL)
(BR-10214 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7065)
(RIGHT CPLX0-5553)
(:CREATOR |martin|)
(:CREATION-DATE 3349097225) )
NIL)
(BR-10215 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7066)
(RIGHT CPLX0-5552)
(:CREATOR |martin|)
(:CREATION-DATE 3349097278) )
NIL)
(BR-10216 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS-7067)
(RIGHT CPLX0-4555)
(:CREATOR |martin|)
(:CREATION-DATE 3349102550) )
NIL)
(BR-10217 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8786)
(RIGHT CPLX0-7004)
(:CREATOR |martin|)
(:CREATION-DATE 3349107164) )
NIL)
(BR-10221 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7069)
(RIGHT CPLX0-5551)
(:CREATOR |martin|)
(:CREATION-DATE 3349122271) )
NIL)
(BR-10222 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8790)
(RIGHT CPLX0-7003)
(ACTIVATORS CPLX0-5549 CPLX0-5550)
(:CREATOR |martin|)
(:CREATION-DATE 3349122857) )
((ACTIVATORS CPLX0-5549 COMMENT)
(ACTIVATORS CPLX0-5549 CITATIONS "15941987" "7961507")
(ACTIVATORS CPLX0-5550 CITATIONS "15941987" "7961507")))
(BR-10223 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7070)
(RIGHT CPLX0-5550)
(:CREATOR |martin|)
(:CREATION-DATE 3349123010) )
NIL)
(BR-10224 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7071)
(RIGHT CPLX0-5549)
(:CREATOR |martin|)
(:CREATION-DATE 3349123100) )
NIL)
(BR-10225 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM-8792)
(RIGHT CPLX0-7002)
(:CREATOR |martin|)
(:CREATION-DATE 3349182788) )
NIL)
(BR-10226 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT CPLX0-222 PM-8793)
(RIGHT CPLX0-7001)
(:CREATOR |martin|)
(:CREATION-DATE 3349462421) )
NIL)
(BR-10227 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8794)
(RIGHT CPLX0-7000)
(ACTIVATORS CPLX0-5547 CPLX0-5548)
(:CREATOR |martin|)
(:CREATION-DATE 3349470938) )
((ACTIVATORS CPLX0-5548 CITATIONS) (ACTIVATORS CPLX0-5548 COMMENT)))
(BR-10228 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7072)
(RIGHT CPLX0-5548)
(:CREATOR |martin|)
(:CREATION-DATE 3349471046) )
NIL)
(BR-10229 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7073)
(RIGHT CPLX0-5547)
(:CREATOR |martin|)
(:CREATION-DATE 3349471201) )
NIL)
(BR-10231 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8797)
(RIGHT CPLX0-6999)
(ACTIVATORS CPLX0-5548 CPLX0-5547)
(:CREATOR |martin|)
(:CREATION-DATE 3349543360) )
((ACTIVATORS CPLX0-5548 CITATIONS) (ACTIVATORS CPLX0-5548 COMMENT)
(ACTIVATORS CPLX0-5547 CITATIONS) (ACTIVATORS CPLX0-5547 COMMENT)))
(BR-10232 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM-8798)
(RIGHT CPLX0-6998)
(ACTIVATORS CPLX0-5545 CPLX0-5546)
(:CREATOR |martin|)
(:CREATION-DATE 3349550231) )
((ACTIVATORS CPLX0-5545 CITATIONS "15941987") (ACTIVATORS CPLX0-5545 COMMENT)
(ACTIVATORS CPLX0-5546 CITATIONS "15941987")))
(BR-10233 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8800)
(RIGHT CPLX0-6997)
(:CREATOR |asantos|)
(:CREATION-DATE 3349551928) )
NIL)
(BR-10234 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7074)
(RIGHT CPLX0-5546)
(:CREATOR |martin|)
(:CREATION-DATE 3349553927) )
NIL)
(BR-10235 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-3930 BS-7075)
(RIGHT CPLX0-5545)
(:CREATOR |martin|)
(:CREATION-DATE 3349554041) )
NIL)
(BR-10236 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8803)
(RIGHT CPLX0-6996)
(:CREATOR |asantos|)
(:CREATION-DATE 3349554326) )
NIL)
(BR-10237 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8805)
(RIGHT CPLX0-6995)
(:CREATOR |asantos|)
(:CREATION-DATE 3349558201) )
NIL)
(BR-10238 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8807)
(RIGHT CPLX0-6994)
(:CREATOR |asantos|)
(:CREATION-DATE 3349558487) )
NIL)
(BR-10239 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8808)
(RIGHT CPLX0-6962)
(:CREATOR |asantos|)
(:CREATION-DATE 3349620094) )
NIL)
(BR-10240 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8809)
(RIGHT CPLX0-6967)
(:CREATOR |asantos|)
(:CREATION-DATE 3349620420) )
NIL)
(BR-10241 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM-8813)
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(:CREATOR |martin|)
(:CREATION-DATE 3340711414) )
NIL)
(BR0-10044 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6953)
(RIGHT CPLX0-5513)
(:CREATOR |asantos|)
(:CREATION-DATE 3340717172) )
NIL)
(BR0-10045 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6954)
(RIGHT CPLX0-5675)
(:CREATOR |asantos|)
(:CREATION-DATE 3340717338) )
NIL)
(BR0-10046 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6955)
(RIGHT CPLX0-5674)
(:CREATOR |asantos|)
(:CREATION-DATE 3340717565) )
NIL)
(BR0-10047 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6956)
(RIGHT CPLX0-5673)
(:CREATOR |asantos|)
(:CREATION-DATE 3340718270) )
NIL)
(BR0-10048 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6957)
(RIGHT CPLX0-5493)
(:CREATOR |asantos|)
(:CREATION-DATE 3340718448) )
NIL)
(BR0-10049 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6958)
(RIGHT CPLX0-5492)
(:CREATOR |asantos|)
(:CREATION-DATE 3340720395) )
NIL)
(BR0-10050 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6959)
(RIGHT CPLX0-5512)
(:CREATOR |asantos|)
(:CREATION-DATE 3340720965) )
NIL)
(BR0-10051 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6960)
(RIGHT CPLX0-5508)
(:CREATOR |asantos|)
(:CREATION-DATE 3340721139) )
NIL)
(BR0-10052 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6961)
(RIGHT CPLX0-5505)
(:CREATOR |asantos|)
(:CREATION-DATE 3340722318) )
NIL)
(BR0-10053 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6962)
(RIGHT CPLX0-5510)
(:CREATOR |asantos|)
(:CREATION-DATE 3340722385) )
NIL)
(BR0-10054 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6963)
(RIGHT CPLX0-5485)
(:CREATOR |asantos|)
(:CREATION-DATE 3340722553) )
NIL)
(BR0-10055 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6964)
(RIGHT CPLX0-5484)
(:CREATOR |asantos|)
(:CREATION-DATE 3340723851) )
NIL)
(BR0-10056 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6965)
(RIGHT CPLX0-5483)
(:CREATOR |asantos|)
(:CREATION-DATE 3340724149) )
NIL)
(BR0-10057 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6966)
(RIGHT CPLX0-5482)
(:CREATOR |asantos|)
(:CREATION-DATE 3340724252) )
NIL)
(BR0-10058 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6967)
(RIGHT CPLX0-5481)
(:CREATOR |asantos|)
(:CREATION-DATE 3340724332) )
NIL)
(BR0-10060 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6969)
(RIGHT CPLX0-5480)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727209) )
NIL)
(BR0-10061 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6970)
(RIGHT CPLX0-5479)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727309) )
NIL)
(BR0-10062 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6971)
(RIGHT CPLX0-5470)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727700) )
NIL)
(BR0-10063 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6972)
(RIGHT CPLX0-5469)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727834) )
NIL)
(BR0-10064 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6973)
(RIGHT CPLX0-5468)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727883) )
NIL)
(BR0-10065 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00260 BS0-6974)
(RIGHT CPLX0-5467)
(:CREATOR |asantos|)
(:CREATION-DATE 3340727940) )
NIL)
(BR0-10066 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6975)
(RIGHT CPLX0-5466)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753338) )
NIL)
(BR0-10067 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6976)
(RIGHT CPLX0-5465)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753400) )
NIL)
(BR0-10068 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6977)
(RIGHT CPLX0-5464)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753484) )
NIL)
(BR0-10069 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6978)
(RIGHT CPLX0-5478)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753536) )
NIL)
(BR0-10070 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6979)
(RIGHT CPLX0-5477)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753623) )
NIL)
(BR0-10071 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6980)
(RIGHT CPLX0-5476)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753683) )
NIL)
(BR0-10072 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6981)
(RIGHT CPLX0-5475)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753732) )
NIL)
(BR0-10073 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6982)
(RIGHT CPLX0-5474)
(:CREATOR |asantos|)
(:CREATION-DATE 3340753858) )
NIL)
(BR0-10074 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6983)
(RIGHT CPLX0-5473)
(:CREATOR |asantos|)
(:CREATION-DATE 3340754052) )
NIL)
(BR0-10077 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6986)
(RIGHT CPLX0-5472)
(:CREATOR |asantos|)
(:CREATION-DATE 3340754206) )
NIL)
(BR0-10078 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6987)
(RIGHT CPLX0-5471)
(:CREATOR |asantos|)
(:CREATION-DATE 3340754250) )
NIL)
(BR0-10079 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6988)
(RIGHT CPLX0-5463)
(:CREATOR |asantos|)
(:CREATION-DATE 3340754754) )
NIL)
(BR0-10080 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS0-6989)
(RIGHT CPLX0-5462)
(:CREATOR |asantos|)
(:CREATION-DATE 3340754948) )
NIL)
(BR0-10081 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARP BS0-6990)
(RIGHT CPLX0-5461)
(:CREATOR |asantos|)
(:CREATION-DATE 3340755036) )
NIL)
(BR0-10082 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-6991)
(RIGHT CPLX0-5622)
(:CREATOR |martin|)
(:CREATION-DATE 3341665985) )
NIL)
(BR0-10083 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-6992)
(RIGHT CPLX0-5621)
(:CREATOR |martin|)
(:CREATION-DATE 3341671856) )
NIL)
(BR0-10084 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8714)
(RIGHT CPLX0-7076)
(ACTIVATORS CPLX0-5620)
(:CREATOR |martin|)
(:CREATION-DATE 3341676585) )
((ACTIVATORS CPLX0-5620 CITATIONS "10850996")
(ACTIVATORS CPLX0-5620 COMMENT
"Rob is a transcriptional regulator related with the increase in resistance to antibiotics and is expressed constitutively. Bennik et al have shown that this regulator activates the transcription of ybiS gene |CITS [ 10850996 ]|.")))
(BR0-10085 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04418 BS0-6993)
(RIGHT CPLX0-5620)
(:CREATOR |martin|)
(:CREATION-DATE 3341676732) )
NIL)
(BR0-10086 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8715)
(RIGHT CPLX0-7075)
(ACTIVATORS CPLX0-5619)
(:CREATOR |martin|)
(:CREATION-DATE 3341676847) )
((ACTIVATORS CPLX0-5619 CITATIONS "10850996") (ACTIVATORS CPLX0-5619 COMMENT)))
(BR0-10087 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04418 BS0-6994)
(RIGHT CPLX0-5619)
(:CREATOR |martin|)
(:CREATION-DATE 3341676898) )
NIL)
(BR0-10088 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8716)
(RIGHT CPLX0-7074)
(:CREATOR |martin|)
(:CREATION-DATE 3341689669) )
NIL)
(BR0-10089 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6995)
(RIGHT CPLX0-5618)
(:CREATOR |asantos|)
(:CREATION-DATE 3341860155) )
NIL)
(BR0-10090 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6996)
(RIGHT CPLX0-5617)
(:CREATOR |asantos|)
(:CREATION-DATE 3341860317) )
NIL)
(BR0-10091 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6997)
(RIGHT CPLX0-5616)
(:CREATOR |asantos|)
(:CREATION-DATE 3341863434) )
NIL)
(BR0-10092 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6998)
(RIGHT CPLX0-5615)
(:CREATOR |asantos|)
(:CREATION-DATE 3341863797) )
NIL)
(BR0-10093 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8717)
(RIGHT CPLX0-7073)
(:CREATOR |martin|)
(:CREATION-DATE 3342191559) )
NIL)
(BR0-10094 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8718)
(RIGHT CPLX0-7072)
(:CREATOR |martin|)
(:CREATION-DATE 3342191636) )
NIL)
(BR0-10095 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8719)
(RIGHT CPLX0-7071)
(:CREATOR |martin|)
(:CREATION-DATE 3342191672) )
NIL)
(BR0-10096 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-6999)
(RIGHT CPLX0-5506)
(:CREATOR |asantos|)
(:CREATION-DATE 3342195364) )
NIL)
(BR0-10097 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-7000)
(RIGHT CPLX0-5507)
(:CREATOR |asantos|)
(:CREATION-DATE 3342196098) )
NIL)
(BR0-10098 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-7001)
(RIGHT CPLX0-5488)
(:CREATOR |asantos|)
(:CREATION-DATE 3342196977) )
NIL)
(BR0-10099 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-7002)
(RIGHT CPLX0-5614)
(:CREATOR |asantos|)
(:CREATION-DATE 3342197205) )
NIL)
(BR0-10100 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-7003)
(RIGHT CPLX0-5613)
(:CREATOR |asantos|)
(:CREATION-DATE 3342197549) )
NIL)
(BR0-10101 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7004)
(RIGHT CPLX0-5612)
(:CREATOR |sgama|)
(:CREATION-DATE 3342299488) )
NIL)
(BR0-10102 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7005)
(RIGHT CPLX0-5611)
(:CREATOR |asantos|)
(:CREATION-DATE 3342361879) )
NIL)
(BR0-10103 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7006)
(RIGHT CPLX0-5610)
(:CREATOR |asantos|)
(:CREATION-DATE 3342362484) )
NIL)
(BR0-10104 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7007)
(RIGHT CPLX0-5609)
(:CREATOR |asantos|)
(:CREATION-DATE 3342372714) )
NIL)
(BR0-10105 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7008)
(RIGHT CPLX0-5608)
(:CREATOR |asantos|)
(:CREATION-DATE 3342375136) )
NIL)
(BR0-10106 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7009)
(RIGHT CPLX0-5607)
(:CREATOR |asantos|)
(:CREATION-DATE 3342375763) )
NIL)
(BR0-10107 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7010)
(RIGHT CPLX0-5606)
(:CREATOR |asantos|)
(:CREATION-DATE 3342376107) )
NIL)
(BR0-10108 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-7011)
(RIGHT CPLX0-5605)
(:CREATOR |asantos|)
(:CREATION-DATE 3342377739) )
NIL)
(BR0-10109 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-7012)
(RIGHT CPLX0-5604)
(:CREATOR |martin|)
(:CREATION-DATE 3342388810) )
NIL)
(BR0-10110 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-2487 BS0-7013)
(RIGHT CPLX0-5603)
(:CREATOR |martin|)
(:CREATION-DATE 3342456403) )
NIL)
(BR0-10111 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT CPLX0-222 PM0-8720)
(RIGHT CPLX0-7069)
(:CREATOR |martin|)
(:CREATION-DATE 3342459970) )
NIL)
(BR0-10112 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-8721)
(RIGHT CPLX0-7068)
(:CREATOR |martin|)
(:CREATION-DATE 3342462052) )
NIL)
(BR0-10114 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8723)
(RIGHT CPLX0-7066)
(ACTIVATORS CPLX0-5602)
(:CREATOR |martin|)
(:CREATION-DATE 3342823765) )
((ACTIVATORS CPLX0-5602 CITATIONS "12754220")
(ACTIVATORS CPLX0-5602 COMMENT
"By making use of micro arrays analysis it was concluded that FNR activates sbm-argK-ygfGH operon expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
(BR0-10115 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8726)
(RIGHT CPLX0-7065)
(:CREATOR |martin|)
(:CREATION-DATE 3342982762) )
NIL)
(BR0-10116 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7015)
(RIGHT CPLX0-5490)
(:CREATOR |sgama|)
(:CREATION-DATE 3342995517) )
NIL)
(BR0-10117 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7016)
(RIGHT CPLX0-5489)
(:CREATOR |sgama|)
(:CREATION-DATE 3342995702) )
NIL)
(BR0-10118 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8727)
(RIGHT CPLX0-7064)
(ACTIVATORS CPLX0-5599)
(:CREATOR |sgama|)
(:CREATION-DATE 3342996232) )
((ACTIVATORS CPLX0-5599 CITATIONS "12754220")
(ACTIVATORS CPLX0-5599 COMMENT
"By making use of micro arrays analysis it was concluded that FNR activates acrEF operon expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
(BR0-10120 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7018)
(RIGHT CPLX0-5602)
(:CREATOR |sgama|)
(:CREATION-DATE 3343059572) )
NIL)
(BR0-10121 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7019)
(RIGHT CPLX0-5601)
(:CREATOR |sgama|)
(:CREATION-DATE 3343060481) )
NIL)
(BR0-10122 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-8728)
(RIGHT CPLX0-7063)
(INHIBITORS CPLX0-5587 CPLX0-5589)
(ACTIVATORS CPLX0-5600)
(:CREATOR |sgama|)
(:CREATION-DATE 3343061240) )
((INHIBITORS CPLX0-5587 CITATIONS "15995204") (INHIBITORS CPLX0-5587 COMMENT)
(INHIBITORS CPLX0-5589 CITATIONS "15995204")
(ACTIVATORS CPLX0-5600 CITATIONS "12754220")
(ACTIVATORS CPLX0-5600 COMMENT
"By making use of micro arrays analysis it was concluded that FNR activates dcuSR operon expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
(BR0-10123 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7020)
(RIGHT CPLX0-5600)
(:CREATOR |sgama|)
(:CREATION-DATE 3343061488) )
NIL)
(BR0-10124 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7021)
(RIGHT CPLX0-5599)
(:CREATOR |sgama|)
(:CREATION-DATE 3343069670) )
NIL)
(BR0-10125 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-8730)
(RIGHT CPLX0-7062)
(:CREATOR |asantos|)
(:CREATION-DATE 3343069885) )
NIL)
(BR0-10126 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-8731)
(RIGHT CPLX0-7061)
(:CREATOR |asantos|)
(:CREATION-DATE 3343070465) )
NIL)
(BR0-10127 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-8732)
(RIGHT CPLX0-7060)
(:CREATOR |asantos|)
(:CREATION-DATE 3343071481) )
NIL)
(BR0-10128 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-8733)
(RIGHT CPLX0-7059)
(:CREATOR |asantos|)
(:CREATION-DATE 3343071885) )
NIL)
(BR0-10129 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-8734)
(RIGHT CPLX0-7058)
(:CREATOR |asantos|)
(:CREATION-DATE 3343072061) )
NIL)
(BR0-10130 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8735)
(RIGHT CPLX0-7054)
(ACTIVATORS CPLX0-5598)
(:CREATOR |sgama|)
(:CREATION-DATE 3343072894) )
((ACTIVATORS CPLX0-5598 CITATIONS "12754220")
(ACTIVATORS CPLX0-5598 COMMENT
"By making use of micro arrays analysis it was concluded that FNR activates bcsBZ operon expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
(BR0-10131 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-7022)
(RIGHT CPLX0-5598)
(:CREATOR |sgama|)
(:CREATION-DATE 3343073018) )
NIL)
(BR0-10132 NIL (
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"By making use of micro arrays analysis it was concluded that anaerobiosis do not affect the expression of gapC operon, although FNR appears to repress it. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
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(:CREATOR |martin|)
(:CREATION-DATE 3360589996) )
NIL)
(BR0-10447 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8934)
(RIGHT CPLX0-6920)
(:CREATOR |martin|)
(:CREATION-DATE 3360590036) )
NIL)
(BR0-10448 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8935)
(RIGHT CPLX0-6921)
(:CREATOR |martin|)
(:CREATION-DATE 3360590314) )
NIL)
(BR0-10449 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8936)
(RIGHT CPLX0-6922)
(:CREATOR |martin|)
(:CREATION-DATE 3360590410) )
NIL)
(BR0-10450 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8937)
(RIGHT CPLX0-6923)
(:CREATOR |martin|)
(:CREATION-DATE 3360590725) )
NIL)
(BR0-10451 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7326-MONOMER BS0-7167)
(RIGHT CPLX0-5501)
(:CREATOR |martin|)
(:CREATION-DATE 3360593385) )
NIL)
(BR0-10452 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7326-MONOMER BS0-7168)
(RIGHT CPLX0-5502)
(:CREATOR |martin|)
(:CREATION-DATE 3360606638) )
NIL)
(BR0-10453 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7326-MONOMER BS0-7169)
(RIGHT CPLX0-5503)
(:CREATOR |martin|)
(:CREATION-DATE 3360607126) )
NIL)
(BR0-10454 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7326-MONOMER BS0-7170)
(RIGHT CPLX0-5504)
(:CREATOR |martin|)
(:CREATION-DATE 3360611775) )
NIL)
(BR0-10455 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8938)
(RIGHT CPLX0-6924)
(:CREATOR |martin|)
(:CREATION-DATE 3360623921) )
NIL)
(BR0-10456 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8939)
(RIGHT CPLX0-6941)
(:CREATOR |sgama|)
(:CREATION-DATE 3360674482) )
NIL)
(BR0-10457 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8940)
(RIGHT CPLX0-6925)
(:CREATOR |martin|)
(:CREATION-DATE 3360679935) )
NIL)
(BR0-10458 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8941)
(RIGHT CPLX0-6926)
(:CREATOR |martin|)
(:CREATION-DATE 3360680013) )
NIL)
(BR0-10459 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8942)
(RIGHT CPLX0-6927)
(:CREATOR |martin|)
(:CREATION-DATE 3360680146) )
NIL)
(BR0-10460 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8943)
(RIGHT CPLX0-6928)
(:CREATOR |martin|)
(:CREATION-DATE 3360680218) )
NIL)
(BR0-10461 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8944)
(RIGHT CPLX0-6929)
(:CREATOR |martin|)
(:CREATION-DATE 3360680360) )
NIL)
(BR0-10462 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8945)
(RIGHT CPLX0-6930)
(:CREATOR |martin|)
(:CREATION-DATE 3360680399) )
NIL)
(BR0-10463 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8946)
(RIGHT CPLX0-6931)
(:CREATOR |martin|)
(:CREATION-DATE 3360680476) )
NIL)
(BR0-10464 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8947)
(RIGHT CPLX0-6932)
(:CREATOR |martin|)
(:CREATION-DATE 3360680539) )
NIL)
(BR0-10465 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8948)
(RIGHT CPLX0-6933)
(:CREATOR |martin|)
(:CREATION-DATE 3360680582) )
NIL)
(BR0-10466 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8949)
(RIGHT CPLX0-6934)
(:CREATOR |martin|)
(:CREATION-DATE 3360680623) )
NIL)
(BR0-10467 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8950)
(RIGHT CPLX0-6935)
(:CREATOR |martin|)
(:CREATION-DATE 3360680767) )
NIL)
(BR0-10468 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8951)
(RIGHT CPLX0-6936)
(:CREATOR |martin|)
(:CREATION-DATE 3360680885) )
NIL)
(BR0-10469 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8952)
(RIGHT CPLX0-6937)
(:CREATOR |martin|)
(:CREATION-DATE 3360680934) )
NIL)
(BR0-10470 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8953)
(RIGHT CPLX0-6938)
(:CREATOR |martin|)
(:CREATION-DATE 3360681392) )
NIL)
(BR0-10471 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8954)
(RIGHT CPLX0-6939)
(:CREATOR |martin|)
(:CREATION-DATE 3360681438) )
NIL)
(BR0-10472 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8955)
(RIGHT CPLX0-6940)
(:CREATOR |martin|)
(:CREATION-DATE 3360681470) )
NIL)
(BR0-10474 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8957)
(RIGHT CPLX0-6942)
(:CREATOR |martin|)
(:CREATION-DATE 3360961649) )
NIL)
(BR0-10475 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8958)
(RIGHT CPLX0-6943)
(:CREATOR |martin|)
(:CREATION-DATE 3360961698) )
NIL)
(BR0-10476 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8959)
(RIGHT CPLX0-6944)
(:CREATOR |martin|)
(:CREATION-DATE 3360961744) )
NIL)
(BR0-10477 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8960)
(RIGHT CPLX0-6945)
(:CREATOR |martin|)
(:CREATION-DATE 3360961791) )
NIL)
(BR0-10478 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8961)
(RIGHT CPLX0-6946)
(:CREATOR |martin|)
(:CREATION-DATE 3360961934) )
NIL)
(BR0-10479 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8962)
(RIGHT CPLX0-6947)
(:CREATOR |martin|)
(:CREATION-DATE 3360962045) )
NIL)
(BR0-10480 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8963)
(RIGHT CPLX0-6948)
(:CREATOR |martin|)
(:CREATION-DATE 3360962100) )
NIL)
(BR0-10481 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8964)
(RIGHT CPLX0-6949)
(:CREATOR |martin|)
(:CREATION-DATE 3360962136) )
NIL)
(BR0-10482 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8965)
(RIGHT CPLX0-6950)
(:CREATOR |martin|)
(:CREATION-DATE 3360962185) )
NIL)
(BR0-10483 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8966)
(RIGHT CPLX0-6951)
(:CREATOR |martin|)
(:CREATION-DATE 3360962261) )
NIL)
(BR0-10484 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8967)
(RIGHT CPLX0-6952)
(:CREATOR |martin|)
(:CREATION-DATE 3360962324) )
NIL)
(BR0-10485 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8968)
(RIGHT CPLX0-6958)
(:CREATOR |martin|)
(:CREATION-DATE 3360962377) )
NIL)
(BR0-10486 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8969)
(RIGHT CPLX0-7133)
(:CREATOR |martin|)
(:CREATION-DATE 3360962435) )
NIL)
(BR0-10487 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8970)
(RIGHT CPLX0-6957)
(:CREATOR |martin|)
(:CREATION-DATE 3360962472) )
NIL)
(BR0-10488 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8971)
(RIGHT CPLX0-6956)
(:CREATOR |martin|)
(:CREATION-DATE 3360962545) )
NIL)
(BR0-10489 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8972)
(RIGHT CPLX0-6955)
(:CREATOR |martin|)
(:CREATION-DATE 3360962580) )
NIL)
(BR0-10490 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8973)
(RIGHT CPLX0-6954)
(:CREATOR |martin|)
(:CREATION-DATE 3360962608) )
NIL)
(BR0-10491 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8974)
(RIGHT CPLX0-6953)
(:CREATOR |martin|)
(:CREATION-DATE 3360962659) )
NIL)
(BR0-10492 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8975)
(RIGHT CPLX0-6961)
(:CREATOR |martin|)
(:CREATION-DATE 3360962725) )
NIL)
(BR0-10493 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8976)
(RIGHT CPLX0-6960)
(:CREATOR |martin|)
(:CREATION-DATE 3360962760) )
NIL)
(BR0-10494 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8977)
(RIGHT CPLX0-6959)
(:CREATOR |martin|)
(:CREATION-DATE 3360962800) )
NIL)
(BR0-10495 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8978)
(RIGHT CPLX0-6969)
(:CREATOR |martin|)
(:CREATION-DATE 3360963500) )
NIL)
(BR0-10496 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8979)
(RIGHT CPLX0-6970)
(:CREATOR |martin|)
(:CREATION-DATE 3360963533) )
NIL)
(BR0-10497 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8980)
(RIGHT CPLX0-6968)
(:CREATOR |martin|)
(:CREATION-DATE 3360963574) )
NIL)
(BR0-10498 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8981)
(RIGHT CPLX0-6966)
(:CREATOR |martin|)
(:CREATION-DATE 3360963621) )
NIL)
(BR0-10499 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8982)
(RIGHT CPLX0-6965)
(:CREATOR |martin|)
(:CREATION-DATE 3360963668) )
NIL)
(BR0-10500 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8983)
(RIGHT CPLX0-7042)
(:CREATOR |martin|)
(:CREATION-DATE 3360963726) )
NIL)
(BR0-10501 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8984)
(RIGHT CPLX0-6980)
(:CREATOR |martin|)
(:CREATION-DATE 3360963765) )
NIL)
(BR0-10502 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8985)
(RIGHT CPLX0-6979)
(:CREATOR |martin|)
(:CREATION-DATE 3360963832) )
NIL)
(BR0-10503 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8986)
(RIGHT CPLX0-6977)
(:CREATOR |martin|)
(:CREATION-DATE 3360963875) )
NIL)
(BR0-10504 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8987)
(RIGHT CPLX0-6976)
(:CREATOR |martin|)
(:CREATION-DATE 3360963914) )
NIL)
(BR0-10505 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8988)
(RIGHT CPLX0-6974)
(:CREATOR |martin|)
(:CREATION-DATE 3360963946) )
NIL)
(BR0-10506 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8989)
(RIGHT CPLX0-6973)
(:CREATOR |martin|)
(:CREATION-DATE 3360963991) )
NIL)
(BR0-10507 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8990)
(RIGHT CPLX0-7067)
(:CREATOR |martin|)
(:CREATION-DATE 3360964082) )
NIL)
(BR0-10508 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8991)
(RIGHT CPLX0-7051)
(:CREATOR |martin|)
(:CREATION-DATE 3360964117) )
NIL)
(BR0-10509 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8992)
(RIGHT CPLX0-7050)
(:CREATOR |martin|)
(:CREATION-DATE 3360964153) )
NIL)
(BR0-10510 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8993)
(RIGHT CPLX0-7098)
(:CREATOR |martin|)
(:CREATION-DATE 3360964253) )
NIL)
(BR0-10511 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8994)
(RIGHT CPLX0-7091)
(:CREATOR |martin|)
(:CREATION-DATE 3360964290) )
NIL)
(BR0-10512 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8995)
(RIGHT CPLX0-7024)
(:CREATOR |martin|)
(:CREATION-DATE 3360964323) )
NIL)
(BR0-10513 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8996)
(RIGHT CPLX0-7020)
(:CREATOR |martin|)
(:CREATION-DATE 3360964359) )
NIL)
(BR0-10514 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8997)
(RIGHT CPLX0-7015)
(:CREATOR |martin|)
(:CREATION-DATE 3360964393) )
NIL)
(BR0-10515 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8998)
(RIGHT CPLX0-6984)
(:CREATOR |martin|)
(:CREATION-DATE 3360964429) )
NIL)
(BR0-10516 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8999)
(RIGHT CPLX0-6983)
(:CREATOR |martin|)
(:CREATION-DATE 3360964462) )
NIL)
(BR0-10517 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9000)
(RIGHT CPLX0-7077)
(:CREATOR |martin|)
(:CREATION-DATE 3360964496) )
NIL)
(BR0-10518 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9001)
(RIGHT CPLX0-7070)
(:CREATOR |martin|)
(:CREATION-DATE 3360964534) )
NIL)
(BR0-10519 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9002)
(RIGHT CPLX0-7080)
(:CREATOR |martin|)
(:CREATION-DATE 3360964616) )
NIL)
(BR0-10520 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9003)
(RIGHT CPLX0-7079)
(:CREATOR |martin|)
(:CREATION-DATE 3360964646) )
NIL)
(BR0-10521 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9004)
(RIGHT CPLX0-7078)
(:CREATOR |martin|)
(:CREATION-DATE 3360964704) )
NIL)
(BR0-10522 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9005)
(RIGHT CPLX0-7143)
(:CREATOR |martin|)
(:CREATION-DATE 3360964733) )
NIL)
(BR0-10523 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9007)
(RIGHT CPLX0-7144)
(:CREATOR |asantos|)
(:CREATION-DATE 3361129452) )
NIL)
(BR0-10524 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9008)
(RIGHT CPLX0-7154)
(:CREATOR |asantos|)
(:CREATION-DATE 3361129882) )
NIL)
(BR0-10525 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9009)
(RIGHT CPLX0-7155)
(:CREATOR |asantos|)
(:CREATION-DATE 3361193736) )
NIL)
(BR0-10526 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9010)
(RIGHT CPLX0-7156)
(:CREATOR |asantos|)
(:CREATION-DATE 3361193815) )
NIL)
(BR0-10527 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9011)
(RIGHT CPLX0-7157)
(:CREATOR |asantos|)
(:CREATION-DATE 3361193875) )
NIL)
(BR0-10528 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9012)
(RIGHT CPLX0-7158)
(:CREATOR |asantos|)
(:CREATION-DATE 3361193998) )
NIL)
(BR0-10529 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9013)
(RIGHT CPLX0-7159)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194029) )
NIL)
(BR0-10530 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9014)
(RIGHT CPLX0-7160)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194345) )
NIL)
(BR0-10531 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9015)
(RIGHT CPLX0-7161)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194394) )
NIL)
(BR0-10532 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9016)
(RIGHT CPLX0-7169)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194524) )
NIL)
(BR0-10533 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9018)
(RIGHT CPLX0-7170)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194574) )
NIL)
(BR0-10534 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9019)
(RIGHT CPLX0-7162)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194626) )
NIL)
(BR0-10535 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9020)
(RIGHT CPLX0-7163)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194743) )
NIL)
(BR0-10536 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9021)
(RIGHT CPLX0-7164)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194792) )
NIL)
(BR0-10537 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9022)
(RIGHT CPLX0-7165)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194837) )
NIL)
(BR0-10538 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9023)
(RIGHT CPLX0-7166)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194877) )
NIL)
(BR0-10539 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9024)
(RIGHT CPLX0-7167)
(:CREATOR |asantos|)
(:CREATION-DATE 3361194992) )
NIL)
(BR0-10540 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9025)
(RIGHT CPLX0-7168)
(:CREATOR |asantos|)
(:CREATION-DATE 3361195033) )
NIL)
(BR0-10541 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9026)
(RIGHT CPLX0-7178)
(:CREATOR |asantos|)
(:CREATION-DATE 3361196713) )
NIL)
(BR0-10542 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-9027)
(RIGHT CPLX0-7179)
(:CREATOR |asantos|)
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"This site was determined by computational searches and its inducibility analyzed by Northern analysis in a variety of lexA backgrounds.
The sequence of the site is as follows: CTGGATAAAATTACAG, and its absolute position is 2194478.5.
We have given the absolute position in the genome of E. coli of this site instead of the central position since the +1 of the transcription initiation has not yet been determined |CITS:[ 10760155]|.
")))
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(:CREATION-DATE 3213469922)
(:CREATOR |sgama|) )
NIL)
(BR0-1102 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(RIGHT CPLX0-5460)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3220041393) )
NIL)
(BR0-1103 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3220041473) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3220637921) )
NIL)
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(:CREATION-DATE 3214840398)
(:CREATOR |sgama|) )
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3220880725) )
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(:CREATION-DATE 3214840398)
(:CREATOR |sgama|) )
NIL)
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(INHIBITORS CPLX0-4177 CITATIONS "[98233760]" "11101675" "15659676")))
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(:CREATOR |sgama|)
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NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3221237348) )
NIL)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3221237351) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATION-DATE 3215804518)
(:CREATOR |sgama|) )
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATION-DATE 3216067107)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5211 CITATIONS) (INHIBITORS CPLX0-5211 COMMENT)))
(BR0-1182 NIL (
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(:CREATION-DATE 3216067107)
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((INHIBITORS CPLX0-5211 CITATIONS) (INHIBITORS CPLX0-5211 COMMENT)))
(BR0-1183 NIL (
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(:CREATION-DATE 3216067107)
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((INHIBITORS CPLX0-5210 CITATIONS) (INHIBITORS CPLX0-5210 COMMENT)))
(BR0-1184 NIL (
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(:CREATION-DATE 3216067107)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4171 CITATIONS) (ACTIVATORS CPLX0-4171 COMMENT)))
(BR0-1185 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1123 RNAPS-CPLX)
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(ACTIVATORS CPLX0-4171)
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(:CREATION-DATE 3216067107)
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((ACTIVATORS CPLX0-4171 CITATIONS) (ACTIVATORS CPLX0-4171 COMMENT)))
(BR0-1186 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3216067107)
(:CREATOR |sgama|) )
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(BR0-1187 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-1125)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3216408222)
(:CREATOR |sgama|) )
NIL)
(BR0-1188 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-981)
(RIGHT CPLX0-5452)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3221594686) )
NIL)
(BR0-12 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-11)
(RIGHT CPLX0-5668)
(:CREATOR |asantos|)
(:CREATION-DATE 3338668939) )
NIL)
(BR0-1201 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-1162)
(RIGHT CPLX0-6887)
(OFFICIAL-EC? T)
(:CREATION-DATE 3217096357)
(:CREATOR |sgama|) )
NIL)
(BR0-1202 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-1163)
(RIGHT CPLX0-6886)
(ACTIVATORS CPLX0-4022 CPLX0-4023 CPLX0-4024 CPLX0-4025 CPLX0-4062 CPLX0-4063
CPLX0-4064)
(OFFICIAL-EC? T)
(:CREATION-DATE 3217096357)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4064 CITATIONS "21999255")
(ACTIVATORS CPLX0-4063 CITATIONS "21999255")
(ACTIVATORS CPLX0-4062 CITATIONS "21999255")
(ACTIVATORS CPLX0-4025 CITATIONS "21999255")
(ACTIVATORS CPLX0-4025 COMMENT
"ArgR enhances expression from astCp2 promoter but is not essential for its expression.")
(ACTIVATORS CPLX0-4024 CITATIONS "21999255")
(ACTIVATORS CPLX0-4024 COMMENT
"ArgR enhances expression from astCp2 promoter but is not essential for its expression.")
(ACTIVATORS CPLX0-4023 CITATIONS "21999255")
(ACTIVATORS CPLX0-4023 COMMENT
"ArgR enhances expression from astCp2 promoter but is not essential for its expression.")
(ACTIVATORS CPLX0-4022 CITATIONS "21999255")
(ACTIVATORS CPLX0-4022 COMMENT
"ArgR enhances expression from astCp2 promoter but is not essential for its expression.")))
(BR0-1203 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-1164)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3217096357)
(:CREATOR |sgama|) )
NIL)
(BR0-1204 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-1001)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3221840481) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-1002)
(RIGHT CPLX0-5450)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3221847416) )
NIL)
(BR0-1221 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1181)
(RIGHT CPLX0-6884)
(OFFICIAL-EC? T)
(:CREATION-DATE 3219587926)
(:CREATOR |sgama|) )
NIL)
(BR0-1222 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1182)
(RIGHT CPLX0-6883)
(INHIBITORS CPLX0-4099)
(OFFICIAL-EC? T)
(:CREATION-DATE 3219785458)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4099 COMMENT) (INHIBITORS CPLX0-4099 CITATIONS "20553180")))
(BR0-1241 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-1201)
(RIGHT CPLX0-6882)
(ACTIVATORS CPLX0-5621 CPLX0-5649)
(OFFICIAL-EC? T)
(:CREATION-DATE 3221504949)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5621 CITATIONS "10542180") (ACTIVATORS CPLX0-5621 COMMENT)
(ACTIVATORS CPLX0-5649 CITATIONS "10542180")))
(BR0-1242 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-6 BS0-1021)
(RIGHT CPLX0-5449)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222612372) )
NIL)
(BR0-1243 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1022)
(RIGHT CPLX0-5448)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222612525) )
NIL)
(BR0-1244 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-6 BS0-1023)
(RIGHT CPLX0-5447)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222617831) )
NIL)
(BR0-1261 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-1221)
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(BASAL-TRANSCRIPTION-VALUE 95187304)
(OFFICIAL-EC? T)
(:CREATION-DATE 3221595417)
(ACTIVATORS CPLX0-5452)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5452 COMMENT)
(ACTIVATORS CPLX0-5452 CITATIONS "[97302968]" "[97302967]")))
(BR0-1262 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-1222)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3221595417)
(:CREATOR |sgama|) )
NIL)
(BR0-1263 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM00564)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3221595417)
(:CREATOR |sgama|) )
NIL)
(BR0-1264 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00565)
(RIGHT CPLX0-6878)
(OFFICIAL-EC? T)
(:CREATION-DATE 3221595417)
(:CREATOR |sgama|) )
NIL)
(BR0-1265 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-1041)
(RIGHT CPLX0-5446)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222784115) )
NIL)
(BR0-1266 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00969 BS0-1042)
(RIGHT CPLX0-5445)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222784117) )
NIL)
(BR0-1267 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-6 BS0-1061)
(RIGHT CPLX0-5444)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3222805007) )
NIL)
(BR0-1268 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-1062)
(RIGHT CPLX0-5443)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3223145691) )
NIL)
(BR0-1269 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01896 BS0-1063)
(RIGHT CPLX0-5442)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3223145837) )
NIL)
(BR0-1270 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01896 BS0-1064)
(RIGHT CPLX0-5441)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3223146000) )
NIL)
(BR0-1272 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-1066)
(RIGHT CPLX0-5440)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3223324850) )
NIL)
(BR0-1273 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT BS0-1065 PD00197)
(RIGHT CPLX0-5439)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3223324893) )
NIL)
(BR0-1281 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00138 RNAPS-CPLX)
(RIGHT CPLX0-6877)
(OFFICIAL-EC? T)
(:CREATION-DATE 3222546402)
(ACTIVATORS CPLX0-5655 CPLX0-4626)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4626 CITATIONS)
(ACTIVATORS CPLX0-5655 CITATIONS "8626281") (ACTIVATORS CPLX0-5655 COMMENT)
(ACTIVATORS CPLX0-4626 COMMENT
"AppY protein is also involved in anaerobic induction of the hya operon, which encodes hydrogenase 1 and is located immediately upstream from the appCBA operon. AppY protein regulates AppA synthesis by activating transcription from appCp promoter. Furthermore, the appY gene might be autoregulated.
