abbreviation officialName formula charge casNumber KEGG-cmpd-ID notes ecocyc-id analysis metacyc-id ile-L L-Isoleucine C6H13NO2 0 73-32-5 C00407 KEGG - C00407 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR ILE hom-L L-Homoserine C4H9NO3 0 672-15-1 C00263 KEGG - C00263 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR HOMO-SER trdox Oxidized thioredoxin X 0 C00343 KEGG - C00343 SMP OX-THIOREDOXIN-MONOMER mthgxl Methylglyoxal C3H4O2 0 78-98-8 C00546 KEGG - C00546 Neutral Compound SMP CHS METHYL-GLYOXAL h2mb4p 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate C5H9O8P2 -3 C11811 KEGG C11811 JLR see PMID 12010124 HYDROXY-METHYL-BUTENYL-DIP fdp D-Fructose 1,6-bisphosphate C6H10O12P2 -4 488-69-7 C00354 KEGG - C00354 Neutral MF = C6H14O12P2 SMP CHS FRUCTOSE-16-DIPHOSPHATE hkntd 2-hydroxy-6-ketononatrienedioate C9H6O6 -2 No Kegg entry, see PMID: 9603882 Neutral- C9H8O6 JLR Changed to -2 charge unknown but diene exists in metacyc 3ophb 3-Octaprenyl-4-hydroxybenzoate C47H69O3 -1 C05809 KEGG - C05809 Neutral MF = C47H70O3 SMP CHS 3-OCTAPRENYL-4-HYDROXYBENZOATE gdpmann GDP-D-mannose C16H23N5O16P2 -2 C00096 KEGG C00096 Neutral:C16H25N5O16P2 JLR Checked N-groups JLR GDP-MANNOSE dtdp dTDP C10H13N2O11P2 -3 C00363 KEGG - C00363 Neutral MF = C10H16N2O11P2 SMP CHS TDP spmd Spermidine C7H22N3 3 124-20-9 C00315 KEGG - C00315 Neutral Compound SMP CHS Changed according to Genomatica JLR SPERMIDINE hisp L-Histidinol phosphate C6H11N3O4P -1 25679-93-0 C01100 KEGG - C01100 Neutral MF = C6H12N3O4P SMP CHS Changed according to Genomatica JLR L-HISTIDINOL-P fe3dhbzs ferric 2,3-dihydroxybenzoylserine C10H10NO6Fe 2 AMF CPD0-641 octeACP Octadecenoyl-ACP (n-C18:1ACP) C29H53N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty 5dh4dglc 5-Dehydro-4-deoxy-D-glucarate C6H6O7 -2 C00679 KEGG - C00679 Neutral-C6H8O7 JLR 5-KETO-4-DEOXY-D-GLUCARATE kphphhlipa kdo-phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C139H241N2O70P4 -11 AMF unknown lys-L L-Lysine C6H15N2O2 1 56-87-1 C00047 KEGG - C00047 Neutral MF = C6H14N2O2 SMP CHS Changed according to Genomatica JLR LYS btn Biotin C10H15N2O3S -1 58-85-5 C00120 KEGG - C00120 Neutral MF = C10H16N2O3S SMP CHS Checked N-groups JLR BIOTIN glx Glyoxylate C2H1O3 -1 298-12-4 C00048 KEGG - C00048 Neutral MF = C2H2O3 SMP CHS GLYOX glyclt Glycolate C2H3O3 -1 79-14-1 C00160 KEGG - C00160 Neutral MF = C2H4O3 SMP CHS GLYCOLLATE cobalt2 Co2+ Co 2 7440-48-4 C00175 KEGG - C00175 CO+2 mn2 Mn2+ Mn 2 None C00034 KEGG - C00034 SMP CHS MN+2 3sala 3-Sulfino-L-alanine C3H5NO4S -2 1115-65-7 C00606 KEGG - C00606 Neutral MF = C3H7NO4S SMP CHS 3-SULFINOALANINE gdpfuc GDP-L-fucose C16H23N5O15P2 -2 C00325 KEGG - C00325 KEGG glycan: G10615 Neutral: C16H25N5O15P2 JLR GUANOSINE_DIPHOSPHATE_FUCOSE gdptp Guanosine 3'-diphosphate 5'-triphosphate C10H11N5O20P5 -7 C04494 KEGG - C04494 Neutral MF = C10H18N5O20P5 SMP CHS GDP-TP man D-Mannose C6H12O6 0 3458-28-4 C00159 KEGG - C00159 Neutral Compound SMP CHS MANNOSE urate Urate C5H4N4O3 0 69-93-2 C00366 KEGG - C00366 Neutral Compound SMP CHS URATE ppt Phosphonate HO3P -2 13598-36-2 C06701 KEGG - C06701 JLR Pka- 2 and 6.58 (http://research.chem.psu.edu/brpgroup/pKa_compilation.pdf) metacyc PHOSPHONATE PHOSPHONATE fum Fumarate C4H2O4 -2 110-17-8 C00122 KEGG - C00122 Neutral MF = C4H4O4 SMP CHS FUM ckdo CMP-3-deoxy-D-manno-octulosonate C17H24N3O15P -2 JLR- like KEGG C04121 except ring structure (see NH page 1044) CMP-KDO dpcoa Dephospho-CoA C21H33N7O13P2S -2 C00882 KEGG - C00882 Neutral MF = C21H35N7O13P2S SMP CHS Checked N-groups JLR DEPHOSPHO-COA murein5px4p two disacharide linked murein units, pentapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain) C77H117N15O40 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->D-ala other structure is unclear gln-L L-Glutamine C5H10N2O3 0 56-85-9 C00064 KEGG - C00064 Neutral MF = C5H10N2O3 SMP CHS GLN murein3px3p two disacharide linked murein units, tripeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain) C68H102N12O37 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->A2pm unknown fru D-Fructose C6H12O6 0 57-48-7 C00095 KEGG - C00095 Deleted KEGG -C01496 (fructose) Neutral Compound SMP CHS FRU uri Uridine C9H12N2O6 0 58-96-8 C00299 KEGG - C00299 Neutral Compound SMP CHS Checked N-groups JLR URIDINE 3otdcoa 3-Oxotetradecanoyl-CoA C35H56N7O18P3S -4 C05261 KEGG - C05261 Neutral MF = C35H60N7O18P3S SMP fatty mettrna L-Methionyl-tRNA (Met) C5H10NOSR 1 C02430 KEGG - C02430 SMP adjusted for Genomatica's change to aa - NCD |Charged-MET-tRNAs| 4hthr 4-Hydroxy-L-threonine C4H9NO4 0 C06056 KEGG C06056 JLR Checked N JLR unknown glcn D-Gluconate C6H11O7 -1 526-95-4 C00257 KEGG - C00257 Neutral MF = C6H12O7 SMP CHS GLUCONATE dmlz 6,7-Dimethyl-8-(1-D-ribityl)lumazine C13H18N4O6 0 C04332 KEGG - C04332 Neutral Compound SMP CHS Checked N-groups, agrees with ACD software, JLR, NCD DIMETHYL-D-RIBITYL-LUMAZINE glcr D-Glucarate C6H8O8 -2 87-73-0 C00818 KEGG - C00818 KEGG - C00767 has Glucarate is deleted from the database Neutral MF = C6H10O8 SMP CHS D-GLUCARATE urdglyc (-)-Ureidoglycolate C3H5N2O4 -1 C00603 KEGG - C00603 Neutral- C4H6N2O4 JLR Checked N-groups JLR CPD-1091 ncam Nicotinamide C6H6N2O 0 98-92-0 C00153 KEGG - C00153 SMP CHS Checked N-groups JLR NIACINAMIDE actACP Acetoacetyl-ACP C15H25N2O9PRS -1 