56: an orthophosphoric monoester subsumes r5p, and an alcohol subsumes rib-D 56: COMMENT: "WIDE SPECIFICITY. ALSO CATALYSES TRANSPHOSPHORYLATIONS." 56: equivalent to ALKAPHOSPHA-RXN in terms of stoichiometry. But context 56 B4055 [p] : h2o + r5p --> pi + rib-D R5PPpp 56 EG11934 aphA H_2_O + an orthophosphoric monoester = phosphate + an alcohol ACID-PHOSPHATASE-RXN 57: Generic reaction. a sugar phosphate subsumes r5p and a sugar subsumes rib-D 57 B0822 [c] : h2o + r5p --> pi + rib-D R5PP 57 G6425 ybiV H_2_O + a sugar phosphate = a sugar + phosphate SUGAR-PHOSPHATASE-RXN 58: PYDXPP is an orphan enzyme? Closest matches are the following: (union (reactions-of-compound 'pyridoxal_phosphate) (reactions-of-compound 'pyridoxal)) (PMPOXI-RXN PNPOXI-RXN PYRDAMPTRANS-RXN PYRIDOXKIN-RXN PYROXALTRANSAM-RXN) EC(48): (intersection (reactions-of-compound 'pyridoxal_phosphate) (reactions-of-compound 'pyridoxal)) (PYRIDOXKIN-RXN) EC(49): (substrates-of-reaction 'pyridoxkin-rxn) (PYRIDOXAL ATP ADP PYRIDOXAL_PHOSPHATE) 58 no-b-gene [c] : h2o + pydx5p --> pi + pydx PYDXPP 60: Generic reaction. an orthophosphoric monoester subsumes thrp, and an alcohol subsumes thr-L. 60 B4055 [p] : h2o + thrp --> pi + thr-L PTHRpp 60 EG11934 aphA H_2_O + an orthophosphoric monoester = phosphate + an alcohol ACID-PHOSPHATASE-RXN 61: PSSA_EC According to compound notes, tv org: Hpylori, Ecoli scaled up (50x) of phosphatidylserine with an average 2 fatty acid chain (C1686H3148O100) Checked N JLR 61 B2585 [c] : (0.02) cdpdag_EC + ser-L <==> cmp + h + (0.02) ps_EC PSSA_EC 61 EG10781 pssA CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine PHOSPHASERSYN-RXN 62: PSD_EC ps_EC and pe_EC are scaled up (50x) 62 B4160 [c] : h + (0.02) ps_EC --> co2 + (0.02) pe_EC PSD_EC 62 EG10775 psd L-1-phosphatidylserine = L-1-phosphatidyl-ethanolamine + CO_2_ PHOSPHASERDECARB-RXN 65: ALKAPHOSPHA-RXn subsumes PPTHpp because an orthophosphoric monoester subsumes ppt, and an alcohol subsumes h2. 65 B0383 [p] : h2o + ppt --> h2 + pi PPTHpp 65 EG10727 phoA an orthophosphoric monoester + H_2_O = an alcohol + phosphate ALKAPHOSPHA-RXN 67: Update: 2.7.4.1 is a generic reaction. How did iJR904 get PPKr? 67: PPKr NIL polyphosphate kinase [c] : atp + pi <==> adp + ppi Update 2.7.4.1 b2501 67 B2501 [c] : atp + pi <==> adp + ppi PPKr 67 EG11510 ppk long chain polyphosphate + ATP = long chain polyphosphate + ADP POLYPHOSPHATE-KINASE-RXN 68: Update: 2.7.4.1 is a generic reaction. How did iJR904 get PPK2r? 68: PPK2r NIL polyphosphate kinase [c] : atp + ppi <==> adp + pppi Update 2.7.4.1 b2501 68 B2501 [c] : atp + ppi <==> adp + pppi PPK2r 68 EG11510 ppk long chain polyphosphate + ATP = long chain polyphosphate + ADP POLYPHOSPHATE-KINASE-RXN 70: The PHYT-RXN only releases 1 phosphate. PHYTSpp releases all 6. Unfortunately, there is no reaction that releases the other 5 reactions down to 0 in EcoCyc. Palsson wins. 70: Note: RXN-1001 is a duplicate