Genetic analysis of the appCp promoter region indicates that the presence of sequences upstream from the -10 region are required for activation of the appCp promoter by AppY protein and anaerobiosis, suggesting that this region has an AppY binding site.")))
(BR0-1282 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1282)
(RIGHT CPLX0-6876)
(OFFICIAL-EC? T)
(:CREATION-DATE 3222546402)
(INHIBITORS CPLX0-5448 CPLX0-5449)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5449 COMMENT)
(INHIBITORS CPLX0-5449 CITATIONS "[98125743]")
(INHIBITORS CPLX0-5448 CITATIONS "[98125743]")
(INHIBITORS CPLX0-5448 COMMENT "
")))
(BR0-1283 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00436 BS0-1081)
(RIGHT CPLX0-5438)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3224353350) )
NIL)
(BR0-13 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00214 BS0-8)
(RIGHT CPLX0-5669)
(:CREATOR |asantos|)
(:CREATION-DATE 3338740037) )
NIL)
(BR0-1301 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1283)
(RIGHT CPLX0-6875)
(INHIBITORS CPLX0-4206)
(OFFICIAL-EC? T)
(:CREATION-DATE 3222784149)
(ACTIVATORS CPLX0-5446)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5446 CITATIONS "[20545450]")))
(BR0-1302 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1284)
(RIGHT CPLX0-6874)
(OFFICIAL-EC? T)
(:CREATION-DATE 3222784149)
(ACTIVATORS CPLX0-5664 CPLX0-5445)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5664 CITATIONS "9044285")
(ACTIVATORS CPLX0-5664 COMMENT
"Based on moaA gel shift assays and moaA-lacZ operon fusions , molybdate had no effect on the ModE binding to the moaAp2 |CITS: [9044285]|.")
(ACTIVATORS CPLX0-5445 COMMENT)
(ACTIVATORS CPLX0-5445 CITATIONS "[20545450]")))
(BR0-1303 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-1121)
(RIGHT CPLX0-4661)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227021048) )
NIL)
(BR0-1304 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1122)
(RIGHT CPLX0-4665)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227036924) )
NIL)
(BR0-1305 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1123)
(RIGHT CPLX0-4664)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227036966) )
NIL)
(BR0-1306 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1124)
(RIGHT CPLX0-4663)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227037015) )
NIL)
(BR0-1307 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1125)
(RIGHT CPLX0-4659)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227037081) )
NIL)
(BR0-1308 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-1126)
(RIGHT CPLX0-4658)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3227037126) )
NIL)
(BR0-1321 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-1301)
(RIGHT CPLX0-6873)
(OFFICIAL-EC? T)
(:CREATION-DATE 3223147044)
(INHIBITORS CPLX0-5248 CPLX0-5250 CPLX0-5249 CPLX0-5304 CPLX0-5305 CPLX0-5306
CPLX0-5307 CPLX0-5308 CPLX0-5442)
(ACTIVATORS CPLX0-5308 CPLX0-5307 CPLX0-5309 CPLX0-5443)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5443 COMMENT) (INHIBITORS CPLX0-5248 CITATIONS "15252051")
(INHIBITORS CPLX0-5248 COMMENT
"The addition of CRP decreased the ArcA-specific protection on binding sites -51.5 and -97.5, and the CRP-specific protection was decreased, implying that ArcA and CRP compete with each other for the binding to the ptsGp1 promoter.")
(INHIBITORS CPLX0-5250 CITATIONS "15252051") (INHIBITORS CPLX0-5250 COMMENT)
(INHIBITORS CPLX0-5249 CITATIONS "15252051")
(INHIBITORS CPLX0-5249 COMMENT
"The addition of CRP decreased the ArcA-specific protection on binding sites -51.5 and -97.5, and the CRP-specific protection was decreased, implying that ArcA and CRP compete with each other for the binding to the ptsGp1 promoter.")
(INHIBITORS CPLX0-5308 COMMENT
"Fis binding to site I and II can co-activate ptsGp1 transcription with CRP.")
(ACTIVATORS CPLX0-5308 CITATIONS "12588863")
(ACTIVATORS CPLX0-5308 COMMENT
"Fis binding to site I and II can co-activate ptsGp1 transcription with CRP.")
(INHIBITORS CPLX0-5442 COMMENT
"Mlc showed better repression of ptsGp1 in the presence of Fis.")
(INHIBITORS CPLX0-5304 CITATIONS "12588863") (INHIBITORS CPLX0-5304 COMMENT)
(INHIBITORS CPLX0-5305 CITATIONS "12588863") (INHIBITORS CPLX0-5305 COMMENT)
(INHIBITORS CPLX0-5306 CITATIONS "12588863") (INHIBITORS CPLX0-5306 COMMENT)
(INHIBITORS CPLX0-5307 CITATIONS "12588863")
(INHIBITORS CPLX0-5307 COMMENT
"Fis binding to site I and II can coativate ptsGp1 transcription with CRP.")
(ACTIVATORS CPLX0-5307 CITATIONS "12588863")
(ACTIVATORS CPLX0-5307 COMMENT
"Fis binding to site I and II can coativate ptsGp1 transcription with CRP.")
(INHIBITORS CPLX0-5308 CITATIONS "12588863") (ACTIVATORS CPLX0-5309 COMMENT)
(ACTIVATORS CPLX0-5309 CITATIONS "12588863")
(INHIBITORS CPLX0-5442 CITATIONS "[99000512]")
(ACTIVATORS CPLX0-5443 CITATIONS "[99000512]" "15520470")))
(BR0-1322 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(ACTIVATORS CPLX0-5243 COMMENT
"It is suggested that ArcA relieves the repression mediated by the far upstream FNR dimer by competing for occupation of the -93 site of the yfiD promoter.")
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(INHIBITORS CPLX0-5241 COMMENT
"PdhR is a weak repressor of yfiD expression.")
(INHIBITORS CPLX0-5241 CITATIONS "11932447")
(INHIBITORS CPLX0-5439 CITATIONS "99000517" "21106004" "11932447"
"15988767")
(ACTIVATORS CPLX0-5439 CITATIONS "99000517" "21106004" "11932447"
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(INHIBITORS CPLX0-5440 CITATIONS "21106004" "99000517" "11932447")))
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"Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the
efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
")
(ACTIVATORS CPLX0-4095 CITATIONS "21475775")
(ACTIVATORS CPLX0-4098 CITATIONS "21475775")
(ACTIVATORS CPLX0-4102 CITATIONS "21475775")
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Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream r egions; as a result, they help the
efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
")
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"Paradoxically, even though H-NS is an inhibitor it drives the bound RNA
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")
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"Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
In a DNase I footprinting analysis of the rrnEp region, several regions of Lrp protection can be observed extending from position -100 upstream into the downstream transcription region. Specific central positions for Lrp transcriptional regulator were not determined. It is important to note that the same sequence is strongly protected by H-NS-DNA complex |CITS: [16238633]|.")
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Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the
efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
")
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"Paradoxically, even though H-NS is an inhibitor it drives the bound RNA
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")
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"Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
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efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
")
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"Paradoxically, even though H-NS is an inhibitor it drives the bound RNA
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")
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Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the
efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
")
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"Paradoxically, even though H-NS is an inhibitor it drives the bound RNA
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")
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(:CREATOR |sgama|) )
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(:CREATOR |sgama|) )
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(:CREATOR |sgama|) )
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(:CREATOR |sgama|) )
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(:CREATOR |sgama|)
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")
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(INHIBITORS CPLX0-4641 COMMENT
"The regulatory effect of MetJ on the promoter metKp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4641 CITATIONS "11448880")
(INHIBITORS CPLX0-4511 CITATIONS "11448880")))
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"The regulatory effect of Fur on the promoter fhuE is as of yet not known. However, we assigned a negative effect to this regulatory interaction based on two facts: (1) the protein binding site is 16 bp downstream the transcription start site; and (2) Fur is known to act, so far without exceptions, as a negative regulator.")))
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")
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")))
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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"By making use of micro arrays analysis it was concluded that FNR activates xdhA gene expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this gene |CITS: [12754220]|.")))
(BR0-3081 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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((INHIBITORS CPLX0-4289 COMMENT
"Under anaerobiosis, FNR repress cydAB operon expression |CITS: [12754220]|.")
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(INHIBITORS CPLX0-4007 CITATIONS "20453462" "12754220" "16140031")
(INHIBITORS CPLX0-4006 CITATIONS "20572078")
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"Hns most strongly represses cydAp4 promoter and has a moderate effect on cydAp1, cydAp2 and cydAp3 promoters.
Hns regulates the cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.")
(INHIBITORS CPLX0-4289 CITATIONS "20453462" "12754220" "16140031")))
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((INHIBITORS CPLX0-4289 COMMENT
"Under anaerobiosis, FNR repress cydAB operon expression |CITS: [12754220]|.")
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"Hns most strongly represses cydAp4 promoter and has a moderate effect on cydAp1, cydAp2 and cydAp3 promoters.
Hns regulates the cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.")
(INHIBITORS CPLX0-4289 CITATIONS "20453462" "12754220" "16140031")))
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(:CREATION-DATE 3273259774) )
NIL)
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NIL)
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NIL)
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(:CREATION-DATE 3273499051) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3273499132) )
NIL)
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(:CREATOR |sgama|)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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(LEFT PM00376)
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NIL)
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NIL)
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NIL)
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(LEFT PD00288 BS0-2442)
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(:CREATOR |sgama|)
(:CREATION-DATE 3274816239) )
NIL)
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((ACTIVATORS CPLX0-4046 CITATIONS "12617754")
(ACTIVATORS CPLX0-4045 CITATIONS "12617754")
(INHIBITORS CPLX0-4060 COMMENT
"The regulatory effect of IHF on the promoter ygjGp is not known.")
(INHIBITORS CPLX0-4060 CITATIONS "12617754")
(ACTIVATORS CPLX0-4046 COMMENT
"The regulatory effect of NtrC on the promoter ygjGp is as yet not known.
However, we assigned a negative positive to this regulatory interaction based on the facts that NtrC activates sigma54 promoters and the promoter ygjGp is one of them.")
(ACTIVATORS CPLX0-4045 COMMENT
"The regulatory effect of NtrC on the promoter ygjGp is as yet not known.
However, we assigned a negative positive to this regulatory interaction
based on the facts that NtrC activates sigma54 promoters and the promoter ygjGp is one of them.")
(INHIBITORS CPLX0-4061 COMMENT
"The regulatory effect of Fis on the promoter ygjGp is not known.
")
(INHIBITORS CPLX0-4061 CITATIONS "12617754")))
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(:CREATOR |martin|)
(:CREATION-DATE 3339864454) )
NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3277576432) )
NIL)
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NIL)
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(:CREATOR |martin|)
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NIL)
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NIL)
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NIL)
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NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-3582)
(RIGHT CPLX0-6735)
(INHIBITORS CPLX0-4079 CPLX0-4080)
(:CREATOR |sgama|)
(:CREATION-DATE 3277584455) )
((INHIBITORS CPLX0-4080 CITATIONS "20553180")
(INHIBITORS CPLX0-4079 CITATIONS "20553180")))
(BR0-3491 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00009 BS0-2549)
(RIGHT CPLX0-4080)
(:CREATOR |sgama|)
(:CREATION-DATE 3277584576) )
NIL)
(BR0-3492 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00009 BS0-2550)
(RIGHT CPLX0-4079)
(:CREATOR |sgama|)
(:CREATION-DATE 3277584635) )
NIL)
(BR0-3493 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2551)
(RIGHT CPLX0-4078)
(:CREATOR |martin|)
(:CREATION-DATE 3277644956) )
NIL)
(BR0-3494 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2552)
(RIGHT CPLX0-4081)
(:CREATOR |martin|)
(:CREATION-DATE 3277645031) )
NIL)
(BR0-3495 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2553)
(RIGHT CPLX0-4086)
(:CREATOR |martin|)
(:CREATION-DATE 3277645106) )
NIL)
(BR0-3496 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2554)
(RIGHT CPLX0-4085)
(:CREATOR |martin|)
(:CREATION-DATE 3277645219) )
NIL)
(BR0-3497 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2555)
(RIGHT CPLX0-4084)
(:CREATOR |martin|)
(:CREATION-DATE 3277645269) )
NIL)
(BR0-3498 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2556)
(RIGHT CPLX0-4083)
(:CREATOR |martin|)
(:CREATION-DATE 3277646139) )
NIL)
(BR0-3499 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2557)
(RIGHT CPLX0-4082)
(:CREATOR |martin|)
(:CREATION-DATE 3277646177) )
NIL)
(BR0-35 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-21)
(RIGHT CPLX0-5644)
(:CREATOR |asantos|)
(:CREATION-DATE 3340052353) )
NIL)
(BR0-3500 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2558)
(RIGHT CPLX0-4554)
(:CREATOR |martin|)
(:CREATION-DATE 3277646233) )
NIL)
(BR0-3501 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2559)
(RIGHT CPLX0-4551)
(:CREATOR |martin|)
(:CREATION-DATE 3277646275) )
NIL)
(BR0-3502 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2560)
(RIGHT CPLX0-4550)
(:CREATOR |martin|)
(:CREATION-DATE 3277646371) )
NIL)
(BR0-3506 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2564)
(RIGHT CPLX0-4557)
(:CREATOR |martin|)
(:CREATION-DATE 3277647579) )
NIL)
(BR0-3507 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2565)
(RIGHT CPLX0-4553)
(:CREATOR |martin|)
(:CREATION-DATE 3277647616) )
NIL)
(BR0-3508 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2566)
(RIGHT CPLX0-4552)
(:CREATOR |martin|)
(:CREATION-DATE 3277647650) )
NIL)
(BR0-3510 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2568)
(RIGHT CPLX0-4531)
(:CREATOR |martin|)
(:CREATION-DATE 3277648839) )
NIL)
(BR0-3511 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2569)
(RIGHT CPLX0-4530)
(:CREATOR |martin|)
(:CREATION-DATE 3277648880) )
NIL)
(BR0-3512 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2570)
(RIGHT CPLX0-4529)
(:CREATOR |martin|)
(:CREATION-DATE 3277648929) )
NIL)
(BR0-3513 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2571)
(RIGHT CPLX0-4528)
(:CREATOR |martin|)
(:CREATION-DATE 3277649031) )
NIL)
(BR0-3521 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-3601)
(RIGHT CPLX0-6734)
(INHIBITORS CPLX0-5135 CPLX0-4576)
(:CREATOR |sgama|)
(:CREATION-DATE 3277663268) )
((INHIBITORS CPLX0-5135 COMMENT)
(INHIBITORS CPLX0-5135 CITATIONS "20553180" "11917098")
(INHIBITORS CPLX0-4576 CITATIONS "20553180" "11917098")))
(BR0-3522 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00009 BS0-2572)
(RIGHT CPLX0-4576)
(:CREATOR |sgama|)
(:CREATION-DATE 3277663427) )
NIL)
(BR0-3524 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-3603)
(RIGHT CPLX0-6733)
(INHIBITORS CPLX0-4099)
(:CREATOR |sgama|)
(:CREATION-DATE 3277666751) )
((INHIBITORS CPLX0-4099 CITATIONS "20553180")))
(BR0-3541 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3621)
(RIGHT CPLX0-6732)
(:CREATOR |sgama|)
(:CREATION-DATE 3278097448) )
NIL)
(BR0-3542 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3622)
(RIGHT CPLX0-6731)
(:CREATOR |sgama|)
(:CREATION-DATE 3278097921) )
NIL)
(BR0-3543 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3623)
(RIGHT CPLX0-6730)
(INHIBITORS CPLX0-5192)
(:CREATOR |sgama|)
(:CREATION-DATE 3278168174) )
((INHIBITORS CPLX0-5192 CITATIONS "11953442")))
(BR0-3544 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3624)
(RIGHT CPLX0-6729)
(INHIBITORS CPLX0-5190)
(:CREATOR |sgama|)
(:CREATION-DATE 3278168545) )
((INHIBITORS CPLX0-5190 CITATIONS "11953442")
(INHIBITORS CPLX0-5190 COMMENT
"This is an unusual site because it is 151 base pairs downstream of psdp promoter.")))
(BR0-3545 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3625)
(RIGHT CPLX0-6728)
(ACTIVATORS CPLX0-5191)
(:CREATOR |sgama|)
(:CREATION-DATE 3278169021) )
((ACTIVATORS CPLX0-5191 CITATIONS "11953442")))
(BR0-3546 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3626)
(RIGHT CPLX0-6727)
(:CREATOR |sgama|)
(:CREATION-DATE 3278169339) )
NIL)
(BR0-3561 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM0-3663)
(RIGHT CPLX0-6726)
(:CREATOR |sgama|)
(:CREATION-DATE 3278259215) )
NIL)
(BR0-3562 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3664)
(RIGHT CPLX0-6725)
(:CREATOR |sgama|)
(:CREATION-DATE 3278260505) )
NIL)
(BR0-3563 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3665)
(RIGHT CPLX0-6724)
(:CREATOR |sgama|)
(:CREATION-DATE 3278260804) )
NIL)
(BR0-3564 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3681)
(RIGHT CPLX0-6723)
(:CREATOR |sgama|)
(:CREATION-DATE 3278266825) )
NIL)
(BR0-3565 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-3684)
(RIGHT CPLX0-6722)
(:CREATOR |sgama|)
(:CREATION-DATE 3278268020) )
NIL)
(BR0-3581 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-UHPA BS0-2581)
(RIGHT CPLX0-4494)
(:CREATOR |martin|)
(:CREATION-DATE 3278691318) )
NIL)
(BR0-3582 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7072-MONOMER BS0-2583)
(RIGHT CPLX0-4493)
(:CREATOR |sgama|)
(:CREATION-DATE 3278706945) )
NIL)
(BR0-3601 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2601)
(RIGHT CPLX0-5359)
(:CREATOR |martin|)
(:CREATION-DATE 3278777931) )
NIL)
(BR0-3602 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2602)
(RIGHT CPLX0-5358)
(:CREATOR |martin|)
(:CREATION-DATE 3278778312) )
NIL)
(BR0-3622 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00442)
(RIGHT CPLX0-6721)
(:CREATOR |martin|)
(:CREATION-DATE 3278860046) )
NIL)
(BR0-3641 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2641)
(RIGHT CPLX0-5357)
(:CREATOR |sgama|)
(:CREATION-DATE 3278944864) )
NIL)
(BR0-3642 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7072-MONOMER BS0-2642)
(RIGHT CPLX0-5356)
(:CREATOR |sgama|)
(:CREATION-DATE 3278945139) )
NIL)
(BR0-3643 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7072-MONOMER BS0-2643)
(RIGHT CPLX0-5355)
(:CREATOR |sgama|)
(:CREATION-DATE 3278945264) )
NIL)
(BR0-3662 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00667)
(RIGHT CPLX0-6720)
(:CREATOR |sgama|)
(:CREATION-DATE 3279306174) )
NIL)
(BR0-3663 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00649)
(RIGHT CPLX0-6719)
(:CREATOR |sgama|)
(:CREATION-DATE 3279307151) )
NIL)
(BR0-3664 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00650)
(RIGHT CPLX0-6718)
(:CREATOR |sgama|)
(:CREATION-DATE 3279307241) )
NIL)
(BR0-3665 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00651)
(RIGHT CPLX0-6717)
(:CREATOR |sgama|)
(:CREATION-DATE 3279307303) )
NIL)
(BR0-3666 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-3761)
(RIGHT CPLX0-6716)
(:CREATOR |sgama|)
(:CREATION-DATE 3279307533) )
NIL)
(BR0-3681 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3781)
(RIGHT CPLX0-6715)
(ACTIVATORS CPLX0-5354)
(:CREATOR |sgama|)
(:CREATION-DATE 3279548949) )
((ACTIVATORS CPLX0-5354 CITATIONS "20570538")))
(BR0-3682 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2661)
(RIGHT CPLX0-5354)
(:CREATOR |sgama|)
(:CREATION-DATE 3279554757) )
NIL)
(BR0-3701 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3802)
(RIGHT CPLX0-6713)
(ACTIVATORS CPLX0-6714 CPLX0-5153 CPLX0-5154)
(:CREATOR |sgama|)
(:CREATION-DATE 3279636603) )
((ACTIVATORS CPLX0-6714 CITATIONS) (ACTIVATORS CPLX0-6714 COMMENT)
(ACTIVATORS CPLX0-5153 CITATIONS) (ACTIVATORS CPLX0-5153 COMMENT)
(ACTIVATORS CPLX0-5154 CITATIONS "15805526")))
(BR0-3721 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3821)
(RIGHT CPLX0-6712)
(ACTIVATORS CPLX0-4634)
(:CREATOR |sgama|)
(:CREATION-DATE 3279636966) )
((ACTIVATORS CPLX0-4634 CITATIONS "20570538")))
(BR0-3722 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2681)
(RIGHT CPLX0-4634)
(:CREATOR |sgama|)
(:CREATION-DATE 3279637253) )
NIL)
(BR0-3723 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3822)
(RIGHT CPLX0-6711)
(ACTIVATORS CPLX0-4633)
(:CREATOR |sgama|)
(:CREATION-DATE 3279637499) )
((ACTIVATORS CPLX0-4633 CITATIONS "20570538")))
(BR0-3724 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2682)
(RIGHT CPLX0-4633)
(:CREATOR |sgama|)
(:CREATION-DATE 3279637632) )
NIL)
(BR0-3725 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3823)
(RIGHT CPLX0-6710)
(ACTIVATORS CPLX0-4632)
(:CREATOR |sgama|)
(:CREATION-DATE 3279638133) )
((ACTIVATORS CPLX0-4632 CITATIONS "20570538")))
(BR0-3726 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2683)
(RIGHT CPLX0-4632)
(:CREATOR |sgama|)
(:CREATION-DATE 3279638511) )
NIL)
(BR0-3741 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-3841)
(RIGHT CPLX0-6709)
(:CREATOR |martin|)
(:CREATION-DATE 3279894904) )
NIL)
(BR0-3742 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-3842)
(RIGHT CPLX0-6708)
(:CREATOR |martin|)
(:CREATION-DATE 3279897699) )
NIL)
(BR0-3743 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3843)
(RIGHT CPLX0-6707)
(:CREATOR |sgama|)
(:CREATION-DATE 3279897850) )
NIL)
(BR0-3744 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-3846)
(RIGHT CPLX0-6706)
(:CREATOR |sgama|)
(:CREATION-DATE 3279898468) )
NIL)
(BR0-3745 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-3847)
(RIGHT CPLX0-6705)
(ACTIVATORS CPLX0-5574 CPLX0-5605 CPLX0-5353)
(:CREATOR |sgama|)
(:CREATION-DATE 3279915494) )
((ACTIVATORS CPLX0-5574 CITATIONS "15699038")
(ACTIVATORS CPLX0-5574 COMMENT
"ArcA activates ycdG gene expression, although oxygen does not appear to regulate the gene . A putative ArcA binding site 112 bp upstream of this gene was identified, but the sequence of it was not showed |CITS: [15699038]|.")
(ACTIVATORS CPLX0-5605 CITATIONS "15883881")
(ACTIVATORS CPLX0-5605 COMMENT
"The sequence of this site is: ACTATGTCACGTGTTAA, and its absolute central position is 1073356. The distance with respect to the ATG of the translation start is -1270 |CITS:[15883881]|.
We have given the absolute central position in the genome of E. coli of these sites instead of the central position since the +1 of the transcription initiation has not yet been determined.")
(ACTIVATORS CPLX0-5353 CITATIONS "20570538")))
(BR0-3761 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS0-2701)
(RIGHT CPLX0-5353)
(:CREATOR |sgama|)
(:CREATION-DATE 3279987101) )
NIL)
(BR0-3781 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-1781 BS0-2721)
(RIGHT CPLX0-5352)
(:CREATOR |martin|)
(:CREATION-DATE 3280241336) )
NIL)
(BR0-3801 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-3921)
(RIGHT CPLX0-6704)
(INHIBITORS CPLX0-4309 CPLX0-4310)
(:CREATOR |sgama|)
(:CREATION-DATE 3282571661) )
((INHIBITORS CPLX0-4309 CITATIONS "11929525")
(INHIBITORS CPLX0-4309 COMMENT
"IHF binding to this site strongly represses acsP1 promoter and weakly represses nrfAp, a promoter that is overlapping and divergent to acsP1.")
(INHIBITORS CPLX0-4310 CITATIONS "11929525")
(INHIBITORS CPLX0-4310 COMMENT
"Fis binding to this site strongly represses acsP1 promoter and weakly represses nrfAp, a promoter that is overlapping and divergent to acsP1.")))
(BR0-3804 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2743)
(RIGHT CPLX0-4310)
(:CREATOR |sgama|)
(:CREATION-DATE 3282572830) )
NIL)
(BR0-3805 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-2744)
(RIGHT CPLX0-4309)
(:CREATOR |sgama|)
(:CREATION-DATE 3282572921) )
NIL)
(BR0-3806 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-3923)
(RIGHT CPLX0-6703)
(INHIBITORS CPLX0-4299 CPLX0-4300 CPLX0-4301 CPLX0-4307)
(ACTIVATORS CPLX0-4299 CPLX0-4311 CPLX0-4305)
(:CREATOR |sgama|)
(:CREATION-DATE 3282576073) )
((INHIBITORS CPLX0-4299 CITATIONS "14651625")
(INHIBITORS CPLX0-4299 COMMENT
"The regulatory effect of this IHF site is as yet not known.
")
(ACTIVATORS CPLX0-4299 CITATIONS "14651625")
(ACTIVATORS CPLX0-4299 COMMENT
"The regulatory effect of this IHF site is as yet not known.
")
(INHIBITORS CPLX0-4300 CITATIONS "14651625")
(INHIBITORS CPLX0-4300 COMMENT
"IHF binding to this site functions as anti-activator of CRP.
")
(INHIBITORS CPLX0-4301 CITATIONS "14651625")
(INHIBITORS CPLX0-4301 COMMENT
"Fis binding to this site functions as anti-activator of CRP.")
(INHIBITORS CPLX0-4307 CITATIONS "14651625")
(INHIBITORS CPLX0-4307 COMMENT
"Fis binding to this site functions as anti-activator of CRP.")
(ACTIVATORS CPLX0-4311 CITATIONS "12923087" "10894724")
(ACTIVATORS CPLX0-4311 COMMENT
"Activation of the acsp2 promoter absolutely requires a CRP site centered at position -69.5, while optimal expression requires an aditional site centered at position -122.5.")
(ACTIVATORS CPLX0-4305 CITATIONS "12923087" "10894724")
(ACTIVATORS CPLX0-4305 COMMENT
"Activation of the acsp2 promoter absolutely requires a CRP site centered at position -69.5, while optimal expression requires an additional site centered at positions -122.5.")))
(BR0-3807 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-2745)
(RIGHT CPLX0-4305)
(:CREATOR |sgama|)
(:CREATION-DATE 3282577624) )
NIL)
(BR0-3808 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-2746)
(RIGHT CPLX0-4311)
(:CREATOR |sgama|)
(:CREATION-DATE 3282577707) )
NIL)
(BR0-3809 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2747)
(RIGHT CPLX0-4307)
(:CREATOR |sgama|)
(:CREATION-DATE 3282590476) )
NIL)
(BR0-3810 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2748)
(RIGHT CPLX0-4301)
(:CREATOR |sgama|)
(:CREATION-DATE 3282590586) )
NIL)
(BR0-3811 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-2749)
(RIGHT CPLX0-4300)
(:CREATOR |sgama|)
(:CREATION-DATE 3282590970) )
NIL)
(BR0-3812 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-2750)
(RIGHT CPLX0-4299)
(:CREATOR |sgama|)
(:CREATION-DATE 3282591280) )
NIL)
(BR0-3822 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00490)
(RIGHT CPLX0-6702)
(ACTIVATORS CPLX0-5606)
(INHIBITORS CPLX0-4184 CPLX0-4186 CPLX0-4620 CPLX0-4617 CPLX0-4618 CPLX0-4619
CPLX0-4294)
(:CREATOR |sgama|)
(:CREATION-DATE 3282676094) )
((INHIBITORS CPLX0-4294 COMMENT) (ACTIVATORS CPLX0-5606 CITATIONS "15883881")
(ACTIVATORS CPLX0-5606 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it checked for the presence of its regulatory motif in the promoter region |CITS: [15883881]|.")
(INHIBITORS CPLX0-4294 CITATIONS "2419307" "16515535")
(INHIBITORS CPLX0-4184 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4184 CITATIONS "11448880" "16515535" "2419307")
(INHIBITORS CPLX0-4186 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4186 CITATIONS "11448880" "2419307")
(INHIBITORS CPLX0-4617 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4617 CITATIONS "11448880" "2419307")
(INHIBITORS CPLX0-4619 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4619 CITATIONS "11448880" "2419307")
(INHIBITORS CPLX0-4620 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4620 CITATIONS "11448880" "2419307")
(INHIBITORS CPLX0-4618 COMMENT
"The regulatory effect of MetJ on the promoter metBp is as yet not known. However, we assigned a negative effect
to this regulatory interaction based on two facts: the protein's binding site is very close to the promoter,
and MetJ is known to act, so far without exceptions, as a negative regulator.")
(INHIBITORS CPLX0-4618 CITATIONS "11448880" "2419307")))
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(:CREATOR |sgama|)
(:CREATION-DATE 3282917006) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATION-DATE 3284309015) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3338308745) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |martin|)
(:CREATION-DATE 3284474204) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00969 BS0-2801)
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(:CREATOR |martin|)
(:CREATION-DATE 3284740864) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-4102)
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(:CREATOR |martin|)
(:CREATION-DATE 3284742900) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-2821)
(RIGHT CPLX0-4088)
(:CREATOR |sgama|)
(:CREATION-DATE 3284746716) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2841)
(RIGHT CPLX0-5351)
(:CREATOR |sgama|)
(:CREATION-DATE 3284816716) )
NIL)
(BR0-3982 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2842)
(RIGHT CPLX0-5350)
(:CREATOR |sgama|)
(:CREATION-DATE 3284820201) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-2843)
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(:CREATOR |sgama|)
(:CREATION-DATE 3284822225) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS0-2844)
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(:CREATOR |sgama|)
(:CREATION-DATE 3284822336) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS0-2845)
(RIGHT CPLX0-5347)
(:CREATOR |sgama|)
(:CREATION-DATE 3284822473) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-2846)
(RIGHT CPLX0-5346)
(:CREATOR |sgama|)
(:CREATION-DATE 3284822549) )
NIL)
(BR0-3987 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-2847)
(RIGHT CPLX0-5345)
(:CREATOR |sgama|)
(:CREATION-DATE 3284822824) )
NIL)
(BR0-4 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-3)
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(:CREATOR |asantos|)
(:CREATION-DATE 3338668556) )
((INHIBITORS CPLX0-5668 CITATIONS "3037486")
(INHIBITORS CPLX0-5668 COMMENT
"The promoter region of the recN gene contained two 16 bp sequences, separated by 6 bp, that match the consensus sequence (SOS box) for binding LexA protein |CITS:[ 3037486]|.")
(INHIBITORS CPLX0-5667 CITATIONS "3037486")
(INHIBITORS CPLX0-5667 COMMENT
"The promoter region of the recN gene contained two 16 bp sequences, separated by 6 bp, that match the consensus sequence (SOS box) for binding LexA protein |CITS:[ 3037486]|.")))
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-2861)
(RIGHT CPLX0-4541)
(:CREATOR |martin|)
(:CREATION-DATE 3284836171) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00084 BS0-2862)
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(:CREATOR |martin|)
(:CREATION-DATE 3284902992) )
NIL)
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(:CREATOR |sgama|)
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(ACTIVATORS CPLX0-4562 CITATIONS "11292794") (ACTIVATORS CPLX0-4562 COMMENT)))
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(:CREATOR |sgama|)
(:CREATION-DATE 3285078970) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3285078998) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(RIGHT CPLX0-4564)
(:CREATOR |sgama|)
(:CREATION-DATE 3285079237) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01520 BS0-2901)
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(:CREATOR |sgama|)
(:CREATION-DATE 3285343628) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2902)
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(:CREATOR |martin|)
(:CREATION-DATE 3285423517) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2921)
(RIGHT CPLX0-4641)
(:CREATOR |martin|)
(:CREATION-DATE 3285435648) )
NIL)
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(LEFT MONOMER0-157 BS0-2922)
(RIGHT CPLX0-4646)
(:CREATOR |martin|)
(:CREATION-DATE 3285436219) )
NIL)
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(LEFT MONOMER0-157 BS0-2923)
(RIGHT CPLX0-4645)
(:CREATOR |martin|)
(:CREATION-DATE 3285436860) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2941)
(RIGHT CPLX0-4619)
(:CREATOR |martin|)
(:CREATION-DATE 3285437499) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2942)
(RIGHT CPLX0-4618)
(:CREATOR |martin|)
(:CREATION-DATE 3285437652) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2943)
(RIGHT CPLX0-4617)
(:CREATOR |martin|)
(:CREATION-DATE 3285438132) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2944)
(RIGHT CPLX0-4620)
(:CREATOR |martin|)
(:CREATION-DATE 3285438585) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2961)
(RIGHT CPLX0-4186)
(:CREATOR |martin|)
(:CREATION-DATE 3285438947) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2962)
(RIGHT CPLX0-4184)
(:CREATOR |martin|)
(:CREATION-DATE 3285439029) )
NIL)
(BR0-4103 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2963)
(RIGHT CPLX0-4183)
(:CREATOR |martin|)
(:CREATION-DATE 3285439663) )
NIL)
(BR0-4104 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2964)
(RIGHT CPLX0-4187)
(:CREATOR |martin|)
(:CREATION-DATE 3285439971) )
NIL)
(BR0-4105 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2965)
(RIGHT CPLX0-4191)
(:CREATOR |martin|)
(:CREATION-DATE 3285440325) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-157 BS0-2966)
(RIGHT CPLX0-4190)
(:CREATOR |martin|)
(:CREATION-DATE 3285440386) )
NIL)
(BR0-4108 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM00607)
(RIGHT CPLX0-6699)
(ACTIVATORS CPLX0-4188)
(:CREATOR |martin|)
(:CREATION-DATE 3285516369) )
((ACTIVATORS CPLX0-4188 CITATIONS "11555297")))
(BR0-4109 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD02198 BS0-2967)
(RIGHT CPLX0-4188)
(:CREATOR |martin|)
(:CREATION-DATE 3285516741) )
NIL)
(BR0-4110 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD02198 BS0-2968)
(RIGHT CPLX0-4164)
(:CREATOR |martin|)
(:CREATION-DATE 3285517337) )
NIL)
(BR0-4121 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4201)
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(ACTIVATORS CPLX0-5204)
(INHIBITORS CPLX0-5204)
(:CREATOR |sgama|)
(:CREATION-DATE 3285703976) )
((ACTIVATORS CPLX0-5204 CITATIONS "12367523" "11222606")
(ACTIVATORS CPLX0-5204 COMMENT
"Generally Fur binds to 19 bp in DNA, but in this case it binds to 25 bp upstream from entSp1 promoter.")
(INHIBITORS CPLX0-5204 COMMENT
"Generally Fur binds to 19 bp in DNA, but in this case it binds to 25 bp upstream from entSp1 promoter.")
(INHIBITORS CPLX0-5204 CITATIONS "12367523" "11222606")))
(BR0-4122 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4202)
(RIGHT CPLX0-6697)
(:CREATOR |sgama|)
(:CREATION-DATE 3285704204) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4203)
(RIGHT CPLX0-6696)
(:CREATOR |sgama|)
(:CREATION-DATE 3285706752) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4241 RNAPS-CPLX)
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(ACTIVATORS CPLX0-5344 CPLX0-4076 CPLX0-4077)
(:CREATOR |martin|)
(:CREATION-DATE 3286115319) )
((ACTIVATORS CPLX0-4076 COMMENT
"Lrp protected at multiple sites extending at least between positions -14 and -102 and the effects of cAMP-CRP and Lrp were additive.")