C05744 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) ACETOACETYL-S-ACP maltpt Maltopentaose C30H52O26 0 Not in Kegg JLR metacyc MALTOPENTAOSE MALTOPENTAOSE tdcoa Tetradecanoyl-CoA (n-C14:0CoA) C35H58N7O17P3S -4 C02593 KEGG - C02593 Neutral MF = C35H62N7O17P3S SMP changed compound class from peptides to fatty acids - NCD metacyc TETRADECANOYL-COA TETRADECANOYL-COA athr-L L-Allo-threonine C4H9NO3 0 28954-12-3 C05519 KEGG - C05519 AMF L-ALLO-THREONINE cbl1 Cob(I)alamin C62H88CoN13O14P -1 18534-66-2 C00853 KEGG - C00853 Kegg shows C62H93CoN13O14P (removed 3 H from ring, 1H from phosphate group, 1H from ribazole group) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR Note: (Updated with Pipeline Pilot Calculations (1 H from the phosphate group removed) RM)-dind't take this into account 8/2004 REDONE old values were C62H89CoN13O14P charge +6 (by JLR) COB-I-ALAMIN hmfurn 4-hydroxy-5-methyl-3(2H)-furanone C5H6O3 0 No Kegg Entry See PMID: 11489131 JLR unknown imacp 3-(Imidazol-4-yl)-2-oxopropyl phosphate C6H7N2O5P -2 C01267 KEGG - C01267 Neutral MF = C6H9N2O5P SMP CHS Checked N-groups JLR IMIDAZOLE-ACETOL-P td2coa trans-Tetradec-2-enoyl-CoA C35H56N7O17P3S -4 C05273 KEGG - C05273 Neutral MF = C35H60N7O17P3S SMP fatty oxam Oxamate C2H2NO3 -1 471-47-6 C01444 KEGG - C01444 JLR- Checked protonation state OXAMATE 4per 4-Phospho-D-erythronate C4H6O8P -3 C03393 KEGG - C03393 Neutral MF = C4H9O8P SMP CHS ERYTHRONATE-4P inost myo-Inositol C6H12O6 0 87-89-8 C00137 KEGG - C00137 Neutral Compound SMP CHS MYO-INOSITOL ggptrc gamma-glutamyl-putrescine C9H20O3N3 1 MKA AMF GAMMA-GLUTAMYL-PUTRESCINE sulfac sulfoacetate C2H2O5S -2 AMF unknown cpe_EC Phosphatidylethanolamine (ecoli) C1986H3848N50O400P50 0 AMF org: Hpylori, Ecoli scaled up (50x) of ps with 2 ave fatty acids L-1-PHOSPHATIDYL-ETHANOLAMINE fmettrna N-Formylmethionyl-tRNA C6H9NO2SR 0 C03294 KEGG - C03294 SMP |fMET-tRNAs| ggagicolipa glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C163H281N2O89P4 -11 AMF unknown pan4p Pantetheine 4'-phosphate C11H21N2O7PS -2 C01134 KEGG - C01134 Neutral MF = C11H23N2O7PS SMP CHS Checked N-groups JLR PANTETHEINE-P so2 sulfur dioxide O2S 0 C09306 AMF SULFUR-DIOXIDE rbflvrd Reduced riboflavin C17H22N4O6 0 C01007 KEGG - C01007 metacyc CPD-316 CPD-316 seramp L-seryl-AMP C13H19N6O9P 0 See EcoCyc- L-seryl-AMP JLR Checked N-groups JLR SERYL-AMP phpyr Phenylpyruvate C9H7O3 -1 156-06-9 C00166 KEGG - C00166 Neutral MF = C9H8O3 SMP CHS PHENYL-PYRUVATE melib Melibiose C12H22O11 0 585-99-9 C05402 KEGG - C05402 Neutral compound CAS # covers alpha-D-(+)-Melibiose hydrate SMP CHS MELIBIOSE ragund rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C69H113N1O16P2 -2 AMF unknown hqn Hydroquinone C6H6O2 0 123-31-9 C00530 KEGG - C00530 SMP metacyc HYDROQUINONE HYDROQUINONE uacmamu UDP-N-acetyl-D-mannosaminouronate C17H22N3O18P2 -3 90-02-8 C06240 KEGG - C06240 Neutral-C17H25N3O18P2 JLR Checked N-groups JLR UDP-MANNACA hhlipa heptosyl-heptosyl-kdo2-lipidA C124H220N2O51P2 -6 AMF unknown , probably trnaser tRNA(Ser) R 0 C01650 KEGG - C01650 SMP |SER-tRNAs| xmp Xanthosine 5'-phosphate C10H11N4O9P -2 523-98-8 C00655 KEGG - C00655 Neutral MF = C10H13N4O9P SMP CHS Checked N-groups JLR XANTHOSINE-5-PHOSPHATE ribflv Riboflavin C17H20N4O6 0 83-88-5 C00255 KEGG - C00255 Neutral Compound SMP CHS RIBOFLAVIN 3mob 3-Methyl-2-oxobutanoate C5H7O3 -1 C00141 KEGG - C00141 Neutral MF = C5H8O3 SMP CHS 2-KETO-ISOVALERATE cit Citrate C6H5O7 -3 77-92-9 C00158 KEGG - C00158 Neutral MF = C6H8O7 SMP CHS CIT acgal N-Acetyl-D-galactosamine C8H15NO6 0 14215-68-0; 1811-31-0 C01132 KEGG - C01132 Neutral Compound SMP NCD metacyc CPD-3604 CPD-3604 3ohdcoa 3-Oxohexadecanoyl-CoA C37H60N7O18P3S -4 C05259 KEGG - C05259 Neutral MF = C37H64N7O18P3S SMP metacyc 3-OXOPALMITOYL-COA 3-OXOPALMITOYL-COA hxa Hexanoate (n-C6:0) C6H11O2 -1 142-62-1 C01585 KEGG - C01585 Neutral MF = C6H12O2 SMP changed compound class from peptides - NCD synmeta HEXANOATE HEXANOATE mal-L L-Malate C4H4O5 -2 97-67-6 C00149 KEGG - C00149 Neutral MF = C4H6O5 SMP CHS MAL r15bp D-Ribose 1,5-bisphosphate C5H8O11P2 -4 None C01151 KEGG - C01151 Neutral MF = C5H12O11P2 SMP CHS RIBOSE-15-BISPHOSPHATE synonym RIBOSE-15-BISPHOSPHATE 3mop (S)-3-Methyl-2-oxopentanoate C6H9O3 -1 C00671 KEGG - C00671 Neutral MF = C6H10O3 C003465 and C03911 are deleted SMP CHS 2-KETO-3-METHYL-VALERATE phom O-Phospho-L-homoserine C4H8NO6P -2 C01102 KEGG - C01102 Neutral MF = C4H10NO6P SMP CHS Changed according to Genomatica JLR O-PHOSPHO-L-HOMOSERINE mana D-Mannonate C6H11O7 -1 C00514 KEGG - C00514 Neutral MF = C6H12O7 SMP D-MANNONATE pi Phosphate HO4P -2 14265-44-2 C00009 KEGG - C00009 Neutral MF = H3O4P SMP CHS Formula changed to HPO4 (Charge -2) on Feb-26-2002 |Pi| 4ppcys N-((R)-4-Phosphopantothenoyl)-L-cysteine C12H20N2O9PS -3 C04352 KEGG - C04352 Neutral MF = C12H23N2O9PS SMP CHS Checked N-groups JLR R-4-PHOSPHOPANTOTHENOYL-L-CYSTEINE frulys fructoselysine C12H25N2O7 1 MKA FRUCTOSELYSINE alatrna L-Alanyl-tRNA(Ala) C3H6NOR 1 C00886 KEGG - C00886 SMP adjusted for Genomatica's change to aa - NCD |Charged-ALA-tRNAs| 4ppan D-4'-Phosphopantothenate C9H15NO8P -3 C03492 KEGG - C03492 Neutral MF = C9H18NO8P SMP CHS Checked N-groups JLR 4-P-PANTOTHENATE cynt Cyanate CNO -1 420-05-3 C01417 KEGG - C01417 Neutral-CHNO JLR Checked