of PHYT-RXN 70 B0980 [p] : (6) h2o + minohp --> inost + (6) pi PHYTSpp 70 EG10049 appA H_2_O + phytate = phosphate + D-_myo_-inositol (1,2,3,4,5)-penta_kis_phosphate 6-PHYT-RXN 70 EG10049 appA GTP + H_2_O = GDP + phosphate RXN0-1021 73: (50x) problem again 73 B1912 [c] : (0.02) cdpdag_EC + glyc3p <==> cmp + h + (0.02) pgp_EC PGSA_EC 73 EG10706 pgsA CDP-diacylglycerol + glycerol-3-phosphate = CMP + L-1-phosphatidylglycerol-phosphate PHOSPHAGLYPSYN-RXN 75: Glucose-1-phosp subsumes Alpha-D-Glucose! 75 B0688 [c] : g1p <==> g6p PGMT 75 EG12144 pgm α-D-glucose 1-phosphate = α-D-glucose-6-phosphate PHOSPHOGLUCMUT-RXN 75 B2690 [c] : g1p <==> g6p PGMT 76: (50x) problem again 76 B3546 [p] : lipa + (0.02) pe_EC --> (0.02) 12dgr_EC + enlipa PETNTpp 76 EG12267 eptB KDO_2_-lipid IV_A_ + Phosphatidylethenolamine = 1,2-diacylglycerol + phosphatidylethanolamine-KDO_2_-lipidA RXN0-4581 77: (50x) problem again 77 no-b-gene [c] : cmp + h + (0.02) pe_EC <==> (0.02) 12dgr_EC + cdpea PEPT_EC 77 This reaction is closest to ETHANOLAMINEPHOSPHOTRANSFERASE-RXN, but this reaction only exists in MetaCyc, not EcoCyc. An orphan enzyme? 78: 3.6.3.39-RXN subsumes PEabcpp. 78 B0914 atp[c] + h2o[c] + pe_EC[c] --> adp[c] + h[c] + pe_EC[p] + pi[c] PEabcpp 78 EG10613 msbA a lipopolysaccharide_[cytosol]_ + H_2_O + ATP =a lipopolysaccharide_[out]_ + phosphate + ADP 3.6.3.39-RXN 79: Closest to PNKIN-RXN. No EC number. No gene indicates possible orphan enzyme? Where is the evidence? 79 no-b-gene [c] : h2o + pdx5p --> pi + pydxn PDXPP 80: This is a combination of PDXA-RXN and PDXJ-RXN. 80 B0052 [c] : dxyl5p + nad + phthr --> co2 + h + (2) h2o + nadh + pdx5p + pi PDX5PS 80 EG10691 pdxA phospho-hydroxy-threonine + NAD_+_ = 1-amino-propan-2-one-3-phosphate + NADH + CO_2_ PDXA-RXN 80 B2564 [c] : dxyl5p + nad + phthr --> co2 + h + (2) h2o + nadh + pdx5p + pi PDX5PS 80 EG10693 pdxJ 1-amino-propan-2-one-3-phosphate + 1-deoxy-D-xylulose 5-phosphate = pyridoxine-5'-phosphate + phosphate + 2 H_2_O PDXJ-RXN 82: Another (50x) problem. No gene. orphan enzyme? Same as PHOSPHATIDATE-PHOSPHATASE-RXN in MetaCyc. no evidence. 82 no-b-gene [c] : h2o + (0.02) pa_EC --> (0.02) 12dgr_EC + pi PAPA_EC 82 no-b-gene [c] : h2o + (0.02) pa_EC --> (0.02) 12dgr_EC + pi PAPA_EC 83: PYRROLINECARBREDUCT-RXN subsumes P5CR, because NAD(P)H is a generic compound. 83 B0386 [c] : 1pyr5c + (2) h + nadph --> nadp + pro-L P5CR 83 EG10769 proC pyrroline 5-carboxylate + NAD(P)H + H_+_ = L-proline + NAD(P)_+_ PYRROLINECARBREDUCT-RXN 85: This is odd. OPPSYN-RXN does not include octaprenyl-diphosphate (octdp) as a substrate, but it mentions it in the comments. OCTDPS seems to combine compounds in OPPSYN-RXN and FPPSYN-RXN. 85 B3187 [c] : frdp + (5) ipdp --> octdp + (5) ppi OCTDPS 85 EG10017 ispB _trans_-polyisoprenyl_n_-PP + Δ_3_-isopentenyl-PP = _trans_-polyisoprenyl_n+1_-PP + pyrophosphate OPPSYN-RXN 86: There appears to some correspondence to reactions in