(ACTIVATORS CPLX0-4076 CITATIONS "9512707")
(ACTIVATORS CPLX0-4077 CITATIONS "11532138" "9512707")
(ACTIVATORS CPLX0-5344 COMMENT
"H-NS modulate csiD expression by influencing activation by cAMP-CRP")
(ACTIVATORS CPLX0-5344 CITATIONS "11532138")
(INHIBITORS CPLX0-5303 CITATIONS "14731280")))
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |martin|)
(:CREATION-DATE 3286118148) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS0-3002)
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(:CREATOR |martin|)
(:CREATION-DATE 3286119839) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286205986) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3286206946) )
NIL)
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(LEFT PD00288 BS0-3022)
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(:CREATOR |martin|)
(:CREATION-DATE 3286207056) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-3041)
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(:CREATOR |martin|)
(:CREATION-DATE 3286285975) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-3061)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286553758) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-3081)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286560426) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286564041) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00589)
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(:CREATOR |martin|)
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((ACTIVATORS CPLX0-5522 CITATIONS "16377617") (ACTIVATORS CPLX0-5522 COMMENT)))
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(:CREATOR |sgama|)
(:CREATION-DATE 3286719364) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286892348) )
NIL)
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(:CREATOR |sgama|)
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((ACTIVATORS CPLX0-4058 CITATIONS "11274153")))
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(LEFT RNAPE-CPLX PM0-4383)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286895116) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286895371) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3286912207) )
NIL)
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NIL)
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(LEFT PM0-4422)
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(:CREATOR |sgama|)
(:CREATION-DATE 3287166400) )
NIL)
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NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3287168584) )
NIL)
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(ACTIVATORS CPLX0-4009 CITATIONS "11357510")
(ACTIVATORS CPLX0-4008 CITATIONS "11357510")
(ACTIVATORS CPLX0-4003 CITATIONS "11357510")))
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(:CREATOR |sgama|)
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NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3287236142) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3287236461) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3287236594) )
NIL)
(BR0-4406 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4428)
(RIGHT CPLX0-5775)
(ACTIVATORS CPLX0-5692)
(INHIBITORS CPLX0-4093 CPLX0-4092)
(:CREATOR |sgama|)
(:CREATION-DATE 3287238787) )
((ACTIVATORS CPLX0-5692 CITATIONS "15520470") (ACTIVATORS CPLX0-5692 COMMENT)
(INHIBITORS CPLX0-4092 CITATIONS "1460045")
(INHIBITORS CPLX0-4093 CITATIONS "1460045")))
(BR0-4407 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4430)
(RIGHT CPLX0-5772)
(:CREATOR |sgama|)
(:CREATION-DATE 3287240545) )
NIL)
(BR0-4408 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4432)
(RIGHT CPLX0-5776)
(:CREATOR |sgama|)
(:CREATION-DATE 3287240646) )
NIL)
(BR0-4409 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4433)
(RIGHT CPLX0-5774)
(:CREATOR |sgama|)
(:CREATION-DATE 3287242434) )
NIL)
(BR0-4410 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4435)
(RIGHT CPLX0-5758)
(:CREATOR |sgama|)
(:CREATION-DATE 3287244750) )
NIL)
(BR0-4411 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4436)
(RIGHT CPLX0-5757)
(ACTIVATORS CPLX0-4057)
(:CREATOR |sgama|)
(:CREATION-DATE 3287245423) )
((ACTIVATORS CPLX0-4057 COMMENT) (ACTIVATORS CPLX0-4057 CITATIONS "11274153")))
(BR0-4421 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00367)
(RIGHT CPLX0-5787)
(ACTIVATORS CPLX0-3979 CPLX0-4021)
(INHIBITORS CPLX0-4020)
(:CREATOR |martin|)
(:CREATION-DATE 3287250112) )
((ACTIVATORS CPLX0-4021 CITATIONS "8550494" "8071201")
(ACTIVATORS CPLX0-3979 CITATIONS "8071201")
(INHIBITORS CPLX0-4020 CITATIONS "8550494" "8071201")
(INHIBITORS CPLX0-4020 COMMENT)))
(BR0-4422 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00366)
(RIGHT CPLX0-5786)
(:CREATOR |martin|)
(:CREATION-DATE 3287250371) )
NIL)
(BR0-4423 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-3161)
(RIGHT CPLX0-4020)
(:CREATOR |martin|)
(:CREATION-DATE 3287250819) )
NIL)
(BR0-4424 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4443)
(RIGHT CPLX0-5784)
(:CREATOR |sgama|)
(:CREATION-DATE 3287251304) )
NIL)
(BR0-4425 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4444)
(RIGHT CPLX0-5788)
(:CREATOR |sgama|)
(:CREATION-DATE 3287251909) )
NIL)
(BR0-4426 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3162)
(RIGHT CPLX0-4021)
(:CREATOR |martin|)
(:CREATION-DATE 3287252903) )
NIL)
(BR0-4427 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4445)
(RIGHT CPLX0-5785)
(:CREATOR |sgama|)
(:CREATION-DATE 3287253090) )
NIL)
(BR0-4441 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS0-3181)
(RIGHT CPLX0-3979)
(:CREATOR |martin|)
(:CREATION-DATE 3287253278) )
NIL)
(BR0-4442 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4461)
(RIGHT CPLX0-5753)
(:CREATOR |sgama|)
(:CREATION-DATE 3287253925) )
NIL)
(BR0-4461 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4462)
(RIGHT CPLX0-6682)
(:CREATOR |sgama|)
(:CREATION-DATE 3287254631) )
NIL)
(BR0-4462 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4482)
(RIGHT CPLX0-6681)
(:CREATOR |sgama|)
(:CREATION-DATE 3287256358) )
NIL)
(BR0-4463 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01520 BS0-3201)
(RIGHT CPLX0-4092)
(:CREATOR |martin|)
(:CREATION-DATE 3287326447) )
NIL)
(BR0-4464 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01520 BS0-3202)
(RIGHT CPLX0-4093)
(:CREATOR |martin|)
(:CREATION-DATE 3287326501) )
NIL)
(BR0-4481 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-3221)
(RIGHT CPLX0-4058)
(:CREATOR |sgama|)
(:CREATION-DATE 3287340063) )
NIL)
(BR0-4482 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-3222)
(RIGHT CPLX0-4057)
(:CREATOR |sgama|)
(:CREATION-DATE 3287340237) )
NIL)
(BR0-4483 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-CPXR BS0-3223)
(RIGHT CPLX0-4056)
(:CREATOR |sgama|)
(:CREATION-DATE 3287340291) )
NIL)
(BR0-4501 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4524)
(RIGHT CPLX0-6680)
(:CREATOR |sgama|)
(:CREATION-DATE 3287410152) )
NIL)
(BR0-4503 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4525)
(RIGHT CPLX0-6679)
(:CREATOR |sgama|)
(:CREATION-DATE 3287410272) )
NIL)
(BR0-4504 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM0-4527)
(RIGHT CPLX0-6678)
(:CREATOR |sgama|)
(:CREATION-DATE 3287412158) )
NIL)
(BR0-4505 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4528)
(RIGHT CPLX0-6677)
(ACTIVATORS CPLX0-4489)
(INHIBITORS CPLX0-4555 CPLX0-4491)
(:CREATOR |martin|)
(:CREATION-DATE 3287412654) )
((INHIBITORS CPLX0-4555 CITATIONS) (INHIBITORS CPLX0-4555 COMMENT)
(ACTIVATORS CPLX0-4489 CITATIONS "8755903") (ACTIVATORS CPLX0-4489 COMMENT)))
(BR0-4506 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD04099 BS0-3241)
(RIGHT CPLX0-4491)
(:CREATOR |martin|)
(:CREATION-DATE 3287413437) )
NIL)
(BR0-4507 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01520 BS0-3242)
(RIGHT CPLX0-4489)
(:CREATOR |martin|)
(:CREATION-DATE 3287413783) )
NIL)
(BR0-4521 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-160 BS0-3261)
(RIGHT CPLX0-4501)
(:CREATOR |martin|)
(:CREATION-DATE 3287495138) )
NIL)
(BR0-4561 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4583)
(RIGHT CPLX0-6676)
(:CREATOR |sgama|)
(:CREATION-DATE 3287760499) )
NIL)
(BR0-4581 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00266 BS0-3281)
(RIGHT CPLX0-4395)
(:CREATOR |martin|)
(:CREATION-DATE 3287930943) )
NIL)
(BR0-4582 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4621)
(RIGHT CPLX0-6675)
(ACTIVATORS CPLX0-5126 CPLX0-5338)
(INHIBITORS CPLX0-5126 CPLX0-5338 CPLX0-5339 CPLX0-4395)
(:CREATOR |martin|)
(:CREATION-DATE 3287931560) )
((ACTIVATORS CPLX0-5126 COMMENT) (INHIBITORS CPLX0-5126 CITATIONS "1848637")
(ACTIVATORS CPLX0-5126 CITATIONS "1848637")
(INHIBITORS CPLX0-4395 COMMENT
"CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.")
(INHIBITORS CPLX0-4395 CITATIONS "11139621" "9469834" "7934873")
(INHIBITORS CPLX0-5339 COMMENT
"CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.")
(INHIBITORS CPLX0-5339 CITATIONS "11139621" "9469834" "7934873")
(ACTIVATORS CPLX0-5338 COMMENT
"CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.")
(ACTIVATORS CPLX0-5338 CITATIONS "11139621" "7934873" "9469834" "1848637")
(INHIBITORS CPLX0-5338 COMMENT
"CAP and NagC can bind simultaneously and produce a more stable complex than binary NagC-DNA complex.")
(INHIBITORS CPLX0-5338 CITATIONS "11139621" "7934873" "9469834" "1848637")))
(BR0-4601 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4641)
(RIGHT CPLX0-6674)
(:CREATOR |sgama|)
(:CREATION-DATE 3288016197) )
NIL)
(BR0-4602 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4642)
(RIGHT CPLX0-6673)
(:CREATOR |sgama|)
(:CREATION-DATE 3288017478) )
NIL)
(BR0-4603 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4643)
(RIGHT CPLX0-6672)
(:CREATOR |sgama|)
(:CREATION-DATE 3288019453) )
NIL)
(BR0-4604 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4644)
(RIGHT CPLX0-6671)
(:CREATOR |sgama|)
(:CREATION-DATE 3288020699) )
NIL)
(BR0-4605 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4645)
(RIGHT CPLX0-6670)
(:CREATOR |sgama|)
(:CREATION-DATE 3288021000) )
NIL)
(BR0-4622 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00266 BS0-3302)
(RIGHT CPLX0-5339)
(:CREATOR |martin|)
(:CREATION-DATE 3288097139) )
NIL)
(BR0-4623 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3303)
(RIGHT CPLX0-5338)
(:CREATOR |martin|)
(:CREATION-DATE 3288097407) )
NIL)
(BR0-4641 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4684)
(RIGHT CPLX0-6669)
(INHIBITORS CPLX0-5337)
(:CREATOR |martin|)
(:CREATION-DATE 3288373450) )
((INHIBITORS CPLX0-5337 CITATIONS "11254141") (INHIBITORS CPLX0-5337 COMMENT)))
(BR0-4642 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-2021 BS0-3321)
(RIGHT CPLX0-5337)
(:CREATOR |martin|)
(:CREATION-DATE 3288373664) )
NIL)
(BR0-4643 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM0-4681)
(RIGHT CPLX0-6668)
(INHIBITORS CPLX0-5656 CPLX0-5657 CPLX0-5234 CPLX0-5244 CPLX0-5245 CPLX0-5246)
(ACTIVATORS CPLX0-5235 CPLX0-5236 CPLX0-5237 CPLX0-5327)
(:CREATOR |sgama|)
(:CREATION-DATE 3288379027) )
((ACTIVATORS CPLX0-5327 COMMENT
"NorR (-87 site) is considered of high-affinity and the occupation of this site facilitates further binding of NorR to the adjacent site (s). Is possible that NorR at -87 binding site (high-affinity) is primarily required for NorR-dependent norVW regulation, while one or both of the lower affinity sites are involved in norR autoregulation. It contains the inverted repeat GTCA-(N3)-TGAC.
Although NorR regulator protein can bind independently to each of the three binding sites in the norV promoter region controlling the flavorubredoxin gene expression, the presence of these three sites is required for in vivo induction of norVW operon. Using protein cross-linking experiments it was demonstrated that NorR binds to the promoter of flavorubredoxin gene as a trimer |CITS: [15694381]|.")
(INHIBITORS CPLX0-5246 COMMENT) (INHIBITORS CPLX0-5656 CITATIONS "12586421")
(INHIBITORS CPLX0-5656 COMMENT) (INHIBITORS CPLX0-5657 CITATIONS "12586421")
(INHIBITORS CPLX0-5657 COMMENT) (INHIBITORS CPLX0-5246 CITATIONS "12586421")
(INHIBITORS CPLX0-5244 COMMENT
"NarP or NarL repress the transcription of nor operon when E. coli is grown with nitrite, it suggest that NarL and NarP proteins are competing with a transcriptional activator wich is activated by nitrite, and may bind to the nucleotide region in the vacinity of the putative NarL/NarP binding site (PubMed: 12586421)")
(INHIBITORS CPLX0-5244 CITATIONS "12586421")
(INHIBITORS CPLX0-5245 COMMENT
"NarP or NarL repress the transcription of nor operon when E. coli is grown with nitrite, it suggest that NarL and NarP proteins are competing with a transcriptional activator which is activated by nitrite, and may bind to the nucleotide region in the vicinity of the putative NarL/NarP binding site |CITS:[12586421]|.")
(INHIBITORS CPLX0-5245 CITATIONS "12586421")
(ACTIVATORS CPLX0-5236 COMMENT
"NorR (-132) is considered of low-affinity. It contains the inversed repeat GTCA-(N3)-TGAC. NorR (-87 site) is considered of high-affinity and the occupation of this site facilitates further binding of NorR to the adjacent site (s). Is possible that NorR at -87 binding site (high-affinity) is primarily required for NorR-dependent norVW regulation, while one or both of the lower affinity sites are involved in norR autoregulation.
Although NorR regulator protein can bind independently to each of the three binding sites in the norV promoter region controlling the flavorubredoxin gene expression, the presence of these three sites is required for in vivo induction of norVW operon. Using protein cross-linking experiments it was demonstrated that NorR binds to the promoter of flavorubredoxin gene as a trimer |CITS: [15694381]|.")
(ACTIVATORS CPLX0-5236 CITATIONS "11751865" "12142437" "12529359" "15375149"
"15694381")
(ACTIVATORS CPLX0-5237 COMMENT
"NorR (-111 site) is considered of low-affinity. It contains the inverted repeat
GTCA-(N3)-CGAC. NorR (87 site) is considered of high-affinity and the occupation of this site facilitates further binding of NorR to the adjacent site (s). Is possible that NorR at -87 binding site (high-affinity) is primarily required for NorR-dependent norVW regulation, while one or both of the lower affinity sites are involved in norR autoregulation.
Although NorR regulator protein can bind independently to each of the three binding sites in the norV promoter region controlling the flavorubredoxin gene expression, the presence of these three sites is required for in vivo induction of norVW operon. Using protein cross-linking experiments it was demonstrated that NorR binds to the promoter of flavorubredoxin gene as a trimer |CITS: [15694381]|.")
(ACTIVATORS CPLX0-5237 CITATIONS "11751865" "12142437" "12529359" "15375149"
"15694381")
(ACTIVATORS CPLX0-5327 CITATIONS "11751865" "12142437" "12529359" "15375149"
"15667300" "15694381")
(INHIBITORS CPLX0-5234 CITATIONS "15375149")
(INHIBITORS CPLX0-5234 COMMENT
"IHF (17 site) is considered a low affinity IHF binding site.
By the position it is inferred that it causes a negative effect.
By the position and compared with a similar described csgD regulation, is inferred that it causes a positive effect.")
(ACTIVATORS CPLX0-5235 CITATIONS "15375149")
(ACTIVATORS CPLX0-5235 COMMENT
"IHF (-48 site) is fully occupied at IHF concentration lower than those for IHF (17 site). The location of this binding-site is consistent with a role for IHF in bending DNA to bring NorR into contact with RNA polymerase.
")))
(BR0-4661 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3341)
(RIGHT CPLX0-5336)
(:CREATOR |martin|)
(:CREATION-DATE 3288529155) )
NIL)
(BR0-4662 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3342)
(RIGHT CPLX0-5335)
(:CREATOR |martin|)
(:CREATION-DATE 3288529231) )
NIL)
(BR0-4663 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3343)
(RIGHT CPLX0-5334)
(:CREATOR |martin|)
(:CREATION-DATE 3288529367) )
NIL)
(BR0-4664 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3344)
(RIGHT CPLX0-5333)
(:CREATOR |martin|)
(:CREATION-DATE 3288529422) )
NIL)
(BR0-4666 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3346)
(RIGHT CPLX0-5332)
(:CREATOR |martin|)
(:CREATION-DATE 3288529535) )
NIL)
(BR0-4667 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3347)
(RIGHT CPLX0-5331)
(:CREATOR |martin|)
(:CREATION-DATE 3288529617) )
NIL)
(BR0-4668 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3348)
(RIGHT CPLX0-5330)
(:CREATOR |martin|)
(:CREATION-DATE 3288529660) )
NIL)
(BR0-4669 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-3349)
(RIGHT CPLX0-5329)
(:CREATOR |martin|)
(:CREATION-DATE 3288529913) )
NIL)
(BR0-4671 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-3351)
(RIGHT CPLX0-5328)
(:CREATOR |martin|)
(:CREATION-DATE 3288530143) )
NIL)
(BR0-4672 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12108-MONOMER BS0-3352)
(RIGHT CPLX0-5327)
(:CREATOR |sgama|)
(:CREATION-DATE 3288535871) )
NIL)
(BR0-4673 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6319-MONOMER BS0-3353)
(RIGHT CPLX0-5326)
(:CREATOR |sgama|)
(:CREATION-DATE 3288538545) )
NIL)
(BR0-4674 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3354)
(RIGHT CPLX0-5325)
(:CREATOR |martin|)
(:CREATION-DATE 3288538640) )
NIL)
(BR0-4675 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3355)
(RIGHT CPLX0-5324)
(:CREATOR |martin|)
(:CREATION-DATE 3288538715) )
NIL)
(BR0-4681 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4701)
(RIGHT CPLX0-6667)
(ACTIVATORS CPLX0-4566)
(:CREATOR |martin|)
(:CREATION-DATE 3288555231) )
((ACTIVATORS CPLX0-4566 CITATIONS "10762278" "14645248")
(ACTIVATORS CPLX0-4566 COMMENT
"CdaR responding to the inducers D-glycerate, D-galactarate, D-glucarate, and 2-D-mannosyl-glycerate")))
(BR0-4682 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4702)
(RIGHT CPLX0-6666)
(ACTIVATORS CPLX0-4565)
(:CREATOR |martin|)
(:CREATION-DATE 3288555442) )
((ACTIVATORS CPLX0-4565 CITATIONS "10762278" "14645248")
(ACTIVATORS CPLX0-4565 COMMENT
"CdaR responding to the inducers D-glycerate, D-galactarate, D-glucarate, and 2-D-mannosyl-glycerate")))
(BR0-4683 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4722)
(RIGHT CPLX0-6665)
(INHIBITORS CPLX0-5322 CPLX0-5323)
(:CREATOR |martin|)
(:CREATION-DATE 3288617903) )
((INHIBITORS CPLX0-5322 COMMENT)
(INHIBITORS CPLX0-5322 CITATIONS "14645248" "7805834")
(INHIBITORS CPLX0-5323 CITATIONS "14645248" "7805834")))
(BR0-4684 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00103 BS0-3361)
(RIGHT CPLX0-5323)
(:CREATOR |martin|)
(:CREATION-DATE 3288621844) )
NIL)
(BR0-4685 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00103 BS0-3362)
(RIGHT CPLX0-5322)
(:CREATOR |martin|)
(:CREATION-DATE 3288621996) )
NIL)
(BR0-4686 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4723)
(RIGHT CPLX0-6664)
(INHIBITORS CPLX0-4580)
(:CREATOR |sgama|)
(:CREATION-DATE 3288622247) )
((INHIBITORS CPLX0-4580 COMMENT)
(INHIBITORS CPLX0-4580 CITATIONS "8576032" "10559180")))
(BR0-4701 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4741)
(RIGHT CPLX0-6663)
(ACTIVATORS CPLX0-4568)
(:CREATOR |martin|)
(:CREATION-DATE 3288632229) )
((ACTIVATORS CPLX0-4568 CITATIONS "14645248" "10762278")
(ACTIVATORS CPLX0-4568 COMMENT
"CdaR responding to the inducers D-glycerate, D-galactarate, D-glucarate, and 2-D-mannosyl-glycerate")))
(BR0-4702 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12335-MONOMER BS0-3381)
(RIGHT CPLX0-4568)
(:CREATOR |martin|)
(:CREATION-DATE 3288632594) )
NIL)
(BR0-4703 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12335-MONOMER BS0-3382)
(RIGHT CPLX0-4567)
(:CREATOR |martin|)
(:CREATION-DATE 3288633164) )
NIL)
(BR0-4704 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12335-MONOMER BS0-3383)
(RIGHT CPLX0-4566)
(:CREATOR |martin|)
(:CREATION-DATE 3288633434) )
NIL)
(BR0-4705 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12335-MONOMER BS0-3384)
(RIGHT CPLX0-4565)
(:CREATOR |martin|)
(:CREATION-DATE 3288633559) )
NIL)
(BR0-4706 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4742)
(RIGHT CPLX0-6662)
(INHIBITORS CPLX0-4585)
(:CREATOR |sgama|)
(:CREATION-DATE 3288637486) )
((INHIBITORS CPLX0-4585 COMMENT
"It was not identified which of two promoters of the als operon was repressed by AlsR, but we inferred that both are repressed, because they are very closed.")
(INHIBITORS CPLX0-4585 CITATIONS "9401019")))
(BR0-4721 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4744)
(RIGHT CPLX0-6661)
(INHIBITORS CPLX0-4586)
(:CREATOR |sgama|)
(:CREATION-DATE 3288704386) )
((INHIBITORS CPLX0-4586 COMMENT
"It was not identified which of two promoters of the als operon was repressed by AlsR, but we inferred that both are repressed, because they are very closed.")
(INHIBITORS CPLX0-4586 CITATIONS "9401019")))
(BR0-4722 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7821-MONOMER BS0-3401)
(RIGHT CPLX0-4586)
(:CREATOR |sgama|)
(:CREATION-DATE 3288710992) )
NIL)
(BR0-4723 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7821-MONOMER BS0-3402)
(RIGHT CPLX0-4585)
(:CREATOR |sgama|)
(:CREATION-DATE 3288711052) )
NIL)
(BR0-4724 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7821-MONOMER BS0-3403)
(RIGHT CPLX0-4580)
(:CREATOR |sgama|)
(:CREATION-DATE 3288728720) )
NIL)
(BR0-4741 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4761)
(RIGHT CPLX0-6660)
(:CREATOR |sgama|)
(:CREATION-DATE 3288977338) )
NIL)
(BR0-4742 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4762)
(RIGHT CPLX0-6659)
(:CREATOR |sgama|)
(:CREATION-DATE 3288983238) )
NIL)
(BR0-4743 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4763)
(RIGHT CPLX0-6658)
(:CREATOR |sgama|)
(:CREATION-DATE 3288985192) )
NIL)
(BR0-4761 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4785)
(RIGHT CPLX0-6657)
(:CREATOR |martin|)
(:CREATION-DATE 3289239975) )
NIL)
(BR0-4762 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3421)
(RIGHT CPLX0-4657)
(:CREATOR |martin|)
(:CREATION-DATE 3289311729) )
NIL)
(BR0-4766 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3425)
(RIGHT CPLX0-4668)
(:CREATOR |martin|)
(:CREATION-DATE 3289316170) )
NIL)
(BR0-4767 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3426)
(RIGHT CPLX0-4667)
(:CREATOR |martin|)
(:CREATION-DATE 3289316467) )
NIL)
(BR0-4768 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3427)
(RIGHT CPLX0-4666)
(:CREATOR |martin|)
(:CREATION-DATE 3289316703) )
NIL)
(BR0-4769 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3428)
(RIGHT CPLX0-4662)
(:CREATOR |martin|)
(:CREATION-DATE 3289316803) )
NIL)
(BR0-4781 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4802)
(RIGHT CPLX0-6656)
(ACTIVATORS CPLX0-5321)
(:CREATOR |martin|)
(:CREATION-DATE 3289567917) )
((ACTIVATORS CPLX0-5321 CITATIONS "15073297")))
(BR0-4782 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-DCUR-MONOMER BS0-3441)
(RIGHT CPLX0-5321)
(:CREATOR |martin|)
(:CREATION-DATE 3289568075) )
NIL)
(BR0-4802 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3462)
(RIGHT CPLX0-4263)
(:CREATOR |martin|)
(:CREATION-DATE 3289578634) )
NIL)
(BR0-4803 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3463)
(RIGHT CPLX0-4262)
(:CREATOR |martin|)
(:CREATION-DATE 3289579035) )
NIL)
(BR0-4804 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3464)
(RIGHT CPLX0-4266)
(:CREATOR |martin|)
(:CREATION-DATE 3289579235) )
NIL)
(BR0-4805 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3465)
(RIGHT CPLX0-4265)
(:CREATOR |martin|)
(:CREATION-DATE 3289579512) )
NIL)
(BR0-4806 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3466)
(RIGHT CPLX0-4264)
(:CREATOR |martin|)
(:CREATION-DATE 3289580387) )
NIL)
(BR0-4807 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3467)
(RIGHT CPLX0-4267)
(:CREATOR |martin|)
(:CREATION-DATE 3289580548) )
NIL)
(BR0-4809 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00365 BS0-3469)
(RIGHT CPLX0-4268)
(:CREATOR |sgama|)
(:CREATION-DATE 3289657720) )
NIL)
(BR0-4810 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00406 BS0-3470)
(RIGHT CPLX0-4245)
(:CREATOR |sgama|)
(:CREATION-DATE 3289658581) )
NIL)
(BR0-4811 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00406 BS0-3471)
(RIGHT CPLX0-4244)
(:CREATOR |sgama|)
(:CREATION-DATE 3289661232) )
NIL)
(BR0-4812 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3472)
(RIGHT CPLX0-4243)
(:CREATOR |martin|)
(:CREATION-DATE 3289672589) )
NIL)
(BR0-4813 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3473)
(RIGHT CPLX0-4242)
(:CREATOR |martin|)
(:CREATION-DATE 3289672865) )
NIL)
(BR0-4814 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3474)
(RIGHT CPLX0-4246)
(:CREATOR |martin|)
(:CREATION-DATE 3289672961) )
NIL)
(BR0-4822 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3482)
(RIGHT CPLX0-4291)
(:CREATOR |martin|)
(:CREATION-DATE 3289737528) )
NIL)
(BR0-4823 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3483)
(RIGHT CPLX0-4290)
(:CREATOR |martin|)
(:CREATION-DATE 3289737777) )
NIL)
(BR0-4824 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3484)
(RIGHT CPLX0-4283)
(:CREATOR |martin|)
(:CREATION-DATE 3289739260) )
NIL)
(BR0-4825 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3485)
(RIGHT CPLX0-4282)
(:CREATOR |martin|)
(:CREATION-DATE 3289739336) )
NIL)
(BR0-4826 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3486)
(RIGHT CPLX0-4281)
(:CREATOR |martin|)
(:CREATION-DATE 3289751585) )
NIL)
(BR0-4827 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3487)
(RIGHT CPLX0-4285)
(:CREATOR |martin|)
(:CREATION-DATE 3289752914) )
NIL)
(BR0-4828 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3488)
(RIGHT CPLX0-4284)
(:CREATOR |martin|)
(:CREATION-DATE 3289753675) )
NIL)
(BR0-4829 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3489)
(RIGHT CPLX0-4286)
(:CREATOR |martin|)
(:CREATION-DATE 3289754599) )
NIL)
(BR0-4841 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS0-3501)
(RIGHT CPLX0-4239)
(:CREATOR |martin|)
(:CREATION-DATE 3289822889) )
NIL)
(BR0-4842 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4844)
(RIGHT CPLX0-6655)
(INHIBITORS CPLX0-4238)
(:CREATOR |martin|)
(:CREATION-DATE 3289837227) )
((INHIBITORS CPLX0-4238 COMMENT)
(INHIBITORS CPLX0-4238 CITATIONS "11397910" "10816566")))
(BR0-4843 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-2487 BS0-3502)
(RIGHT CPLX0-4238)
(:CREATOR |martin|)
(:CREATION-DATE 3289837701) )
NIL)
(BR0-4861 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4863)
(RIGHT CPLX0-6654)
(ACTIVATORS CPLX0-4342)
(:CREATOR |martin|)
(:CREATION-DATE 3289919169) )
((ACTIVATORS CPLX0-4342 CITATIONS "10608803" "10048032")))
(BR0-4862 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11969-MONOMER BS0-3521)
(RIGHT CPLX0-4342)
(:CREATOR |martin|)
(:CREATION-DATE 3289919893) )
NIL)
(BR0-4863 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-4864)
(RIGHT CPLX0-6653)
(ACTIVATORS CPLX0-4343)
(:CREATOR |sgama|)
(:CREATION-DATE 3289931749) )
((ACTIVATORS CPLX0-4343 CITATIONS "12100559")
(ACTIVATORS CPLX0-4343 COMMENT
"There are four putative sites to bind MarA but just one at position -41.5 is necessary to activate the transcription of nfnB.
In vitro, but not in vivo, the proteins Rob and SoxS activate the transcription of nfnB and they bind to MarA binding site when they are in a high concentration.")))
(BR0-4864 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00365 BS0-3522)
(RIGHT CPLX0-4343)
(:CREATOR |sgama|)
(:CREATION-DATE 3289932071) )
NIL)
(BR0-4881 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4882)
(RIGHT CPLX0-6652)
(INHIBITORS CPLX0-5603)
(:CREATOR |martin|)
(:CREATION-DATE 3290782354) )
((INHIBITORS CPLX0-5603 CITATIONS "9680209" "10816566")
(INHIBITORS CPLX0-5603 COMMENT
"The Zur binding site for the znuA transcription unit is exactly the same site for the znuCB operon. But, it can not be correctly
positioned for znuA because it has no transcription initiation position determined.")))
(BR0-4901 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PUTA-MONOMER BS0-3541)
(RIGHT CPLX0-5320)
(:CREATOR |martin|)
(:CREATION-DATE 3290957663) )
NIL)
(BR0-4902 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00009 BS0-3542)
(RIGHT CPLX0-5319)
(:CREATOR |martin|)
(:CREATION-DATE 3290972098) )
NIL)
(BR0-4921 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3561)
(RIGHT CPLX0-5318)
(:CREATOR |martin|)
(:CREATION-DATE 3291404464) )
NIL)
(BR0-4922 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG10143-MONOMER BS0-3562)
(RIGHT CPLX0-5317)
(:CREATOR |martin|)
(:CREATION-DATE 3291404600) )
NIL)
(BR0-4923 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG10143-MONOMER BS0-3563)
(RIGHT CPLX0-3978)
(:CREATOR |martin|)
(:CREATION-DATE 3291404713) )
NIL)
(BR0-4924 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00266 BS0-3564)
(RIGHT CPLX0-5316)
(:CREATOR |martin|)
(:CREATION-DATE 3291405368) )
NIL)
(BR0-4925 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00266 BS0-3565)
(RIGHT CPLX0-5315)
(:CREATOR |martin|)
(:CREATION-DATE 3291405442) )
NIL)
(BR0-4961 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4921)
(RIGHT CPLX0-6651)
(INHIBITORS CPLX0-5259 CPLX0-5258 CPLX0-5257)
(ACTIVATORS CPLX0-5261 CPLX0-5291 CPLX0-5260)
(:CREATOR |martin|)
(:CREATION-DATE 3292089146) )
((ACTIVATORS CPLX0-5260 COMMENT) (ACTIVATORS CPLX0-5261 COMMENT)
(ACTIVATORS CPLX0-5291 COMMENT) (INHIBITORS CPLX0-5258 COMMENT)
(INHIBITORS CPLX0-5257 COMMENT) (ACTIVATORS CPLX0-5291 CITATIONS "14593252")
(INHIBITORS CPLX0-5259 CITATIONS "14593252")
(INHIBITORS CPLX0-5258 CITATIONS "14593252")
(INHIBITORS CPLX0-5257 CITATIONS "14593252")
(ACTIVATORS CPLX0-5261 CITATIONS "14973046" "14593252")
(ACTIVATORS CPLX0-5260 CITATIONS "14593252")))
(BR0-4962 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4922)
(RIGHT CPLX0-6650)
(INHIBITORS CPLX0-5257 CPLX0-5258 CPLX0-5259)
(ACTIVATORS CPLX0-5260 CPLX0-5291 CPLX0-5261)
(:CREATOR |martin|)
(:CREATION-DATE 3292089357) )
((ACTIVATORS CPLX0-5291 COMMENT) (ACTIVATORS CPLX0-5261 CITATIONS "14593252")
(ACTIVATORS CPLX0-5260 CITATIONS "14593252")
(ACTIVATORS CPLX0-5291 CITATIONS "14593252" "9658018")
(INHIBITORS CPLX0-5257 CITATIONS "14593252") (INHIBITORS CPLX0-5257 COMMENT)
(INHIBITORS CPLX0-5259 CITATIONS "14593252")
(INHIBITORS CPLX0-5258 CITATIONS "14593252") (INHIBITORS CPLX0-5258 COMMENT)))
(BR0-4981 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4941)
(RIGHT CPLX0-6649)
(INHIBITORS CPLX0-5314)
(:CREATOR |martin|)
(:CREATION-DATE 3292602536) )
((INHIBITORS CPLX0-5314 CITATIONS "1649816")))
(BR0-4982 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4942)
(RIGHT CPLX0-6648)
(INHIBITORS CPLX0-5314)
(:CREATOR |martin|)
(:CREATION-DATE 3292602633) )
((INHIBITORS CPLX0-5314 CITATIONS "1649816")))
(BR0-4983 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-4943)
(RIGHT CPLX0-6647)
(:CREATOR |martin|)
(:CREATION-DATE 3292602807) )
NIL)
(BR0-4985 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3622)
(RIGHT CPLX0-5314)
(:CREATOR |martin|)
(:CREATION-DATE 3292613782) )
NIL)
(BR0-5 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARP BS0-2)
(RIGHT CPLX0-5656)
(:CREATOR |sgama|)
(:CREATION-DATE 3339339610) )
NIL)
(BR0-5022 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00357)
(RIGHT CPLX0-6646)
(:CREATOR |martin|)
(:CREATION-DATE 3293376947) )
NIL)
(BR0-5041 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-5001)
(RIGHT CPLX0-6645)
(:CREATOR |martin|)
(:CREATION-DATE 3294416596) )
NIL)
(BR0-5062 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00412)
(RIGHT CPLX0-6644)
(:CREATOR |martin|)
(:CREATION-DATE 3294498587) )
NIL)
(BR0-5065 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-5023)
(RIGHT CPLX0-6643)
(ACTIVATORS CPLX0-5312 CPLX0-5313)
(:CREATOR |sgama|)
(:CREATION-DATE 3294499574) )
((ACTIVATORS CPLX0-5312 COMMENT
"The operon nrdDG is induced under anaerobiosis in the stationary phase, this induction is FNR dependent.")
(ACTIVATORS CPLX0-5313 COMMENT
"The operon nrdDG is induced under anaerobiosis in the stationary phase, this induction is FNR dependent.")
(ACTIVATORS CPLX0-5312 CITATIONS "12923108")
(ACTIVATORS CPLX0-5313 CITATIONS "12923108")))
(BR0-5066 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00411)
(RIGHT CPLX0-6642)
(:CREATOR |martin|)
(:CREATION-DATE 3294499587) )
NIL)
(BR0-5067 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-3661)
(RIGHT CPLX0-5313)
(:CREATOR |sgama|)
(:CREATION-DATE 3294500629) )
NIL)
(BR0-5068 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-3662)
(RIGHT CPLX0-5312)
(:CREATOR |sgama|)
(:CREATION-DATE 3294500770) )
NIL)
(BR0-5069 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00634)
(RIGHT CPLX0-6641)
(:CREATOR |martin|)
(:CREATION-DATE 3294501361) )
NIL)
(BR0-5081 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5042)
(RIGHT CPLX0-6640)
(INHIBITORS CPLX0-5302 CPLX0-5300 CPLX0-5301)
(ACTIVATORS CPLX0-5299)
(:CREATOR |martin|)
(:CREATION-DATE 3294582234) )
((ACTIVATORS CPLX0-5299 COMMENT)
(INHIBITORS CPLX0-5301 COMMENT "FIS-site II overlaps the -35 box.")
(INHIBITORS CPLX0-5301 CITATIONS "20223650")
(INHIBITORS CPLX0-5300 COMMENT
"FIS-site I partially overlaps the CAP binding site")
(INHIBITORS CPLX0-5300 CITATIONS "20223650")
(ACTIVATORS CPLX0-5299 CITATIONS "20253547" "15520470")
(INHIBITORS CPLX0-5302 COMMENT
"Hns is necessary but is not sufficient for repression of bglB gene, it was suggested that other cellular factors are involved in the repression of this gene.
Repression at this site requires the termination factor Rho and is reduced by translation of the bglG mRNA
|CITS: [15066043]|.")
(INHIBITORS CPLX0-5302 CITATIONS "15066043" "96279746")))
(BR0-5082 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3681)
(RIGHT CPLX0-5311)
(:CREATOR |sgama|)
(:CREATION-DATE 3294586869) )
NIL)
(BR0-5101 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-3701)
(RIGHT CPLX0-5310)
(:CREATOR |sgama|)
(:CREATION-DATE 3294590413) )
NIL)
(BR0-5121 NIL (
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(:CREATOR |martin|)
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NIL)
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(LEFT PD00196 BS0-3728)
(RIGHT CPLX0-5308)
(:CREATOR |martin|)
(:CREATION-DATE 3294687551) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3729)
(RIGHT CPLX0-5307)
(:CREATOR |martin|)
(:CREATION-DATE 3294688409) )
NIL)
(BR0-5130 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3730)
(RIGHT CPLX0-5306)
(:CREATOR |martin|)
(:CREATION-DATE 3294688782) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3731)
(RIGHT CPLX0-5305)
(:CREATOR |martin|)
(:CREATION-DATE 3294688998) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3732)
(RIGHT CPLX0-5304)
(:CREATOR |martin|)
(:CREATION-DATE 3294689173) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5062)
(RIGHT CPLX0-6639)
(:CREATOR |martin|)
(:CREATION-DATE 3294754268) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-5063)
(RIGHT CPLX0-6638)
(:CREATOR |sgama|)
(:CREATION-DATE 3294756617) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12386-MONOMER BS0-3733)
(RIGHT CPLX0-5303)
(:CREATOR |sgama|)
(:CREATION-DATE 3294762838) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-3742)
(RIGHT CPLX0-5302)
(:CREATOR |martin|)
(:CREATION-DATE 3296416528) )
NIL)
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(LEFT PD00196 BS0-3743)
(RIGHT CPLX0-5301)
(:CREATOR |martin|)
(:CREATION-DATE 3296416632) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-3744)
(RIGHT CPLX0-5300)
(:CREATOR |martin|)
(:CREATION-DATE 3296416739) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-3745)
(RIGHT CPLX0-5299)
(:CREATOR |martin|)
(:CREATION-DATE 3296416878) )
NIL)
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(LEFT PHOSPHO-NARL BS0-3761)
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(:CREATOR |sgama|)
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NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARP BS0-3762)
(RIGHT CPLX0-5297)
(:CREATOR |sgama|)
(:CREATION-DATE 3296835048) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-6 BS0-3763)
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(:CREATOR |sgama|)
(:CREATION-DATE 3296840975) )
NIL)
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(LEFT RNAP70-CPLX PM0-5121)
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(:CREATOR |martin|)
(:CREATION-DATE 3296913279) )
NIL)
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(LEFT PM0-5141)
(RIGHT CPLX0-6636)
(:CREATOR |sgama|)
(:CREATION-DATE 3296929720) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5142)
(RIGHT CPLX0-6635)
(:CREATOR |sgama|)
(:CREATION-DATE 3296929913) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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((INHIBITORS CPLX0-3987 CITATIONS "8455549")
(INHIBITORS CPLX0-3987 COMMENT
"The H-NS site for the hdeD regulatory region hasn't been determined, but Yoshida93 suggest that H-NS
has two sites: one site near hdeD and the other one close to hdeA (the upstream opposite direction operon); and that
H-NS represses transcription through the DNA dinding to supercoil it or DNA already supercoiled.
Futrher experiments are requiered to test this proposal.")
(ACTIVATORS CPLX0-4598 CITATIONS "14702398") (ACTIVATORS CPLX0-4598 COMMENT)
(ACTIVATORS CPLX0-5288 CITATIONS "14702398") (ACTIVATORS CPLX0-5288 COMMENT)))
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(LEFT EG11544-MONOMER BS0-3781)
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(:CREATOR |sgama|)
(:CREATION-DATE 3296934291) )
NIL)
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(LEFT PD03585 BS0-3782)
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(:CREATOR |martin|)
(:CREATION-DATE 3296934882) )
NIL)
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(LEFT EG11544-MONOMER BS0-3783)
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(:CREATOR |sgama|)
(:CREATION-DATE 3296935351) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00577)
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(:CREATOR |sgama|)
(:CREATION-DATE 3296936579) )
NIL)
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(LEFT RNAP70-CPLX PM00578)
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(LEFT RNAP70-CPLX PM00579)
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(:CREATOR |sgama|)
(:CREATION-DATE 3296936639) )
NIL)
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(LEFT MONOMER0-1301 BS0-3784)
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(:CREATOR |martin|)
(:CREATION-DATE 3296938525) )
NIL)
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(LEFT MONOMER0-1301 BS0-3803)
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(:CREATION-DATE 3297003889) )
NIL)
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(LEFT EG11544-MONOMER BS0-3804)
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(:CREATION-DATE 3297012389) )
NIL)
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(LEFT PM0-5164)
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(:CREATOR |martin|)
(:CREATION-DATE 3297015179) )
NIL)
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(LEFT EG11544-MONOMER BS0-3805)
(RIGHT CPLX0-5289)
(:CREATOR |sgama|)
(:CREATION-DATE 3297015179) )
NIL)
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(LEFT EG11544-MONOMER BS0-3806)
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(:CREATION-DATE 3297015657) )
NIL)
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(LEFT EG11544-MONOMER BS0-3807)
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(:CREATION-DATE 3297017205) )
NIL)
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(LEFT EG11544-MONOMER BS0-3808)
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(:CREATION-DATE 3297018228) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3297019371) )
NIL)
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(LEFT RNAP70-CPLX PM00134)
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(ACTIVATORS CPLX0-5284)
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((ACTIVATORS CPLX0-5284 CITATIONS "14702398") (ACTIVATORS CPLX0-5284 COMMENT)))
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(LEFT EG11544-MONOMER BS0-3810)
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(:CREATOR |sgama|)
(:CREATION-DATE 3297021009) )
NIL)
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(LEFT PM0-5167)
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(INHIBITORS CPLX0-5255 CITATIONS "9537375" "98324953")))
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(LEFT PM0-5168)
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(ACTIVATORS CPLX0-5283)
(:CREATOR |martin|)
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(INHIBITORS CPLX0-5282 CITATIONS "9537375" "9358057" "98324953")
(ACTIVATORS CPLX0-5283 CITATIONS "9537375" "98324953")))
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(LEFT CPLX0-226 BS0-3812)
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(:CREATION-DATE 3297088939) )
NIL)
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(LEFT PD03585 BS0-3814)
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(:CREATOR |martin|)
(:CREATION-DATE 3297090103) )
NIL)
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(LEFT PM00344)
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(ACTIVATORS CPLX0-5281)
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(LEFT EG12243-MONOMER BS0-3815)
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(:CREATION-DATE 3297092903) )
NIL)
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(LEFT EG12243-MONOMER BS0-3816)
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(:CREATION-DATE 3297093518) )
NIL)
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(LEFT EG12243-MONOMER BS0-3817)
(RIGHT CPLX0-5279)
(:CREATOR |sgama|)
(:CREATION-DATE 3297095276) )
NIL)
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(LEFT EG12243-MONOMER BS0-3821)
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(:CREATOR |sgama|)
(:CREATION-DATE 3297194205) )
NIL)
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(LEFT EG12243-MONOMER BS0-3822)
(RIGHT CPLX0-5277)
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(:CREATION-DATE 3297194206) )
NIL)
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((ACTIVATORS CPLX0-5695 CITATIONS "15520470") (ACTIVATORS CPLX0-5695 COMMENT)
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(INHIBITORS CPLX0-5221 CITATIONS "15516583") (INHIBITORS CPLX0-5221 COMMENT)
(ACTIVATORS CPLX0-4631 COMMENT
"gntP gene is subject to strong catabolite repression.")