N-groups JLR CPD-69 ps_EC phosphatidylserine (Ecoli) C1986H3698N50O500P50 -50 C02737 tv org: Hpylori, Ecoli scaled up (50x) of phosphatidylserine with an average 2 fatty acid chain (C1686H3148O100) Checked N JLR L-1-PHOSPHATIDYL-SERINE oc2coa trans-Oct-2-enoyl-CoA C29H44N7O17P3S -4 C05276 KEGG - C05276 Neutral MF = C29H48N7O18P3S SMP fatty 5mthf 5-Methyltetrahydrofolate C20H24N7O6 -1 C00440 KEGG - C00440 Neutral MF = C20H25N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Note that Kegg structure is incorrect, in one of the rings there should be a N rather than a C (see thf) Agrees with pipeline pilot 5-METHYL-THF 4pasp 4-Phospho-L-aspartate C4H6NO7P -2 C03082 KEGG - C03082 Neutral MF = C4H8NO7P SMP CHS Changed according to Genomatica JLR L-BETA-ASPARTYL-P lipa KDO(2)-lipid (A) C110H196N2O39P2 -6 598-35-6 C06026 KEGG - C06026 NH page 1043 JLR KDO2-LIPID-A dttp dTTP C10H13N2O14P3 -4 C00459 KEGG - C00459 Neutral MF = C10H17N2O14P3 SMP CHS TTP glu-D D-Glutamate C5H8NO4 -1 56-86-0 C00217 KEGG - C00217 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR D-GLT 3hodcoa (S)-3-Hydroxyoctadecanoyl-CoA C39H66N7O18P3S -4 NCD fatty sbzcoa O-Succinylbenzoyl-CoA C32H39N7O20P3S -5 C03160 KEGG - C03160 Neutral MF = C32H44N7O20P3S SMP CHS O-SUCCINYLBENZOYL-COA pyam5p Pyridoxamine 5'-phosphate C8H12N2O5P -1 529-96-4 C00647 KEGG - C00647 Neutral MF = C8H13N2O5P SMP CHS Checked N-groups JLR, AMF PYRIDOXAMINE-5P sarcs Sarcosine C3H7NO2 0 107-97-1 C00213 KEGG - C00213 SAB SARCOSINE feoxam-un ferroxamine minus Fe(3) C25H46N6O8 -2 siderophore unknown galctn-D D-Galactonate C6H11O7 -1 C00880 KEGG - C00880 Neutral-C6H12O7 JLR D-GALACTONATE 5dglcn 5-Dehydro-D-gluconate C6H9O7 -1 C01062 KEGG - C01062 Neutral-C6H10O7 JLR 5K-GLUCONATE trnagly tRNA(Gly) R 0 C01642 KEGG - C01642 SMP |GLY-tRNAs| dxyl5p 1-deoxy-D-xylulose 5-phosphate C5H9O7P -2 C11437 KEGG C11437 Used by enzymes (EC 4.1.3.37 & 1.1.1.267) Neutral MF = C5H11O7P SMP DEOXYXYLULOSE-5P gua Guanine C5H5N5O 0 73-40-5 C00242 KEGG - C00242 Neutral Compound SMP CHS GUANINE 26dap-LL LL-2,6-Diaminoheptanedioate C7H14N2O4 0 583-93-7 C00666 KEGG - C00666 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR LL-DIAMINOPIMELATE 2amsa 2-Aminomalonate semialdehyde C3H5NO3 0 C11822 0 2-AMINOMALONATE-SEMIALDEHYDE glu-L L-Glutamate C5H8NO4 -1 56-86-0 C00025 KEGG - C00025 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR GLT fadh2 Flavin adenine dinucleotide reduced C27H33N9O15P2 -2 C01352 KEGG - C01352 Neutral MF = C27H35N9O15P2 (FADH2) SMP Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD FADH2 ctbtcoa crotonobetainyl-CoA C28H44N8O17P3S -3 No Kegg Entry crotonobetaine with a CoA attached +1 charge on crotonobetaine -4 charge on CoA JLR Checked N-groups JLR CROTONOBETAINYL-COA 25dkglcn 2,5-diketo-D-gluconate C6H7O7 -1 C02780 KEGG C02780 Neutal - C6H8O7 JLR 25-DIDEHYDRO-D-GLUCONATE h2s Hydrogen sulfide H2S 0 06/04/7783 C00283 KEGG - C00283 Neutral Compound SMP CHS HS octa octanoate (n-C8:0) C8H15O2 -1 124-07-2 C06423 KEGG - C06423 Neutral MF = C8H16O2 SMP changed compound class from peptides - NCD CPD-195 dxyl 1-deoxy-D-xylulose C5H10O4 0 C06257 KEGG C06257 tv Neidhardt pg 683 CPD-1093 ipdp Isopentenyl diphosphate C5H9O7P2 -3 C00129 KEGG - C00129 Neutral MF = C5H12O7P2 SMP |delta(3)-isopentenyl-pp| 2dh3dgal 2-Dehydro-3-deoxy-D-galactonate C6H9O6 -1 C01216 KEGG - C01216 Neutral-C6H10O6 JLR 2-DEHYDRO-3-DEOXY-D-GALACTONATE lald-L L-Lactaldehyde C3H6O2 0 598-35-6 C00424 KEGG - C00424 Neutral Compound SMP CHS LACTALD dhpmp Dihydroneopterin monophosphate C9H12N5O7P -2 C05925 KEGG - C05925 MM JLR- Neidhardt pg 667 Checked N-groups, ACD indicates that the N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked AMF DIHYDRONEOPTERIN-P acolipa 4-Amino-4-deoxy-L-arabinose modified core oligosaccharide lipid A C181H314N3O103P4 -9 AMF unknown odecoa Octadecenoyl-CoA (n-C18:1CoA) C39H64N7O17P3S -4 NCD KEGG - C00510 C18:1 C18H33O2 (charge -1) CoA - C21H32N7O16P3S charge (-4) NJ fatty gam1p D-Glucosamine 1-phosphate C6H13NO8P -1 C06156 KEGG - C06156 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR GLUCOSAMINE-1P trnaala tRNA(Ala) R 0 C01635 KEGG - C01635 SMP |ALA-tRNAs| gam6p D-Glucosamine 6-phosphate C6H13NO8P -1 3616-42-0 C00352 KEGG - C00352 Neutral MF = C6H14NO8P SMP CHS Changed according to Genomatica JLR D-GLUCOSAMINE-6-P dhptd 4,5-dihydroxy-2,3-pentanedione C5H8O4 0 C11838 KEGG C11838 See PMID: 11489131 JLR unknown od2coa trans-Octadec-2-enoyl-CoA C39H64N7O17P3S -4 NCD C18:1 - C18H33O2 (charge -1) C21H32N7O16P3S (charge -4) NJ fatty garagund glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C77H125N1O22P2 -2 AMF other O-antigen biosynthesis no3 Nitrate NO3 -1 C00244 KEGG - C00244 Neutral MF = HNO3 SMP CHS Checked N-goups JLR NITRATE dcmp dCMP C9H12N3O7P -2 1032-65-1 C00239 KEGG - C00239 Neutral MF = C9H14N3O7P SMP CHS metacyc DCMP DCMP orot5p Orotidine 5'-phosphate C10H10N2O11P -3 2149-82-8 C01103 KEGG - C01103 Neutral MF = C10H13N2O11P SMP Checked N-groups JLR OROTIDINE-5-PHOSPHATE glyc3p Glycerol 3-phosphate C3H7O6P -2 C00093 KEGG - C00093 Neutral MF = C3H9O6P SMP GLYCEROL-3P fpram 2-(Formamido)-N1-(5-phospho-D-ribosyl)acetamidine C8H15N3O8P -1 C04640 KEGG - C04640 Neutral MF = C8H16N3O8P SMP CHS Changed according to Genomatica JLR 