the same pathway, but which is not clear: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=ANARESPACC-PWY 86: 1.7.7.2-RXN contains cytochrome, which is a protein. It is unclear if these reactions are the same. 86 B4070 (2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p] NTRIR4pp 86 EG11781 nrfA NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 86 B4071 (2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p] NTRIR4pp 86 EG11945 nrfB NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 86 B4072 (2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p] NTRIR4pp 86 EG11946 nrfC NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 86 B4073 (2) h[p] + (3) mql8[c] + no2[p] --> (2) h2o[p] + (3) mqn8[c] + nh4[p] NTRIR4pp 86 EG11947 nrfD NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 87: Cytochrome is *not* the same as quinone. 87: NOTE CAS number and KEGG ID for quinone are algorithms. 87 B4070 (2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c] NTRIR3pp 87 EG11781 nrfA NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 87 B4071 (2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c] NTRIR3pp 87 EG11945 nrfB NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 87 B4072 (2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c] NTRIR3pp 87 EG11946 nrfC NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 87 B4073 (2) h[p] + no2[p] + (3) q8h2[c] --> (2) h2o[p] + nh4[p] + (3) q8[c] NTRIR3pp 87 EG11947 nrfD NO_2__-_ + 6 reduced cytochrome _c552_ + 7 H_+_ -> ammonia + 6 oxidized cytochrome _c552_ + 2 H_2_O 1.7.7.2-RXN 88: NITRITEREDUCT-RXN subsumes NTRIR2x because NAD(P)H makes it a generic reaction. 88 B3365 [c] : (5) h + (3) nadh + no2 --> (2) h2o + (3) nad + nh4 NTRIR2x 88 EG10653 nirB 3 NAD(P)_+_ + NH(4)OH + H_2_O -> 3 NAD(P)H + NO_2__-_ NITRITREDUCT-RXN 88 B3366 [c] : (5) h + (3) nadh + no2 --> (2) h2o + (3) nad + nh4 NTRIR2x 88 EG10655 nirD 3 NAD(P)_+_ + NH(4)OH + H_2_O -> 3 NAD(P)H + NO_2__-_ NITRITREDUCT-RXN 91: RXN0-1041 subsumes NTPP8 becuase a nucleoside triphosphate makes it RXN0-1041 a generic reaction. 91 B2781 [c] : h2o + utp --> h + ppi + ump NTPP8 91 EG10572 mazG a nucleoside triphosphate + H_2_O -> a nucleoside monophosphate + pyrophosphate RXN0-1041 92: RXN0-1041 subsumes NTPP7 becuase a nucleoside triphosphate makes it RXN0-1041 a generic reaction. 92 B2781 [c] : dttp + h2o --> dtmp + h + ppi NTPP7 92 EG10572 mazG a nucleoside triphosphate + H_2_O -> a nucleoside monophosphate + pyrophosphate RXN0-1041 95: doesn't quite fit into either reaction. dgmp and dgsn are deoxy-ribonucleosides, not ribonucleosides. 