(ACTIVATORS CPLX0-4631 CITATIONS "15516583" "15520470")))
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(LEFT CPLX0-226 BS0-3841)
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(:CREATION-DATE 3297446628) )
NIL)
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NIL)
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(:CREATION-DATE 3297519354) )
NIL)
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(:CREATION-DATE 3297519670) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3297535268) )
NIL)
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(LEFT PD03585 BS0-3882)
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(:CREATOR |martin|)
(:CREATION-DATE 3297537900) )
NIL)
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(LEFT CPLX0-226 BS0-3883)
(RIGHT CPLX0-4332)
(:CREATOR |martin|)
(:CREATION-DATE 3297537997) )
NIL)
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((ACTIVATORS CPLX0-4347 CITATIONS) (ACTIVATORS CPLX0-4347 COMMENT)))
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(LEFT PC00027 BS0-3901)
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(:CREATOR |martin|)
(:CREATION-DATE 3297606261) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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NIL)
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(ACTIVATORS CPLX0-5743 COMMENT
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(INHIBITORS CPLX0-4471 COMMENT) (INHIBITORS CPLX0-4471 CITATIONS "6357945")))
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(:CREATOR |martin|)
(:CREATION-DATE 3298063278) )
NIL)
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(LEFT PD03270 BS0-3923)
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(:CREATION-DATE 3298067633) )
NIL)
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(INHIBITORS CPLX0-4474 CITATIONS "6406797" "3929016")
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(LEFT EG20249-MONOMER BS0-3924)
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NIL)
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(LEFT PD03270 BS0-3925)
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(:CREATOR |martin|)
(:CREATION-DATE 3298119792) )
NIL)
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(INHIBITORS CPLX0-4521)
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(LEFT PD03270 BS0-3926)
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(:CREATOR |martin|)
(:CREATION-DATE 3298125733) )
NIL)
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(LEFT CPLX0-226 BS0-3927)
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(:CREATOR |martin|)
(:CREATION-DATE 3298126539) )
NIL)
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(LEFT EG20249-MONOMER BS0-3928)
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(:CREATOR |martin|)
(:CREATION-DATE 3298126571) )
NIL)
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(LEFT PD03270 BS0-3929)
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(:CREATOR |martin|)
(:CREATION-DATE 3298126785) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-5301)
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(:CREATOR |martin|)
(:CREATION-DATE 3298201175) )
NIL)
(BR0-5382 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-5302)
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(:CREATOR |martin|)
(:CREATION-DATE 3298207508) )
NIL)
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(LEFT PM0-5321)
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(:CREATOR |martin|)
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((INHIBITORS CPLX0-5275 COMMENT
"Expression of the regulated gene is affected as a result of mutating the regulatory protein. Note that this evidence does not eliminate the possibility of an indirect effect of the regulator on the regulated gene.")
(INHIBITORS CPLX0-5274 COMMENT
"Expression of the regulated gene is affected as a result of mutating the regulatory protein. Note that this evidence does not eliminate the possiblity of an indirect effect of the regulator on the regulated gene.")
(ACTIVATORS CPLX0-5273 CITATIONS "3934044")
(ACTIVATORS CPLX0-5273 COMMENT
"Expression of the regulated gene is affected as a result of mutating the regulatory protein. Note that this evidence does not eliminate the possiblity of an indirect effect of the regulator on the regulated gene.")
(INHIBITORS CPLX0-5274 CITATIONS "3934044" "3079718")
(INHIBITORS CPLX0-5275 CITATIONS "3934044" "3079718")))
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(:CREATOR |martin|)
(:CREATION-DATE 3298243053) )
NIL)
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NIL)
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(:CREATION-DATE 3298243408) )
NIL)
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(:CREATION-DATE 3298243454) )
NIL)
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(:CREATION-DATE 3298646874) )
NIL)
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(:CREATION-DATE 3298647745) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3298648024) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3298649231) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3298649619) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3298732460) )
NIL)
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(LEFT RNAPE-CPLX PM0-5361)
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(:CREATOR |sgama|)
(:CREATION-DATE 3298831509) )
NIL)
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(INHIBITORS CPLX0-5266 CITATIONS "14996803" "12374842" "12644495")
(INHIBITORS CPLX0-4162 CITATIONS "14996803" "12374842" "12644495")))
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(LEFT G7854-MONOMER BS0-3981)
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(:CREATOR |martin|)
(:CREATION-DATE 3301768613) )
NIL)
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(INHIBITORS CPLX0-4073 CITATIONS "12374842" "14996803")
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(:CREATION-DATE 3301769230) )
NIL)
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(LEFT PM00405)
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(:CREATOR |martin|)
(:CREATION-DATE 3301920683) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5423)
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(:CREATOR |martin|)
(:CREATION-DATE 3301922822) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00406)
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(:CREATOR |martin|)
(:CREATION-DATE 3301923210) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5426)
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(:CREATOR |martin|)
(:CREATION-DATE 3301928168) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5441)
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(:CREATOR |martin|)
(:CREATION-DATE 3301931600) )
NIL)
(BR0-5522 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-5442)
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(:CREATOR |martin|)
(:CREATION-DATE 3301932441) )
NIL)
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(LEFT PM0-5461)
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(ACTIVATORS CPLX0-5264)
(:CREATOR |martin|)
(:CREATION-DATE 3301937657) )
((ACTIVATORS CPLX0-5264 CITATIONS "11844765")))
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(LEFT PD00196 BS0-4021)
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(:CREATOR |martin|)
(:CREATION-DATE 3301937685) )
NIL)
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(LEFT PD00197 BS0-4022)
(RIGHT CPLX0-5263)
(:CREATOR |sgama|)
(:CREATION-DATE 3301947338) )
NIL)
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(LEFT PHOSPHO-OMPR BS0-4041)
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(:CREATOR |sgama|)
(:CREATION-DATE 3302018782) )
NIL)
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(LEFT RNAP70-CPLX PM0-5501)
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(:CREATOR |sgama|)
(:CREATION-DATE 3302536741) )
NIL)
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(LEFT CPLX-125 BS0-4061)
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(:CREATOR |paley|)
(:CREATION-DATE 3302673073) )
NIL)
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(:CREATOR |paley|)
(:CREATION-DATE 3302673073) )
NIL)
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(LEFT CPLX-125 BS0-4063)
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(:CREATOR |paley|)
(:CREATION-DATE 3302673073) )
NIL)
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(LEFT CPLX-125 BS0-4064)
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(:CREATOR |paley|)
(:CREATION-DATE 3302673073) )
NIL)
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(:CREATOR |paley|)
(:CREATION-DATE 3302673073) )
NIL)
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(:CREATION-DATE 3302978564) )
NIL)
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(LEFT G7854-MONOMER BS0-4082)
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(:CREATOR |martin|)
(:CREATION-DATE 3302982550) )
NIL)
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(LEFT PM0-5561)
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(:CREATOR |sgama|)
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(LEFT PM0-5562)
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(:CREATION-DATE 3302986380) )
NIL)
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(LEFT PC00027 BS0-4101)
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(:CREATOR |martin|)
(:CREATION-DATE 3303044451) )
NIL)
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(:CREATION-DATE 3303045141) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3303046420) )
NIL)
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(:CREATION-DATE 3303053273) )
NIL)
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NIL)
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(:CREATION-DATE 3303138757) )
NIL)
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(:CREATION-DATE 3303139041) )
NIL)
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(:CREATION-DATE 3303139440) )
NIL)
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(:CREATION-DATE 3303139527) )
NIL)
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(:CREATION-DATE 3303244118) )
NIL)
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(:CREATION-DATE 3303565358) )
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NIL)
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NIL)
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NIL)
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(:CREATION-DATE 3303668731) )
NIL)
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(:CREATION-DATE 3303669145) )
NIL)
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(:CREATION-DATE 3303669298) )
NIL)
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(LEFT PC00027 BS0-4207)
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(:CREATOR |asantos|)
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NIL)
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(:CREATOR |asantos|)
(:CREATION-DATE 3303669843) )
NIL)
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(LEFT PM0-5661)
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(:CREATOR |martin|)
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NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3304104316) )
NIL)
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NIL)
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(:CREATION-DATE 3304106916) )
NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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The binding of each of two regulators (CRP and ArgR) to the regulatory region of argG gene, interferes with the binding of each other, but ArgR binding overrides CRP binding.
")
(INHIBITORS CPLX0-4643 CITATIONS "12730174" "1640456")
(INHIBITORS CPLX0-4642 CITATIONS "12730174" "1640456")
(INHIBITORS CPLX0-4642 COMMENT
"It has been sugested that a DNA loop is formed when ArgR is binding to the three Arg boxes.
The binding of each of two regulators (CRP and ArgR) to the regulatory region of argG gene, interferes with the binding of each other, but ArgR binding overrides CRP binding.
")
(INHIBITORS CPLX0-4644 CITATIONS "12730174" "1640456")
(INHIBITORS CPLX0-4644 COMMENT
"It has been sugested that a DNA loop is formed when ArgR is binding to the three Arg boxes.
The binding of each of two regulators (CRP and ArgR) to the regulatory region of argG gene, interferes with the binding of each other, but ArgR binding overrides CRP binding.
")
(ACTIVATORS CPLX0-4640 CITATIONS "12730174")
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"CRP binds in just one site, activates argG gene expression and represses the expression of the divergent operon metY-yhbC-nusA-infB.")))
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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Near to the ung promoter, in the CpxR box, there is an AT- rich sequence corresponding to the UP element. It is probable that CpxR binding to the ung promoter represses its transcription by interfering with the ability of the alpha-CTD to bind to the UP element.
")
(INHIBITORS CPLX0-5152 CITATIONS "15576781")))
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(:CREATOR |martin|)
(:CREATION-DATE 3321745113) )
((INHIBITORS CPLX0-5730 CITATIONS "16140472") (INHIBITORS CPLX0-5730 COMMENT)
(INHIBITORS CPLX0-5731 CITATIONS "16140472") (INHIBITORS CPLX0-5731 COMMENT)
(INHIBITORS CPLX0-5732 CITATIONS) (INHIBITORS CPLX0-5732 COMMENT)
(INHIBITORS CPLX0-5733 CITATIONS "16140472") (INHIBITORS CPLX0-5733 COMMENT)))
(BR0-7556 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00432)
(RIGHT CPLX0-6523)
(:CREATOR |martin|)
(:CREATION-DATE 3321745499) )
NIL)
(BR0-7557 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00431)
(RIGHT CPLX0-6522)
(:CREATOR |martin|)
(:CREATION-DATE 3321745596) )
NIL)
(BR0-7558 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00430)
(RIGHT CPLX0-6521)
(:CREATOR |martin|)
(:CREATION-DATE 3321745737) )
NIL)
(BR0-7561 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-6881)
(RIGHT CPLX0-5755)
(ACTIVATORS CPLX0-4505)
(INHIBITORS CPLX0-4506 CPLX0-4502 CPLX0-4503)
(:CREATOR |sgama|)
(:CREATION-DATE 3321815024) )
((INHIBITORS CPLX0-4503 CITATIONS "14731281")
(INHIBITORS CPLX0-4502 CITATIONS "14731281")
(INHIBITORS CPLX0-4506 CITATIONS "14731281")
(ACTIVATORS CPLX0-4505 CITATIONS "14731281")
(INHIBITORS CPLX0-4503 COMMENT
"The operator sequence recognized by AgaR in this position is not a directly sequence.")))
(BR0-7562 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-6882)
(RIGHT CPLX0-5754)
(INHIBITORS CPLX0-4350 CPLX0-4349)
(:CREATOR |sgama|)
(:CREATION-DATE 3321817849) )
((INHIBITORS CPLX0-4350 CITATIONS "14731281")
(INHIBITORS CPLX0-4349 CITATIONS "14731281")))
(BR0-7581 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-6883)
(RIGHT CPLX0-6520)
(INHIBITORS CPLX0-4390 CPLX0-4391 CPLX0-4509 CPLX0-4507 CPLX0-4508 CPLX0-4504)
(:CREATOR |sgama|)
(:CREATION-DATE 3321818250) )
((INHIBITORS CPLX0-4390 CITATIONS "14731281")
(INHIBITORS CPLX0-4390 COMMENT
"The AgaR operators sites farthest to the transcriptional start sites of agaS have not been experimentaly verified.
They were inferred by computational analysis, based on similarity to consensus sequence.")
(INHIBITORS CPLX0-4391 CITATIONS "14731281")
(INHIBITORS CPLX0-4391 COMMENT
"The AgaR operators sites farthest to the transcriptional start sites of agaS have not been experimentally verified.
They were inferred by computational analysis, based on similarity to consensus sequence.")
(INHIBITORS CPLX0-4509 CITATIONS "14731281")
(INHIBITORS CPLX0-4507 CITATIONS "14731281") (INHIBITORS CPLX0-4507 COMMENT)
(INHIBITORS CPLX0-4508 CITATIONS "14731281") (INHIBITORS CPLX0-4508 COMMENT)
(INHIBITORS CPLX0-4504 CITATIONS "14731281")
(INHIBITORS CPLX0-4504 COMMENT
"This operator sequence recognized by AgaR in this position is not a directly sequence.")))
(BR0-7622 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5442)
(RIGHT CPLX0-4503)
(:CREATOR |sgama|)
(:CREATION-DATE 3322246824) )
NIL)
(BR0-7623 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5443)
(RIGHT CPLX0-4502)
(:CREATOR |sgama|)
(:CREATION-DATE 3322249016) )
NIL)
(BR0-7624 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5444)
(RIGHT CPLX0-4506)
(:CREATOR |sgama|)
(:CREATION-DATE 3322249512) )
NIL)
(BR0-7625 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-5445)
(RIGHT CPLX0-4505)
(:CREATOR |sgama|)
(:CREATION-DATE 3322250224) )
NIL)
(BR0-7626 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5446)
(RIGHT CPLX0-4504)
(:CREATOR |sgama|)
(:CREATION-DATE 3322253410) )
NIL)
(BR0-7627 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5447)
(RIGHT CPLX0-4508)
(:CREATOR |sgama|)
(:CREATION-DATE 3322254320) )
NIL)
(BR0-7628 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5448)
(RIGHT CPLX0-4507)
(:CREATOR |sgama|)
(:CREATION-DATE 3322254814) )
NIL)
(BR0-7629 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5449)
(RIGHT CPLX0-4509)
(:CREATOR |sgama|)
(:CREATION-DATE 3322255056) )
NIL)
(BR0-7630 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5450)
(RIGHT CPLX0-4391)
(:CREATOR |sgama|)
(:CREATION-DATE 3322255493) )
NIL)
(BR0-7632 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-5451)
(RIGHT CPLX0-4390)
(:CREATOR |sgama|)
(:CREATION-DATE 3322311693) )
NIL)
(BR0-7641 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00615)
(RIGHT CPLX0-6519)
(ACTIVATORS CPLX0-5719 CPLX0-5718 CPLX0-5717)
(:CREATOR |martin|)
(:CREATION-DATE 3322356291) )
((ACTIVATORS CPLX0-5719 CITATIONS "9670013")
(ACTIVATORS CPLX0-5719 COMMENT
"This promoter is may coupled to CpxR-CpxA-dependent transcription |CITS: [9670013]|.")
(ACTIVATORS CPLX0-5718 CITATIONS "9670013")
(ACTIVATORS CPLX0-5718 COMMENT
"This promoter is may coupled to CpxR-CpxA-dependent transcription |CITS: [9670013]|.")
(ACTIVATORS CPLX0-5717 CITATIONS "9670013")
(ACTIVATORS CPLX0-5717 COMMENT
"This promoter is may coupled to CpxR-CpxA-dependent transcription |CITS: [9670013]|.")))
(BR0-7642 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00584)
(RIGHT CPLX0-6518)
(:CREATOR |martin|)
(:CREATION-DATE 3322356839) )
NIL)
(BR0-7643 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00429)
(RIGHT CPLX0-6517)
(:CREATOR |martin|)
(:CREATION-DATE 3322357107) )
NIL)
(BR0-7644 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00374)
(RIGHT CPLX0-6516)
(:CREATOR |martin|)
(:CREATION-DATE 3322357262) )
NIL)
(BR0-7645 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00508)
(RIGHT CPLX0-6515)
(:CREATOR |martin|)
(:CREATION-DATE 3322392286) )
NIL)
(BR0-7646 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00387)
(RIGHT CPLX0-6514)
(:CREATOR |martin|)
(:CREATION-DATE 3322392463) )
NIL)
(BR0-7648 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00325)
(RIGHT CPLX0-6513)
(INHIBITORS CPLX0-4367 CPLX0-4368)
(:CREATOR |martin|)
(:CREATION-DATE 3322393770) )
((INHIBITORS CPLX0-4367 CITATIONS "15988767")
(INHIBITORS CPLX0-4367 COMMENT
"It appears that the negative effect of ArcA and Fnr on aceE is not additive |CITS:[15988767]|.")
(INHIBITORS CPLX0-4368 COMMENT
"FNR represses aceEp promoter under anaerobic conditions.")
(INHIBITORS CPLX0-4368 CITATIONS "8057842" "15988767")))
(BR0-7649 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00472)
(RIGHT CPLX0-6512)
(:CREATOR |martin|)
(:CREATION-DATE 3322393895) )
NIL)
(BR0-7650 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00471)
(RIGHT CPLX0-6511)
(:CREATOR |martin|)
(:CREATION-DATE 3322394014) )
NIL)
(BR0-7661 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00508)
(RIGHT CPLX0-6510)
(:CREATOR |martin|)
(:CREATION-DATE 3322421822) )
NIL)
(BR0-7662 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00387)
(RIGHT CPLX0-6509)
(:CREATOR |martin|)
(:CREATION-DATE 3322421927) )
NIL)
(BR0-7663 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00507)
(RIGHT CPLX0-6508)
(:CREATOR |martin|)
(:CREATION-DATE 3322422095) )
NIL)
(BR0-7664 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00330)
(RIGHT CPLX0-6507)
(:CREATOR |martin|)
(:CREATION-DATE 3322422351) )
NIL)
(BR0-7665 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00331)
(RIGHT CPLX0-6506)
(:CREATOR |martin|)
(:CREATION-DATE 3322422381) )
NIL)
(BR0-7666 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00352)
(RIGHT CPLX0-6505)
(:CREATOR |martin|)
(:CREATION-DATE 3322422490) )
NIL)
(BR0-7667 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00398)
(RIGHT CPLX0-6504)
(:CREATOR |martin|)
(:CREATION-DATE 3322423174) )
NIL)
(BR0-7668 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00477)
(RIGHT CPLX0-6503)
(:CREATOR |martin|)
(:CREATION-DATE 3322423392) )
NIL)
(BR0-7669 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00345)
(RIGHT CPLX0-6502)
(:CREATOR |martin|)
(:CREATION-DATE 3322423508) )
NIL)
(BR0-7670 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00419)
(RIGHT CPLX0-6501)
(:CREATOR |martin|)
(:CREATION-DATE 3322423612) )
NIL)
(BR0-7671 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00438)
(RIGHT CPLX0-6500)
(:CREATOR |martin|)
(:CREATION-DATE 3322424359) )
NIL)
(BR0-7673 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00375)
(RIGHT CPLX0-6499)
(INHIBITORS CPLX0-5147)
(:CREATOR |martin|)
(:CREATION-DATE 3322425336) )
((INHIBITORS CPLX0-5147 CITATIONS "12754220")
(INHIBITORS CPLX0-5147 COMMENT
"Under anaerobiosis, FNR repress rplT gene expression, but it is not known if this regulation is direct or indirect |CITS: [12754220]|.")))
(BR0-7674 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00450)
(RIGHT CPLX0-6498)
(:CREATOR |martin|)
(:CREATION-DATE 3322425450) )
NIL)
(BR0-7675 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00439)
(RIGHT CPLX0-6497)
(:CREATOR |martin|)
(:CREATION-DATE 3322425652) )
NIL)
(BR0-7681 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00386)
(RIGHT CPLX0-6496)
(INHIBITORS CPLX0-4221 CPLX0-4219)
(:CREATOR |martin|)
(:CREATION-DATE 3322429849) )
((INHIBITORS CPLX0-4219 COMMENT) (INHIBITORS CPLX0-4219 CITATIONS "88314937")))
(BR0-7682 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00385)
(RIGHT CPLX0-6495)
(INHIBITORS CPLX0-4220 CPLX0-4218)
(:CREATOR |martin|)
(:CREATION-DATE 3322430009) )
((INHIBITORS CPLX0-4218 CITATIONS "88314937")))
(BR0-7683 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00641)
(RIGHT CPLX0-6494)
(:CREATOR |martin|)
(:CREATION-DATE 3322430307) )
NIL)
(BR0-7701 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00428)
(RIGHT CPLX0-6493)
(:CREATOR |martin|)
(:CREATION-DATE 3322511064) )
NIL)
(BR0-7702 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00481)
(RIGHT CPLX0-6492)
(:CREATOR |martin|)
(:CREATION-DATE 3322511489) )
NIL)
(BR0-7703 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00332)
(RIGHT CPLX0-6491)
(:CREATOR |martin|)
(:CREATION-DATE 3322512886) )
NIL)
(BR0-7721 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00455)
(RIGHT CPLX0-6490)
(:CREATOR |martin|)
(:CREATION-DATE 3322516314) )
NIL)
(BR0-7781 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5461)
(RIGHT CPLX0-4277)
(:CREATOR |martin|)
(:CREATION-DATE 3322925698) )
NIL)
(BR0-7782 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5462)
(RIGHT CPLX0-4276)
(:CREATOR |martin|)
(:CREATION-DATE 3322926040) )
NIL)
(BR0-7783 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5463)
(RIGHT CPLX0-4275)
(:CREATOR |martin|)
(:CREATION-DATE 3322926102) )
NIL)
(BR0-7787 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5467)
(RIGHT CPLX0-4273)
(:CREATOR |martin|)
(:CREATION-DATE 3322929845) )
NIL)
(BR0-7788 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5468)
(RIGHT CPLX0-4279)
(:CREATOR |martin|)
(:CREATION-DATE 3322929911) )
NIL)
(BR0-7789 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5469)
(RIGHT CPLX0-4278)
(:CREATOR |martin|)
(:CREATION-DATE 3322929991) )
NIL)
(BR0-7791 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5471)
(RIGHT CPLX0-4255)
(:CREATOR |martin|)
(:CREATION-DATE 3322930965) )
NIL)
(BR0-7792 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5472)
(RIGHT CPLX0-4253)
(:CREATOR |martin|)
(:CREATION-DATE 3322930997) )
NIL)
(BR0-7793 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5473)
(RIGHT CPLX0-4251)
(:CREATOR |martin|)
(:CREATION-DATE 3322931036) )
NIL)
(BR0-7794 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-5474)
(RIGHT CPLX0-4257)
(:CREATOR |martin|)
(:CREATION-DATE 3322931064) )
NIL)
(BR0-7801 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-5481)
(RIGHT CPLX0-5184)
(:CREATOR |martin|)
(:CREATION-DATE 3323016508) )
NIL)
(BR0-7802 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5482)
(RIGHT CPLX0-5183)
(:CREATOR |martin|)
(:CREATION-DATE 3323016614) )
NIL)
(BR0-7803 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5483)
(RIGHT CPLX0-5182)
(:CREATOR |martin|)
(:CREATION-DATE 3323016672) )
NIL)
(BR0-7804 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5484)
(RIGHT CPLX0-5181)
(:CREATOR |martin|)
(:CREATION-DATE 3323016725) )
NIL)
(BR0-7841 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00391)
(RIGHT CPLX0-6489)
(:CREATOR |sgama|)
(:CREATION-DATE 3323028350) )
NIL)
(BR0-7861 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7141)
(RIGHT CPLX0-5766)
(:CREATOR |sgama|)
(:CREATION-DATE 3323030545) )
NIL)
(BR0-7881 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-7161)
(RIGHT CPLX0-6488)
(:CREATOR |martin|)
(:CREATION-DATE 3323103665) )
NIL)
(BR0-7882 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-7162)
(RIGHT CPLX0-6487)
(:CREATOR |martin|)
(:CREATION-DATE 3323103831) )
NIL)
(BR0-7883 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7163)
(RIGHT CPLX0-6486)
(ACTIVATORS CPLX0-5180)
(:CREATOR |martin|)
(:CREATION-DATE 3323103923) )
((ACTIVATORS CPLX0-5180 CITATIONS "1848300" "12867454" "2163388")
(ACTIVATORS CPLX0-5180 COMMENT)))
(BR0-7884 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-5501)
(RIGHT CPLX0-5180)
(:CREATOR |martin|)
(:CREATION-DATE 3323105088) )
NIL)
(BR0-7901 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7183)
(RIGHT CPLX0-6485)
(ACTIVATORS CPLX0-5176)
(INHIBITORS CPLX0-5174 CPLX0-5175 CPLX0-5177 CPLX0-5178 CPLX0-5179)
(:CREATOR |martin|)
(:CREATION-DATE 3323110333) )
((INHIBITORS CPLX0-5174 COMMENT) (INHIBITORS CPLX0-5175 CITATIONS "15743943")
(INHIBITORS CPLX0-5178 COMMENT) (INHIBITORS CPLX0-5179 COMMENT)
(ACTIVATORS CPLX0-5176 CITATIONS "15743943")
(INHIBITORS CPLX0-5177 CITATIONS "15743943")
(INHIBITORS CPLX0-5178 CITATIONS "15743943")
(INHIBITORS CPLX0-5179 CITATIONS "15743943")))
(BR0-7902 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5521)
(RIGHT CPLX0-5179)
(:CREATOR |martin|)
(:CREATION-DATE 3323114062) )
NIL)
(BR0-7903 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5522)
(RIGHT CPLX0-5178)
(:CREATOR |martin|)
(:CREATION-DATE 3323114113) )
NIL)
(BR0-7904 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7678-MONOMER BS0-5523)
(RIGHT CPLX0-5177)
(:CREATOR |martin|)
(:CREATION-DATE 3323114613) )
NIL)
(BR0-7905 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-5524)
(RIGHT CPLX0-5176)
(:CREATOR |martin|)
(:CREATION-DATE 3323114802) )
NIL)
(BR0-7906 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00322)
(RIGHT CPLX0-6484)
(:CREATOR |martin|)
(:CREATION-DATE 3323116041) )
NIL)
(BR0-7921 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00321)
(RIGHT CPLX0-6483)
(:CREATOR |martin|)
(:CREATION-DATE 3323122848) )
NIL)
(BR0-7922 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00323)
(RIGHT CPLX0-6482)
(:CREATOR |martin|)
(:CREATION-DATE 3323122901) )
NIL)
(BR0-7923 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00497)
(RIGHT CPLX0-6481)
(:CREATOR |martin|)
(:CREATION-DATE 3323124269) )
NIL)
(BR0-7924 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00319)
(RIGHT CPLX0-6480)
(:CREATOR |martin|)
(:CREATION-DATE 3323124697) )
NIL)
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NIL)
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NIL)
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NIL)
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(:CREATION-DATE 3323207517) )
NIL)
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NIL)
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NIL)
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(:CREATOR |martin|)
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NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3323618045) )
NIL)
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(LEFT PM00498)
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(:CREATOR |martin|)
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NIL)
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"Under anaerobiosis, FNR represses rpsJ gene expression, but it is not known if this regulation is direct or indirect |CITS: [12754220]|. We assigned this regulation to the rrpsJ-rplCDWB-rpsS-rplV-rpsC-rplP-rpmC-rpsQ operon because it is known that rpsJ gene is transcribed as a part of this operon.")))
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NIL)
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NIL)
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NIL)
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NIL)
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(:CREATOR |martin|)
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NIL)
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(:CREATOR |martin|)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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(:CREATION-DATE 3323810351) )
NIL)
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(:CREATION-DATE 3323811140) )
NIL)
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(:CREATION-DATE 3325882590) )
NIL)
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(:CREATION-DATE 3325882711) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3325950020) )
NIL)
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NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3326136291) )
NIL)
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NIL)
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(:CREATION-DATE 3326486506) )
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(:CREATOR |sgama|)
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(:CREATOR |sgama|)
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NIL)
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NIL)
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NIL)
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NIL)
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(:CREATION-DATE 3328299983) )
NIL)
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NIL)
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(:CREATION-DATE 3328376513) )
NIL)
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(:CREATION-DATE 3328454915) )
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(:CREATION-DATE 3329571822) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3329574076) )
NIL)
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(LEFT PD00261 BS0-5966)
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(:CREATOR |martin|)
(:CREATION-DATE 3329574393) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3329666672) )
NIL)
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(LEFT PD00197 BS0-6001)
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(:CREATOR |sgama|)
(:CREATION-DATE 3329677090) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3329678394) )
NIL)
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(ACTIVATORS CPLX0-4372 COMMENT
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3330131162) )
NIL)
(BR0-8705 NIL (
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(LEFT PM0-7621)
(RIGHT CPLX0-6445)
(:CREATOR |martin|)
(:CREATION-DATE 3330185133) )
NIL)
(BR0-8706 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7622)
(RIGHT CPLX0-6444)
(:CREATOR |martin|)
(:CREATION-DATE 3330185673) )
NIL)
(BR0-8721 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7641)
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(:CREATOR |martin|)
(:CREATION-DATE 3330269169) )
NIL)
(BR0-8741 NIL (
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(INHIBITORS CPLX0-4236 CPLX0-4237)
(:CREATOR |sgama|)
(:CREATION-DATE 3331903967) )
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(INHIBITORS CPLX0-4236 COMMENT
"Mn2+ represses mntH expression. This repression is mediated by MntR, a transcriptional regulator that binds to a 25 nt region, positioned 23.5 nt upstream of the mntH gene start |CITS: [11466284]|.")
(INHIBITORS CPLX0-4237 CITATIONS "11466284")
(INHIBITORS CPLX0-4237 COMMENT
"Iron represses mntH expression. This repression is mediated by Fur, a transcriptional regulator that binds 59 nt upstream of the mntH gene start |CITS: [11466284]|.")))
(BR0-8742 NIL (
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(LEFT PC00009 BS0-6061)
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(:CREATOR |sgama|)
(:CREATION-DATE 3331904377) )
NIL)
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(:CREATION-DATE 3331907459) )
NIL)
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(:CREATION-DATE 3331990150) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3331992350) )
NIL)
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(:CREATOR |martin|)
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NIL)
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(:CREATION-DATE 3332794549) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3332796738) )
NIL)
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((ACTIVATORS CPLX0-5150 CITATIONS "2542226") (ACTIVATORS CPLX0-5150 COMMENT)))
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(:CREATOR |martin|)
(:CREATION-DATE 3332801560) )
NIL)
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(LEFT PM00616)
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(:CREATOR |martin|)
(:CREATION-DATE 3332801982) )
NIL)
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((INHIBITORS CPLX0-5149 CITATIONS "9023215") (INHIBITORS CPLX0-5149 COMMENT)))
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(LEFT PC00061 BS0-6101)
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(:CREATOR |martin|)
(:CREATION-DATE 3332863625) )
NIL)
(BR0-8862 NIL (
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(LEFT PM0-7781)
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(:CREATOR |martin|)
(:CREATION-DATE 3332876286) )
NIL)
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(LEFT PM0-7801)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333115937) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-7803)
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(:CREATOR |martin|)
(:CREATION-DATE 3333139672) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-6182)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333209103) )
NIL)
(BR0-8943 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-6183)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333209509) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-6184)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333210142) )
NIL)
(BR0-8945 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333210513) )
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"Under anaerobiosis, FNR represses rplS and trmD gene expression, but it is not known if this regulation is direct or indirect |CITS: [12754220]|. We assigned this regulation to the rpsP-rimM-trmD-rplS operon because it is known that rplS and trmD genes are transcribed as a part of this operon.")))
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(:CREATOR |sgama|)
(:CREATION-DATE 3333210682) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(:CREATOR |martin|)
(:CREATION-DATE 3333299174) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3333312721) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7)
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(:CREATOR |martin|)
(:CREATION-DATE 3338053835) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATOR |martin|)
(:CREATION-DATE 3333389657) )
NIL)
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(LEFT PM0-7881)
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(:CREATOR |martin|)
(:CREATION-DATE 3333457466) )
NIL)
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(LEFT PC00061 BS0-6241)
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(:CREATOR |martin|)
(:CREATION-DATE 3333459958) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS0-6261)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333564823) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7901)
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(:CREATOR |sgama|)
(:CREATION-DATE 3333728427) )
NIL)
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6321)
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(:CREATOR |asantos|)
(:CREATION-DATE 3333745061) )
NIL)
(BR0-9121 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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((ACTIVATORS CPLX0-5141 COMMENT)
(ACTIVATORS CPLX0-5141 CITATIONS "9532784" "12694615")))
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-7941)
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(ACTIVATORS CPLX0-5141)
(:CREATOR |martin|)
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((ACTIVATORS CPLX0-5141 COMMENT)
(ACTIVATORS CPLX0-5141 CITATIONS "9532784" "12694615")))
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-EVGA BS0-6341)
(RIGHT CPLX0-5141)
(:CREATOR |martin|)
(:CREATION-DATE 3333823810) )
NIL)
(BR0-9181 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(:CREATOR |asantos|)
(:CREATION-DATE 3333913721) )
((INHIBITORS CPLX0-5140 CITATIONS "1577702")
(INHIBITORS CPLX0-5140 COMMENT
"polB(dinA) regulatory region contains both a perfect match to LexA binding site and a sequences with the extended dyad symmetry (CTGT....ACAG) seen in the consensus sequence for LexA operators.")))
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6361)
(RIGHT CPLX0-5140)
(:CREATOR |asantos|)
(:CREATION-DATE 3333916096) )
NIL)
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(INHIBITORS CPLX0-5139)
(BASAL-TRANSCRIPTION-VALUE 1577702)
(:CREATOR |asantos|)
(:CREATION-DATE 3333917894) )
((INHIBITORS CPLX0-5139 CITATIONS "1577702")
(INHIBITORS CPLX0-5139 COMMENT
"dinH regulatory region contains both a perfect match to LexA binding site and a sequences with the extended dyad symmetry (CTGT....ACAG) seen in the consensus sequence for LexA operators.")))
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(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6362)
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(:CREATOR |asantos|)
(:CREATION-DATE 3333918073) )
NIL)
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(INHIBITORS CPLX0-5138)
(:CREATOR |martin|)
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(BR0-9202 NIL (
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(LEFT G6276-MONOMER BS0-6381)
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(:CREATOR |martin|)
(:CREATION-DATE 3333983241) )
NIL)
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(INHIBITORS CPLX0-5138)
(:CREATOR |martin|)
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((INHIBITORS CPLX0-5138 CITATIONS "12460564")))
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(:CREATOR |martin|)
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((INHIBITORS CPLX0-5137 CITATIONS "12460564")))
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(LEFT G6276-MONOMER BS0-6382)
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(:CREATOR |martin|)
(:CREATION-DATE 3333985821) )
NIL)
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(:CREATOR |martin|)
(:CREATION-DATE 3333992955) )
NIL)
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(LEFT PC00009 BS0-6441)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334076060) )
NIL)
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(LEFT PC00009 BS0-6461)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334085966) )
NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334086133) )
NIL)
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((INHIBITORS CPLX0-4604 CITATIONS "11101675")
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(BR0-9304 NIL (
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(LEFT PC00009 BS0-6463)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334086879) )
NIL)
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(LEFT PC00009 BS0-6464)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334086925) )
NIL)
(BR0-9321 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8102)
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(:CREATOR |sgama|)
(:CREATION-DATE 3334096605) )
NIL)
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(LEFT PM0-8121)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334323862) )
NIL)
(BR0-9342 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8123)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334325658) )
NIL)
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(LEFT PM0-8124)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334326158) )
NIL)
(BR0-9344 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8125)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334326451) )
NIL)
(BR0-9345 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8126)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334326764) )
NIL)
(BR0-9346 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-6481)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334328961) )
NIL)
(BR0-9347 NIL (
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(LEFT PD00288 BS0-6482)
(RIGHT CPLX0-4674)
(:CREATOR |asantos|)
(:CREATION-DATE 3334330726) )
NIL)
(BR0-9348 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-6483)
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(:CREATOR |asantos|)
(:CREATION-DATE 3334331936) )
NIL)
(BR0-9361 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8161)
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(ACTIVATORS CPLX0-5134)
(:CREATOR |martin|)
(:CREATION-DATE 3334352985) )
((ACTIVATORS CPLX0-5134 CITATIONS "12813061" "15883881")
(ACTIVATORS CPLX0-5134 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it checked for the presence of its regulatory motif in the promoter region |CITS: [15883881]|.")))
(BR0-9362 NIL (
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(LEFT PHOSPHO-PHOP BS0-6501)
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(:CREATOR |martin|)
(:CREATION-DATE 3334353194) )
NIL)
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(ACTIVATORS CPLX0-5133)
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((ACTIVATORS CPLX0-5133 CITATIONS "12813061") (ACTIVATORS CPLX0-5133 COMMENT)))
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(:CREATOR |martin|)
(:CREATION-DATE 3334354031) )
NIL)
(BR0-9365 NIL (
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(LEFT PM0-8164)
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(:CREATOR |martin|)
(:CREATION-DATE 3334354543) )
((ACTIVATORS CPLX0-5132 CITATIONS "12813061" "15883881")
(ACTIVATORS CPLX0-5132 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it checked for the presence of its regulatory motif in the promoter region |CITS: [15883881]|.")))
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(LEFT PHOSPHO-PHOP BS0-6503)
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(:CREATOR |martin|)
(:CREATION-DATE 3334354633) )
NIL)
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(:CREATOR |martin|)
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((ACTIVATORS CPLX0-5131 CITATIONS "12813061")))
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(LEFT PHOSPHO-PHOP BS0-6522)
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(:CREATOR |martin|)
(:CREATION-DATE 3334421251) )
NIL)
(BR0-9384 NIL (
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(LEFT PM0-8183)
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(:CREATOR |martin|)
(:CREATION-DATE 3334421387) )
((INHIBITORS CPLX0-5131 CITATIONS "12813061") (INHIBITORS CPLX0-5131 COMMENT)))
(BR0-9386 NIL (
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(:CREATOR |sgama|)
(:CREATION-DATE 3334425935) )
((INHIBITORS CPLX0-5679 CITATIONS "16478729") (INHIBITORS CPLX0-5679 COMMENT)))
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(:CREATOR |martin|)
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((ACTIVATORS CPLX0-5130 CITATIONS "12813061") (ACTIVATORS CPLX0-5130 COMMENT)))
(BR0-9388 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-6524)
(RIGHT CPLX0-5130)
(:CREATOR |martin|)
(:CREATION-DATE 3334432897) )
NIL)
(BR0-9389 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8186)
(RIGHT CPLX0-6406)
(ACTIVATORS CPLX0-5129)
(:CREATOR |martin|)
(:CREATION-DATE 3334433667) )
((ACTIVATORS CPLX0-5129 CITATIONS "12813061") (ACTIVATORS CPLX0-5129 COMMENT)))
(BR0-9390 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-6525)
(RIGHT CPLX0-5129)
(:CREATOR |martin|)
(:CREATION-DATE 3334433723) )
NIL)
(BR0-9401 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8201)
(RIGHT CPLX0-6405)
(ACTIVATORS CPLX0-5128)
(:CREATOR |martin|)
(:CREATION-DATE 3334435530) )
((ACTIVATORS CPLX0-5128 CITATIONS "15126461")))
(BR0-9402 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-6541)
(RIGHT CPLX0-5128)
(:CREATOR |martin|)
(:CREATION-DATE 3334435605) )
NIL)
(BR0-9403 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8202)
(RIGHT CPLX0-6404)
(ACTIVATORS CPLX0-5127)
(:CREATOR |martin|)
(:CREATION-DATE 3334435811) )
((ACTIVATORS CPLX0-5127 CITATIONS "15126461") (ACTIVATORS CPLX0-5127 COMMENT)))
(BR0-9404 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-PHOP BS0-6542)
(RIGHT CPLX0-5127)
(:CREATOR |martin|)
(:CREATION-DATE 3334435905) )
NIL)
(BR0-9405 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8203)
(RIGHT CPLX0-6403)
(:CREATOR |martin|)
(:CREATION-DATE 3334436358) )
NIL)
(BR0-9441 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6561)
(RIGHT CPLX0-5126)
(:CREATOR |martin|)
(:CREATION-DATE 3334599013) )
NIL)
(BR0-9481 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11544-MONOMER BS0-6581)
(RIGHT CPLX0-5125)
(:CREATOR |asantos|)
(:CREATION-DATE 3334604851) )
NIL)
(BR0-9482 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6582)
(RIGHT CPLX0-5124)
(:CREATOR |asantos|)
(:CREATION-DATE 3334605795) )
NIL)
(BR0-9483 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8222)
(RIGHT CPLX0-6402)
(:CREATOR |sgama|)
(:CREATION-DATE 3334607627) )
NIL)
(BR0-9484 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8224)
(RIGHT CPLX0-6401)
(:CREATOR |sgama|)
(:CREATION-DATE 3334608045) )
NIL)
(BR0-9501 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS0-6601)
(RIGHT CPLX0-3987)
(:CREATOR |martin|)
(:CREATION-DATE 3334676750) )
NIL)
(BR0-9502 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8241)
(RIGHT CPLX0-5762)
(ACTIVATORS CPLX0-3988)
(INHIBITORS CPLX0-3986)
(:CREATOR |martin|)
(:CREATION-DATE 3334679372) )
((ACTIVATORS CPLX0-3988 CITATIONS "15743955")
(INHIBITORS CPLX0-3986 CITATIONS "15743955") (INHIBITORS CPLX0-3986 COMMENT)))
(BR0-9503 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6799-MONOMER BS0-6621)
(RIGHT CPLX0-3986)
(:CREATOR |martin|)
(:CREATION-DATE 3334680303) )
NIL)
(BR0-9504 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6622)
(RIGHT CPLX0-3989)
(:CREATOR |asantos|)
(:CREATION-DATE 3334691151) )
NIL)
(BR0-9505 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6623)
(RIGHT CPLX0-3988)
(:CREATOR |martin|)
(:CREATION-DATE 3334693767) )
NIL)
(BR0-9506 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00598 RNAPS-CPLX)
(RIGHT CPLX0-5763)
(ACTIVATORS CPLX0-4888 CPLX0-4887)
(INHIBITORS CPLX0-5503 CPLX0-5386 CPLX0-5387 CPLX0-5388 CPLX0-5389)
(:CREATOR |martin|)
(:CREATION-DATE 3334694670) )
((INHIBITORS CPLX0-5503 CITATIONS "16677314") (INHIBITORS CPLX0-5503 COMMENT)
(INHIBITORS CPLX0-5388 CITATIONS) (INHIBITORS CPLX0-5388 COMMENT)
(INHIBITORS CPLX0-5387 CITATIONS) (INHIBITORS CPLX0-5387 COMMENT)
(INHIBITORS CPLX0-5389 CITATIONS) (INHIBITORS CPLX0-5389 COMMENT)))
(BR0-9507 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8261)
(RIGHT CPLX0-5764)
(ACTIVATORS CPLX0-5645 CPLX0-3990)
(:CREATOR |martin|)
(:CREATION-DATE 3334697509) )
((ACTIVATORS CPLX0-5645 CITATIONS "15686558")
(ACTIVATORS CPLX0-5645 COMMENT
"CpxR regulator binds to the mdtA regulatory region at two sites: -161.5 and -98.5, all of them with respect to the start codon of mdtA gene since the +1 of the transcription initiation has not been determined yet. The site -98.5 of CpxR overlaps to the BaeR site. These sites were determined by Gen Expression Analysis and Purified Proteins.