5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE synonym 5-PHOSPHORIBOSYL-N-FORMYLGLYCINEAMIDINE suchms O-Succinyl-L-homoserine C8H12NO6 -1 1492-23-5 C01118 KEGG - C01118 Neutral MF = C8H13NO6 SMP CHS Changed according to Genomatica JLR O-SUCCINYL-L-HOMOSERINE mqn8 Menaquinone 8 C51H72O2 0 84-81-1 C00828 KEGG - C00828 General Formula = C16H16O2(C5H8)n; n = 7 for mqn8; See also mq SMP CHS VITAMIN_K_{2} murein5p5p two linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) C80H124N16O42 -4 AMF this is formed when two uaagmda units come together and lose their undecprenyl chains [GlcNac-MurNac-pentapeptide(beta1->4)GlcNac-MurNac-pentapeptide] unit only the leading oxygen from the ether bond to the next unit is kept on the MurNac, the one from the previous unit connected to the terminal GlcNac is not considered PMID: 9751644 has a good figure other structure is unclear 4hoxpacd 4-Hydroxyphenylacetaldehyde C8H8O2 0 60-11-7 C03765 KEGG - C03765 SAB HYDRPHENYLAC-CPD 23dhba (2,3-Dihydroxybenzoyl)adenylate C17H17N5O10P -1 C04030 KEGG - C04030 Neutral MF = C17H18N5O10P SMP CHS Check groups AMF, JLR, SAB CPD-62 fe3hox Fe(III)hydroxamate C9H18O6N3Fe 0 C06227 KEGG - C06227 formula corrected, 3/24/05 MKA contains "R" groups - replaced with ethyl groups other structure is unclear pac Phenylacetic acid C8H7O2 -1 CAS: 103-82-2 C07086 Kegg C07086 Neutral-C8H8O2 JLR PHENYLACETATE cl Chloride Cl -1 C00115 0 CL- trnahis tRNA(His) R 0 C01643 KEGG - C01643 SMP |HIS-tRNAs| 3hcinnm 3-hydroxycinnamic acid C9H7O3 -1 No Kegg entry see PMID: 9603882 Neutral-C9H8O3 JLR unknown 4h2opntn 4-Hydroxy-2-oxopentanoate C5H7O4 -1 111844-33-8 C03589 KEGG - C03589 Neutral-C5H8O4 JLR 4-HYDROXY-2-KETOVALERATE u23ga UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine C43H75N3O20P2 -2 C04652 KEGG - C04652 Neutral MF = C43H77N3O20P2 SMP CHS Checked N-groups JLR OH-MYRISTOYL LalaLglu L-alanine-L-glutamate C8H13N2O5 -1 AMF dont think its the same as gluala unknown hxan Hypoxanthine C5H4N4O 0 68-94-0 C00262 KEGG - C00262 Neutral Compound SMP CHS Checked N-groups JLR HYPOXANTHINE lipa_cold cold adapted KDO(2)-lipid (A) C114H202N2O39P2 -6 see PMID 10092655 Neutral C114H208N2O39P2 JLR KDO2-LIPID-IVA-COLD acgam1p N-Acetyl-D-glucosamine 1-phosphate C8H14NO9P -2 None C04256 KEGG - C04256 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR N-ACETYL-D-GLUCOSAMINE-1-P fmn FMN C17H19N4O9P -2 146-17-8 C00061 KEGG - C00061 Neutral MF = C17H21N4O9P SMP CHS Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD FMN 5mdr1p 5-Methylthio-5-deoxy-D-ribose 1-phosphate C6H11O7PS -2 C04188 KEGG - C04188 Neutral MF = C6H13O7PS SMP CHS metacyc CPD-444 CPD-444 hco3 Bicarbonate CHO3 -1 71-52-3 C00288 KEGG - C00288 SMP CHS HCO3 tungs tungstate O4W1 -2 AMF TUNGSTATE gal D-Galactose C6H12O6 0 59-23-4 C00124 KEGG - C00124 Deleted KEGG - C01582 (Galactose) Neutral Compound SMP CHS GALACTOSE fe3hox-un Fe(III)hydoxamate, unloaded C9H18O6N3 -3 not produced by K-12 ecoli formula not certain - contains "R" group (replaced w/ ethyl groups); Fe(III)hydroxamate chemistry unclear, but must lose Fe within cell to be recycled MKA other structure is unclear, probably a class butso3 butanesulfonate C4H9O3S -1 AMF metacyc CPD-3744 CPD-3744 cpgn coprogen C35H52N6O13Fe -1 AMF unknown 25drapp 2,5-Diamino-6-(ribosylamino)-4-(3H)-pyrimidinone 5'-phosphate C9H14N5O8P -2 Neidhardt, pg 658 JLR- similar to 25dhpp except ketone group in the nitrogen ring rather than the OH group Checked N-groups, agrees with ACD software, JLR DIAMINO-OH-PHOSPHORIBOSYLAMINO-PYR cystrna L-Cysteinyl-tRNA(Cys) C3H6NOSR 1 C03125 KEGG - C03125 SMP adjusted for Genomatica's change to aa - NCD |Charged-CYS-tRNAs| 23cgmp 2',3'-Cyclic GMP C10H11N5O7P -1 C06194 KEGG - C06194 AMF synmeta CPD-3709 CPD-3709 3dhq 3-Dehydroquinate C7H9O6 -1 C00944 KEGG - C00944 Neutral MF = C7H10O6 SMP CHS DEHYDROQUINATE enter Enterochelin C30H27N3O15 0 Similar to KEGG - C05821 The side chains should be the same, in Kegg one has an alcohol instead of a ketone. See PMID 9214294 for picture. JLR ENTEROBACTIN g6p D-Glucose 6-phosphate C6H11O9P -2 56-73-5 C00092 KEGG - C00092 Neutral MF = C6H13O9P SMP CHS GLC-6-P other is this alpha or beta ??? 23camp 2',3'-Cyclic AMP C10H11N5O6P -1 9014-63-5 C02353 KEGG - C02353 AMF synmeta CPD-3707 CPD-3707 ascb6p L-ascorbate-6-phosphate C6H7O9P -2 No Kegg Entry JLR L-ASCORBATE-6-PHOSPHATE glu5p L-Glutamate 5-phosphate C5H8NO7P -2 C03287 KEGG - C03287 Neutral MF = C5H10NO7P SMP Changed according to Genomatica JLR L-GLUTAMATE-5-P 23ccmp 2',3'-Cyclic CMP C9H11N3O7P -1 C02354 KEGG - C02354 AMF unknown o16a2und (O16 antigen)x2 undecaprenyl diphosphate C123H200N2O57P2 -2 AMF other structure is unclear gthrd Reduced glutathione C10H16N3O6S -1 70-18-8 C00051 KEGG - C00051 Neutral MF = C10H17N3O6S SMP CHS Changed according to Genomatica JLR GLUTATHIONE cdpdag_EC CDPdiacylglycerol (E coli) C2286H3998N150O750P100 -100 C00269 scaled up (50x) of CDP diacylglycerol with 2 ave fatty acids should be charge of -100 CDPDIACYLGLYCEROL hack CDPDIACYLGLYCEROL etha Ethanolamine C2H8NO 1 141-43-5 C00189 KEGG - C00189 Checked N-groups JLR ETHANOL-AMINE scl sirohydrochlorin C42H39N4O16 -7 C05778 KEGG - C05778 Neutral MF = C42H46N4O16 SMP Checked N-groups, JLR SIROHYDROCHLORIN pyr Pyruvate C3H3O3 -1 127-17-3 C00022 KEGG - C00022 