95: RXN0-3741 subsumes NTD8pp because dgmp is a deoxyribonucleoside monophosphate and dgsn is a deoxyribonucleoside 95: b0480 and b4055 have a function in iJR904 that EcoCyc does not. 95 B0480 [p] : dgmp + h2o --> dgsn + pi NTD8pp 95 EG11060 ushA a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN 95 EG11060 ushA a UDP-sugar + H_2_O = UMP + a sugar-1-phosphate UDPSUGARHYDRO-RXN 95 B4055 [p] : dgmp + h2o --> dgsn + pi NTD8pp 95 EG11934 aphA H_2_O + an orthophosphoric monoester = phosphate + an alcohol ACID-PHOSPHATASE-RXN 96: RXN0-3741 subsumes NTD8 because dgmp is a deoxyribonucleoside monophosphate and dgsn is a deoxyribonucleoside 96 B2291 [c] : dgmp + h2o --> dgsn + pi NTD8 96 G7185 yfbR a deoxyribonucleoside 5'-monophosphate + H_2_O -> a deoxyribonucleoside + phosphate RXN0-3741 96 B2744 [c] : dgmp + h2o --> dgsn + pi NTD8 96 EG11817 surE a nucleoside 3'-phosphate + H_2_O = a ribonucleoside + phosphate 3-NUCLEOTID-RXN 96 EG11817 surE a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN 97: RXN0-3741 subsumes NTD8 because damp is a deoxyribonucleoside monophosphate and dad-2 is a deoxyribonucleoside. 97: b0480 and b4055 have a function in iJR904 that EcoCyc does not. 97 B0480 [p] : damp + h2o --> dad-2 + pi NTD6pp 97 EG11060 ushA a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN 97 EG11060 ushA a UDP-sugar + H_2_O = UMP + a sugar-1-phosphate UDPSUGARHYDRO-RXN 97 B4055 [p] : damp + h2o --> dad-2 + pi NTD6pp 97 EG11934 aphA H_2_O + an orthophosphoric monoester = phosphate + an alcohol ACID-PHOSPHATASE-RXN 98: RXN0-3741 subsumes NTD6pp because damp is a deoxyribonucleoside monophosphate and dad-2 is a deoxyribonucleoside 98: NOTE: deoxyribonucleoside monophosphate and a deoxyribonucleoside should be class frames, and should have (damp,dcmp, dtmp, dgmp) and (deoxyadenosine, deoxycytidine, deoxyguanosine, deoxythiamine) respectively as instances. 98: 5'-NUCLEOTID-RXN is resolved in 100 98 B2291 [c] : damp + h2o --> dad-2 + pi NTD6 98 G7185 yfbR a deoxyribonucleoside 5'-monophosphate + H_2_O -> a deoxyribonucleoside + phosphate RXN0-3741 98 B2744 [c] : damp + h2o --> dad-2 + pi NTD6 98 EG11817 surE a nucleoside 3'-phosphate + H_2_O = a ribonucleoside + phosphate 3-NUCLEOTID-RXN 98 EG11817 surE a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN 99: 5'-NUCLEOTID-RXN subsumes NTD4pp because cmp is a ribonucleoside monophosphate and cytd is a ribonucleoside 99: NTD4pp NIL 5'-nucleotidase (CMP) [p] : cmp + h2o --> cytd + pi Update 3.1.3.5 ( b0480 or b4055 ) 99 B0480 [p] : cmp + h2o --> cytd + pi NTD4pp 99 EG11060 ushA a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN 99 EG11060 ushA a UDP-sugar + H_2_O = UMP + a sugar-1-phosphate UDPSUGARHYDRO-RXN 99 B4055 [p] : cmp + h2o --> cytd + pi NTD4pp 99 EG11934 aphA H_2_O + an orthophosphoric monoester = phosphate + an alcohol ACID-PHOSPHATASE-RXN 100: 5'-NUCLEOTID-RXN subsumes NTD4 because cmp is a ribonucleoside monophosphate and cytd is a ribonucleoside 100 B2744 [c] : cmp + h2o --> cytd + pi NTD4 100 EG11817 surE a nucleoside 3'-phosphate + H_2_O = a ribonucleoside + phosphate 3-NUCLEOTID-RXN 100 EG11817 surE a ribonucleoside monophosphate + H_2_O = a ribonucleoside + phosphate 5'-NUCLEOTID-RXN Notes: Add compound classes into owl.