CpxAR signaling depends on the BaeRS system and CpxR binds to multiple distal regions to modulate the effect of BaeR.
|CITS:[15686558]|.
")
(ACTIVATORS CPLX0-3990 COMMENT
"BaeR regulator binds to the mdtA regulatory region to -62.5 with respect to the start codon of mdtA gene since the +1 of the transcription initiation has not been determined. This site was determined by Gen Expression Analysis and Purified Proteins. It is overlapped by the site -98.5 of CpxR |CITS:[15686558]|.
The central position of the BaeR binding site (TTTTTCTCCCTTATTGGC) has been identified by similarity to the consensus sequence TTTTTCTCCATDATTGGC (using the Align ACE program)|CITS:[15716448]|. D = G, A or T.
The induction of mdtA gene is mediated by indole via BaeR |CITS:[15686558]|.
")
(ACTIVATORS CPLX0-3990 CITATIONS "12107133" "15686558" "15716448")))
(BR0-9508 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-BAER BS0-6641)
(RIGHT CPLX0-3990)
(:CREATOR |martin|)
(:CREATION-DATE 3334697699) )
NIL)
(BR0-9521 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00231 RNAPS-CPLX)
(RIGHT CPLX0-5778)
(ACTIVATORS CPLX0-4994)
(INHIBITORS CPLX0-4545 CPLX0-5420 CPLX0-4517)
(:CREATOR |martin|)
(:CREATION-DATE 3334946200) )
((INHIBITORS CPLX0-5420 CITATIONS "11287152")
(INHIBITORS CPLX0-5420 COMMENT
"The regulatory effect of FlhDC in the mglB operon transcription has been proved just by microarray analysis by |CITS: [21184412]|")
(ACTIVATORS CPLX0-4994 CITATIONS "93106962" "15520470")
(ACTIVATORS CPLX0-4994 COMMENT)))
(BR0-9522 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8281)
(RIGHT CPLX0-5777)
(INHIBITORS CPLX0-5121)
(:CREATOR |martin|)
(:CREATION-DATE 3334947036) )
((INHIBITORS CPLX0-5121 CITATIONS "7860604")
(INHIBITORS CPLX0-5121 COMMENT
"Both Fis and RpoS negatively regulate to mglA in a gene expression analysis. The rpoS effect could be indirect |CITS: [7860604]|.")))
(BR0-9541 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8342)
(RIGHT CPLX0-6400)
(INHIBITORS CPLX0-4068)
(:CREATOR |asantos|)
(:CREATION-DATE 3335108192) )
((INHIBITORS CPLX0-4068 CITATIONS "15616579")
(INHIBITORS CPLX0-4068 COMMENT
"Between the dhaKLM operon and the dhaR gene there is a 190-bp-long intergenic region that divergently transcribes them. DhaR is an (auto) repressor of the dhaR gene and an activator of the dhaKLM operon |CITS: [15616579]|.")))
(BR0-9542 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6628-MONOMER BS0-6661)
(RIGHT CPLX0-4068)
(:CREATOR |asantos|)
(:CREATION-DATE 3335109892) )
NIL)
(BR0-9561 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8361)
(RIGHT CPLX0-6399)
(ACTIVATORS CPLX0-5123)
(:CREATOR |asantos|)
(:CREATION-DATE 3335128497) )
((ACTIVATORS CPLX0-5123 CITATIONS "15616579")
(ACTIVATORS CPLX0-5123 COMMENT
"Between the dhaKLM operon and the dhaR gene there is a 190-bp-long intergenic region that divergently transcribes them. DhaR is an (auto) repressor of the dhaR gene and an activator of the dhaKLM operon |CITS: [15616579]|.")))
(BR0-9562 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6628-MONOMER BS0-6681)
(RIGHT CPLX0-5123)
(:CREATOR |asantos|)
(:CREATION-DATE 3335128732) )
NIL)
(BR0-9563 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6682)
(RIGHT CPLX0-5122)
(:CREATOR |asantos|)
(:CREATION-DATE 3335188455) )
NIL)
(BR0-9564 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6683)
(RIGHT CPLX0-5121)
(:CREATOR |asantos|)
(:CREATION-DATE 3335188806) )
NIL)
(BR0-9565 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8381)
(RIGHT CPLX0-6398)
(INHIBITORS CPLX0-5120)
(:CREATOR |asantos|)
(:CREATION-DATE 3335189036) )
((INHIBITORS CPLX0-5120 CITATIONS "7860604")
(INHIBITORS CPLX0-5120 COMMENT
"Fis negatively regulates to glnQ gene expression and rpoS lightly regulates its expression |CITS: [7860604]|.")))
(BR0-9566 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS0-6684)
(RIGHT CPLX0-5120)
(:CREATOR |asantos|)
(:CREATION-DATE 3335189448) )
NIL)
(BR0-9581 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8401)
(RIGHT CPLX0-6397)
(ACTIVATORS CPLX0-5644 CPLX0-5118 CPLX0-5119)
(:CREATOR |asantos|)
(:CREATION-DATE 3335196192) )
((ACTIVATORS CPLX0-5644 CITATIONS "15686558")
(ACTIVATORS CPLX0-5644 COMMENT
"CpxR regulator binds to the acrD regulatory region at three sites: -141.5, -174.5 and -115.5, all of them with respect to the start codon of acrD gene since the +1 of the transcription initiation has not been determined yet. It possible that the -115.5 site of CpxR overlaps to the BaeR site, in this region. These sites were determined by Gen Expression Analysis and Purified Proteins.
CpxAR signaling depends on the BaeRS system and CpxR binds to multiple distal regions to modulate the effect of BaeR.
|CITS:[15686558]|.
")
(ACTIVATORS CPLX0-5118 CITATIONS "12951338" "15686558" "15716448")
(ACTIVATORS CPLX0-5118 COMMENT
"Through of overexpression analysis, baeR and evgA mediated B-lactam as result of induction of multidrug exporter acrD gene expression indirect |CITS: [12951338]|.
BaeR regulator binds to the acrD regulatory region at -79.5 with respect to the start codon of acrD gene since the +1 of the transcription initiation has not been determined yet. It is possible that this site is overlapped by the site -115.5 of CpxR in this region. This site was determined by Gen Expression Analysis and Purified Proteins. |CITS:[15686558]|.
The central position of the BaeR binding site (TTTTTCTCCACGATTGGC) has been identified by similarity to the consensus sequence TTTTTCTCCATDATTGGC (using the Align ACE program)|CITS:[15716448]|. D = G, A or T.
The induction of acrD gene is mediated by indole via BaeR |CITS:[15686558]|.")
(ACTIVATORS CPLX0-5119 CITATIONS "12951338")
(ACTIVATORS CPLX0-5119 COMMENT
"Through of overexpression analysis, BaeR and EvgA mediated B-lactam as result of induction of multidrug exporter acrD gene expression indirect |CITS: [12951338]|.")))
(BR0-9582 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-EVGA BS0-6701)
(RIGHT CPLX0-5119)
(:CREATOR |asantos|)
(:CREATION-DATE 3335196307) )
NIL)
(BR0-9583 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-BAER BS0-6702)
(RIGHT CPLX0-5118)
(:CREATOR |asantos|)
(:CREATION-DATE 3335196413) )
NIL)
(BR0-9601 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00369 BS0-6721)
(RIGHT CPLX0-4336)
(:CREATOR |martin|)
(:CREATION-DATE 3335722864) )
NIL)
(BR0-9621 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-6741)
(RIGHT CPLX0-4349)
(:CREATOR |martin|)
(:CREATION-DATE 3335725755) )
NIL)
(BR0-9622 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7630-MONOMER BS0-6742)
(RIGHT CPLX0-4350)
(:CREATOR |martin|)
(:CREATION-DATE 3335725824) )
NIL)
(BR0-9625 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8424)
(RIGHT CPLX0-6396)
(:CREATOR |martin|)
(:CREATION-DATE 3335731291) )
NIL)
(BR0-9641 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8441)
(RIGHT CPLX0-6395)
(:CREATOR |martin|)
(:CREATION-DATE 3336315771) )
NIL)
(BR0-9642 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS0-6761)
(RIGHT CPLX0-4317)
(:CREATOR |martin|)
(:CREATION-DATE 3336319858) )
NIL)
(BR0-9661 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-8461)
(RIGHT CPLX0-6394)
(:CREATOR |martin|)
(:CREATION-DATE 3336399930) )
NIL)
(BR0-9663 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8464)
(RIGHT CPLX0-6393)
(:CREATOR |martin|)
(:CREATION-DATE 3336408006) )
NIL)
(BR0-9681 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6781)
(RIGHT CPLX0-4218)
(:CREATOR |martin|)
(:CREATION-DATE 3336415690) )
NIL)
(BR0-9682 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6782)
(RIGHT CPLX0-4220)
(:CREATOR |martin|)
(:CREATION-DATE 3336415882) )
NIL)
(BR0-9683 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6783)
(RIGHT CPLX0-4219)
(:CREATOR |martin|)
(:CREATION-DATE 3336416848) )
NIL)
(BR0-9684 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00205 BS0-6784)
(RIGHT CPLX0-4221)
(:CREATOR |martin|)
(:CREATION-DATE 3336417033) )
NIL)
(BR0-9701 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8481)
(RIGHT CPLX0-6392)
(:CREATOR |martin|)
(:CREATION-DATE 3336759624) )
NIL)
(BR0-9721 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8501)
(RIGHT CPLX0-6391)
(:CREATOR |martin|)
(:CREATION-DATE 3336776755) )
NIL)
(BR0-9743 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8523)
(RIGHT CPLX0-6390)
(:CREATOR |martin|)
(:CREATION-DATE 3336790627) )
NIL)
(BR0-9744 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8525)
(RIGHT CPLX0-6389)
(:CREATOR |martin|)
(:CREATION-DATE 3336791171) )
NIL)
(BR0-9745 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8526)
(RIGHT CPLX0-6388)
(:CREATOR |martin|)
(:CREATION-DATE 3336791471) )
NIL)
(BR0-9746 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8527)
(RIGHT CPLX0-6387)
(:CREATOR |martin|)
(:CREATION-DATE 3336792290) )
NIL)
(BR0-9747 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8528)
(RIGHT CPLX0-6386)
(:CREATOR |martin|)
(:CREATION-DATE 3336792354) )
NIL)
(BR0-9748 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-8529)
(RIGHT CPLX0-6385)
(:CREATOR |martin|)
(:CREATION-DATE 3336816958) )
NIL)
(BR0-9749 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8530)
(RIGHT CPLX0-6384)
(:CREATOR |martin|)
(:CREATION-DATE 3336822619) )
NIL)
(BR0-9761 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8541)
(RIGHT CPLX0-6383)
(:CREATOR |martin|)
(:CREATION-DATE 3336839495) )
NIL)
(BR0-9762 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8542)
(RIGHT CPLX0-6382)
(:CREATOR |martin|)
(:CREATION-DATE 3336839873) )
NIL)
(BR0-9781 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8561)
(RIGHT CPLX0-6381)
(:CREATOR |martin|)
(:CREATION-DATE 3336858454) )
NIL)
(BR0-9782 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM0-8562)
(RIGHT CPLX0-6380)
(:CREATOR |martin|)
(:CREATION-DATE 3336863883) )
NIL)
(BR0-9801 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8581)
(RIGHT CPLX0-6379)
(:CREATOR |martin|)
(:CREATION-DATE 3336919907) )
NIL)
(BR0-9802 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8582)
(RIGHT CPLX0-6378)
(:CREATOR |martin|)
(:CREATION-DATE 3336920018) )
NIL)
(BR0-9803 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM0-8583)
(RIGHT CPLX0-6377)
(:CREATOR |martin|)
(:CREATION-DATE 3336920110) )
NIL)
(BR0-9821 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8601)
(RIGHT CPLX0-6376)
(INHIBITORS CPLX0-5115 CPLX0-5116)
(ACTIVATORS CPLX0-5117)
(:CREATOR |asantos|)
(:CREATION-DATE 3336927013) )
((INHIBITORS CPLX0-5115 CITATIONS "2543976") (INHIBITORS CPLX0-5115 COMMENT)
(INHIBITORS CPLX0-5116 CITATIONS "2543976")
(ACTIVATORS CPLX0-5117 CITATIONS "2543976")
(ACTIVATORS CPLX0-5117 COMMENT
"MetR is perhaps be responsible for both the activation of expression of metE as well as the autoregulation of metR gene.")))
(BR0-9822 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8603)
(RIGHT CPLX0-6375)
(INHIBITORS CPLX0-5117 CPLX0-5115 CPLX0-5116)
(:CREATOR |asantos|)
(:CREATION-DATE 3336930117) )
((INHIBITORS CPLX0-5116 COMMENT
"Both sites of the MetJ regulator in the intergenic-region of metE and metR could be negatively regulating both promoters metRp2 and metRp1.")
(INHIBITORS CPLX0-5117 CITATIONS "2543976")
(INHIBITORS CPLX0-5117 COMMENT
"MetR is perhaps be responsible for both the activation of expression of metE as well as the autoregulation of metR gene.")
(INHIBITORS CPLX0-5115 CITATIONS "2543976")
(INHIBITORS CPLX0-5115 COMMENT
"Both sites of the MetJ regulator in the intergenic-region of metE and metR could be negatively regulating both promoters metRp2 and metRp1.")
(INHIBITORS CPLX0-5116 CITATIONS "2543976")))
(BR0-9823 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM0-8604)
(RIGHT CPLX0-6374)
(INHIBITORS CPLX0-5117 CPLX0-5115 CPLX0-5116)
(:CREATOR |asantos|)
(:CREATION-DATE 3336931934) )
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(INHIBITORS CPLX0-5115 CITATIONS "2543976")
(INHIBITORS CPLX0-5115 COMMENT
"Both sites of the MetJ regulator in the intergenic-region of metE and metR could be negatively regulating both promoters metRp2 and metRp1.")
(INHIBITORS CPLX0-5116 CITATIONS "2543976")
(INHIBITORS CPLX0-5116 COMMENT
"Both sites of the MetJ regulator in the intergenic-region of metE and metR could be negatively regulating both promoters metRp2 and metRp1.")))
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Both sites were determined by computational searches and their inducibility was analyzed by Northern analysis in a variety of lexA backgrounds and by footprinting analysis.
The sequence of the box 1 is as the follows: CTGTACGTATCGACAG, and its absolute position is 1808210.5. The sequence of the box 2 is the follow it: CTGTATAAAAATCCTA, and its absolute position is 1808192.5.
We have given the absolute position in the genome of E. coli of these sites instead of the central position since the +1 of the transcription initiation has not yet been determined |CITS:[ 10760155]|.
")))
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The sequence of the site is as follows: CTGTATTTGTCTCCAG, and its absolute position is 3719642.5
We have given the absolute position in the genome of E. coli of this site instead of the central position since the +1 of the transcription initiation has not yet been determined |CITS:[ 10760155]|.
")))
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The sequence of the site is as the follows: CTGTATGATTATCCAG, and its absolute position is 3646013.5
We have given the absolute position in the genome of E. coli of this site instead of the central position since the +1 of the transcription initiation has not yet been determined
|CITS:[ 10760155]|.")))
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(:CREATION-DATE 3163452702) )
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(CITATIONS "[83272947]")
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(:CREATION-DATE 3163452702) )
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
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(CITATIONS "[88288052]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[89012001]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[86085676]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[86085676]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[86085676]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[92104984]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[79093990]" "[89336774]" "[92062732]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(LEFT PC00009 BS00040)
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(CITATIONS "[89123101]")
(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATION-DATE 3163452702) )
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(:CREATION-DATE 3163452702) )
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(:CREATION-DATE 3163452702) )
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(:CREATION-DATE 3163452702) )
NIL)
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(CITATIONS "[87004572]" "[89336786]")
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(:CREATION-DATE 3163452702) )
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATOR |collado|)
(:CREATION-DATE 3163452702) )
NIL)
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(:CREATION-DATE 3163452702) )
NIL)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188316688) )
NIL)
(BR124 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM176)
(RIGHT CPLX0-6321)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188317374) )
NIL)
(BR125 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00214)
(RIGHT CPLX0-6320)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188590408)
(ACTIVATORS CPLX0-5444)
(INHIBITORS CPLX0-4405 CPLX0-4815 CPLX0-4483)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4483 CITATIONS "[94164309]")
(INHIBITORS CPLX0-4815 CITATIONS "[89263708]" "[94164309]")
(INHIBITORS CPLX0-4405 CITATIONS "[94164309]")
(ACTIVATORS CPLX0-5444 CITATIONS "[99140136]")
(ACTIVATORS CPLX0-5444 COMMENT
"A model is proposed in which ModE-molybdate serves as a secondary transcriptional activator of both the hyc and narXL operons which are activated primarily by the transcriptional activators, FhlA and NarL, respectively.")))
(BR126 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM177)
(RIGHT CPLX0-6319)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188318096) )
NIL)
(BR127 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM178)
(RIGHT CPLX0-6318)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188324787) )
NIL)
(BR128 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM179)
(RIGHT CPLX0-6317)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188325817) )
NIL)
(BR129 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM180)
(RIGHT CPLX0-6316)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188326694) )
NIL)
(BR130 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM181)
(RIGHT CPLX0-6315)
(ACTIVATORS CPLX0-5414)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188327874) )
((ACTIVATORS CPLX0-5414 COMMENT)
(ACTIVATORS CPLX0-5414 CITATIONS "[99200496]" "[96323034]" "[20032357]")))
(BR131 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM194)
(RIGHT CPLX0-6314)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188328700) )
NIL)
(BR132 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM195)
(RIGHT CPLX0-6313)
(OFFICIAL-EC? T)
(ACTIVATORS CPLX0-4760)
(:CREATOR |sgama|)
(:CREATION-DATE 3188330153) )
((ACTIVATORS CPLX0-4760 COMMENT
"Shalel-Levanon et al |CITS: [15988767]| suggested that FNR has a minor positive effect or no effect on arcA expression under the conditions that they used.")
(ACTIVATORS CPLX0-4760 CITATIONS "[94293769]")))
(BR133 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM196)
(RIGHT CPLX0-6312)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188331132) )
NIL)
(BR137 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS105)
(RIGHT CPLX0-4485)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188571601) )
NIL)
(BR140 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS108)
(RIGHT CPLX0-4820)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188572685) )
NIL)
(BR141 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS109)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188573330) )
NIL)
(BR142 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM324)
(RIGHT CPLX0-6311)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168973663)
(INHIBITORS CPLX0-5494 CPLX0-5214 CPLX0-5215 CPLX0-5216 CPLX0-4501 CPLX0-4479
CPLX0-4478)
(ACTIVATORS CPLX0-4477)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5494 CITATIONS "16377617") (INHIBITORS CPLX0-5494 COMMENT)
(ACTIVATORS CPLX0-4477 CITATIONS "9202484")
(INHIBITORS CPLX0-5214 CITATIONS "10071223") (INHIBITORS CPLX0-5214 COMMENT)
(INHIBITORS CPLX0-4478 CITATIONS "10071223") (INHIBITORS CPLX0-4478 COMMENT)
(INHIBITORS CPLX0-5215 CITATIONS "10071223") (INHIBITORS CPLX0-5215 COMMENT)
(INHIBITORS CPLX0-5216 CITATIONS "10071223") (INHIBITORS CPLX0-5216 COMMENT)
(INHIBITORS CPLX0-4479 CITATIONS "10071223") (INHIBITORS CPLX0-4479 COMMENT)
(INHIBITORS CPLX0-4501 CITATIONS "11160809")))
(BR143 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM325)
(RIGHT CPLX0-6310)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168975272)
(:CREATOR |sgama|) )
NIL)
(BR144 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM326)
(RIGHT CPLX0-6309)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168977678)
(ACTIVATORS CPLX0-5357 CPLX0-5422)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5422 COMMENT) (ACTIVATORS CPLX0-5357 CITATIONS "20570538")
(ACTIVATORS CPLX0-5422 CITATIONS "[96105196]")))
(BR145 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM327)
(RIGHT CPLX0-6308)
(ACTIVATORS CPLX0-4146 CPLX0-4147)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168978324)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4147 CITATIONS "8596457")
(ACTIVATORS CPLX0-4146 CITATIONS "95286540")))
(BR146 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM327)
(RIGHT CPLX0-6307)
(ACTIVATORS CPLX0-4146 CPLX0-4147)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168978324)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4147 CITATIONS "8596457")
(ACTIVATORS CPLX0-4146 CITATIONS "95286540")))
(BR147 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM328)
(RIGHT CPLX0-6306)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169213116)
(:CREATOR |sgama|) )
NIL)
(BR148 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM329)
(RIGHT CPLX0-6305)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169214175)
(:CREATOR |sgama|) )
NIL)
(BR149 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM330)
(RIGHT CPLX0-6304)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(:CREATOR |sgama|) )
NIL)
(BR150 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM331 RNAP70-CPLX)
(RIGHT CPLX0-6303)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(:CREATOR |sgama|) )
NIL)
(BR151 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM332 RNAP70-CPLX)
(RIGHT CPLX0-6302)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(ACTIVATORS CPLX0-4421 CPLX0-4725)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4421 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4725 COMMENT)
(ACTIVATORS CPLX0-4725 CITATIONS "[97055421]" "[20032357]")))
(BR152 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM332)
(RIGHT CPLX0-6301)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(ACTIVATORS CPLX0-4421 CPLX0-4725)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4421 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4725 COMMENT)
(ACTIVATORS CPLX0-4725 CITATIONS "[97055421]" "[20032357]")))
(BR153 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM333)
(RIGHT CPLX0-6300)
(ACTIVATORS CPLX0-5199 CPLX0-5200 CPLX0-4351)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5199 CITATIONS "98411361")
(ACTIVATORS CPLX0-5199 COMMENT
"The regulatory effect of IHF on the rtcB promoter is not known yet.
However, we assigned a positive effect to this regulatory interaction based on the protein?s binding site which is upstream to the promoter (62 bp upstream to the transcription start site).")
(ACTIVATORS CPLX0-5200 CITATIONS "98411361")
(ACTIVATORS CPLX0-5200 COMMENT
"The regulatory effect of IHF on the rtcB promoter is as yet not known.
However, we assigned a positive effect to this regulatory interaction based on the protein?s binding site is upstream to the promoter (52 bp upstream to the transcription start site).")
(ACTIVATORS CPLX0-4351 CITATIONS "[98411361]")
(ACTIVATORS CPLX0-4351 COMMENT
"RtcR with its N-terminal truncated activates the transcription of rtcBA operon.")))
(BR154 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM334)
(RIGHT CPLX0-6299)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(INHIBITORS CPLX0-4730 CPLX0-4731)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4730 CITATIONS "[20252593]")
(INHIBITORS CPLX0-4731 CITATIONS "[20252593]")))
(BR155 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM335)
(RIGHT CPLX0-6298)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169217401)
(:CREATOR |sgama|) )
NIL)
(BR156 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM336)
(RIGHT CPLX0-6297)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169218122)
(:CREATOR |sgama|) )
NIL)
(BR157 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS110)
(RIGHT CPLX0-4484)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188573581) )
NIL)
(BR158 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM338)
(RIGHT CPLX0-6296)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169225922)
(INHIBITORS CPLX0-5103 CPLX0-4496)
(ACTIVATORS CPLX0-4404 CPLX0-4611)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5103 CITATIONS "8631699") (INHIBITORS CPLX0-5103 COMMENT)
(INHIBITORS CPLX0-4496 CITATIONS "[96200092]")
(INHIBITORS CPLX0-4496 COMMENT)
(ACTIVATORS CPLX0-4404 CITATIONS "[96200092]")
(ACTIVATORS CPLX0-4404 COMMENT
"Four other putative half sites for FNR were detected upstream of this site, but the functionality of these elements is puzzling because of their location with respect to the transcription start site |CITS: [8631699]|")
(ACTIVATORS CPLX0-4611 CITATIONS "[96200092]")))
(BR159 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM339)
(RIGHT CPLX0-6295)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169227982)
(ACTIVATORS CPLX0-5542 CPLX0-4774 CPLX0-4775 CPLX0-4803 CPLX0-4804)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5542 CITATIONS "16377617" "12754220")
(ACTIVATORS CPLX0-4803 COMMENT
"CaiF and CRP bind co-operatively to the cai-fix intergenic region to activate the fixA promoter")
(ACTIVATORS CPLX0-4774 CITATIONS "[20032369]")
(ACTIVATORS CPLX0-4774 COMMENT
"CaiF and CRP bind co-operatively to the cai-fix intergenic region to activate the fixA promoter.")
(ACTIVATORS CPLX0-4775 CITATIONS "[20032369]")
(ACTIVATORS CPLX0-4775 COMMENT
"CaiF and CRP bind co-operatively to the cai-fix intergenic region to activate the fixA promoter.")
(ACTIVATORS CPLX0-4804 COMMENT
"CaiF and CRP bind co-operatively to the cai-fix intergenic region to activate the fixA promoter")
(ACTIVATORS CPLX0-4803 CITATIONS "[96200092]" "[98241519]" "[20032369]")
(ACTIVATORS CPLX0-4804 CITATIONS "[96200092]" "[98241519]" "[20032369]")))
(BR160 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM340 RNAP70-CPLX)
(RIGHT CPLX0-6294)
(OFFICIAL-EC? T)
(:CREATION-DATE 3169229209)
(:CREATOR |sgama|) )
NIL)
(BR161 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM421)
(RIGHT CPLX0-6293)
(OFFICIAL-EC? T)
(:CREATION-DATE 3170524798)
(:CREATOR |sgama|) )
NIL)
(BR162 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS111)
(RIGHT CPLX0-4818)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188573811) )
NIL)
(BR163 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS112)
(RIGHT CPLX0-4817)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188574335) )
NIL)
(BR164 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS113)
(RIGHT CPLX0-4816)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188574587) )
NIL)
(BR165 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS114)
(RIGHT CPLX0-4600)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188574837) )
NIL)
(BR166 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS115)
(RIGHT CPLX0-4400)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188575224) )
NIL)
(BR167 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS116)
(RIGHT CPLX0-4483)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188575586) )
NIL)
(BR168 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS117)
(RIGHT CPLX0-4815)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188575926) )
NIL)
(BR169 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00349)
(RIGHT CPLX0-6292)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188576986)
(:CREATOR |sgama|) )
NIL)
(BR170 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS118)
(RIGHT CPLX0-4814)
(OFFICIAL-EC? T)
(CITATIONS "94335636")
(:CREATOR |sgama|)
(:CREATION-DATE 3188576622) )
NIL)
(BR171 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM201)
(RIGHT CPLX0-6291)
(OFFICIAL-EC? T)
(INHIBITORS CPLX0-4760)
(:CREATOR |sgama|)
(:CREATION-DATE 3188577933) )
((INHIBITORS CPLX0-4760 COMMENT)
(INHIBITORS CPLX0-4760 CITATIONS "[94293769]")))
(BR172 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM202 RNAP70-CPLX)
(RIGHT CPLX0-6290)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188584384) )
NIL)
(BR174 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM204 RNAP70-CPLX)
(RIGHT CPLX0-6289)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188586142) )
NIL)
(BR175 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM205)
(RIGHT CPLX0-6288)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188587245) )
NIL)
(BR176 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM206)
(RIGHT CPLX0-6287)
(INHIBITORS CPLX0-5320)
(ACTIVATORS CPLX0-4268)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188588174) )
((INHIBITORS CPLX0-5320 CITATIONS "11294639" "1618807")
(INHIBITORS CPLX0-5320 COMMENT
"The binding of PutA to the put intergenic DNA has been shown to the complex with significant curvature of the put intergenic region.")
(ACTIVATORS CPLX0-4268 CITATIONS "11395452") (ACTIVATORS CPLX0-4268 COMMENT)))
(BR181 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00559)
(RIGHT CPLX0-6286)
(INHIBITORS CPLX0-5529)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188673649)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5529 CITATIONS "9922259" "9352908" "9595659")
(INHIBITORS CPLX0-5529 COMMENT)))
(BR2 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM4)
(RIGHT CPLX0-6285)
(INHIBITORS CPLX0-4623)
(ACTIVATORS CPLX0-4624 CPLX0-4621)
(OFFICIAL-EC? T)
(:CREATION-DATE 3181069760)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4623 CITATIONS "20229831") (INHIBITORS CPLX0-4623 COMMENT)
(ACTIVATORS CPLX0-4624 CITATIONS "20229831")
(ACTIVATORS CPLX0-4624 COMMENT
"This site of IHF binding is also used to regulate the divergent promoter paaAp promoter.")
(ACTIVATORS CPLX0-4621 CITATIONS "20229831")
(ACTIVATORS CPLX0-4621 COMMENT
"This site of CRP binding is also used to regulate the divergent promoter paaAp promoter.")))
(BR201 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM501)
(RIGHT CPLX0-6284)
(OFFICIAL-EC? T)
(:CREATION-DATE 3177705408)
(ACTIVATORS CPLX0-4781 CPLX0-4413)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4781 CITATIONS "[96032385]" "[99328987]")
(ACTIVATORS CPLX0-4413 CITATIONS "[96032385]" "[99328987]")))
(BR202 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM502)
(RIGHT CPLX0-6283)
(OFFICIAL-EC? T)
(:CREATION-DATE 3177762772)
(ACTIVATORS CPLX0-4794 CPLX0-4795 CPLX0-4796 CPLX0-4797)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4794 CITATIONS "[98062196]")
(ACTIVATORS CPLX0-4797 CITATIONS "[98062196]")
(ACTIVATORS CPLX0-4797 COMMENT)
(ACTIVATORS CPLX0-4795 CITATIONS "[98062196]")
(ACTIVATORS CPLX0-4795 COMMENT)
(ACTIVATORS CPLX0-4796 CITATIONS "[98062196]")
(ACTIVATORS CPLX0-4796 COMMENT)))
(BR203 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS00667)
(RIGHT CPLX0-4813)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188761250) )
NIL)
(BR204 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS00662)
(RIGHT CPLX0-4812)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188761496) )
NIL)
(BR205 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS00663)
(RIGHT CPLX0-4608)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188761600) )
NIL)
(BR206 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM221)
(RIGHT CPLX0-6282)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188762202)
(INHIBITORS CPLX0-4799 CPLX0-4800 CPLX0-4801 CPLX0-4802)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4801 CITATIONS "91358373")
(INHIBITORS CPLX0-4799 CITATIONS "91358373") (INHIBITORS CPLX0-4799 COMMENT)
(INHIBITORS CPLX0-4800 CITATIONS "91358373")
(INHIBITORS CPLX0-4802 CITATIONS "92121102")))
(BR207 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS141)
(RIGHT CPLX0-4488)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188831485) )
NIL)
(BR208 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS142)
(RIGHT CPLX0-4811)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188831689) )
NIL)
(BR209 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS143)
(RIGHT CPLX0-4810)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188831930) )
NIL)
(BR21 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM182)
(RIGHT CPLX0-6281)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166796730)
(:CREATOR |sgama|) )
NIL)
(BR210 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS144)
(RIGHT CPLX0-4809)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188832180) )
NIL)
(BR211 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS145)
(RIGHT CPLX0-4808)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188832677) )
NIL)
(BR212 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS146)
(RIGHT CPLX0-4807)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188833028) )
NIL)
(BR213 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS147)
(RIGHT CPLX0-4806)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188833209) )
NIL)
(BR214 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS148)
(RIGHT CPLX0-4805)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188833380) )
NIL)
(BR215 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS149)
(RIGHT CPLX0-4612)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188833576) )
NIL)
(BR216 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS150)
(RIGHT CPLX0-4405)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188833852) )
NIL)
(BR217 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM222)
(RIGHT CPLX0-6280)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188850689)
(ACTIVATORS CPLX0-4802)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4802 CITATIONS "92121102") (ACTIVATORS CPLX0-4802 COMMENT)))
(BR218 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM223)
(RIGHT CPLX0-6279)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188850689)
(INHIBITORS CPLX0-4802)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4802 CITATIONS "92121102") (INHIBITORS CPLX0-4802 COMMENT)))
(BR22 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM183)
(RIGHT CPLX0-6278)
(ACTIVATORS CPLX0-3978 CPLX0-5317 CPLX0-5318)
(INHIBITORS CPLX0-5317 CPLX0-3978 CPLX0-5315 CPLX0-5316)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166799730)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5317 CITATIONS "15066032")
(INHIBITORS CPLX0-5317 COMMENT
"ChbR and NagC appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(INHIBITORS CPLX0-3978 CITATIONS "15066032")
(INHIBITORS CPLX0-3978 COMMENT
"ChbR and NagC appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(INHIBITORS CPLX0-5315 CITATIONS "15066032")
(INHIBITORS CPLX0-5315 COMMENT
"NagC and ChbR appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(INHIBITORS CPLX0-5316 CITATIONS "15066032")
(INHIBITORS CPLX0-5316 COMMENT
"NagC and ChbR appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(ACTIVATORS CPLX0-3978 CITATIONS "15066032")
(ACTIVATORS CPLX0-3978 COMMENT
"ChbR and NagC appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(ACTIVATORS CPLX0-5317 CITATIONS "15066032")
(ACTIVATORS CPLX0-5317 COMMENT
"ChbR and NagC appear to act as repressor for the chbB operon in the absence of the inducing sugar chitobiose.")
(ACTIVATORS CPLX0-5318 CITATIONS "15066032" "15520470")))
(BR221 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS121)
(RIGHT CPLX0-4804)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3171801841) )
NIL)
(BR222 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM521)
(RIGHT CPLX0-6277)
(ACTIVATORS CPLX0-5699)
(OFFICIAL-EC? T)
(:CREATION-DATE 3177765029)
(INHIBITORS CPLX0-5447)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5699 CITATIONS "15520470") (ACTIVATORS CPLX0-5699 COMMENT)
(INHIBITORS CPLX0-5447 CITATIONS "[99377070]")))
(BR224 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS124)
(RIGHT CPLX0-4803)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3171803779) )
NIL)
(BR225 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS125)
(RIGHT CPLX0-4611)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3171809294) )
NIL)
(BR226 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS126)
(RIGHT CPLX0-4404)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3171809356) )
NIL)
(BR227 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS127)
(RIGHT CPLX0-4496)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3171809442) )
NIL)
(BR229 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS154)
(RIGHT CPLX0-4802)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188842347) )
NIL)
(BR230 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS155)
(RIGHT CPLX0-4801)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188842533) )
NIL)
(BR231 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS156)
(RIGHT CPLX0-4800)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188842717) )
NIL)
(BR232 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS157)
(RIGHT CPLX0-4799)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188843141) )
NIL)
(BR233 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00208 BS158)
(RIGHT CPLX0-4798)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188843938) )
NIL)
(BR236 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-161 BS161)
(RIGHT CPLX0-4403)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188845841) )
NIL)
(BR237 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-161 BS162)
(RIGHT CPLX0-4495)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188846069) )
NIL)
(BR238 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-2781 BS163)
(RIGHT CPLX0-4797)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188846523) )
NIL)
(BR239 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-2781 BS164)
(RIGHT CPLX0-4796)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188846675) )
NIL)
(BR24 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM185)
(RIGHT CPLX0-6276)
(INHIBITORS CPLX0-4284)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166800509)
(ACTIVATORS CPLX0-4793)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4793 CITATIONS "[97047984]")
(INHIBITORS CPLX0-4284 CITATIONS "14711822")))
(BR240 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-2781 BS165)
(RIGHT CPLX0-4795)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188846801) )
NIL)
(BR241 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G7071-MONOMER BS166)
(RIGHT CPLX0-4794)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188846962) )
NIL)
(BR242 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM224)
(RIGHT CPLX0-6275)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188850689)
(INHIBITORS CPLX0-4359 CPLX0-4284)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4284 CITATIONS "8892825")
(INHIBITORS CPLX0-4359 CITATIONS "[97047984]")))
(BR244 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11088-MONOMER BS168)
(RIGHT CPLX0-4793)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188910267) )
NIL)
(BR25 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM186)
(RIGHT CPLX0-6274)
(ACTIVATORS CPLX0-5720)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166801292)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5720 CITATIONS "11287152")
(ACTIVATORS CPLX0-5720 COMMENT
"The regulatory effect of FlhDC in the mreB operon transcription has been proved just by microarray analysis by |CITS: [21184412]|")))
(BR26 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM187)
(RIGHT CPLX0-6273)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166801292)
(:CREATOR |sgama|) )
NIL)
(BR261 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM241)
(RIGHT CPLX0-6272)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188937346)
(ACTIVATORS CPLX0-4791 CPLX0-4705 CPLX0-4614 CPLX0-4786 CPLX0-4787 CPLX0-4792)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4787 CITATIONS "[94364945]" "[98175452]")
(ACTIVATORS CPLX0-4786 CITATIONS "[94364945]" "[98175452]")
(ACTIVATORS CPLX0-4614 CITATIONS "[98175452]")
(ACTIVATORS CPLX0-4705 CITATIONS "[87279947]" "[97054006]")
(ACTIVATORS CPLX0-4705 COMMENT
"IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.")
(ACTIVATORS CPLX0-4792 CITATIONS "[87279947]" "[97054006]")
(ACTIVATORS CPLX0-4792 COMMENT
"IHF plays a dual role in controlling fimA expression: it is required both for inversion of the fimA control region and for efficient expression from the fimA promoter.")
(ACTIVATORS CPLX0-4791 CITATIONS "[98420106]")))
(BR262 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM242)
(RIGHT CPLX0-6271)
(OFFICIAL-EC? T)
(:CREATION-DATE 3188937346)
(ACTIVATORS CPLX0-5526 CPLX0-4406)
(INHIBITORS CPLX0-4615)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5526 CITATIONS "16207912")
(ACTIVATORS CPLX0-5526 COMMENT
"By means of gen expression and mutation analysis, it was determined that the LrhA protein
regulator positively regulates the fimE expression, leading the repression of the fimA
operon through the ON-OFF switch at fimA |CITS: [16207912]|.")