Neutral MF = C3H4O3 SMP CHS PYRUVATE pheme Protoheme C34H30FeN4O4 -2 14875-96-8 C00032 KEGG - C00032 Neutral MF = C34H32FeN4O4 Note that chemfinder has the incorrect formula SMP CHS Checked N-groups, JLR PROTOHEME damp dAMP C10H12N5O6P -2 653-63-4 C00360 KEGG - C00360 Neutral MF = C10H14N5O6P SMP CHS DAMP dtdp4d6dg dTDP-4-dehydro-6-deoxy-D-glucose C16H22N2O15P2 -2 C00687 KEGG - C00687 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR DTDP-DEOH-DEOXY-GLUCOSE gdpddman GDP-4-dehydro-6-deoxy-D-mannose C16H21N5O15P2 -2 C01222 KEGG - C01222 Neutral: C16H23N5O15P2 JLR Checked N-groups JLR GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE tyr-L L-Tyrosine C9H11NO3 0 60-18-4 C00082 KEGG - C00082 Neutral MF = C9H11NO3 SMP CHS Changed according to Genomatica JLR TYR ala-D D-Alanine C3H7NO2 0 338-69-2 C00133 KEGG - C00133 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR D-ALANINE ctbt crotonobetaine C7H13NO2 0 6666-46-2 C04114 KEGG - C04114 Compound is neutral at pH 7, +1 on N, -1 on O JLR Checked N-groups JLR CROTONO-BETAINE dgmp dGMP C10H12N5O7P -2 902-04-5 C00362 KEGG - C00362 Neutral MF = C10H14N5O7P SMP CHS DGMP fad Flavin adenine dinucleotide oxidized C27H31N9O15P2 -2 146-14-5 C00016 KEGG - C00016 Neutral MF = C27H33N9O15P2 (FAD) SMP Checked N-groups, appears that one N would lose an H (according to ACD software), but left this alone to match genomatica rules JLR,NCD FAD altrn D-Altronate C6H11O7 -1 C00817 KEGG - C00817 Neutral MF = C6H12O7 No L-altronate found in Chemfinder SMP CHS D-ALTRONATE 3php 3-Phosphohydroxypyruvate C3H2O7P -3 C03232 KEGG - C03232 Neutral MF = C3H5O7P SMP CHS 3-P-HYDROXYPYRUVATE 13dpg 3-Phospho-D-glyceroyl phosphate C3H4O10P2 -4 None C00236 KEGG - C00236 Neutral MF = C3H8O10P2 SMP CHS DPG gly Glycine C2H5NO2 0 56-40-6 C00037 KEGG - C00037 Nonchiral compound Neutral MF = C2H5NO2 SMP CHS Changed according to Genomatica JLR GLY xylu-D D-Xylulose C5H10O5 0 551-84-8 C00310 KEGG - C00310 Neutral Compound SMP CHS D-XYLULOSE apg_EC acyl phosphatidylglycerol (E.coli) C2829H5272O550P50 -50 acyl group is attached to the second glycerol molecule Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 apg_EC is really one molecule of apg. JLR fatty adprib ADPribose C15H21N5O14P2 -2 C00301 KEGG - C00301 Neutral MF = C15H23N5O14P2 SMP CHS checked N groups - NCD ADENOSINE_DIPHOSPHATE_RIBOSE 5prdmbz N1-(5-Phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole C14H17N2O7P -2 C04778 KEGG - C04778 Neutral MF = C14H19N2O7P SMP JLR Checked N-groups JLR ALPHA-RIBAZOLE-5-P lyx-L L-Lyxose C5H10O5 0 1949-78-6 C01508 KEGG - C01508 JLR L-LYXOSE 23dhmb (R)-2,3-Dihydroxy-3-methylbutanoate C5H9O4 -1 C04272 KEGG - C04272 (C04039 Deleted) Neutral MF = C5H10O4 SMP CHS DIOH-ISOVALERATE fecrm Ferrichrome C27H42FeN9O12 0 90-02-8 C06228 KEGG - C06228 AMF CHEMID (015630645) unknown could be under |Ferric-Hydroxamate-Complexes| dtdp4aaddg dTDP-4-acetamido-4,6-dideoxy-D-galactose C18H27N3O15P2 -2 No Kegg entry (similar to C04268 excent amino group on sugar is has an acetyl group on it) Neutral-C18H29N3O15P2 JLR Checked N-groups JLR TDP-FUC4NAC o16a4und (O16 antigen)x4 undecaprenyl diphosphate C191H310N4O107P2 -2 AMF other structure is unclear ala-L L-Alanine C3H7NO2 0 56-41-7 C00041 KEGG - C00041 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR L-ALPHA-ALANINE fuc-L L-Fucose C6H12O5 0 2438-80-4 C01019 KEGG - C01019 Neutral Compound SMP L-FUCOSE citr-L L-Citrulline C6H13N3O3 0 372-75-8 C00327 KEGG - C00327 Neutral MF = C6H13N3O3 SMP CHS Changed according to Genomatica JLR L-CITRULLINE hacolipa hepta-acylated core oligosaccharide lipid A (E. coli) C192H333N2O101P4 -11 AMF other structure is unclear dcamp N6-(1,2-Dicarboxyethyl)-AMP C14H14N5O11P -4 C03794 KEGG - C03794 Neutral MF = C14H18N5O11P SMP CHS Checked N-groups JLR ADENYLOSUCC 23dhb 2,3-Dihydroxybenzoate C7H5O4 -1 303-38-8 C00196 KEGG - C00196 Neutral MF = C7H6O4 SMP CHS 2-3-DIHYDROXYBENZOATE duri Deoxyuridine C9H12N2O5 0 951-78-0 C00526 KEGG - C00526 Neutral Compound SMP CHS Checked N-groups JLR DEOXYURIDINE ametam S-Adenosylmethioninamine C14H24N6O3S 2 C01137 KEGG - C01137 SMP Changed according to Genomatica JLR S-ADENOSYLMETHIONINAMINE aspsa L-Aspartate 4-semialdehyde C4H7NO3 0 None C00441 KEGG - C00441 Neutral MF = C4H7NO3 SMP CHS Changed according to Genomatica JLR L-ASPARTATE-SEMIALDEHYDE murein4px4p4p three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala), one uncrosslinked tetrapaptide) (middle of chain) C111H169N21O59 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala unknown gdpofuc GDP-4-oxo-L-fucose C16H21N5O15P2 -2 583-08-4 C05389 KEGG - C05389 Neutral: C16H23N5O15P2 JLR Checked N-Groups JLR unknown but metacyc has some close ones rmn L-Rhamnose C6H12O5 0 3615-41-6 C00507 KEGG - C00507 SMP RHAMNOSE mercppyr Mercaptopyruvate C3H3O3S -1 C00957 KEGG - C00957 3-MERCAPTO-PYRUVATE grxox glutaredoxin (oxidized) X 0 AMf C07293 GLUTAREDOXIN-MONOMER b2coa trans-But-2-enoyl-CoA C25H36N7O17P3S -4 102680-35-3 C00877 KEGG - C00877 Neutral MF = C25H40N7O17P3S SMP CROTONYL-COA dimp dIMP C10H11N4O7P -2 C06196 KEGG - C06196 (figure in Kegg is inconsistent with other inosine bases) IT Neutral MF = C10H15N4O7P SMP CHS DIMP eca4colipa (enterobacterial common antigen)x4 core oligosaccharide lipid A C272H447N14O160P4 -15 AMF