(INHIBITORS CPLX0-4615 COMMENT)
(ACTIVATORS CPLX0-4406 CITATIONS "[94364945]" "[98175452]")
(ACTIVATORS CPLX0-4406 COMMENT)
(INHIBITORS CPLX0-4615 CITATIONS "[94178716]" "[98258023]")))
(BR263 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS181)
(RIGHT CPLX0-4792)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188935073) )
NIL)
(BR264 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS182)
(RIGHT CPLX0-4791)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188935253) )
NIL)
(BR265 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS183)
(RIGHT CPLX0-4615)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188935379) )
NIL)
(BR266 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS184)
(RIGHT CPLX0-4406)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188935576) )
NIL)
(BR267 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS185)
(RIGHT CPLX0-4492)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189171484) )
NIL)
(BR268 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11088-MONOMER BS186)
(RIGHT CPLX0-4790)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189175748) )
NIL)
(BR269 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS187)
(RIGHT CPLX0-4789)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189176006) )
NIL)
(BR27 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM188)
(RIGHT CPLX0-6270)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166801292)
(:CREATOR |sgama|) )
NIL)
(BR271 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS189)
(RIGHT CPLX0-4788)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189177654) )
NIL)
(BR272 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS190)
(RIGHT CPLX0-4787)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189178828) )
NIL)
(BR273 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS191)
(RIGHT CPLX0-4786)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189178995) )
NIL)
(BR275 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS193)
(RIGHT CPLX0-4614)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189179115) )
NIL)
(BR28 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM189)
(RIGHT CPLX0-6269)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166801292)
(:CREATOR |sgama|) )
NIL)
(BR281 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00324)
(RIGHT CPLX0-6268)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189873179)
(INHIBITORS CPLX0-4785 CPLX0-4814)
(ACTIVATORS CPLX0-5481 CPLX0-5482 CPLX0-5483 CPLX0-5484 CPLX0-4613 CPLX0-4612
CPLX0-4814)
(:CREATOR |paley|) )
((ACTIVATORS CPLX0-5481 CITATIONS "15659676") (ACTIVATORS CPLX0-5481 COMMENT)
(ACTIVATORS CPLX0-5482 CITATIONS "15659676") (ACTIVATORS CPLX0-5482 COMMENT)
(ACTIVATORS CPLX0-5483 CITATIONS "15659676") (ACTIVATORS CPLX0-5483 COMMENT)
(ACTIVATORS CPLX0-5484 CITATIONS "15659676") (ACTIVATORS CPLX0-5484 COMMENT)
(ACTIVATORS CPLX0-4612 COMMENT)
(INHIBITORS CPLX0-4814 COMMENT
"FNR affects pdhRp promoter under anaerobic conditions.")
(ACTIVATORS CPLX0-4814 COMMENT
"FNR affects pdhRp promoter under anaerobic conditions.")
(ACTIVATORS CPLX0-4613 CITATIONS "[94335636]" "15659676")
(INHIBITORS CPLX0-4785 CITATIONS "[94335636]" "[95302963]")
(INHIBITORS CPLX0-4814 CITATIONS "[94335636]" "12754220" "16377617")
(ACTIVATORS CPLX0-4612 CITATIONS "[94335636]" "15659676")
(ACTIVATORS CPLX0-4814 CITATIONS "[94335636]" "12754220" "16377617")))
(BR282 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00574)
(RIGHT CPLX0-6267)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189873179)
(ACTIVATORS CPLX0-5263 CPLX0-4467)
(:CREATOR |paley|) )
((ACTIVATORS CPLX0-5263 COMMENT
"FNR activates the hypB transcription under anaerobiosis.")
(ACTIVATORS CPLX0-5263 CITATIONS "14612240")
(ACTIVATORS CPLX0-4467 COMMENT
"FNR activates the hypB transcription under anaerobiosis.")
(ACTIVATORS CPLX0-4467 CITATIONS "14612240")))
(BR284 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11088-MONOMER BS201)
(RIGHT CPLX0-4785)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189884208) )
NIL)
(BR285 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS202)
(RIGHT CPLX0-4613)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3189884295) )
NIL)
(BR286 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00512)
(RIGHT CPLX0-6266)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR287 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00513)
(RIGHT CPLX0-6265)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR288 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00420)
(RIGHT CPLX0-6264)
(ACTIVATORS CPLX0-5696)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5696 CITATIONS "15520470") (ACTIVATORS CPLX0-5696 COMMENT)))
(BR289 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00441)
(RIGHT CPLX0-6263)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR29 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM190)
(RIGHT CPLX0-6262)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166802732)
(:CREATOR |sgama|) )
NIL)
(BR290 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00340)
(RIGHT CPLX0-6261)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR291 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00316)
(RIGHT CPLX0-6260)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR292 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00317)
(RIGHT CPLX0-6259)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR293 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00566)
(RIGHT CPLX0-6258)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR294 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00341)
(RIGHT CPLX0-6257)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR295 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00437)
(RIGHT CPLX0-6256)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR296 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00418)
(RIGHT CPLX0-6255)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR297 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00339)
(RIGHT CPLX0-6254)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR298 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00485)
(RIGHT CPLX0-6253)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR299 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00556)
(RIGHT CPLX0-6252)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR3 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM5)
(RIGHT CPLX0-6251)
(INHIBITORS CPLX0-4601)
(ACTIVATORS CPLX0-4624 CPLX0-4621)
(OFFICIAL-EC? T)
(:CREATION-DATE 3181069760)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4621 COMMENT
"This site of CRP binding is also used to regulate the divergent promoter paaZp promoter.")
(ACTIVATORS CPLX0-4621 CITATIONS "20229831")
(ACTIVATORS CPLX0-4624 COMMENT
"This site of IHF binding is also used to regulate the divergent promoter paaZp promoter.")
(ACTIVATORS CPLX0-4624 CITATIONS "20229831")
(INHIBITORS CPLX0-4601 CITATIONS "20229831")))
(BR30 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM191)
(RIGHT CPLX0-6250)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166807585)
(:CREATOR |sgama|) )
NIL)
(BR300 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00381)
(RIGHT CPLX0-6249)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR301 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00552)
(RIGHT CPLX0-6248)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189958660)
(:CREATOR |sgama|) )
NIL)
(BR302 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00435)
(RIGHT CPLX0-6247)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189964140)
(:CREATOR |sgama|) )
NIL)
(BR303 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00436)
(RIGHT CPLX0-6246)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189964140)
(:CREATOR |sgama|) )
NIL)
(BR304 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00434)
(RIGHT CPLX0-6245)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189964140)
(:CREATOR |sgama|) )
NIL)
(BR305 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00433)
(RIGHT CPLX0-6244)
(OFFICIAL-EC? T)
(:CREATION-DATE 3189964140)
(:CREATOR |sgama|) )
NIL)
(BR31 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM192)
(RIGHT CPLX0-6243)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166807585)
(:CREATOR |sgama|) )
NIL)
(BR32 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM193)
(RIGHT CPLX0-6242)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166807585)
(:CREATOR |sgama|) )
NIL)
(BR33 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM65)
(RIGHT CPLX0-6241)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166814486)
(INHIBITORS CPLX0-4670)
(ACTIVATORS CPLX0-4671)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4670 COMMENT)
(INHIBITORS CPLX0-4670 CITATIONS "[98155143]")
(ACTIVATORS CPLX0-4671 CITATIONS "[98155143]")))
(BR34 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM197)
(RIGHT CPLX0-6240)
(INHIBITORS CPLX0-5382 CPLX0-5383 CPLX0-5384 CPLX0-5385)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166814486)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5382 COMMENT)
(INHIBITORS CPLX0-5384 CITATIONS "[20005604]")
(INHIBITORS CPLX0-5383 CITATIONS "[20005604]")
(INHIBITORS CPLX0-5382 CITATIONS "[20005604]")
(INHIBITORS CPLX0-5385 CITATIONS "[20005604]")))
(BR343 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00511)
(RIGHT CPLX0-6239)
(ACTIVATORS CPLX0-5279)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190648067)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5279 CITATIONS "14702398") (ACTIVATORS CPLX0-5279 COMMENT)))
(BR345 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00380)
(RIGHT CPLX0-6238)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190648067)
(:CREATOR |sgama|) )
NIL)
(BR346 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00514)
(RIGHT CPLX0-6237)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190648067)
(INHIBITORS CPLX0-5537 CPLX0-5193 CPLX0-5194 CPLX0-5427)
(ACTIVATORS CPLX0-5428 CPLX0-5429 CPLX0-5430)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5537 CITATIONS "16238633")
(INHIBITORS CPLX0-5537 COMMENT
"Based on studies of binding sites with gel shift and footprinting with Lrp and H-NS regulator proteins, it was demonstrated that
both proteins interact with obvious synergism in the repression of all seven E. coli rrn P1 promoter upstream regions; as a result, they help the
efficient shutdown of rRNA synthesis. Likewise, both proteins could be a transient heteromer via protein-protein interaction interfering with the RNA
polymerase, and of this way it alters the DNA of the upstream regions of the all seven ribosomal P1 promoters |CITS: [16238633]|.
Many Lrp and H-NS sites were observed through a DNase I footprinting analysis in the rrnBp upstream region. Although no specific central
positions were determined, the Lrp is clustering between positions -20 and -90. It is important note th at the same sequence is strongly protected by
H-NS-DNA complex |CITS: [16238633]|.")
(ACTIVATORS CPLX0-5429 CITATIONS "96091159" "96240676" "98294054"
"98175677")
(ACTIVATORS CPLX0-5430 CITATIONS "98175677" "98294054" "96240676"
"96091159")
(ACTIVATORS CPLX0-5428 CITATIONS "96091159" "96240676" "98175677"
"98294054")
(INHIBITORS CPLX0-5427 COMMENT
"H-NS antagonizes the Fis-mediated activation of P1 promoter through a
conformational changes in the DNA.
")
(INHIBITORS CPLX0-5427 CITATIONS "7512187")
(INHIBITORS CPLX0-5194 COMMENT
"H-NS antagonizes the Fis-mediated activation of P1 promoter through a
comformational changes in the DNA.
")
(INHIBITORS CPLX0-5194 CITATIONS "7512187")
(INHIBITORS CPLX0-5193 COMMENT
"H-NS antagonizes the Fis-mediated activation of P1 promoter through a
comformational changes in the DNA.
")
(INHIBITORS CPLX0-5193 CITATIONS "7512187")))
(BR347 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00547)
(RIGHT CPLX0-6236)
(ACTIVATORS CPLX0-5370 CPLX0-5371 CPLX0-5372)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190648067)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5372 CITATIONS "20223627")
(ACTIVATORS CPLX0-5371 CITATIONS "20223627")
(ACTIVATORS CPLX0-5370 CITATIONS "20223627")))
(BR348 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP32-CPLX PM00614)
(RIGHT CPLX0-6235)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190648067)
(:CREATOR |sgama|) )
NIL)
(BR349 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM321)
(RIGHT CPLX0-6234)
(OFFICIAL-EC? T)
(:CREATION-DATE 3190989412)
(:CREATOR |sgama|) )
NIL)
(BR35 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00383)
(RIGHT CPLX0-6233)
(OFFICIAL-EC? T)
(:CREATION-DATE 3166817990)
(:CREATOR |sgama|) )
NIL)
(BR350 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00501)
(RIGHT CPLX0-6232)
(OFFICIAL-EC? T)
(:CREATION-DATE 3191702880)
(:CREATOR |sgama|) )
NIL)
(BR36 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM66)
(RIGHT CPLX0-6231)
(INHIBITORS CPLX0-4258)
(OFFICIAL-EC? T)
(:CREATION-DATE 3183479114)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4258 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it checked for the presence of its regulatory motif in the promoter region |CITS: [15883881]|.")
(INHIBITORS CPLX0-4258 CITATIONS "[99395066]" "12813061" "15126461"
"15883881")))
(BR362 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM341)
(RIGHT CPLX0-6230)
(OFFICIAL-EC? T)
(:CREATION-DATE 3191952919)
(ACTIVATORS CPLX0-4784)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4784 CITATIONS) (ACTIVATORS CPLX0-4784 COMMENT)))
(BR363 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM342)
(RIGHT CPLX0-6229)
(OFFICIAL-EC? T)
(:CREATION-DATE 3191952919)
(:CREATOR |sgama|) )
NIL)
(BR364 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM343)
(RIGHT CPLX0-6228)
(OFFICIAL-EC? T)
(:CREATION-DATE 3191952919)
(:CREATOR |sgama|) )
NIL)
(BR37 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM67)
(RIGHT CPLX0-6227)
(ACTIVATORS CPLX0-4258)
(OFFICIAL-EC? T)
(:CREATION-DATE 3183479114)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4258 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it checked for the presence of its regulatory motif in the promoter region |CITS: [15883881]|.")
(ACTIVATORS CPLX0-4258 CITATIONS "12813061" "15126461" "15883881")))
(BR38 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM68)
(RIGHT CPLX0-6226)
(OFFICIAL-EC? T)
(:CREATION-DATE 3183479617)
(ACTIVATORS CPLX0-5189 CPLX0-4779 CPLX0-4780)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5189 CITATIONS "9371449") (ACTIVATORS CPLX0-5189 COMMENT)
(ACTIVATORS CPLX0-4779 CITATIONS "98037500")
(ACTIVATORS CPLX0-4780 CITATIONS "98037500")))
(BR381 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS241)
(RIGHT CPLX0-4784)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3191952742) )
NIL)
(BR382 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM00637)
(RIGHT CPLX0-6225)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192368516)
(:CREATOR |sgama|) )
NIL)
(BR383 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM361)
(RIGHT CPLX0-6224)
(INHIBITORS CPLX0-5678)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192388037)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5678 CITATIONS "11953442") (INHIBITORS CPLX0-5678 COMMENT)))
(BR39 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM69)
(RIGHT CPLX0-6223)
(ACTIVATORS CPLX0-5575)
(OFFICIAL-EC? T)
(:CREATION-DATE 3183485037)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5575 CITATIONS "15699038")
(ACTIVATORS CPLX0-5575 COMMENT
"ArcA activates xylR gene expression under anaerobiosis. A putative ArcA binding site 112 bp upstream of this gene was identified, but the sequence of it was not shown |CITS: [15699038]|.")))
(BR4 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM7)
(RIGHT CPLX0-6222)
(OFFICIAL-EC? T)
(:CREATION-DATE 3181070475)
(:CREATOR |sgama|) )
NIL)
(BR40 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM70)
(RIGHT CPLX0-6221)
(INHIBITORS CPLX0-5122)
(OFFICIAL-EC? T)
(:CREATION-DATE 3183485356)
(ACTIVATORS CPLX0-5189 CPLX0-4777 CPLX0-4778)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5189 COMMENT) (ACTIVATORS CPLX0-5189 CITATIONS "9371449")
(INHIBITORS CPLX0-5122 CITATIONS "7860604")
(INHIBITORS CPLX0-5122 COMMENT
"Fis and RpoS inhibit xylF expression in a rpoS fis double mutant strain. The rpoS effects could be indirect |CITS: [7860604]|.")
(ACTIVATORS CPLX0-4777 CITATIONS "9371449")
(ACTIVATORS CPLX0-4778 CITATIONS "98037500")))
(BR401 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM383)
(RIGHT CPLX0-6220)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192564932)
(:CREATOR |sgama|) )
NIL)
(BR402 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM384)
(RIGHT CPLX0-6219)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192564932)
(:CREATOR |sgama|) )
NIL)
(BR403 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS263)
(RIGHT CPLX0-4783)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192381662) )
NIL)
(BR404 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS264)
(RIGHT CPLX0-4782)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192382144) )
NIL)
(BR405 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS265)
(RIGHT CPLX0-4556)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192382247) )
NIL)
(BR407 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11146-MONOMER BS267)
(RIGHT CPLX0-4413)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454431) )
NIL)
(BR408 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11146-MONOMER BS268)
(RIGHT CPLX0-4781)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454581) )
NIL)
(BR409 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-165 BS269)
(RIGHT CPLX0-4780)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454764) )
NIL)
(BR410 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-165 BS270)
(RIGHT CPLX0-4779)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454862) )
NIL)
(BR411 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-165 BS271)
(RIGHT CPLX0-4778)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454926) )
NIL)
(BR412 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-165 BS272)
(RIGHT CPLX0-4777)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192454983) )
NIL)
(BR42 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS41)
(RIGHT CPLX0-4477)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188056705) )
NIL)
(BR422 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS282)
(RIGHT CPLX0-4776)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3192808517) )
NIL)
(BR425 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM404)
(RIGHT CPLX0-6218)
(INHIBITORS CPLX0-5148)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192904370)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5148 CITATIONS "12754220")
(INHIBITORS CPLX0-5148 COMMENT
"FNR represses rplM-rps operon expression under anaerobiosis. A putative FNR binding site, which is not shown in the paper, was identified upstream of this operon |CITS: [12754220]|.")))
(BR427 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM406)
(RIGHT CPLX0-6217)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192904370)
(:CREATOR |sgama|) )
NIL)
(BR428 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM407)
(RIGHT CPLX0-6216)
(OFFICIAL-EC? T)
(:CREATION-DATE 3192904370)
(:CREATOR |sgama|) )
NIL)
(BR43 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS42)
(RIGHT CPLX0-4478)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188057627) )
NIL)
(BR44 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS43)
(RIGHT CPLX0-4479)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188059672) )
NIL)
(BR443 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6088-MONOMER BS301)
(RIGHT CPLX0-4775)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193079493) )
NIL)
(BR444 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6088-MONOMER BS302)
(RIGHT CPLX0-4774)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193079602) )
NIL)
(BR445 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6088-MONOMER BS303)
(RIGHT CPLX0-4563)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193079695) )
NIL)
(BR446 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6088-MONOMER BS304)
(RIGHT CPLX0-4358)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193079761) )
NIL)
(BR447 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM435)
(RIGHT CPLX0-6215)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193156723)
(:CREATOR |sgama|) )
NIL)
(BR448 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM437)
(RIGHT CPLX0-6214)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193424730)
(INHIBITORS CPLX0-4770 CPLX0-4771)
(ACTIVATORS CPLX0-4772 CPLX0-4773)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4770 COMMENT)
(ACTIVATORS CPLX0-4773 CITATIONS "[94335635]")
(ACTIVATORS CPLX0-4772 CITATIONS "[94335635]")
(INHIBITORS CPLX0-4771 CITATIONS "[94335635]")
(INHIBITORS CPLX0-4770 CITATIONS "[94335635]")))
(BR449 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM439)
(RIGHT CPLX0-6213)
(INHIBITORS CPLX0-4002 CPLX0-4289)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193426578)
(ACTIVATORS CPLX0-4007 CPLX0-4761)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4007 COMMENT) (ACTIVATORS CPLX0-4761 COMMENT)
(INHIBITORS CPLX0-4289 COMMENT
"Under anaerobiosis, FNR repress cydAB operon expression |CITS: [12754220]|.")
(ACTIVATORS CPLX0-4761 CITATIONS "[97047984]" "16140031")
(INHIBITORS CPLX0-4002 CITATIONS "20572078")
(INHIBITORS CPLX0-4002 COMMENT
"Hns most strongly represses cydAp4 promoter and has a moderate effect on cydAp1, cydAp2 and cydAp3 promoters.
Hns regulates the cydAB expression negatively in anaerobiosis and aerobiosis, but ArcA antagonizes its action in anaerobiosis.")
(ACTIVATORS CPLX0-4007 CITATIONS "20453462" "12754220" "16140031")
(INHIBITORS CPLX0-4289 CITATIONS "20453462" "12754220" "16140031")))
(BR45 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS44)
(RIGHT CPLX0-4480)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188060315) )
NIL)
(BR450 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM440)
(RIGHT CPLX0-6212)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193512392)
(:CREATOR |sgama|) )
NIL)
(BR451 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM442)
(RIGHT CPLX0-6211)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193512392)
(:CREATOR |sgama|) )
NIL)
(BR452 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM443)
(RIGHT CPLX0-6210)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193512392)
(:CREATOR |sgama|) )
NIL)
(BR453 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM444)
(RIGHT CPLX0-6209)
(ACTIVATORS CPLX0-5722 CPLX0-5296)
(INHIBITORS CPLX0-5653 CPLX0-5654 CPLX0-5298 CPLX0-5297)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193595302)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5722 CITATIONS "11287152")
(ACTIVATORS CPLX0-5722 COMMENT
"The regulatory effect of FlhDC in the napF operon transcription has been proved just by microarray analysis by |CITS: [21184412]|")
(INHIBITORS CPLX0-5653 CITATIONS "13129959")
(INHIBITORS CPLX0-5654 CITATIONS "13129959") (INHIBITORS CPLX0-5654 COMMENT)
(ACTIVATORS CPLX0-5296 COMMENT) (INHIBITORS CPLX0-5298 CITATIONS "13129959")
(INHIBITORS CPLX0-5297 CITATIONS "13129959")
(ACTIVATORS CPLX0-5296 CITATIONS "13129959")
(INHIBITORS CPLX0-5298 COMMENT
"The napFp2 promoter is inhibited by NarL in response to nitrate.")
(INHIBITORS CPLX0-5297 COMMENT
"The napFp2 promoter is inhibited by NarP in response to nitrate.")))
(BR454 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM446)
(RIGHT CPLX0-6208)
(OFFICIAL-EC? T)
(:CREATION-DATE 3193600983)
(INHIBITORS CPLX0-5652 CPLX0-4769)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5652 CITATIONS "2509902" "8057377")
(INHIBITORS CPLX0-4769 CITATIONS "[95379749]")
(INHIBITORS CPLX0-4769 COMMENT)))
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(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM449)
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(OFFICIAL-EC? T)
(:CREATION-DATE 3193771009)
(INHIBITORS CPLX0-5212 CPLX0-4415)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5212 COMMENT
"The regulatory effect of IHF on the promoter yiaJp is as yet not known.
However, we assigned a negative effect to this regulatory interaction based on the fact that the protein binding site is very close to the promoter (4 bp upstream the transcription start site).")
(INHIBITORS CPLX0-5212 CITATIONS "20372646")
(INHIBITORS CPLX0-4415 CITATIONS "10913096") (INHIBITORS CPLX0-4415 COMMENT)))
(BR456 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
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(RIGHT CPLX0-6206)
(INHIBITORS CPLX0-5124 CPLX0-4675 CPLX0-5394)
(ACTIVATORS CPLX0-5125 CPLX0-5395 CPLX0-5396)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194115297)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5124 CITATIONS "11238978")
(INHIBITORS CPLX0-5124 COMMENT
"This potential site could belong to the CRP regulator since it possesses 9 of the 16 consensus nucleotides associated with CRP binding |CITS: [11238978]|. GadE and CRP bind to this site controlling gadA expression during both acid and stationary phases.")
(ACTIVATORS CPLX0-5125 CITATIONS "12940989" "11238978")
(ACTIVATORS CPLX0-5125 COMMENT
"GadE is required both for gadA/gadBC expression during exponential growth and stationary phase expression. GadE is an acid-induced regulator since it is involved in the acid induction of gadA/gadBC operons during exponential growth. The expression of these operons is maybe one of the most intensively regulated system in Escherichia coli since it is regulated by different factors. GadE and GadX could simultaneously bind to the GAD box region of gadA/gadBC and form a complex |CITS: [12940989]|.
")
(INHIBITORS CPLX0-4675 CITATIONS "10383761" "8455549")
(INHIBITORS CPLX0-5394 CITATIONS "[22336325]")
(INHIBITORS CPLX0-5394 COMMENT
"GadW regulates positive expression of the gadBC in the absence of GadX only to pH 8. ")
(ACTIVATORS CPLX0-5395 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5395 COMMENT)
(ACTIVATORS CPLX0-5396 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5396 COMMENT)))
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(:CREATOR |sgama|)
(:CREATION-DATE 3188064941) )
NIL)
(BR461 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
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(RIGHT CPLX0-4773)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193684479) )
NIL)
(BR462 NIL (
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193684616) )
NIL)
(BR463 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS323)
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(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193684757) )
NIL)
(BR464 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-OMPR BS324)
(RIGHT CPLX0-4770)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193684808) )
NIL)
(BR465 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS325)
(RIGHT CPLX0-4558)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193685102) )
NIL)
(BR466 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11962-MONOMER BS326)
(RIGHT CPLX0-4359)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193685233) )
NIL)
(BR467 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS327)
(RIGHT CPLX0-4415)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193770426) )
NIL)
(BR468 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00010 BS328)
(RIGHT CPLX0-4769)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3193770811) )
NIL)
(BR470 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS330)
(RIGHT CPLX0-4768)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194033711) )
NIL)
(BR479 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00631)
(RIGHT CPLX0-6205)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194269023)
(INHIBITORS CPLX0-4762 CPLX0-5362 CPLX0-5366 CPLX0-5367 CPLX0-4763 CPLX0-4424
CPLX0-4765 CPLX0-4766 CPLX0-4767)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5366 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4424 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4424 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4762 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4762 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-5362 CITATIONS "[95095955]")
(INHIBITORS CPLX0-5362 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-5366 CITATIONS "[95095955]")
(INHIBITORS CPLX0-5367 CITATIONS "[95095955]")
(INHIBITORS CPLX0-5367 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4763 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4763 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4765 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4765 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4766 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4766 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")
(INHIBITORS CPLX0-4767 CITATIONS "[95095955]")
(INHIBITORS CPLX0-4767 COMMENT
"Binding of Lrp to one site enhances occupancy of the other sites Lrp in ompCp2 promoter. Leucine does not abolish DNA binding by the ligated Lrp but it may alter the affinity of Lrp for specific sites on DNA.")))
(BR48 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS47)
(RIGHT CPLX0-4482)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188067790) )
NIL)
(BR480 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS340)
(RIGHT CPLX0-4767)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095352) )
NIL)
(BR481 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS341)
(RIGHT CPLX0-4766)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095477) )
NIL)
(BR482 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS342)
(RIGHT CPLX0-4765)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095596) )
NIL)
(BR483 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS343)
(RIGHT CPLX0-4764)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095652) )
NIL)
(BR484 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS344)
(RIGHT CPLX0-4763)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095703) )
NIL)
(BR488 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS348)
(RIGHT CPLX0-4762)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194095934) )
NIL)
(BR489 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM461 RNAPS-CPLX)
(RIGHT CPLX0-6204)
(ACTIVATORS CPLX0-5576 CPLX0-5295 CPLX0-5399 CPLX0-5400 CPLX0-5401 CPLX0-5402)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194270130)
(INHIBITORS CPLX0-5496 CPLX0-3989 CPLX0-4105 CPLX0-5397 CPLX0-5398 CPLX0-4718)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5496 CITATIONS "16377617") (INHIBITORS CPLX0-5496 COMMENT)
(ACTIVATORS CPLX0-5576 CITATIONS "15699038")
(ACTIVATORS CPLX0-5576 COMMENT
"ArcA appears to activate gadAX operon expression under anaerobiosis. A putative ArcA binding site was identified 567 bp upstream of this operon |CITS: [15699038]|, but the sequence was not shown.")
(INHIBITORS CPLX0-3989 CITATIONS "11238978")
(INHIBITORS CPLX0-3989 COMMENT
"This potential site could belong to the CRP regulator since it possesses 9 of the 16 consensus nucleotides associated with CRP binding |CITS: [11238978]|. GadE and CRP bind to this site controlling gadA expression during both acid and stationary phases.")
(INHIBITORS CPLX0-4718 CITATIONS "[21135147]")
(INHIBITORS CPLX0-4105 CITATIONS "12657056")
(ACTIVATORS CPLX0-5295 COMMENT
"GadE is required both for gadA/gadBC expression during exponential growth and stationary phase expression. GadE is an acid-induced regulator since it is involved in the acid induction of gadA/gadBC operons during exponential growth. The expression of these operons is maybe one of the most intensively regulated system in Escherichia coli since it is regulated by different factors. GadE and GadX could simultaneously bind to the GAD box region of gadA/gadBC and form a complex |CITS: [12940989]|.
")
(ACTIVATORS CPLX0-5295 CITATIONS "14702398" "12940989")
(INHIBITORS CPLX0-5397 CITATIONS "[22336325]")
(INHIBITORS CPLX0-5397 COMMENT
"GadW regulates positively the expression of the gadA in the absence of GadX only to pH 8.")
(INHIBITORS CPLX0-5398 CITATIONS "[21972774]" "[22336325]")
(INHIBITORS CPLX0-5398 COMMENT
"H-NS still affects gadA positive expression in a gadXW mutant.")
(ACTIVATORS CPLX0-5399 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5399 COMMENT)
(ACTIVATORS CPLX0-5400 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5400 COMMENT)
(ACTIVATORS CPLX0-5401 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5401 COMMENT)
(ACTIVATORS CPLX0-5402 CITATIONS "[21972774]" "[22336325]")
(ACTIVATORS CPLX0-5402 COMMENT)))
(BR498 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS358)
(RIGHT CPLX0-4761)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194118145) )
NIL)
(BR50 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS49)
(RIGHT CPLX0-4469)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188141551) )
NIL)
(BR500 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS360)
(RIGHT CPLX0-4760)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194118491) )
NIL)
(BR501 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM503)
(RIGHT CPLX0-6203)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194375000)
(ACTIVATORS CPLX0-4726)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4726 COMMENT)
(ACTIVATORS CPLX0-4726 CITATIONS "[97113527]" "[98193134]")))
(BR502 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM504)
(RIGHT CPLX0-6202)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194375000)
(:CREATOR |sgama|) )
NIL)
(BR503 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM505)
(RIGHT CPLX0-6201)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194375000)
(:CREATOR |sgama|) )
NIL)
(BR504 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM506)
(RIGHT CPLX0-6200)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194375000)
(:CREATOR |sgama|) )
NIL)
(BR51 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS50)
(RIGHT CPLX0-4470)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188141840) )
NIL)
(BR52 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS51)
(RIGHT CPLX0-4462)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188142792) )
NIL)
(BR521 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM524 RNAPS-CPLX)
(RIGHT CPLX0-6199)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194638954)
(:CREATOR |sgama|) )
NIL)
(BR522 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM525)
(RIGHT CPLX0-6198)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194705991)
(:CREATOR |sgama|) )
NIL)
(BR523 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM526)
(RIGHT CPLX0-6197)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194808787)
(ACTIVATORS CPLX0-5416 CPLX0-4756)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4756 CITATIONS "8661925")
(ACTIVATORS CPLX0-5416 CITATIONS "[21184412]")
(ACTIVATORS CPLX0-5416 COMMENT
"The regulatory effect of FlhDC in the hydN operon transcription has been proved just by microarray analysis by |CITS: [21184412]|")))
(BR527 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS387)
(RIGHT CPLX0-4424)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194268412) )
NIL)
(BR53 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS52)
(RIGHT CPLX0-4463)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188143477) )
NIL)
(BR54 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS53)
(RIGHT CPLX0-4464)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188144498) )
NIL)
(BR541 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS401)
(RIGHT CPLX0-4759)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194636462) )
NIL)
(BR542 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS402)
(RIGHT CPLX0-4758)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194636666) )
NIL)
(BR543 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS403)
(RIGHT CPLX0-4757)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194708995) )
NIL)
(BR544 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-183 BS404)
(RIGHT CPLX0-4756)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194807834) )
NIL)
(BR545 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM541)
(RIGHT CPLX0-6196)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194897310)
(:CREATOR |sgama|) )
NIL)
(BR546 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM542)
(RIGHT CPLX0-6195)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194897310)
(:CREATOR |sgama|) )
NIL)
(BR547 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM543)
(RIGHT CPLX0-6194)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194897310)
(:CREATOR |sgama|) )
NIL)
(BR55 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS54)
(RIGHT CPLX0-4465)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188145142) )
NIL)
(BR56 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS55)
(RIGHT CPLX0-4466)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188145364) )
NIL)
(BR561 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM561)
(RIGHT CPLX0-6193)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194984331)
(INHIBITORS CPLX0-4755 CPLX0-4578 CPLX0-4746 CPLX0-4747 CPLX0-4748 CPLX0-4749)
(ACTIVATORS CPLX0-4755 CPLX0-4574)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4755 CITATIONS) (ACTIVATORS CPLX0-4755 COMMENT)
(INHIBITORS CPLX0-4578 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4578 COMMENT)
(INHIBITORS CPLX0-4746 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4746 COMMENT)
(INHIBITORS CPLX0-4747 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4747 COMMENT)
(INHIBITORS CPLX0-4748 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4748 COMMENT)
(INHIBITORS CPLX0-4749 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4749 COMMENT)
(ACTIVATORS CPLX0-4574 CITATIONS "[98311086]")
(ACTIVATORS CPLX0-4574 COMMENT)))
(BR562 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM562)
(RIGHT CPLX0-6192)
(OFFICIAL-EC? T)
(:CREATION-DATE 3194984331)
(INHIBITORS CPLX0-4578 CPLX0-4746 CPLX0-4747 CPLX0-4748 CPLX0-4749)
(ACTIVATORS CPLX0-4363 CPLX0-4574)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4578 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4578 COMMENT)
(INHIBITORS CPLX0-4746 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4746 COMMENT)
(INHIBITORS CPLX0-4747 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4747 COMMENT)
(INHIBITORS CPLX0-4748 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4748 COMMENT)
(INHIBITORS CPLX0-4749 CITATIONS "[97113547]" "[99232503]")
(INHIBITORS CPLX0-4749 COMMENT)
(ACTIVATORS CPLX0-4363 CITATIONS "[98311086]")
(ACTIVATORS CPLX0-4574 CITATIONS "[98311086]")
(ACTIVATORS CPLX0-4574 COMMENT)))
(BR564 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS422)
(RIGHT CPLX0-4755)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194983836) )
NIL)
(BR565 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS423)
(RIGHT CPLX0-4574)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194983982) )
NIL)
(BR566 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS424)
(RIGHT CPLX0-4363)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3194984144) )
NIL)
(BR567 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS425)
(RIGHT CPLX0-4425)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195241872) )
NIL)
(BR568 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS426)
(RIGHT CPLX0-4754)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195241929) )
NIL)
(BR569 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS427)
(RIGHT CPLX0-4753)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195242022) )
NIL)
(BR570 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS428)
(RIGHT CPLX0-4752)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195242083) )
NIL)
(BR571 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS429)
(RIGHT CPLX0-4751)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195242203) )
NIL)
(BR572 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS430)
(RIGHT CPLX0-4750)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195242261) )
NIL)
(BR58 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS57)
(RIGHT CPLX0-4467)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188147155) )
NIL)
(BR583 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM582)
(RIGHT CPLX0-6191)
(ACTIVATORS CPLX0-5744 CPLX0-4567)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196453368)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5744 CITATIONS "16377617")
(ACTIVATORS CPLX0-5744 COMMENT
"By making use of micro arrays analysis, Constantinidou et al |CITS: [16377617]| concluded that FNR activates garPLRK-rnpB operon expression. They also identified a putative FNR binding site upstream of the operon, but the sequence was not shown.")
(ACTIVATORS CPLX0-4567 CITATIONS "10762278" "14645248")
(ACTIVATORS CPLX0-4567 COMMENT
"CdaR responding to the inducers D-glycerate, D-galactarate, D-glucarate, and 2-D-mannosyl-glycerate")))
(BR584 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM583)
(RIGHT CPLX0-6190)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196627809)
(:CREATOR |sgama|) )
NIL)
(BR585 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM584)
(RIGHT CPLX0-6189)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196627809)
(:CREATOR |sgama|) )
NIL)
(BR586 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM586)
(RIGHT CPLX0-6188)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196712016)
(ACTIVATORS CPLX0-4443 CPLX0-4375 CPLX0-4583 CPLX0-4740 CPLX0-4741)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4741 CITATIONS "[97070370]")
(ACTIVATORS CPLX0-4740 CITATIONS "[97070370]")
(ACTIVATORS CPLX0-4583 CITATIONS "[97070370]")
(ACTIVATORS CPLX0-4375 CITATIONS "[97070370]")
(ACTIVATORS CPLX0-4443 CITATIONS "[97070370]")))
(BR587 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM587)
(RIGHT CPLX0-6187)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196712016)
(:CREATOR |sgama|) )
NIL)
(BR588 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM588)
(RIGHT CPLX0-6186)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196712016)
(INHIBITORS CPLX0-4582 CPLX0-4737 CPLX0-4738 CPLX0-4739)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4582 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4582 COMMENT)
(INHIBITORS CPLX0-4737 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4737 COMMENT)
(INHIBITORS CPLX0-4738 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4738 COMMENT)
(INHIBITORS CPLX0-4739 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4739 COMMENT)))
(BR589 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM589)
(RIGHT CPLX0-6185)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196712016)
(ACTIVATORS CPLX0-4374)
(INHIBITORS CPLX0-4582 CPLX0-4737 CPLX0-4738 CPLX0-4739)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4374 CITATIONS "[97070370]")
(ACTIVATORS CPLX0-4374 COMMENT)
(INHIBITORS CPLX0-4582 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4582 COMMENT
"FIS represses the hupBp3 promoter only when CRP is absent.")
(INHIBITORS CPLX0-4737 CITATIONS)
(INHIBITORS CPLX0-4737 COMMENT
"FIS represses the hupBp3 promoter only when CRP is absent.")
(INHIBITORS CPLX0-4738 CITATIONS)
(INHIBITORS CPLX0-4738 COMMENT
"FIS represses the hupBp3 promoter only when CRP is absent.")
(INHIBITORS CPLX0-4739 CITATIONS "[97070370]")
(INHIBITORS CPLX0-4739 COMMENT
"FIS represses the hupBp3 promoter only when CRP is absent.")))
(BR59 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS58)
(RIGHT CPLX0-4468)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188147736) )
NIL)
(BR590 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM590)
(RIGHT CPLX0-6184)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196712016)
(:CREATOR |sgama|) )
NIL)
(BR591 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM591)
(RIGHT CPLX0-6183)
(OFFICIAL-EC? T)
(:CREATION-DATE 3196797841)
(INHIBITORS CPLX0-4729)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4729 CITATIONS "[20315956]")
(INHIBITORS CPLX0-4729 COMMENT)))
(BR60 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS59)
(RIGHT CPLX0-4452)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188162191) )
NIL)
(BR601 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS441)
(RIGHT CPLX0-4749)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501059) )
NIL)
(BR602 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS442)
(RIGHT CPLX0-4748)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501165) )
NIL)
(BR603 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS443)
(RIGHT CPLX0-4747)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501256) )
NIL)
(BR604 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS444)
(RIGHT CPLX0-4746)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501321) )
NIL)
(BR605 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS445)
(RIGHT CPLX0-4578)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501399) )
NIL)
(BR606 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS446)
(RIGHT CPLX0-4366)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195501933) )
NIL)
(BR607 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS447)
(RIGHT CPLX0-4435)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195502006) )
NIL)
(BR608 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00365 BS448)
(RIGHT CPLX0-4745)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195589311) )
NIL)
(BR609 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00364 BS449)
(RIGHT CPLX0-4744)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195589465) )
NIL)
(BR61 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00606)
(RIGHT CPLX0-6182)
(OFFICIAL-EC? T)
(:CREATION-DATE 3167134178)
(INHIBITORS CPLX0-4949)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4949 COMMENT)
(INHIBITORS CPLX0-4949 CITATIONS "95403312" "98232508")))
(BR610 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00406 BS450)
(RIGHT CPLX0-4743)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3195589692) )
NIL)
(BR611 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM601)
(RIGHT CPLX0-6181)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197061496)
(:CREATOR |sgama|) )
NIL)
(BR612 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM602)
(RIGHT CPLX0-6180)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197061496)
(:CREATOR |sgama|) )
NIL)
(BR613 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM603)
(RIGHT CPLX0-6179)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197061496)
(:CREATOR |sgama|) )
NIL)
(BR62 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM101)
(RIGHT CPLX0-6178)
(INHIBITORS CPLX0-4196 CPLX0-5221 CPLX0-4518 CPLX0-4519)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185560344)
(ACTIVATORS CPLX0-4631 CPLX0-4808)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4518 COMMENT) (INHIBITORS CPLX0-4196 CITATIONS "7007313")
(ACTIVATORS CPLX0-4631 CITATIONS) (ACTIVATORS CPLX0-4631 COMMENT)
(ACTIVATORS CPLX0-4808 COMMENT) (INHIBITORS CPLX0-4518 CITATIONS "7007313")
(INHIBITORS CPLX0-4519 CITATIONS "6281232" "7007313" "3929016")
(ACTIVATORS CPLX0-4808 CITATIONS "[86174344]")))
(BR622 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-160 BS462)
(RIGHT CPLX0-4742)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196626853) )
NIL)
(BR623 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS463)
(RIGHT CPLX0-4741)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196711325) )
NIL)
(BR624 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS464)
(RIGHT CPLX0-4740)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196711584) )
NIL)
(BR625 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS465)
(RIGHT CPLX0-4583)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196711678) )
NIL)
(BR626 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS466)
(RIGHT CPLX0-4375)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196711763) )
NIL)
(BR627 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS467)
(RIGHT CPLX0-4443)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196711822) )
NIL)
(BR63 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM103)
(RIGHT CPLX0-6177)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185562640)
(:CREATOR |sgama|) )
NIL)
(BR632 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS472)
(RIGHT CPLX0-4739)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196797435) )
NIL)
(BR633 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS473)
(RIGHT CPLX0-4738)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196797494) )
NIL)
(BR634 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS474)
(RIGHT CPLX0-4737)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196797545) )
NIL)
(BR635 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS475)
(RIGHT CPLX0-4582)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196797613) )
NIL)
(BR636 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS476)
(RIGHT CPLX0-4374)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3196797677) )
NIL)
(BR637 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00427)
(RIGHT CPLX0-6176)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197318890)
(:CREATOR |sgama|) )
NIL)
(BR638 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM622)
(RIGHT CPLX0-6175)
(ACTIVATORS CPLX0-4541)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197318890)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4541 COMMENT) (ACTIVATORS CPLX0-4541 CITATIONS "11071896")))
(BR639 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM623)
(RIGHT CPLX0-6174)
(ACTIVATORS CPLX0-4541)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197318890)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4541 CITATIONS "11071896")))
(BR64 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00358)
(RIGHT CPLX0-6173)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185562640)
(:CREATOR |sgama|) )
NIL)
(BR640 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM624)
(RIGHT CPLX0-6172)
(INHIBITORS CPLX0-5612 CPLX0-5633)
(ACTIVATORS CPLX0-5531 CPLX0-4419 CPLX0-4420)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197401733)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5531 CITATIONS "12791142")
(ACTIVATORS CPLX0-5531 COMMENT
"Rob regulates the acrAB operon expression in response to decanoate, but the specific mechanism remains to be
investigated |CITS: [12791142]|. The Rob induction complements the MarA and SoxS effects in this operon.")