unknown actp Acetyl phosphate C2H3O5P -2 19926-71-7 C00227 KEGG - C00227 Neutral MF = C2H5O5P SMP CHS ACETYL-P 2mcacn cis-2-Methylaconitate C7H5O6 -3 99-98-9 C04225 KEGG - C04225 Neutral-C7H8O6 JLR CPD-1136 synonym CPD-1136 dhor-S (S)-Dihydroorotate C5H5N2O4 -1 5988-19-2 C00337 KEGG - C00337 Neutral MF = C5H6N2O4 SMP Checked N-groups JLR DI-H-OROTATE dkmpp 2,3-diketo-5-methylthio-1-phosphopentane C6H9O6PS -2 JLR- no kegg entry metacyc CPD-84 CPD-84 grdp Geranyl diphosphate C10H17O7P2 -3 C00341 KEGG - C00341 Neutral MF = C10H20O7P2 SMP GERANYL-PP 2kmb 2-keto-4-methylthiobutyrate C5H7O3S -1 No KEGG Entry JEM has it as KMB Neutral MF = C5H8O3S SMP metacyc CPD-479 CPD-479 pydx5p Pyridoxal 5'-phosphate C8H8NO6P -2 54-47-7 C00018 KEGG - C00018 Neutral MF = C8H10NO6P SMP CHS Checked N-groups JLR, AMF PYRIDOXAL_PHOSPHATE icolipa inner core oligosaccharide lipid A (E coli) C145H251N2O74P4 -11 AMF other structure is unclear anhgm4p N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide C37H57N7O20 -2 AMF other structure is unclear 3dhguln 3-Dehydro-L-gulonate C6H9O7 -1 C00618 KEGG - C00618 Neutral-C6H10O7 JLR NCD MKA 3-KETO-L-GULONATE cytd Cytidine C9H13N3O5 0 65-46-3 C00475 KEGG - C00475 Neutral Compound SMP CHS Checked N-groups JLR CYTIDINE r1p alpha-D-Ribose 1-phosphate C5H9O8P -2 58459-37-3 C00442 KEGG - C00442 Neutral MF = C5H11O8P SMP CHS RIBOSE-1P mnl D-Mannitol C6H14O6 0 69-65-8 C00392 KEGG - C00392 SMP MANNITOL kdo8p 3-Deoxy-D-manno-octulosonate 8-phosphate C8H12O11P -3 C04478 KEGG - C04478 Neutral MF = C8H15O11P SMP CHS KDO-8P so3 Sulfite O3S -2 7782-99-2 C00094 KEGG - C00094 Neutral MF = H2O3S (sulfurous acid) SMP CHS SO3 pg_EC Phosphatidylglycerol (Ecoli) C1986H3748O500P50 -50 C00344 tv org: Ecoli scaled up (50x) of phosphatidylglycerol with an ave fatty acid of C1686 H3148 O100 L-1-PHOSPHATIDYL-GLYCEROL class L-1-PHOSPHATIDYL-GLYCEROL fatty tagur D-Tagaturonate C6H9O7 -1 None C00558 KEGG - C00558 Neutral MF = C6H10O7 SMP CHS D-TAGATURONATE nadph Nicotinamide adenine dinucleotide phosphate - reduced C21H26N7O17P3 -4 2646-71-1 C00005 KEGG - C00005 Neutral MF = C21H30N7O17P3 SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR NADPH synonym NADPH 6hmhptpp 6-hydroxymethyl-dihydropterin pyrophosphate C7H8N5O8P2 -3 JLR - Neidhardt pg 667, different from 2ahhmd because Ketone vs. OH group on nitrogen ring Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR DIHYDROPTERIN-CH2OH-PP synonym DIHYDROPTERIN-CH2OH-PP glyald D-Glyceraldehyde C3H6O3 0 453-17-8 C00577 KEGG - C00577 KEGG has non-chiral glyceraldehyde (367-47-5) Neutral Compound SMP CHS metacyc GLYCERALD GLYCERALD f1p D-Fructose 1-phosphate C6H11O9P -2 15978-08-2 C02976 KEGG - C02976 Merged with KEGG - C01094 Neutral MF = C6H13O9P SMP CHS FRU1P asntrna L-Asparaginyl-tRNA(Asn) C4H7N2O2R 1 C03402 KEGG - C03402 SMP adjusted for Genomatica's change to aa - NCD |Charged-ASN-tRNAs| dump dUMP C9H11N2O8P -2 964-26-1 C00365 KEGG - C00365 Neutral MF = C9H13N2O8P SMP CHS DUMP 23dhdp 2,3-Dihydrodipicolinate C7H5NO4 -2 C03340 KEGG - C03340 Neutral MF = C7H7NO4 SMP CHS (close compound-dipicolinic acid has a pKa of 2.16 and 4.76) Checked N-groups JLR |2,3-dihydrodipicolinate| no Nitric oxide NO 0 10102-43-9 C00533 KEGG - C00533 SMP CHS NITRIC-OXIDE galt Galactitol C6H14O6 0 608-66-2 C01697 KEGG - C01697 Neutral Compound SMP GALACTITOL halipa hepta-acylated KDO(2)-lipid (A) C126H226N2O40P2 -6 AMF HEPTA-ACYLATED-LIPID-A hack HEPTA-ACYLATED-LIPID-A 6pgc 6-Phospho-D-gluconate C6H10O10P -3 C00345 KEGG - C00345 Neutral MF = C6H13O10P SMP CHS CPD-2961 idp IDP C10H11N4O11P2 -3 86-04-4 C00104 KEGG - C00104 Neutral MF = C10H14N4O11P2 SMP CHS Checked N-groups JLR IDP 2dmmq8 2-Demethylmenaquinone 8 C50H70O2 0 C05818 KEGG - C05818 General Formula = C15H14O2(C5H8)n; n = 7 for 2dmmq8 SMP DEMETHYLMENAQUINONE hack DEMETHYLMENAQUINONE 2ommbl 2-Octaprenyl-3-methyl-6-methoxy- 1,4-benzoquinol C48H74O3 0 Neidhardt page 651 JLR unknown we have the biosynthesis pathway using the quinone compounds rather than the quinols uama UDP-N-acetylmuramoyl-L-alanine C23H33N4O20P2 -3 C01212 KEGG - C01212 Neutral MF = C23H36N4O20P2 SMP CHS Checked N-groups JLR UDP-ACETYLMURAMOYL-ALA pydam Pyridoxamine C8H13N2O2 1 85-87-0 C00534 KEGG - C00534 Neutral Compound SMP CHS Checked N-groups JLR, AMF PYRIDOXAMINE 6pgl 6-phospho-D-glucono-1,5-lactone C6H9O9P -2 None C01236 KEGG - C01236 Neutral MF = C6H11O9P SMP CHS D-6-P-GLUCONO-DELTA-LACTONE hmbil Hydroxymethylbilane C40H38N4O17 -8 73023-76-4 C01024 KEGG - C01024 Neutral MF = C40H46N4O17 SMP CHS Checked N-groups JLR HYDROXYMETHYLBILANE ddcaACP Dodecanoyl-ACP (n-C12:0ACP) C23H43N2O8PRS -1 C05223 KEGG C05223 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty 2ippm 2-Isopropylmaleate C7H8O4 -2 C02631 KEGG - C02631 Neutral MF = C7H10O4 SMP unknown dhf 7,8-Dihydrofolate C19H19N7O6 -2 4033-27-6 C00415 KEGG - C00415 Neutral MF = C19H21N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR DIHYDROFOLATE grxrd glutaredoxin (reduced) XH2 0 AMF C07292 other appropriate class seems missing in ecocyc ahcys S-Adenosyl-L-homocysteine C14H20N6O5S 0 979-92-0 C00021 KEGG - C00021 Neutral MF = C14H20N6O5S SMP CHS Changed according to Genomatica JLR ADENOSYL-HOMO-CYS hdeACP Hexadecenoyl-ACP (n-C16:1ACP) C27H49N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty prbamp 1-(5-Phosphoribosyl)-AMP C15H19N5O14P2 -4 C02741 KEGG - C02741 Neutral MF = C15H23N5O14P2 SMP CHS PHOSPHORIBOSYL-AMP synonym PHOSPHORIBOSYL-AMP galur D-Galacturonate C6H9O7 -1 685-73-4 C00333 KEGG - C00333 Neutral MF = C6H10O7 SMP CHS D-GALACTURONATE ala-B beta-Alanine C3H7NO2 0 107-95-9 C00099 KEGG - C00099 Neutral MF = C3H7NO2 SMP CHS Changed according to Genomatica JLR B-ALANINE glyb Glycine betaine C5H11NO2 0 107-43-7 C00719 KEGG - C00719 SMP Checked N-groups JLR BETAINE glyc Glycerol C3H8O3 0 56-81-5 C00116 KEGG - C00116 Neutral Compound SMP CHS GLYCEROL ssaltpp Succinate semialdehyde-thiamin diphosphate anion C16H21N4O10P2S -3 C05816 KEGG - C05816 Neutral MF = C16H24N4O10P2S SMP JLR Checked N-groups JLR SUCCINATE-SEMIALDEHYDE-THIAMINE-PPI synonym SUCCINATE-SEMIALDEHYDE-THIAMINE-PPI dtdprmn dTDP-L-rhamnose C16H24N2O15P2 -2 572-96-3 C03319 KEGG - C03319 Neutral-C16H26N2O15P2 JLR Checked N-groups JLR DTDP-RHAMNOSE frulysp fructoselysine Phosphate C12H24N2O10P -1 MKA AMF FRUCTOSELYSINE-6-PHOSPHATE hack FRUCTOSELYSINE-6-PHOSPHATE argtrna L-Arginyl-tRNA(Arg) C6H14N4OR 2 C02163 KEGG - C02163 SMP adjusted for Genomatica's change to aa - NCD |Charged-ARG-tRNAs| uamr UDP-N-acetylmuramate C20H28N3O19P2 -3 C01050 KEGG - C01050 Neutral MF = C20H31N3O19P2 SMP CHS Checked N-groups JLR UDP-N-ACETYLMURAMATE 3hbcoa (S)-3-Hydroxybutanoyl-CoA C25H38N7O18P3S -4 C01144 KEGG - C01144 Neutral MF = C25H42N7O18P3S SMP metacyc S-3-HYDROXYBUTANOYL-COA S-3-HYDROXYBUTANOYL-COA 2ddglcn 2-Dehydro-3-deoxy-D-gluconate C6H9O6 -1 None C00204 KEGG - C00204 Neutral MF = C6H10O6 SMP CHS 2-DEHYDRO-3-DEOXY-D-GLUCONATE murein5p5p5p three linked disacharide pentapeptide murein units (uncrosslinked, middle of chain) C120H186N24O63 -6 AMF other structure is unclear ppp9 Protoporphyrin C34H32N4O4 -2 553-12-8 C02191 KEGG - C02191 Neutral MF = C34H34N4O4 SMP CHS PROTOPORPHYRIN_IX ugmd UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate C35H51N7O26P2 -4 C04877 KEGG - C04877 Neutral MF = C35H55N7O26P2 SMP Changed according to Genomatica JLR UDP-AAGM-DIAMINOHEPTANEDIOATE synonym UDP-AAGM-DIAMINOHEPTANEDIOATE uLa4n undecaprenyl phosphate-4-amino-4-deoxy-L-arabinose C60H100N1O7P1 0 AMF other We need to change the reaction of ArnT to correspond to theirs; probably also enter new pathway sucorn N2-Succinyl-L-ornithine C9H15N2O5 -1 80102-04-1 C03415 KEGG - C03415 Neutral: C9H16N2O5 JLR Checked N-groups JLR N2-SUCCINYLORNITHINE unagamu Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate C71H113N2O18P2 -3 No Kegg entry Neutral-C71H116N2O18P2 JLR Checked N-groups JLR C55-PP-GLCNAC-MANNACA synonym C55-PP-GLCNAC-MANNACA cmp CMP C9H12N3O8P -2 84-52-6 C00055 KEGG - C00055 Neutral MF = C9H14N3O8P SMP CHS CMP 2omph 2-Octaprenyl-6-methoxyphenol C47H72O2 0 C05812 KEGG - C05812 SMP CHS 2-OCTAPRENYL-6-METHOXYPHENOL glu1sa L-Glutamate 1-semialdehyde C5H9NO3 0 None C03741 KEGG - C03741 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR GLUTAMATE-1-SEMIALDEHYDE dscl dihydrosirohydrochlorin C42H41N4O16 -7 65207-12-7 C02463 KEGG - C02463 Neutral MF = C42H48N4O16 SMP Checked N-groups, agrees with ACD software, JLR DIHYDROSIROHYDROCHLORIN dms Dimethyl sulfide C2H6S 0 75-18-3 C00580 KEGG - C00580 REDUCED-DMSO glu5sa L-Glutamate 5-semialdehyde C5H9NO3 0 None C01165 KEGG - C01165 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR L-GLUTAMATE_GAMMA-SEMIALDEHYDE u3hga UDP-3-O-(3-hydroxytetradecanoyl)-D-glucosamine C29H50N3O18P2 -1 C06022 KEGG - C06022 Neutral MF = C29H51N3O18P2 SMP CHS Checked N-groups JLR UDP-OHMYR-GLUCOSAMINE synonym UDP-OHMYR-GLUCOSAMINE 2mcit 2-Methylcitrate C7H7O7 -3 96-17-3 C02225 KEGG - C02225 NCD JLR CPD-622 ocdca octadecanoate (n-C18:0) C18H35O2 -1 57-11-4 C01530 KEGG - C01530 Neutral MF = C18H36O2 SID: 38708 CID: 78387 SMP saturated fatty acid, 18 carbons changed compound class from peptides to fatty acids - NCD synmeta STEARIC_ACID STEARIC_ACID myrsACP Myristoyl-ACP (n-C14:0ACP) C25H47N2O8PRS -1 C05761 KEGG C05761 tv myrs component = C14H27O (3/25/03) JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) MYRISTOYL-ACP protein MYRISTOYL-ACP lipidX 2,3-Bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate C34H64NO12P -2 None C04824 KEGG - C04824 Neutral MF = C34H66NO12P SMP CHS Checked N-groups JLR BISOHMYR-GLUCOSAMINYL-1P 4ampm 4-Amino-2-methyl-5-phosphomethylpyrimidine C6H8N3O4P -2 C04556 KEGG - C04556 Neutral MF = C6H10N3O4P SMP CHS Checked N-groups JLR AMINO-HYDROXYMETHYL-METHYL-PYR-P o16aund O16 antigen undecaprenyl diphosphate C89H145N1O32P2 -2 AMF - structure from PMID: 7517391 unknown seln Selenide HSe -1 531-44-2 C01528 KEGG - C01528 Neutral-H2Se JLR CPD-678 murein5p4p two linked disacharide pentapeptide and tetrapeptide murein units (uncrosslinked, middle of chain) C77H119N15O41 -4 AMF PMID: 9751644 has a good figure other structure is unclear acgam N-Acetyl-D-glucosamine C8H15NO6 0 7512-17-6 C00140 KEGG - C00140 Neutral Compound SMP Checked N-groups JLR N-ACETYL-D-GLUCOSAMINE dhpt Dihydropteroate C14H13N6O3 -1 C00921 KEGG - C00921 Neutral MF = C14H14N6O3 SMP CHS Checked N-groups, agrees with ACD software JLR |7,8-dihydropteroate| thm Thiamin C12H17N4OS 1 67-03-8 C00378 KEGG - C00378 +1 Charged Compound SMP CHS neutral forumula was originally listed - NCD Changed according to Genomatica