(INHIBITORS CPLX0-5612 CITATIONS "15883881")
(INHIBITORS CPLX0-5612 COMMENT
"This regulatory interaction was identified by means of PhoPQ-related microarray experiments and it was checked for the presence of the regulatory motif in the promoter region |CITS: [15883881]|.
A repressor function for acrAB operon transcription can be clearly anticipated from the localization of the PhoP binding site, very close to the acrAp promoter core region.")
(INHIBITORS CPLX0-5633 COMMENT
"The acrR gene, which is located upstream of and in the opposite direction of acrAB, encodes AcrR, a negative DNA-binding transcriptional regulator for multidrug efflux pump. The presence of acrR upstream of the acrAB operon in E. coli suggests that the operon may be controlled at the level of transcription by this regulator |CITS [ 8821940]|.")
(INHIBITORS CPLX0-5633 CITATIONS "8821940")
(ACTIVATORS CPLX0-4419 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4419 COMMENT)
(ACTIVATORS CPLX0-4420 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4420 COMMENT)))
(BR641 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD03576 BS481)
(RIGHT CPLX0-4736)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197061296) )
NIL)
(BR642 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD03576 BS482)
(RIGHT CPLX0-4735)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197061473) )
NIL)
(BR644 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00475)
(RIGHT CPLX0-6171)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197401733)
(ACTIVATORS CPLX0-4442 CPLX0-4377)
(INHIBITORS CPLX0-4732 CPLX0-4733 CPLX0-4734)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4442 COMMENT)
(INHIBITORS CPLX0-4734 CITATIONS "[97059088]")
(INHIBITORS CPLX0-4734 COMMENT
"L-Leucine inhibits but does not abolish Lrp binding to its primary and secondary sites in the leader region of the ilvLG_1G_2MEDA.")
(ACTIVATORS CPLX0-4442 CITATIONS "[91107707]" "[92235862]" "[96165539]"
"[96355348]")
(ACTIVATORS CPLX0-4377 CITATIONS "[91107707]" "[96355348]")
(INHIBITORS CPLX0-4732 CITATIONS "[97059088]")
(INHIBITORS CPLX0-4733 CITATIONS "[97059088]")
(INHIBITORS CPLX0-4733 COMMENT
"The results of gel mobility experiments showed that Lrp forms three complexes with an ilv DNA fragment containing this site. In addition, this secondary site possess no sequence similarity to the Lrp consensus site.")))
(BR645 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00476)
(RIGHT CPLX0-6170)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197401733)
(:CREATOR |sgama|) )
NIL)
(BR646 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00474)
(RIGHT CPLX0-6169)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197401733)
(INHIBITORS CPLX0-4442 CPLX0-4377)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4442 CITATIONS) (INHIBITORS CPLX0-4442 COMMENT)
(INHIBITORS CPLX0-4377 CITATIONS) (INHIBITORS CPLX0-4377 COMMENT)))
(BR65 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS60)
(RIGHT CPLX0-4447)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188162652) )
NIL)
(BR66 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS61)
(RIGHT CPLX0-4448)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188163190) )
NIL)
(BR661 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS501)
(RIGHT CPLX0-4734)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197662558) )
NIL)
(BR662 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS502)
(RIGHT CPLX0-4733)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197662680) )
NIL)
(BR663 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-155 BS503)
(RIGHT CPLX0-4732)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197662750) )
NIL)
(BR666 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS506)
(RIGHT CPLX0-4377)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197663193) )
NIL)
(BR667 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS507)
(RIGHT CPLX0-4442)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197663272) )
NIL)
(BR668 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM641)
(RIGHT CPLX0-6168)
(ACTIVATORS CPLX0-4398 CPLX0-4399)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197831597)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4398 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4398 COMMENT)
(ACTIVATORS CPLX0-4399 CITATIONS "[20032357]")
(ACTIVATORS CPLX0-4399 COMMENT)))
(BR669 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM642)
(RIGHT CPLX0-6167)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197831597)
(:CREATOR |sgama|) )
NIL)
(BR67 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS62)
(RIGHT CPLX0-4449)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188217296) )
NIL)
(BR670 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM643)
(RIGHT CPLX0-6166)
(INHIBITORS CPLX0-5615)
(ACTIVATORS CPLX0-5616 CPLX0-5617 CPLX0-5618)
(OFFICIAL-EC? T)
(:CREATION-DATE 3197831597)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5615 CITATIONS "15879709")
(INHIBITORS CPLX0-5615 COMMENT
"The presence of this site could reduce Fis activation and cause inhibition at high Fis concentration. Nevertheless, the authors do not discard the possibility that this effect is due to impurities in the protein preparation |CITS: [15879709]|.")
(ACTIVATORS CPLX0-5616 CITATIONS "15879709")
(ACTIVATORS CPLX0-5616 COMMENT
"Fis activates the rnpB transcription most effectively at moderate salt concentrations |CITS: [15879709]|.")
(ACTIVATORS CPLX0-5617 CITATIONS "15879709")
(ACTIVATORS CPLX0-5617 COMMENT
"Fis activates the rnpB transcription most effectively at moderate salt concentrations |CITS: [15879709]|.")
(ACTIVATORS CPLX0-5618 CITATIONS "15879709")
(ACTIVATORS CPLX0-5618 COMMENT
"Fis activates the rnpB transcription most effectively at moderate salt concentrations |CITS: [15879709]|.")))
(BR671 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM646)
(RIGHT CPLX0-6165)
(OFFICIAL-EC? T)
(:CREATION-DATE 3198246316)
(ACTIVATORS CPLX0-4584)
(INHIBITORS CPLX0-5661 CPLX0-4728)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5661 CITATIONS "10601216") (INHIBITORS CPLX0-5661 COMMENT)
(INHIBITORS CPLX0-4728 CITATIONS "10601216")
(ACTIVATORS CPLX0-4584 CITATIONS "[20069640]")
(ACTIVATORS CPLX0-4584 COMMENT
"Fnr can regulate adhE expression from adhEp2 promoter only in the physical absence of the upstream promoter region.
")))
(BR68 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS63)
(RIGHT CPLX0-4450)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188229337) )
NIL)
(BR681 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS521)
(RIGHT CPLX0-4731)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197920033) )
NIL)
(BR682 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS522)
(RIGHT CPLX0-4730)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197920085) )
NIL)
(BR683 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS523)
(RIGHT CPLX0-4729)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3197920418) )
NIL)
(BR684 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS524)
(RIGHT CPLX0-4728)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198257524) )
NIL)
(BR685 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS525)
(RIGHT CPLX0-4584)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198257593) )
NIL)
(BR686 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS526)
(RIGHT CPLX0-4376)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198257641) )
NIL)
(BR687 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS527)
(RIGHT CPLX0-4444)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198329592) )
NIL)
(BR688 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS528)
(RIGHT CPLX0-4727)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198329758) )
NIL)
(BR689 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM662)
(RIGHT CPLX0-6164)
(OFFICIAL-EC? T)
(:CREATION-DATE 3198600561)
(:CREATOR |sgama|) )
NIL)
(BR69 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS64)
(RIGHT CPLX0-4451)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188229603) )
NIL)
(BR690 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM662 RNAPS-CPLX)
(RIGHT CPLX0-6163)
(OFFICIAL-EC? T)
(:CREATION-DATE 3198600561)
(:CREATOR |sgama|) )
NIL)
(BR691 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM664)
(RIGHT CPLX0-6162)
(OFFICIAL-EC? T)
(:CREATION-DATE 3198847916)
(:CREATOR |sgama|) )
NIL)
(BR692 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00355)
(RIGHT CPLX0-6161)
(OFFICIAL-EC? T)
(:CREATION-DATE 3198847916)
(:CREATOR |sgama|) )
NIL)
(BR70 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS65)
(RIGHT CPLX0-4436)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188229901) )
NIL)
(BR701 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS541)
(RIGHT CPLX0-4726)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198431548) )
NIL)
(BR702 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00406 BS542)
(RIGHT CPLX0-4725)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198595842) )
NIL)
(BR703 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS543)
(RIGHT CPLX0-4724)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198596588) )
NIL)
(BR704 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS544)
(RIGHT CPLX0-4723)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198596941) )
NIL)
(BR705 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS545)
(RIGHT CPLX0-4587)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3198600478) )
NIL)
(BR706 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM681)
(RIGHT CPLX0-6160)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199038984)
(INHIBITORS CPLX0-5188 CPLX0-4721)
(ACTIVATORS CPLX0-5188 CPLX0-4721 CPLX0-5238 CPLX0-4719 CPLX0-4720 CPLX0-4722)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5188 CITATIONS "20507803" "14996792")
(INHIBITORS CPLX0-5188 COMMENT
"Hns modulates the hlyE expression both positively and negatively, this proteins enhances the expression of hlyE CRP-mediated, but Hns inhibits the FNR-mediated hlyE expression.")
(ACTIVATORS CPLX0-5188 CITATIONS "20507803" "14996792")
(ACTIVATORS CPLX0-5188 COMMENT
"Hns modulates the hlyE expression both positively and negatively, this proteins enhances the expression of hlyE CRP-mediated, but Hns inhibits the FNR-mediated hlyE expression.")
(INHIBITORS CPLX0-4721 CITATIONS "20507803" "14996792")
(INHIBITORS CPLX0-4721 COMMENT
"Hns modulates the hlyE expression both positively and negatively, this protein enhances the expression of hlyE CRP-mediated, but it inhibits the FNR-mediated hlyE expression.")
(ACTIVATORS CPLX0-4721 CITATIONS "20507803" "14996792")
(ACTIVATORS CPLX0-4721 COMMENT
"Hns modulates the hlyE expression both positively and negatively, this protein enhances the expression of hlyE CRP-mediated, but it inhibits the FNR-mediated hlyE expression.")
(ACTIVATORS CPLX0-4720 CITATIONS "20507803" "14996792")
(ACTIVATORS CPLX0-4720 COMMENT
"FNR and CRP are in competition for binding at hlyE regulatory region, but FNR occuppies the site more frequently than CRP even under aerobic conditions, but in such conditions FNR is not an active protein, so this protein can not activate trancription of hlyE as efficiently as CRP. The expression of hlyE CRP-mediated activation requires the presence of Hns.")
(ACTIVATORS CPLX0-5238 CITATIONS "99157562" "14996792")
(ACTIVATORS CPLX0-5238 COMMENT
"SlyA activates hlyE transcription by antagonizing the negative action of Hns protein.")
(ACTIVATORS CPLX0-4719 CITATIONS "20507803" "14996792")
(ACTIVATORS CPLX0-4719 COMMENT
"During anaerobic growth Fnr is important for hlyE expression. FNR and CRP are in competition for binding at hlyE regulatory region, but FNR ocuppies the site more frequently than CRP even under aerobic conditions, but in such conditions FNR is not an active protein, so this protein can not activate trancription of hlyE as efficiently as CRP. The expression of hlyE CRP-mediated activation requires the presence of Hns.")
(ACTIVATORS CPLX0-4722 CITATIONS "[99157562]" "14996792" "20507803"
"97014381")
(ACTIVATORS CPLX0-4722 COMMENT
"The close to 40pb size of the footprinting suggests that two dimers of SlyA are binding. Overproduction of SlyA enhances hlyE expresion as a result of antagonizing the negative effects of H-NS.
")))
(BR707 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM682)
(RIGHT CPLX0-6159)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199039396)
(:CREATOR |sgama|) )
NIL)
(BR708 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM683)
(RIGHT CPLX0-6158)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199039396)
(:CREATOR |sgama|) )
NIL)
(BR71 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS66)
(RIGHT CPLX0-4437)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188230532) )
NIL)
(BR72 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS67)
(RIGHT CPLX0-4438)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188230961) )
NIL)
(BR721 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT G6882-MONOMER BS561)
(RIGHT CPLX0-4722)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199111819) )
NIL)
(BR722 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS562)
(RIGHT CPLX0-4721)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199111942) )
NIL)
(BR723 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS563)
(RIGHT CPLX0-4720)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199111998) )
NIL)
(BR724 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS564)
(RIGHT CPLX0-4719)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199112201) )
NIL)
(BR725 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPE-CPLX PM00327)
(RIGHT CPLX0-6157)
(INHIBITORS CPLX0-5573)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199214905)
(ACTIVATORS CPLX0-5713 CPLX0-5451 CPLX0-5453)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5573 CITATIONS "16143461")
(INHIBITORS CPLX0-5573 COMMENT
"Both, Hha and H-NS proteins form the Hha-H-NS complex which negatively controls the htrA osmoregulation |CITS: [16143461]|.")
(ACTIVATORS CPLX0-5713 CITATIONS "97302967" "95189079")
(ACTIVATORS CPLX0-5451 COMMENT)
(ACTIVATORS CPLX0-5451 CITATIONS "97302967" "95189079")
(ACTIVATORS CPLX0-5453 CITATIONS "95189079" "97302967")))
(BR726 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00032 RNAPS-CPLX)
(RIGHT CPLX0-6156)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199214905)
(ACTIVATORS CPLX0-4019)
(INHIBITORS CPLX0-4089 CPLX0-4090 CPLX0-4257 CPLX0-4251 CPLX0-4253 CPLX0-4255
CPLX0-5203 CPLX0-4048 CPLX0-4033)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4090 COMMENT)
(INHIBITORS CPLX0-4048 COMMENT
"HU and GalR, binding two sites, repress the expression of gal operon in the total absence of galactose |CITS: [16524589]|.")
(INHIBITORS CPLX0-4033 COMMENT
"HU and GalR, binding two sites, repress the expression of gal operon in the total absence of galactose |CITS: [16524589]|.")
(INHIBITORS CPLX0-4089 CITATIONS "8982002")
(INHIBITORS CPLX0-4090 CITATIONS "8982002")
(INHIBITORS CPLX0-4033 CITATIONS "97169301" "22882886" "8982002" "15289461")
(INHIBITORS CPLX0-4048 CITATIONS "97169301" "22882886" "8982002" "15289461")
(INHIBITORS CPLX0-5203 COMMENT "GalR is required to bind HU.")
(INHIBITORS CPLX0-5203 CITATIONS "97361846" "20440406" "97169301"
"22882886")
(INHIBITORS CPLX0-4257 CITATIONS "2160266") (INHIBITORS CPLX0-4257 COMMENT)
(INHIBITORS CPLX0-4251 CITATIONS "2160266") (INHIBITORS CPLX0-4251 COMMENT)
(INHIBITORS CPLX0-4253 CITATIONS "2160266") (INHIBITORS CPLX0-4253 COMMENT)
(INHIBITORS CPLX0-4255 CITATIONS "2160266") (INHIBITORS CPLX0-4255 COMMENT)))
(BR728 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS566)
(RIGHT CPLX0-4718)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199475927) )
NIL)
(BR729 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PROTEIN-NRIP BS567)
(RIGHT CPLX0-4717)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3199730578) )
NIL)
(BR741 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM00531)
(RIGHT CPLX0-6155)
(ACTIVATORS CPLX0-5157)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199557508)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5157 COMMENT) (ACTIVATORS CPLX0-5157 CITATIONS "15838058")))
(BR742 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00241 RNAPS-CPLX)
(RIGHT CPLX0-6154)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199644436)
(INHIBITORS CPLX0-4435 CPLX0-4366 CPLX0-4109)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4109 COMMENT
"This site is of low affinity for IHF. The low affinity of IHF binding suggests a simple mechanism for the negative autoregulation of IHF, in which IHF acts as a repressor of transcription initiation only when its level in the cell is high. The increase in the level of IHF as the cells enter the stationary phase is partly caused by the increase in the mRNA level of the two IHF genes.")
(INHIBITORS CPLX0-4366 COMMENT)
(INHIBITORS CPLX0-4435 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4366 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4109 CITATIONS "[99122365]" "[95231284]")))
(BR744 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00279 RNAPS-CPLX)
(RIGHT CPLX0-6153)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199644436)
(ACTIVATORS CPLX0-4727 CPLX0-4444 CPLX0-4376)
(INHIBITORS CPLX0-4728 CPLX0-5661 CPLX0-4107)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4728 COMMENT)
(INHIBITORS CPLX0-4728 CITATIONS "20069640" "92078115")
(INHIBITORS CPLX0-5661 CITATIONS "92078115" "20069640")
(INHIBITORS CPLX0-4107 CITATIONS "98037513")
(INHIBITORS CPLX0-4107 COMMENT
"The effect of FruR repression of adhE gene was studied during aerobic and anaerobic growth conditions, and the
stronger repression was observed during aerobic growth. Both respiratory conditions do not imply a direct regulation,
but they may reflect a difference of fructose or fructose 1,6 diphosphate levels |CITS: [9371462]|.
Later, the FruR site has been localized downstream the promoter, and it is proposed as a repressor site
|CITS: [12083772]|(as it has been observed that other FruR repressor sites are overlapping or downstream the
promoter, see |CITS: [8655535]|).")))
(BR745 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM687)
(RIGHT CPLX0-6152)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199730751)
(ACTIVATORS CPLX0-5277 CPLX0-4717)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4717 CITATIONS "[97000355]")
(ACTIVATORS CPLX0-5277 CITATIONS "14702398") (ACTIVATORS CPLX0-5277 COMMENT)))
(BR746 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00242 RNAPS-CPLX)
(RIGHT CPLX0-6151)
(OFFICIAL-EC? T)
(:CREATION-DATE 3199818143)
(INHIBITORS CPLX0-4658 CPLX0-4659 CPLX0-4663 CPLX0-4664 CPLX0-4665 CPLX0-4139)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4658 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4658 COMMENT)
(INHIBITORS CPLX0-4659 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4659 COMMENT)
(INHIBITORS CPLX0-4663 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4663 COMMENT)
(INHIBITORS CPLX0-4664 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4664 COMMENT)
(INHIBITORS CPLX0-4665 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4665 COMMENT)
(INHIBITORS CPLX0-4139 CITATIONS "[99122365]" "[95231284]")
(INHIBITORS CPLX0-4139 COMMENT)))
(BR748 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM692)
(RIGHT CPLX0-6150)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200080965)
(INHIBITORS CPLX0-4088 CPLX0-4715)
(ACTIVATORS CPLX0-4088 CPLX0-4415 CPLX0-4716)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4415 COMMENT)
(ACTIVATORS CPLX0-4088 COMMENT
"Although Crp has been observed binding to this site, its function remains unknown.")
(INHIBITORS CPLX0-4088 COMMENT
"Although Crp has been observed binding to this site, its function remains unknown.")
(ACTIVATORS CPLX0-4088 CITATIONS "20372646")
(INHIBITORS CPLX0-4088 CITATIONS "20372646")
(ACTIVATORS CPLX0-4415 CITATIONS "10913096")
(INHIBITORS CPLX0-4715 CITATIONS "10913096") (INHIBITORS CPLX0-4715 COMMENT)
(ACTIVATORS CPLX0-4716 CITATIONS "10913096") (ACTIVATORS CPLX0-4716 COMMENT)))
(BR749 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS581)
(RIGHT CPLX0-4716)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200080491) )
NIL)
(BR75 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS69)
(RIGHT CPLX0-4439)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188232137) )
NIL)
(BR751 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG12278-MONOMER BS583)
(RIGHT CPLX0-4715)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200080954) )
NIL)
(BR752 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00466)
(RIGHT CPLX0-6149)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200251553)
(INHIBITORS CPLX0-4381)
(ACTIVATORS CPLX0-4714)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4381 COMMENT)
(ACTIVATORS CPLX0-4714 CITATIONS "[97402541]" "[96423182]")
(ACTIVATORS CPLX0-4714 COMMENT)
(INHIBITORS CPLX0-4381 CITATIONS "[96423182]" "[97402541]")))
(BR753 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00465)
(RIGHT CPLX0-6148)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200251553)
(INHIBITORS CPLX0-4381)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4381 CITATIONS "[96423182]" "[97402541]")
(INHIBITORS CPLX0-4381 COMMENT)))
(BR754 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG10490-MONOMER BS584)
(RIGHT CPLX0-4714)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200251201) )
NIL)
(BR756 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-160 BS586)
(RIGHT CPLX0-4381)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200251295) )
NIL)
(BR757 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS587)
(RIGHT CPLX0-4455)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200337324) )
NIL)
(BR76 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS68)
(RIGHT CPLX0-4433)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188232269) )
NIL)
(BR761 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00363)
(RIGHT CPLX0-6147)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200337416)
(:CREATOR |sgama|) )
NIL)
(BR762 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00364)
(RIGHT CPLX0-6146)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200337416)
(:CREATOR |sgama|) )
NIL)
(BR764 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS601)
(RIGHT CPLX0-4713)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200419947) )
NIL)
(BR765 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS602)
(RIGHT CPLX0-4593)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200420283) )
NIL)
(BR766 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS603)
(RIGHT CPLX0-4384)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200420467) )
NIL)
(BR781 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM721)
(RIGHT CPLX0-6145)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200763897)
(:CREATOR |sgama|) )
NIL)
(BR782 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00625)
(RIGHT CPLX0-6143)
(OFFICIAL-EC? T)
(:CREATION-DATE 3200763897)
(INHIBITORS CPLX0-5660 CPLX0-4709 CPLX0-4710 CPLX0-4458 CPLX0-4383 CPLX0-4592)
(ACTIVATORS CPLX0-6144 CPLX0-4711 CPLX0-4712)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5660 CITATIONS "99069334") (INHIBITORS CPLX0-5660 COMMENT)
(ACTIVATORS CPLX0-6144 COMMENT
"DcuR regulates the expression of dcuBp in response to external C4-dicarboxylates.")
(ACTIVATORS CPLX0-6144 CITATIONS "[22267266]" "[98440434]" "[99138745]"
"14996819" "15073297")
(INHIBITORS CPLX0-4709 CITATIONS "[99069334]")
(INHIBITORS CPLX0-4710 CITATIONS "[99069334]")
(INHIBITORS CPLX0-4710 COMMENT)
(INHIBITORS CPLX0-4458 CITATIONS "[99069334]")
(INHIBITORS CPLX0-4458 COMMENT)
(INHIBITORS CPLX0-4383 CITATIONS "[99069334]")
(INHIBITORS CPLX0-4383 COMMENT)
(INHIBITORS CPLX0-4592 CITATIONS "[99069334]")
(INHIBITORS CPLX0-4592 COMMENT)
(ACTIVATORS CPLX0-4711 CITATIONS "[99069334]")
(ACTIVATORS CPLX0-4712 CITATIONS "[99069334]")
(ACTIVATORS CPLX0-4712 COMMENT
"An unknown factor other than Fnr also contributes to anaerobic induction of dcuB.")))
(BR783 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS621)
(RIGHT CPLX0-4712)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763484) )
NIL)
(BR784 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS622)
(RIGHT CPLX0-4711)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763561) )
NIL)
(BR785 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS623)
(RIGHT CPLX0-4592)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763607) )
NIL)
(BR786 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS624)
(RIGHT CPLX0-4383)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763645) )
NIL)
(BR787 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS625)
(RIGHT CPLX0-4458)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763690) )
NIL)
(BR788 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS626)
(RIGHT CPLX0-4710)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763748) )
NIL)
(BR789 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS627)
(RIGHT CPLX0-4709)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3200763852) )
NIL)
(BR801 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM741)
(RIGHT CPLX0-6142)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201023164)
(INHIBITORS CPLX0-4536 CPLX0-4701)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4701 COMMENT)
(INHIBITORS CPLX0-4701 CITATIONS "[97352675]" "[99445472]")
(INHIBITORS CPLX0-4536 CITATIONS "[97352675]" "[99445472]")))
(BR802 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-160 BS641)
(RIGHT CPLX0-4708)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3201371743) )
NIL)
(BR81 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM261)
(RIGHT CPLX0-6141)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168194184)
(:CREATOR |sgama|) )
NIL)
(BR82 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM261)
(RIGHT CPLX0-6140)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168194184)
(:CREATOR |sgama|) )
NIL)
(BR821 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM761)
(RIGHT CPLX0-6139)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201371850)
(ACTIVATORS CPLX0-4708)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4708 CITATIONS "[97260115]")
(ACTIVATORS CPLX0-4708 COMMENT
"The stimulatory effect of DnaA on polA genes was only observed in stationary-phase.")))
(BR822 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS661)
(RIGHT CPLX0-4707)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3202672180) )
NIL)
(BR823 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS662)
(RIGHT CPLX0-4706)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3202672245) )
NIL)
(BR824 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS663)
(RIGHT CPLX0-4705)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3202841717) )
NIL)
(BR83 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM262)
(RIGHT CPLX0-6138)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168259060)
(INHIBITORS CPLX0-4690 CPLX0-4691)
(ACTIVATORS CPLX0-5151 CPLX0-4692)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5151 CITATIONS "98083735")
(ACTIVATORS CPLX0-5151 COMMENT
"Even though the FruR site has not been determined for the acnA gene, the FruR effect in its transcription is correlated.
And it has been proposed that FruR affects the acnAp2 promoter because this is responsible for the basal level of acnA
during exponential growth as well as redox-stress |CITS: [98083735]|.")
(ACTIVATORS CPLX0-4692 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4691 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4690 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4690 COMMENT)))
(BR84 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM263)
(RIGHT CPLX0-6137)
(OFFICIAL-EC? T)
(:CREATION-DATE 3168259060)
(INHIBITORS CPLX0-4047 CPLX0-4532 CPLX0-4683 CPLX0-4684 CPLX0-4685 CPLX0-4686
CPLX0-4687 CPLX0-4688 CPLX0-4689 CPLX0-4387 CPLX0-4339)
(ACTIVATORS CPLX0-4533)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4047 CITATIONS "9421904")
(INHIBITORS CPLX0-4047 COMMENT
"The direct FruR binding to the acnB has been determined, even though the repressive effect is observed. The different effect of FruR on acnA (activating) and acnB (repressing) is unclear yet. It may be related to the preferencial use of one of the two enzymes in the citric and glyoxilate cycles or stress response (see |CITS: [9421904]|).")
(ACTIVATORS CPLX0-4533 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4339 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4387 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4689 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4688 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4687 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4686 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4685 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4684 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4683 CITATIONS "[98083735]")
(INHIBITORS CPLX0-4532 CITATIONS "[98083735]")))
(BR841 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM00415)
(RIGHT CPLX0-6136)
(INHIBITORS CPLX0-5685 CPLX0-5229)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201877997)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5685 CITATIONS "16428390") (INHIBITORS CPLX0-5685 COMMENT)
(INHIBITORS CPLX0-5229 COMMENT
"Nitric oxide (NO) inactivates the FNR protein, so NO induces hmpA expression .")
(INHIBITORS CPLX0-5229 CITATIONS "96404799" "97340947" "12093725")))
(BR842 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00468)
(RIGHT CPLX0-6135)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201877997)
(:CREATOR |sgama|) )
NIL)
(BR843 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00469)
(RIGHT CPLX0-6134)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201877997)
(:CREATOR |sgama|) )
NIL)
(BR844 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM785)
(RIGHT CPLX0-6133)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201973793)
(:CREATOR |sgama|) )
NIL)
(BR845 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM786)
(RIGHT CPLX0-6132)
(OFFICIAL-EC? T)
(:CREATION-DATE 3201973793)
(:CREATOR |sgama|) )
NIL)
(BR846 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM787)
(RIGHT CPLX0-6131)
(INHIBITORS CPLX0-5310)
(ACTIVATORS CPLX0-5311 CPLX0-5410 CPLX0-5411)
(OFFICIAL-EC? T)
(:CREATION-DATE 3202241461)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5410 CITATIONS "22313470" "14702328")
(ACTIVATORS CPLX0-5311 COMMENT
"CRP and anaerobiosis are required for the hyf operon expression when the HyfR protein is the activator.")
(ACTIVATORS CPLX0-5311 CITATIONS "14702328")
(ACTIVATORS CPLX0-5411 COMMENT
"HypF activates the hyf operon transcription only when it is expressed from a heterologous promoter.")
(ACTIVATORS CPLX0-5411 CITATIONS "22313470" "14702328")
(ACTIVATORS CPLX0-5410 COMMENT
"Only FhlA mutants can activate the transcription of hyf operon.
HycA protein acts as an antiactivator of FhlA |CITS:[12426353]|.")
(INHIBITORS CPLX0-5310 COMMENT
"It seems that Fnr repress the hyf operon expression when it is activated by HyfR. Its is possible that binding of FNR may minimize the binding of HyfR, whose binding site is only 25 bases upstream of the FNR binding site.")
(INHIBITORS CPLX0-5310 CITATIONS "14702328")))
(BR847 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00214 BS681)
(RIGHT CPLX0-4380)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3203274703) )
NIL)
(BR85 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00359)
(RIGHT CPLX0-6130)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185637768)
(:CREATOR |sgama|) )
NIL)
(BR86 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00360)
(RIGHT CPLX0-6129)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185638637)
(INHIBITORS CPLX0-4805 CPLX0-4807 CPLX0-4806)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4805 CITATIONS "[87286425]")
(INHIBITORS CPLX0-4805 COMMENT)
(INHIBITORS CPLX0-4807 CITATIONS "[87286425]")
(INHIBITORS CPLX0-4807 COMMENT)
(INHIBITORS CPLX0-4806 CITATIONS "[87286425]")
(INHIBITORS CPLX0-4806 COMMENT)))
(BR861 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00421)
(RIGHT CPLX0-6128)
(OFFICIAL-EC? T)
(:CREATION-DATE 3202672345)
(INHIBITORS CPLX0-4707)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4707 CITATIONS "11673423" "94165044")))
(BR862 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00421 RNAPS-CPLX)
(RIGHT CPLX0-6127)
(OFFICIAL-EC? T)
(:CREATION-DATE 3202672345)
(INHIBITORS CPLX0-4707)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4707 CITATIONS "11673423" "94165044")))
(BR863 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00423)
(RIGHT CPLX0-6126)
(OFFICIAL-EC? T)
(:CREATION-DATE 3202672345)
(INHIBITORS CPLX0-4630 CPLX0-4653 CPLX0-4649 CPLX0-4650 CPLX0-4654 CPLX0-4655
CPLX0-4648 CPLX0-4651 CPLX0-4652 CPLX0-4647 CPLX0-4706)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4630 CITATIONS "8120010") (INHIBITORS CPLX0-4630 COMMENT)
(INHIBITORS CPLX0-4653 CITATIONS "8120010") (INHIBITORS CPLX0-4653 COMMENT)
(INHIBITORS CPLX0-4649 CITATIONS "8120010") (INHIBITORS CPLX0-4649 COMMENT)
(INHIBITORS CPLX0-4650 CITATIONS "8120010") (INHIBITORS CPLX0-4650 COMMENT)
(INHIBITORS CPLX0-4654 CITATIONS "8120010") (INHIBITORS CPLX0-4654 COMMENT)
(INHIBITORS CPLX0-4655 CITATIONS "8120010") (INHIBITORS CPLX0-4655 COMMENT)
(INHIBITORS CPLX0-4648 CITATIONS "8120010") (INHIBITORS CPLX0-4648 COMMENT)
(INHIBITORS CPLX0-4651 CITATIONS "8120010") (INHIBITORS CPLX0-4651 COMMENT)
(INHIBITORS CPLX0-4652 CITATIONS "8120010") (INHIBITORS CPLX0-4652 COMMENT)
(INHIBITORS CPLX0-4647 CITATIONS "8120010") (INHIBITORS CPLX0-4647 COMMENT)
(INHIBITORS CPLX0-4706 CITATIONS "11673423" "94165044")
(INHIBITORS CPLX0-4706 COMMENT
"Inhibition of this promoter transcription by Hns is reduced in the presence of potassium glutamate.
")))
(BR864 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00422)
(RIGHT CPLX0-6125)
(OFFICIAL-EC? T)
(:CREATION-DATE 3202672345)
(:CREATOR |sgama|) )
NIL)
(BR865 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS701)
(RIGHT CPLX0-4524)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3203708518) )
NIL)
(BR87 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00361)
(RIGHT CPLX0-6124)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185639018)
(:CREATOR |sgama|) )
NIL)
(BR88 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM124)
(RIGHT CPLX0-6123)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185640221)
(:CREATOR |sgama|) )
NIL)
(BR881 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM821)
(RIGHT CPLX0-6122)
(OFFICIAL-EC? T)
(:CREATION-DATE 3203274843)
(ACTIVATORS CPLX0-4380)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4380 CITATIONS "[97440154]")
(ACTIVATORS CPLX0-4380 COMMENT)))
(BR882 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11149-MONOMER BS721)
(RIGHT CPLX0-4704)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3203791860) )
NIL)
(BR883 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS722)
(RIGHT CPLX0-4703)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3203791860) )
NIL)
(BR89 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM125)
(RIGHT CPLX0-6121)
(OFFICIAL-EC? T)
(:CREATION-DATE 3185642532)
(ACTIVATORS CPLX0-5721 CPLX0-5653 CPLX0-5297 CPLX0-5296 CPLX0-4820)
(INHIBITORS CPLX0-5654 CPLX0-5298)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5721 CITATIONS "11287151")
(ACTIVATORS CPLX0-5721 COMMENT
"The regulatory effect of FlhDC in the napF operon transcription has been proved just by microarray analysis by |CITS: [21184412]|")
(INHIBITORS CPLX0-5654 CITATIONS "98361910" "95371106" "13129959")
(INHIBITORS CPLX0-5654 COMMENT)
(ACTIVATORS CPLX0-5653 CITATIONS "13129959" "98361910")
(ACTIVATORS CPLX0-5653 COMMENT)
(ACTIVATORS CPLX0-5297 CITATIONS "13129959" "98361910")
(ACTIVATORS CPLX0-5297 COMMENT) (ACTIVATORS CPLX0-5296 COMMENT)
(INHIBITORS CPLX0-5298 CITATIONS "98361910" "13129959" "95371106")
(ACTIVATORS CPLX0-4820 CITATIONS "98361910" "13129959")
(ACTIVATORS CPLX0-5296 CITATIONS "22024722" "13129959")))
(BR901 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM823)
(RIGHT CPLX0-6120)
(OFFICIAL-EC? T)
(:CREATION-DATE 3203703037)
(:CREATOR |sgama|) )
NIL)
(BR902 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM00527)
(RIGHT CPLX0-6119)
(OFFICIAL-EC? T)
(:CREATION-DATE 3203708802)
(INHIBITORS CPLX0-4622 CPLX0-4524)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4524 CITATIONS "[95286540]")
(INHIBITORS CPLX0-4622 CITATIONS "10802181")))
(BR903 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS741)
(RIGHT CPLX0-4702)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3206813164) )
NIL)
(BR904 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-162 BS742)
(RIGHT CPLX0-4701)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3206813760) )
NIL)
(BR905 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT MONOMER0-162 BS743)
(RIGHT CPLX0-4536)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3206813824) )
NIL)
(BR906 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS744)
(RIGHT CPLX0-4341)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3206814117) )
NIL)
(BR908 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS746)
(RIGHT CPLX0-4700)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3207059121) )
NIL)
(BR909 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS747)
(RIGHT CPLX0-4699)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3207060281) )
NIL)
(BR91 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM162 RNAP70-CPLX)
(RIGHT CPLX0-6118)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188246098) )
NIL)
(BR910 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS748)
(RIGHT CPLX0-4698)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3207060340) )
NIL)
(BR911 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS749)
(RIGHT CPLX0-4697)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3207060395) )
NIL)
(BR913 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-HYDG BS751)
(RIGHT CPLX0-4696)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3207943359) )
NIL)
(BR915 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01896 BS753)
(RIGHT CPLX0-4534)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208199090) )
NIL)
(BR917 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS755)
(RIGHT CPLX0-4385)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208199231) )
NIL)
(BR918 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD01896 BS756)
(RIGHT CPLX0-4695)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208199387) )
NIL)
(BR919 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-TORR BS757)
(RIGHT CPLX0-4694)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208284185) )
NIL)
(BR92 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM163)
(RIGHT CPLX0-6117)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188247217) )
NIL)
(BR920 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-TORR BS758)
(RIGHT CPLX0-4693)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208284251) )
NIL)
(BR921 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00193)
(RIGHT CPLX0-6116)
(OFFICIAL-EC? T)
(:CREATION-DATE 3203791919)
(ACTIVATORS CPLX0-4703)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4703 COMMENT
"As it was described a negative effect in a fruR mutant of S. thyphimurium for the expression of pckA in an earlier
study CITS: |[2496106]|, it was inferred that FruR could activate pckA transcription. Now as the FruR site was found
145bp upstream the transcriptional start site (similar to ace operon site), the suggestion is that FruR is able to
activate gene expression at a considerable distance, possibly looping the DNA in order to contact the
transcriptional initiation complex.")
(ACTIVATORS CPLX0-4703 CITATIONS "[96020647]")))
(BR922 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS759)
(RIGHT CPLX0-4692)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208628896) )
NIL)
(BR923 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS760)
(RIGHT CPLX0-4691)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208628957) )
NIL)
(BR924 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS761)
(RIGHT CPLX0-4690)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629015) )
NIL)
(BR925 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS762)
(RIGHT CPLX0-4533)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629628) )
NIL)
(BR926 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS763)
(RIGHT CPLX0-4339)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629686) )
NIL)
(BR927 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS764)
(RIGHT CPLX0-4387)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629737) )
NIL)
(BR928 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS765)
(RIGHT CPLX0-4689)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629825) )
NIL)
(BR929 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS766)
(RIGHT CPLX0-4688)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629874) )
NIL)
(BR93 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM164)
(RIGHT CPLX0-6115)
(ACTIVATORS CPLX0-5551 CPLX0-4124)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188250019) )
((ACTIVATORS CPLX0-4124 COMMENT)
(ACTIVATORS CPLX0-5551 CITATIONS "15941987" "7961507")
(ACTIVATORS CPLX0-5551 COMMENT)
(ACTIVATORS CPLX0-4124 CITATIONS "[97020029]" "[95050319]")))
(BR930 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS767)
(RIGHT CPLX0-4687)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629934) )
NIL)
(BR931 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS768)
(RIGHT CPLX0-4686)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208629978) )
NIL)
(BR932 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS769)
(RIGHT CPLX0-4685)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208630044) )
NIL)
(BR933 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS770)
(RIGHT CPLX0-4684)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208630098) )
NIL)
(BR934 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS771)
(RIGHT CPLX0-4683)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208630147) )
NIL)
(BR935 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00196 BS772)
(RIGHT CPLX0-4532)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208630200) )
NIL)
(BR936 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS773)
(RIGHT CPLX0-4338)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3208630435) )
NIL)
(BR94 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS81)
(RIGHT CPLX0-4408)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188303648) )
NIL)
(BR941 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM841)
(RIGHT CPLX0-6114)
(OFFICIAL-EC? T)
(:CREATION-DATE 3203873738)
(:CREATOR |sgama|) )
NIL)
(BR95 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS82)
(RIGHT CPLX0-4409)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188304098) )
NIL)
(BR961 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00467)
(RIGHT CPLX0-6113)
(OFFICIAL-EC? T)
(:CREATION-DATE 3204397452)
(:CREATOR |sgama|) )
NIL)
(BR962 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM881)
(RIGHT CPLX0-6112)
(INHIBITORS CPLX0-5662 CPLX0-5352)
(OFFICIAL-EC? T)
(:CREATION-DATE 3204397452)
(ACTIVATORS CPLX0-4341)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5662 CITATIONS "16159764")
(INHIBITORS CPLX0-5662 COMMENT
"NikR and NarLX repress the synthesis of NikABCDE in the presence of nitrate. NarL is phosphorylated by NarX in the presence of NO3-|CITS:[16159764]|.")
(ACTIVATORS CPLX0-4341 COMMENT
"FNR upregulates NikABCDE in the absence of oxygen. This regulator is inactivated by O2 |CITS:[16159764]|.")
(INHIBITORS CPLX0-5352 COMMENT
"The N-terminal domain of NikR is responsible for DNA recognition.
NikR and NarLX repress the synthesis of NikABCDE in the presence of nitrate. NikR also represses NikABCDE expression at higher nickel concentration. This regulator is activated by Ni2+, and its function is inhibited by one or more formate-inducible hydrogenase assembly components |CITS:[16159764]|.")
(INHIBITORS CPLX0-5352 CITATIONS "10787413" "10595554")
(ACTIVATORS CPLX0-4341 CITATIONS "[95020649]" "[20061003]")))
(BR963 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS781)
(RIGHT CPLX0-4682)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3210448045) )
NIL)
(BR964 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-NARL BS782)
(RIGHT CPLX0-4681)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3210448085) )
NIL)
(BR965 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS783)
(RIGHT CPLX0-4535)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3210448130) )
NIL)
(BR966 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00353 BS784)
(RIGHT CPLX0-4335)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3210703624) )
NIL)
(BR967 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00061 BS785)
(RIGHT CPLX0-4386)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3210703919) )
NIL)
(BR97 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT CPLX0-226 BS84)
(RIGHT CPLX0-4410)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188304613) )
NIL)
(BR98 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00197 BS85)
(RIGHT CPLX0-4411)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188305020) )
NIL)
(BR981 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM921)
(RIGHT CPLX0-6111)
(OFFICIAL-EC? T)
(:CREATION-DATE 3207075087)
(ACTIVATORS CPLX0-5218)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-5218 CITATIONS "9171388")))
(BR982 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM922)
(RIGHT CPLX0-6110)
(OFFICIAL-EC? T)
(:CREATION-DATE 3207426970)
(:CREATOR |sgama|) )
NIL)
(BR983 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM923)
(RIGHT CPLX0-6109)
(ACTIVATORS CPLX0-4696)
(OFFICIAL-EC? T)
(:CREATION-DATE 3207944096)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4696 CITATIONS "21140164")
(ACTIVATORS CPLX0-4696 COMMENT
"ZraR activates zraPp promoter in the presence of high Zn2+ and Pb2+ concentrations|CITS: [21140164]|.")))
(BR984 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP54-CPLX PM924)
(RIGHT CPLX0-6108)
(OFFICIAL-EC? T)
(:CREATION-DATE 3207944096)
(ACTIVATORS CPLX0-5697 CPLX0-4696)
(:CREATOR |sgama|) )
((ACTIVATORS CPLX0-4696 COMMENT
"ZraR activates zraSp promoter in the presence of high Zn2+ and Pb2+ concentrations|CITS: [21140164]|.")
(ACTIVATORS CPLX0-5697 CITATIONS "15520470") (ACTIVATORS CPLX0-5697 COMMENT)
(ACTIVATORS CPLX0-4696 CITATIONS "[21140164]")))
(BR985 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM928)
(RIGHT CPLX0-6107)
(INHIBITORS CPLX0-5681 CPLX0-4674)
(ACTIVATORS CPLX0-4210 CPLX0-4595 CPLX0-5289)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208021358)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5681 CITATIONS "14701822") (ACTIVATORS CPLX0-4210 COMMENT)
(INHIBITORS CPLX0-4674 COMMENT
"The H-NS site for the hdeD regulatory region has not been determined, but Yoshida93 suggest that H-NS
has two sites: one site close to hdeA and the other one near to hdeD (the upstream opposite direction operon); and that
H-NS represses transcription through the binding to DNA supercoiled.")
(INHIBITORS CPLX0-4674 CITATIONS "10383761" "8455549")
(ACTIVATORS CPLX0-5289 CITATIONS "14702398")
(ACTIVATORS CPLX0-4595 CITATIONS "14702398")
(ACTIVATORS CPLX0-4210 CITATIONS "12657056")))
(BR986 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM928 RNAPS-CPLX)
(RIGHT CPLX0-6106)
(INHIBITORS CPLX0-5681 CPLX0-4674)
(ACTIVATORS CPLX0-4210 CPLX0-4595 CPLX0-5289)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208021358)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-5681 CITATIONS "14701822") (ACTIVATORS CPLX0-4210 COMMENT)
(INHIBITORS CPLX0-4674 COMMENT
"The H-NS site for the hdeD regulatory region has not been determined, but Yoshida93 suggest that H-NS
has two sites: one site close to hdeA and the other one near to hdeD (the upstream opposite direction operon); and that
H-NS represses transcription through the binding to DNA supercoiled.")
(INHIBITORS CPLX0-4674 CITATIONS "10383761" "8455549")
(ACTIVATORS CPLX0-5289 CITATIONS "14702398")
(ACTIVATORS CPLX0-4595 CITATIONS "14702398")
(ACTIVATORS CPLX0-4210 CITATIONS "12657056")))
(BR987 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAPS-CPLX PM929)
(RIGHT CPLX0-6105)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208021358)
(:CREATOR |sgama|) )
NIL)
(BR988 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM932)
(RIGHT CPLX0-6104)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208021358)
(:CREATOR |sgama|) )
NIL)
(BR989 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM933)
(RIGHT CPLX0-6103)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208021358)
(INHIBITORS CPLX0-4386)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4386 CITATIONS "[97011571]")
(INHIBITORS CPLX0-4386 COMMENT
"FruR site in pfkA gene overlaps with the -35 box, so it is proposed that FruR inhibits pfkA transcription avoiding the
RNA polymerase access to its binding site.")))
(BR99 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PHOSPHO-ARCA BS86)
(RIGHT CPLX0-4412)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3188305289) )
NIL)
(BR990 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM934)
(RIGHT CPLX0-6102)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208199528)
(INHIBITORS CPLX0-4385 CPLX0-4534)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4534 COMMENT)
(INHIBITORS CPLX0-4534 CITATIONS "98143424" "21336590")
(INHIBITORS CPLX0-4385 CITATIONS "21336590")))
(BR991 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM935)
(RIGHT CPLX0-6101)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208199528)
(ACTIVATORS CPLX0-4385)
(INHIBITORS CPLX0-4534)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4534 COMMENT)
(INHIBITORS CPLX0-4534 CITATIONS "[98143424]" "[21336590]")
(ACTIVATORS CPLX0-4385 CITATIONS "[21336590]")
(ACTIVATORS CPLX0-4385 COMMENT
"CRP has a positive effect on mlcp2 transcription directed by Sigma70. However, CRP has little effect on mlcp2 transcription directed by Sigma32.")))
(BR992 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM935 RNAP32-CPLX)
(RIGHT CPLX0-6100)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208199528)
(ACTIVATORS CPLX0-4385)
(INHIBITORS CPLX0-4534)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4534 COMMENT)
(INHIBITORS CPLX0-4534 CITATIONS "[98143424]" "[21336590]")
(ACTIVATORS CPLX0-4385 CITATIONS "[21336590]")
(ACTIVATORS CPLX0-4385 COMMENT
"CRP has a positive effect on mlcp2 transcription directed by Sigma70. However, CRP has little effect on mlcp2 transcription directed by Sigma32.")))
(BR993 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT RNAP70-CPLX PM00672)
(RIGHT CPLX0-6099)
(INHIBITORS CPLX0-4644 CPLX0-4642 CPLX0-4643 CPLX0-4640)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208289609)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4644 CITATIONS "12730174")
(INHIBITORS CPLX0-4644 COMMENT
"It has been sugested that a DNA loop is formed when ArgR is binding to the three Arg boxes.
The binding of each of two regulators (CRP and ArgR) to the regulatory region of metY, interferes with the binding of the other, but ArgR binding overrides CRP binding.
ArgR repress the metY operon only when CRP is present.")
(INHIBITORS CPLX0-4642 CITATIONS "12730174")
(INHIBITORS CPLX0-4642 COMMENT
"It has been sugested that a DNA loop is formed when ArgR is binding to the three Arg boxes.
The binding of each of two regulators (CRP and ArgR) to the regulatory region of metY, interferes with the binding of the other, but ArgR binding overrides CRP binding.
ArgR repress the metY operon only when CRP is present.")
(INHIBITORS CPLX0-4643 CITATIONS "12730174")
(INHIBITORS CPLX0-4643 COMMENT
"It has been sugested that a DNA loop is formed when ArgR is binding to the three Arg boxes.
The binding of each of two regulators (CRP and ArgR) to the regulatory region of metY, interferes with the binding of the other, but ArgR binding overrides CRP binding.
ArgR repress the metY operon only when CRP is present.")
(INHIBITORS CPLX0-4640 CITATIONS "12730174")
(INHIBITORS CPLX0-4640 COMMENT
"CRP binds in just one site activates argG gene expresion and repress the expression of the divergent operon metY-yhbC-nusA-infB.
")))
(BR994 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM168)
(RIGHT CPLX0-6098)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208289609)
(INHIBITORS CPLX0-4694 CPLX0-4693)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4693 COMMENT "
")
(INHIBITORS CPLX0-4693 CITATIONS "[96123439]" "[20115539]")
(INHIBITORS CPLX0-4694 CITATIONS "[96123439]" "[20115539]")
(INHIBITORS CPLX0-4694 COMMENT "
")))
(BR995 NIL (
(OCELOT-GFP::PARENTS |RNA-Polymerase-Binding-Reactions|)
(LEFT PM00483)
(RIGHT CPLX0-6097)
(OFFICIAL-EC? T)
(:CREATION-DATE 3208630561)
(INHIBITORS CPLX0-4338)
(:CREATOR |sgama|) )
((INHIBITORS CPLX0-4338 CITATIONS "[88257027]")
(INHIBITORS CPLX0-4338 COMMENT)))
(BR996 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS801)
(RIGHT CPLX0-4337)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3211047284) )
NIL)
(BR997 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT EG11966-MONOMER BS802)
(RIGHT CPLX0-4389)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3211047389) )
NIL)
(BR998 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PC00027 BS803)
(RIGHT CPLX0-4680)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3211047484) )
NIL)
(BR999 NIL (
(OCELOT-GFP::PARENTS |Transcription-Factor-Binding-Reactions|)
(LEFT PD00288 BS804)
(RIGHT CPLX0-4679)
(OFFICIAL-EC? T)
(:CREATOR |sgama|)
(:CREATION-DATE 3211047980) )
NIL)
(BRANCHED-CHAIN-AA-SYN-PWY NIL (
(OCELOT-GFP::PARENTS AMINO-ACID-FAMILY-SYN)
(:CREATION-DATE 3109711375)
(SUB-PATHWAYS VALSYN-PWY ILEUSYN-PWY LEUSYN-PWY)
(REACTION-LIST ILEUSYN-PWY VALSYN-PWY LEUSYN-PWY)
(COMMON-NAME "superpathway of leucine, valine, and isoleucine biosynthesis")
(PREDECESSORS (2-ISOPROPYLMALATESYN-RXN DIHYDROXYISOVALDEHYDRAT-RXN)
ILEUSYN-PWY VALSYN-PWY LEUSYN-PWY) )
NIL)
(BRANCHED-CHAINAMINOTRANSFER-CPLX NIL (
(OCELOT-GFP::PARENTS |Protein-Complexes|)
(CATALYZES BRANCHED-CHAINAMINOTRANSFERVAL-ENZRXN
BRANCHED-CHAINAMINOTRANSFERILEU-ENZRXN BRANCHED-CHAINAMINOTRANSFERLEU-ENZRXN)
(COMPONENTS BRANCHED-CHAINAMINOTRANSFER-MONOMER)
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
((COMPONENTS BRANCHED-CHAINAMINOTRANSFER-MONOMER COEFFICIENT 6)))
(BRANCHED-CHAINAMINOTRANSFER-MONOMER NIL (
(OCELOT-GFP::PARENTS |Polypeptides|)
(SYNONYMS "B3770" "IlvE")
(COMMON-NAME "IlvE")
(DBLINKS (PFAM "PF01063" IN-FAMILY |pkarp| 3346700417 NIL NIL)
(PDB "1IYE" NIL |pkarp| 3346695114 NIL NIL)
(UNIPROT "P0AB80" NIL |pkarp| 3338704377 NIL NIL)
(REFSEQ "NP_418218" NIL NIL NIL NIL NIL) (PDB "1I1M") (PDB "1I1L")
(PDB "1I1K") (PDB "1A3G"))
(COMPONENT-OF BRANCHED-CHAINAMINOTRANSFER-CPLX)
(PI 5.83d0)
(MOLECULAR-WEIGHT-SEQ 34.09360299999999d0)
(GENE EG10497)
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
NIL)
(BRANCHED-CHAINAMINOTRANSFERILEU-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(SYNONYMS "branched chain amino acid:2-oxoglutarate aminotransferase" "BCAT"
"isoleucine transaminase" "transaminase B")
(COMMON-NAME "branched chain amino acid aminotransferase")
(ALTERNATIVE-SUBSTRATES (VAL ILE LEU))
(REACTION-DIRECTION REVERSIBLE)
(REACTION BRANCHED-CHAINAMINOTRANSFERILEU-RXN)
(COFACTOR-BINDING-COMMENT "Each subunit is bound with approximately 1
mol of pyridoxal 5'-phosphate. |CITS: [89174510]|")
(COMMENT "One enzyme carries out more than one reaction because of
broad substrate specificity.")
(ENZYME BRANCHED-CHAINAMINOTRANSFER-CPLX)
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[79216227]" "[89174510]")))
(BRANCHED-CHAINAMINOTRANSFERILEU-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY ILEUSYN-PWY)
(ENZYMATIC-REACTION BRANCHED-CHAINAMINOTRANSFERILEU-ENZRXN)
(RIGHT 2-KETO-3-METHYL-VALERATE GLT)
(LEFT ILE 2-KETOGLUTARATE)
(EC-NUMBER "2.6.1.42")
(COMMENT "The final reaction in the synthesis of L-isoleucine.")
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
NIL)
(BRANCHED-CHAINAMINOTRANSFERLEU-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(SYNONYMS "leucine transaminase"
"branched chain amino acid:2-oxoglutarate aminotransferase" "BCAT"
"transaminase B")
(COMMON-NAME "branched chain amino acid aminotransferase")
(ALTERNATIVE-SUBSTRATES (VAL ILE LEU))
(REACTION-DIRECTION REVERSIBLE)
(REACTION BRANCHED-CHAINAMINOTRANSFERLEU-RXN)
(COFACTOR-BINDING-COMMENT "Each subunit is bound with approximately 1
mol of pyridoxal 5'-phosphate. |CITS: [89174510]|")
(COMMENT "One enzyme carries out more than one reaction because of
broad substrate specificity.")
(ENZYME BRANCHED-CHAINAMINOTRANSFER-CPLX)
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[79216227]" "[89174510]")))
(BRANCHED-CHAINAMINOTRANSFERLEU-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(IN-PATHWAY LEUSYN-PWY)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? T)
(ENZYMATIC-REACTION LEUAMINOTRANS-ENZRXN
BRANCHED-CHAINAMINOTRANSFERLEU-ENZRXN)
(RIGHT 2K-4CH3-PENTANOATE GLT)
(LEFT LEU 2-KETOGLUTARATE)
(EC-NUMBER "2.6.1.42")
(COMMENT "The final reaction in the synthesis of L-leucine.")
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
NIL)
(BRANCHED-CHAINAMINOTRANSFERVAL-ENZRXN NIL (
(OCELOT-GFP::PARENTS |Enzymatic-Reactions|)
(CITATIONS ":EV-EXP:3279489984:pkarp")
(PROSTHETIC-GROUPS PYRIDOXAL_PHOSPHATE)
(SYNONYMS "valine transaminase"
"branched chain amino acid:2-oxoglutarate aminotransferase" "BCAT"
"transaminase B")
(COMMON-NAME "branched chain amino acid aminotransferase")
(ALTERNATIVE-SUBSTRATES (VAL ILE LEU))
(REACTION-DIRECTION REVERSIBLE)
(REACTION BRANCHED-CHAINAMINOTRANSFERVAL-RXN)
(COFACTOR-BINDING-COMMENT "Each subunit is bound with approximately 1
mol of pyridoxal 5'-phosphate. |CITS: [89174510]|")
(COMMENT "One enzyme carries out more than one reaction because of
broad substrate specificity.")
(ENZYME BRANCHED-CHAINAMINOTRANSFER-CPLX)
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
((ALTERNATIVE-SUBSTRATES :FACET CITATIONS "[79216227]" "[89174510]")))
(BRANCHED-CHAINAMINOTRANSFERVAL-RXN NIL (
(OCELOT-GFP::PARENTS |Small-Molecule-Reactions| EC-2.6.1)
(BALANCE-STATE :BALANCED)
(OFFICIAL-EC? NIL)
(IN-PATHWAY PANTO-PWY ALANINE-VALINESYN-PWY VALSYN-PWY)
(ENZYMATIC-REACTION BRANCHED-CHAINAMINOTRANSFERVAL-ENZRXN)
(RIGHT 2-KETO-ISOVALERATE GLT)
(LEFT VAL 2-KETOGLUTARATE)
(EC-NUMBER "2.6.1.42")
(COMMENT "The final reaction in the synthesis of L-valine.")
(:CREATION-DATE 2969204160)
(:CREATOR |mriley|) )
((EC-NUMBER :FACET COMMENT "EC number 2.6.1.42 refers to a set of
reactions catalyzed by one enzyme.")))
(|Branched-ketoacid-E2| T (
(OCELOT-GFP::PARENTS |Lipoyl-Protein|)
(COMMON-NAME "branched chain α-keto acid dehydrogenase lipoyl carrier") )
NIL)
(|Brassinosteroid-Biosynthesis| T (
(OCELOT-GFP::PARENTS |Plant-Hormone-Biosynthesis|)
(COMMENT
"This class contains pathways of biosynthesis of brassinosteroids, which are plant hormones that trigger cell elongation.")
(COMMON-NAME "Brassinosteroids")
(:CREATION-DATE 3243104630)
(:CREATOR |pkarp|) )
NIL)
(|Brassinosteroids| T (
(OCELOT-GFP::PARENTS |Plant-Hormones| |Steroids|)
(COMMON-NAME "a brassinosteroids")
(:CREATION-DATE 3243104641)
(:CREATOR |pkarp|) )
NIL)
(BRIJ97 NIL (
(OCELOT-GFP::PARENTS |Unclassified-Compounds|)
(ACTIVATORS-UNKMECH-OF CDPDIGLYSYN-ENZRXN)
(:CREATION-DATE 3089989184)
(COMMENT
"This compound is a detergent of the Brij series, which are polyoxyethylene derivatives
of long-chain alkanes.")
(COMMON-NAME "Brij 97") )
NIL)
(BRNQ-MONOMER NIL (
(OCELOT-GFP::PARENTS PC-44)
(MOLECULAR-WEIGHT-SEQ 46.20866299999991d0)
(:CREATION-DATE 3060044036)
(COMMENT "BrnQ is a probable branched chain amino acid transporter. BrnQ
is highly similar to the Salmonella typhimurium BrnQ branched
chain amino acid transporter |CITS: [90241621]| and very probably
corresponds to the Liv-II branched chain amino acid transport
system in E. coli, which has been shown to transport leucine,
valine, and isoleucine |CITS: [79048215]|.
BrnQ is a member of the LIVCS family of branched chain amino acid
transporters and probably functions as a sodium/branched chain amino
acid symporter.")
(SYNONYMS "B0401" "HrbA" "LIV-II" "BrnQ")
(DBLINKS (PFAM "PF05525" IN-FAMILY |pkarp| 3346700317 NIL NIL)
(UNIPROT "P0AD99" NIL |pkarp| 3343984406 NIL NIL)
(REFSEQ "NP_414935" NIL NIL NIL NIL NIL))
(CATALYZES TRANS-ENZRXN-126B TRANS-ENZRXN-126A TRANS-ENZRXN-126)
(GENE EG12168)
(LOCATIONS CCO-PM-BAC-NEG)
(COMMON-NAME "BrnQ branched chain amino acid LIVCS transporter") )
NIL)
(BS-7046 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10176)
(REGULATED-PROMOTER PM-8764)
(RELATIVE-CENTER-DISTANCE NIL)
(CITATIONS "15716448"
"15716448:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3347903345:martin"
"15716448:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3347903345:martin"
"12354228:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3347903183:martin")
(COMMENT
"BaeR regulator binds to the spy regulatory region at -147.5 with respect to the start codon of spy gene since the +1 of the transcription initiation has not been determined yet.
The central position of the BaeR binding site (TTTTTCTCCATAATTGGC) has been identified by similarity to the consensus sequence TTTTTCTCCATDATTGGC (using the Align ACE program) |CITS:[15716448]|. D = G, A or T.")
(COMPONENT-OF CPLX0-5571 TU-8381)
(:CREATOR |martin|)
(:CREATION-DATE 3347903183) )
NIL)
(BS-7047 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10178)
(REGULATED-PROMOTER PM-8765)
(RELATIVE-CENTER-DISTANCE NIL)
(CITATIONS "15716448"
"15716448:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3347903952:martin"
"15716448:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3347903952:martin")
(COMMENT
"BaeR regulator binds to the ycaC regulatory region at -73.5 with respect to the start codon of ycaC gene since the +1 of the transcription initiation has not been determined yet.
The central position of the BaeR binding site (TATTTCCCGTCTATGCTT) has been identified by similarity to the consensus sequence TTTTTCTCCATDATTGGC (using the Align ACE program) |CITS:[15716448]|. D = G, A or T.")
(COMPONENT-OF CPLX0-5570 TU-8382)
(:CREATOR |martin|)
(:CREATION-DATE 3347903952) )
NIL)
(BS-7048 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10184)
(REGULATED-PROMOTER PM-8770)
(RELATIVE-CENTER-DISTANCE 4)
(CITATIONS "16194231" "16135237"
"16194231:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3348863351:martin"
"16194231:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3348923809:martin")
(COMPONENT-OF CPLX0-5569 TU-8387)
(:CREATOR |martin|)
(:CREATION-DATE 3348408854) )
NIL)
(BS-7049 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10195)
(REGULATED-PROMOTER PM-8770)
(RELATIVE-CENTER-DISTANCE -464)
(CITATIONS "16135237" "16194231"
"16194231:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3348923950:martin"
"16194231:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3348923950:martin")
(COMPONENT-OF CPLX0-5568 TU-8387)
(:CREATOR |martin|)
(:CREATION-DATE 3348884019) )
NIL)
(BS-7050 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10198)
(REGULATED-PROMOTER PM-8782)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349040924:martin"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349040924:martin")
(COMPONENT-OF CPLX0-5567 TU00272)
(:CREATOR |martin|)
(:CREATION-DATE 3349040924) )
NIL)
(BS-7051 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10199)
(REGULATED-PROMOTER PM-8782)
(RELATIVE-CENTER-DISTANCE -67.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349041273:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349041273:martin")
(COMPONENT-OF CPLX0-5566 TU00272)
(:CREATOR |martin|)
(:CREATION-DATE 3349041273) )
NIL)
(BS-7052 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10200)
(REGULATED-PROMOTER PM-8783)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349041501:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349041501:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349041501:martin")
(COMPONENT-OF CPLX0-5565 TU00273)
(:CREATOR |martin|)
(:CREATION-DATE 3349041501) )
NIL)
(BS-7053 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10201)
(REGULATED-PROMOTER PM-8783)
(RELATIVE-CENTER-DISTANCE -67.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349041683:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349041683:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349041683:martin")
(COMPONENT-OF CPLX0-5564 TU00273)
(:CREATOR |martin|)
(:CREATION-DATE 3349041683) )
NIL)
(BS-7054 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10203)
(REGULATED-PROMOTER PM-8784)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349043360:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349043360:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349043963:martin")
(COMPONENT-OF CPLX0-5563 TU-8399)
(:CREATOR |martin|)
(:CREATION-DATE 3349043360) )
NIL)
(BS-7055 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10204)
(REGULATED-PROMOTER PM-8784)
(RELATIVE-CENTER-DISTANCE -67.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349043397:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349043397:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349043974:martin")
(COMPONENT-OF CPLX0-5562 TU-8399)
(:CREATOR |martin|)
(:CREATION-DATE 3349043397) )
NIL)
(BS-7056 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10205)
(REGULATED-PROMOTER PM00563)
(RELATIVE-CENTER-DISTANCE -66.5d0)
(CITATIONS "15941987" "10650844" "7961507"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349049449:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349049449:martin"
"10650844:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349049449:martin"
"7961507:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349142337:martin")
(COMPONENT-OF CPLX0-5561 TU00415)
(:CREATOR |martin|)
(:CREATION-DATE 3349049449) )
NIL)
(BS-7057 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10206)
(REGULATED-PROMOTER PM00604)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349051767:martin")
(COMPONENT-OF CPLX0-5560 TU00274)
(:CREATOR |martin|)
(:CREATION-DATE 3349051767) )
NIL)
(BS-7058 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10207)
(REGULATED-PROMOTER PM00604)
(RELATIVE-CENTER-DISTANCE -68.5d0)
(CITATIONS "15941987"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349051819:martin")
(COMPONENT-OF CPLX0-5559 TU00274)
(:CREATOR |martin|)
(:CREATION-DATE 3349051819) )
NIL)
(BS-7059 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10208)
(COMMENT
"The functional confromation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|. |CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
The four small specific sites of the proximal binding site of IclR (-26, -34, -42 and -53) were directly observed at |CITS:[12492863]|.")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -34)
(CITATIONS "12492863" "8682810"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349055235:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349055235:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349055235:martin"
"8682810:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097508:martin"
"8682810:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097508:martin")
(COMPONENT-OF CPLX0-5558 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349055235) )
NIL)
(BS-7060 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10209)
(COMMENT
"The functional confromation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|. |CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
The four small specific sites of the proximal binding site of IclR (-26, -34, -42 and -53) were directly observed at |CITS:[12492863]|.")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -42)
(CITATIONS "12492863" "8682810"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349055340:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349055340:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349055340:martin"
"8682810:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097545:martin"
"8682810:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097545:martin")
(COMPONENT-OF CPLX0-5557 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349055340) )
NIL)
(BS-7061 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10210)
(COMMENT
"The functional confromation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|. |CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
The four small specific sites of the proximal binding site of IclR (-26, -34, -42 and -53) were directly observed at |CITS:[12492863]|.")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -53)
(CITATIONS "12492863" "8682810"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349055431:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349055431:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349055431:martin"
"8682810:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097565:martin"
"8682810:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097565:martin")
(COMPONENT-OF CPLX0-5556 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349055431) )
NIL)
(BS-7063 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10212)
(COMMENT
"The functional conformation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|.|CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
In the specific case of the distal site for IclR at the aceBAK operon, although its existence has not been completely supported by direct (and visual) evidence of footprinting, it has been proved by modified transcription levels due to modifications at the promoter region and an alfa-subunit-RNApolymerase mutant |CITS:[12492863]|.
One specific site for IclR at the distal site (-122) was effectively characterized by footprinting at [12492863]. The other three specific sites (-104, -131 and -141) were identified by the curator studies of the large site sequence.
")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -104)
(CITATIONS "12492863"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349097119:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097119:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097119:martin")
(COMPONENT-OF CPLX0-5555 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349097119) )
NIL)
(BS-7064 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10213)
(COMMENT
"The functional conformation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|.|CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
In the specific case of the distal site for IclR at the aceBAK operon, although its existence has not been completely supported by direct (and visual) evidence of footprinting, it has been proved by modified transcription levels due to modifications at the promoter region and an alfa-subunit-RNApolymerase mutant |CITS:[12492863]|.
One specific site for IclR at the distal site (-122) was effectively characterized by footprinting at [12492863]. The other three specific sites (-104, -131 and -141) were identified by the curator studies of the large site sequence.
")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -122)
(CITATIONS "12492863"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349097180:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097180:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097180:martin")
(COMPONENT-OF CPLX0-5554 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349097180) )
NIL)
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(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10214)
(COMMENT
"The functional conformation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|.|CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
In the specific case of the distal site for IclR at the aceBAK operon, although its existence has not been completely supported by direct (and visual) evidence of footprinting, it has been proved by modified transcription levels due to modifications at the promoter region and an alfa-subunit-RNApolymerase mutant |CITS:[12492863]|.
One specific site for IclR at the distal site (-122) was effectively characterized by footprinting at [12492863]. The other three specific sites (-104, -131 and -141) were identified by the curator studies of the large site sequence.
")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -131)
(CITATIONS "12492863"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349097225:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097225:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097225:martin")
(COMPONENT-OF CPLX0-5553 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349097225) )
NIL)
(BS-7066 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10215)
(COMMENT
"The functional conformation of IclR has been speculated and proposed to be a dimer |CITS:[1447784]| or tetramer |CITS:[11420439]|.|CITS:[12492863] [8682810]| reports the IclR binding sites as large binding regions for the whole IclR complex, at a first glance; with smaller binding sites in more detailed experiments. For seeing a future definition of the IclR functional conformation and to facilitate the studies of these sites, the IclR central positions of the binding sites have been annotated for each subunit (small sites), instead of annotating them as a complete site for the complex.
In the specific case of the distal site for IclR at the aceBAK operon, although its existence has not been completely supported by direct (and visual) evidence of footprinting, it has been proved by modified transcription levels due to modifications at the promoter region and an alfa-subunit-RNApolymerase mutant |CITS:[12492863]|.
One specific site for IclR at the distal site (-122) was effectively characterized by footprinting at [12492863]. The other three specific sites (-104, -131 and -141) were identified by the curator studies of the large site sequence.
")
(REGULATED-PROMOTER PM00001)
(RELATIVE-CENTER-DISTANCE -141)
(CITATIONS "12492863"
"12492863:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349097278:martin"
"12492863:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349097278:martin"
"12492863:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349097278:martin")
(COMPONENT-OF CPLX0-5552 TU00001)
(:CREATOR |martin|)
(:CREATION-DATE 3349097278) )
NIL)
(BS-7067 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10216)
(REGULATED-PROMOTER PM0-4528)
(RELATIVE-CENTER-DISTANCE -11)
(CITATIONS "8682810"
"8682810:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349102549:martin")
(COMPONENT-OF CPLX0-4555 TU0-4288)
(:CREATOR |martin|)
(:CREATION-DATE 3349102549) )
NIL)
(BS-7069 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10221)
(REGULATED-PROMOTER PM164)
(RELATIVE-CENTER-DISTANCE -64.5d0)
(CITATIONS "15941987" "7961507"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349122271:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349122271:martin"
"7961507:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349122455:martin")
(COMPONENT-OF CPLX0-5551 TU00276)
(:CREATOR |martin|)
(:CREATION-DATE 3349122271) )
NIL)
(BS-7070 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10223)
(REGULATED-PROMOTER PM-8790)
(RELATIVE-CENTER-DISTANCE -39.5d0)
(CITATIONS "15941987" "7961507"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349123009:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349123009:martin"
"7961507:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349123832:martin")
(COMPONENT-OF CPLX0-5550 TU-8405)
(:CREATOR |martin|)
(:CREATION-DATE 3349123009) )
NIL)
(BS-7071 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10224)
(REGULATED-PROMOTER PM-8790)
(RELATIVE-CENTER-DISTANCE -66.5d0)
(CITATIONS "15941987" "7961507"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349123099:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349123099:martin"
"7961507:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349123851:martin")
(COMPONENT-OF CPLX0-5549 TU-8405)
(:CREATOR |martin|)
(:CREATION-DATE 3349123099) )
NIL)
(BS-7072 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10228)
(REGULATED-PROMOTER PM-8797)
(RELATIVE-CENTER-DISTANCE -68.5d0)
(CITATIONS "15941987"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349471045:martin")
(COMPONENT-OF CPLX0-5548 TU-8411 TU-8408)
(:CREATOR |martin|)
(:CREATION-DATE 3349471045) )
NIL)
(BS-7073 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10229)
(REGULATED-PROMOTER PM-8797)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349471200:martin")
(COMPONENT-OF CPLX0-5547 TU-8411 TU-8408)
(:CREATOR |martin|)
(:CREATION-DATE 3349471200) )
NIL)
(BS-7074 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10234)
(REGULATED-PROMOTER PM-8798)
(RELATIVE-CENTER-DISTANCE -41.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349553926:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349553926:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349553926:martin")
(COMPONENT-OF CPLX0-5546 TU-8412)
(:CREATOR |martin|)
(:CREATION-DATE 3349553926) )
NIL)
(BS-7075 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10235)
(REGULATED-PROMOTER PM-8798)
(RELATIVE-CENTER-DISTANCE -67.5d0)
(CITATIONS "15941987"
"15941987:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3349554040:martin"
"15941987:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3349554040:martin"
"15941987:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3349554040:martin")
(COMPONENT-OF CPLX0-5545 TU-8412)
(:CREATOR |martin|)
(:CREATION-DATE 3349554040) )
NIL)
(BS-7076 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10253)
(REGULATED-PROMOTER PM361)
(RELATIVE-CENTER-DISTANCE 66)
(CITATIONS "11953442"
"11953442:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3350827528:asantos"
"11953442:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3350827528:asantos")
(COMPONENT-OF CPLX0-5678 TU281)
(:CREATOR |asantos|)
(:CREATION-DATE 3350827528) )
NIL)
(BS-7077 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10254)
(REGULATED-PROMOTER PM0-8184)
(RELATIVE-CENTER-DISTANCE -20)
(CITATIONS "16478729"
"16478729:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3350833462:martin"
"16478729:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3350833462:martin"
"16478729:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3350833462:martin"
"16478729:EV-EXP-IMP-SITE-MUTATION:3350833462:martin")
(COMPONENT-OF CPLX0-5679 TU0-7804)
(:CREATOR |martin|)
(:CREATION-DATE 3350833462) )
NIL)
(BS-7078 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10255)
(REGULATED-PROMOTER PM00536)
(RELATIVE-CENTER-DISTANCE NIL)
(CITATIONS "16000739:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3350845686:asantos")
(COMPONENT-OF CPLX0-5511 TU00392)
(:CREATOR |asantos|)
(:CREATION-DATE 3350845686) )
NIL)
(BS-7079 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10256)
(REGULATED-PROMOTER PM00134)
(RELATIVE-CENTER-DISTANCE -43)
(CITATIONS "14701822"
"14701822:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3350854149:martin"
"14701822:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3350854149:martin"
"14701822:EV-EXP-IMP-SITE-MUTATION:3350854149:martin"
"14701822:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3350854149:martin")
(COMPONENT-OF CPLX0-5680 TU00094)
(:CREATOR |martin|)
(:CREATION-DATE 3350854149) )
NIL)
(BS-7080 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10257)
(REGULATED-PROMOTER PM928)
(RELATIVE-CENTER-DISTANCE -39)
(CITATIONS "14701822" "14701822:EV-EXP-IPI:3350854552:martin"
"14701822:EV-COMP-HINF-SIMILAR-TO-CONSENSUS:3350854552:martin"
"14701822:EV-EXP-IMP-SITE-MUTATION:3350854552:martin"
"14701822:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3350854552:martin")
(COMPONENT-OF CPLX0-5681 TU00282)
(:CREATOR |martin|)
(:CREATION-DATE 3350854552) )
NIL)
(BS-7081 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10258)
(REGULATED-PROMOTER PM169)
(RELATIVE-CENTER-DISTANCE -54.5d0)
(CITATIONS "11918818"
"11918818:EV-EXP-IDA-BINDING-OF-PURIFIED-PROTEINS:3351460172:sgama"
"11918818:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351460172:sgama")
(COMPONENT-OF CPLX0-5682 TU0-6629)
(:CREATOR |sgama|)
(:CREATION-DATE 3351460172) )
NIL)
(BS-7082 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10259)
(REGULATED-PROMOTER PM169)
(RELATIVE-CENTER-DISTANCE NIL)
(CITATIONS "11918818:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351463106:sgama")
(COMPONENT-OF CPLX0-5683 TU0-6629)
(:CREATOR |sgama|)
(:CREATION-DATE 3351463106) )
NIL)
(BS-7083 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10263)
(REGULATED-PROMOTER PM-8827)
(RELATIVE-CENTER-DISTANCE -12)
(CITATIONS "16428390"
"16428390:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351537709:sgama"
"16428390:EV-EXP-IMP-SITE-MUTATION:3351537709:sgama"
"16428390:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351537709:sgama")
(COMPONENT-OF CPLX0-5684 TU-8441)
(:CREATOR |sgama|)
(:CREATION-DATE 3351537575) )
NIL)
(BS-7084 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10264)
(REGULATED-PROMOTER PM00415)
(RELATIVE-CENTER-DISTANCE 1)
(CITATIONS "16428390"
"16428390:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351537809:sgama"
"16428390:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351537809:sgama")
(COMPONENT-OF CPLX0-5685 TU681)
(:CREATOR |sgama|)
(:CREATION-DATE 3351537809) )
NIL)
(BS-7085 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10265)
(REGULATED-PROMOTER PM-8829)
(RELATIVE-CENTER-DISTANCE -7)
(CITATIONS "16428390"
"16428390:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351537889:sgama"
"16428390:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351537889:sgama")
(COMPONENT-OF CPLX0-5686 TU-8443)
(:CREATOR |sgama|)
(:CREATION-DATE 3351537889) )
NIL)
(BS-7086 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10266)
(REGULATED-PROMOTER PM-8830)
(RELATIVE-CENTER-DISTANCE -1)
(CITATIONS "16428390"
"16428390:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351537965:sgama"
"16428390:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351537965:sgama")
(COMPONENT-OF CPLX0-5687 TU00364)
(:CREATOR |sgama|)
(:CREATION-DATE 3351537965) )
NIL)
(BS-7087 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10267)
(REGULATED-PROMOTER PM00536)
(RELATIVE-CENTER-DISTANCE -42.5d0)
(CITATIONS "15520470"
"15520470:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351888399:asantos"
"15520470:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351888399:asantos")
(COMPONENT-OF CPLX0-5688 TU00392)
(:CREATOR |asantos|)
(:CREATION-DATE 3351888399) )
NIL)
(BS-7088 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10268)
(REGULATED-PROMOTER PM00536)
(RELATIVE-CENTER-DISTANCE -170.5d0)
(CITATIONS "15520470"
"15520470:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3351891187:asantos"
"15520470:EV-COMP-AINF-SIMILAR-TO-CONSENSUS:3351891187:asantos")
(COMPONENT-OF CPLX0-5689 TU00392)
(:CREATOR |asantos|)
(:CREATION-DATE 3351891187) )
NIL)
(BS-7089 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR-10269)
(REGULATED-PROMOTER PM00142)
(RELATIVE-CENTER-DISTANCE -191.5d0)
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(TYPE-OF-EVIDENCE :GENE-EXPRESSION-ANALYSIS)
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(RELATIVE-CENTER-DISTANCE -130)
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(:CREATOR |sgama|)
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NIL)
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(COMMENT
"IHF and PspF proteins bind cooperatively to regulate the pspA promoter.")
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NIL)
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(CITATIONS "9148912"
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NIL)
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(TYPE-OF-EVIDENCE :SIMILARITY-TO-CONSENSUS :GENE-EXPRESSION-ANALYSIS)
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(:CREATION-DATE 3255708945) )
NIL)
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(APPEARS-IN-LEFT-SIDE-OF BR0-2001)
(CITATIONS ":EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS"
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(TYPE-OF-EVIDENCE :SIMILARITY-TO-CONSENSUS :GENE-EXPRESSION-ANALYSIS)
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(COMPONENT-OF CPLX0-4399 TU541)
(:CREATOR |sgama|)
(:CREATION-DATE 3255892817) )
NIL)
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(APPEARS-IN-LEFT-SIDE-OF BR0-2002)
(CITATIONS ":EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS"
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(:CREATOR |sgama|)
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NIL)
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(:CREATOR |sgama|)
(:CREATION-DATE 3255978413) )
NIL)
(BS0-1582 NIL (
(OCELOT-GFP::PARENTS |DNA-Binding-Sites|)
(APPEARS-IN-LEFT-SIDE-OF BR0-2022)
(CITATIONS "11395452:EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS:3289656795:sgama"
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(COMPONENT-OF CPLX0-4417 TU0-1841)
(:CREATOR |sgama|)
(:CREATION-DATE 3255978764) )
NIL)
(BS0-1583 NIL (
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(:CREATOR |sgama|)
(:CREATION-DATE 3255978806) )
NIL)
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(COMPONENT-OF CPLX0-4421 TU561)
(:CREATOR |sgama|)
(:CREATION-DATE 3256046224) )
NIL)
(BS0-1585 NIL (
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(APPEARS-IN-LEFT-SIDE-OF BR0-2025)
(CITATIONS ":EV-EXP-IEP-GENE-EXPRESSION-ANALYSIS"
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(TYPE-OF-EVIDENCE :SIMILARITY-TO-CONSENSUS :GENE-EXPRESSION-ANALYSIS)
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(:CREATION-DATE 3256056059) )
NIL)
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