JLR THIAMINE r5p alpha-D-Ribose 5-phosphate C5H9O8P -2 4300-28-1 C00117 KEGG - C00117 Delete KEGG - C03736 Neutral MF = C5H11O8P SMP CHS RIBOSE-5P hack RIBOSE-5P dha Dihydroxyacetone C3H6O3 0 96-26-4 C00184 KEGG - C00184 DIHYDROXYACETONE aso3 arsenite AsO3 -3 C06697 KEGG - C06697 AMF CPD-763 nac Nicotinate C6H4NO2 -1 59-67-6 C00253 KEGG - C00253 Neutral MF = C6H5NO2 SMP CHS Checked N-groups JLR NIACINE aso4 arsenate AsO4 -3 7778-39-4 C01478 KEGG - C01478 AMF ARSENATE sl2a6o N-Succinyl-2-L-amino-6-oxoheptanedioate C11H12NO8 -3 C04462 KEGG - C04462 Neutral MF = C11H15NO8 SMP CHS Checked N-groups JLR N-SUCCINYL-2-AMINO-6-KETOPIMELATE synonym N-SUCCINYL-2-AMINO-6-KETOPIMELATE co2 CO2 CO2 0 124-38-9 C00011 KEGG - C00011 Neutral Compound SMP CHS CARBON-DIOXIDE e4p D-Erythrose 4-phosphate C4H7O7P -2 585-18-2 C00279 KEGG - C00279 Neutral MF = C4H9O7P SMP CHS ERYTHROSE-4P acser O-Acetyl-L-serine C5H9NO4 0 66638-22-0 C00979 KEGG - C00979 Neutral MF = C5H9NO4 SMP CHS Changed according to Genomatica JLR ACETYLSERINE 3hpppn 3-(3-hydroxy-phenyl)propionate C9H9O3 -1 No Kegg entry see PMID: 9603882 Neutral JLR 3-HYDROXYPHENYL-PROPIONATE gal1p alpha-D-Galactose 1-phosphate C6H11O9P -2 2255-14-3 C00446 KEGG - C00446 Neutral MF = C6H13O9P SMP CHS GALACTOSE-1P 4mhetz 4-Methyl-5-(2-hydroxyethyl)-thiazole C6H9NOS 0 137-00-8 C04294 KEGG - C04294 Neutral SMP CHS Checked N-groups JLR THZ thmpp Thiamine diphosphate C12H16N4O7P2S -2 154-87-0 C00068 KEGG - C00068 Neutral MF = C12H19N4O7P2S SMP CHS Changed charged formula; had wrong number of hydrogens -NCD Checked N-groups JLR THIAMINE-PYROPHOSPHATE thmmp Thiamin monophosphate C12H16N4O4PS -1 532-40-1 C01081 KEGG - C01081 +1 Charged MF = C12H18N4O4PS SMP CHS Checked N-groups JLR THIAMINE-P murein3px4p two disacharide linked murein units, tripeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain) C71H107N13O38 -4 AMF PMID: 9751644 has a good figure other structure is unclear dhpppn 3-(2,3-Dihydroxyphenyl)propanoate C9H9O4 -1 145-14-2 C04044 KEGG - C04044 Neutral-C9H10O4 JLR 2-3-DIHYDROXYPHENYL-PROPIONATE pppi Inorganic triphosphate HO10P3 -4 C03279 KEGG - C03279 Neutral MF = H5O10P3 SMP P3I synonym P3I dtdpglu dTDPglucose C16H24N2O16P2 -2 2009-24-7 C00842 KEGG - C00842 Neutral-C16H26N2O16P2 JLR Checked N-groups JLR DTDP-D-GLUCOSE udp UDP C9H11N2O12P2 -3 58-98-0 C00015 KEGG - C00015 Neutral MF = C9H14N2O12P2 SMP CHS UDP cu2 Cu2+ Cu 2 Two entries are made for Cu: Cu3+ and Cu2+ CU+2 urea Urea CH4N2O 0 57-13-6 C00086 KEGG - C00086 Neutral Compound SMP CHS Checked N-groups JLR UREA pppn Phenylpropanoate C9H9O2 -1 2628-17-3 C05629 KEGG - C05629 Neutral-C9H10O2 JLR 3-PHENYLPROPIONATE amob S-Adenosyl-4-methylthio-2-oxobutanoate C15H19N5O6S 0 C04425 KEGG - C04425 Neutral MF = C15H20N5O6S SMP CHS Checked N-groups JLR S-ADENOSYL-4-METHYLTHIO-2-OXOBUTANOATE malcoa Malonyl-CoA C24H33N7O19P3S -5 524-14-1 C00083 KEGG - C00083 Neutral MF = C24H38N7O19P3S SMP CHS MALONYL-COA dhmptp dihydromonapterin-triphosphate C9H12N5O13P3 -4 AMF DIHYDROMONAPTERIN-TRIPHOSPHATE gar N1-(5-Phospho-D-ribosyl)glycinamide C7H14N2O8P -1 C03838 KEGG - C03838 Neutral MF = C7H15N2O8P SMP CHS Changed according to Genomatica JLR 5-PHOSPHO-RIBOSYL-GLYCINEAMIDE synonym 5-PHOSPHO-RIBOSYL-GLYCINEAMIDE kdolipid4 KDO-lipid IV(A) C76H137N2O30P2 -5 C06024 KEGG- C06024 Neutral C76H142N2O30P2 JLR- KDO-LIPID-IVA anhgm N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid C19H29N2O12 -1 AMF unknown glntrna L-Glutaminyl-tRNA(Gln) C5H9N2O2R 1 C02282 KEGG - C02282 SMP adjusted for Genomatica's change to aa - NCD |Charged-GLN-tRNAs| ppa Propionate (n-C3:0) C3H5O2 -1 79-09-4 C00163 KEGG - C00163 Neutral MF = C3H6O2 SMP NCD PROPIONATE hack PROPIONATE ggbutal gamma-glutamyl-gamma-butyraldehyde C9H16O4N2 0 MKA GAMMA-GLUTAMYL-GAMMA-AMINOBUTYRALDEH hack GAMMA-GLUTAMYL-GAMMA-AMINOBUTYRALDEH 23cump 2',3'-Cyclic UMP C9H10N2O8P -1 9014-63-5 C02355 KEGG - C02355 AMF unknown EcoCyc has the general reaction, no specific nucleoside din Deoxyinosine C10H12N4O4 0 890-38-0 C05512 KEGG - C05512 Neutral Compound SMP CHS Checked N-groups JLR DEOXYINOSINE udcpdp Undecaprenyl diphosphate C55H89O7P2 -3 C03543 KEGG - C03543 Neutral MF = C55H92O7P2 SMP CHS UNDECAPRENYL-DIPHOSPHATE xtsn Xanthosine C10H12N4O6 0 146-80-5 C01762 KEGG - C01762 Neutral Compound SMP CHS Checked N-groups JLR XANTHOSINE oaa Oxaloacetate C4H2O5 -2 328-42-7 C00036 KEGG - C00036 Neutral MF = C4H4O5 SMP CHS OXALACETIC_ACID um4p UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine C38H56N8O27P2 -4 AMF UDP-MURNAC-TETRAPEPTIDE synonym UDP-MURNAC-TETRAPEPTIDE fecrm-un Ferrichrome minus Fe(III) C27H42N9O12 -3 CHEMID (015630645) unknown skm5p Shikimate 5-phosphate C7H8O8P -3 C03175 KEGG - C03175 Neutral MF = C7H11O8P SMP CHS SHIKIMATE-5P h2o H2O H2O 0 7732-18-5 C00001 KEGG - C00001 WATER itp ITP C10H11N4O14P3 -4 132-06-9 C00081 KEGG - C00081 Neutral MF = C10H15N4O14P3 SMP CHS Checked N-groups JLR ITP ocdcea octadecenoate (n-C18:1) C18H33O2 -1 monounsaturated fatty acid, 18 carbons KEGG - C00712 NCD updated by NJ metacyc OLEATE-CPD OLEATE-CPD LalaDgluMdapDala L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine C18H30N5O9 -1 AMF other murein recycling stuff; we have a different reaction with UDP-linked compound in EcoCyc gal-bD beta D-Galactose C6H12O6 0 33419-42-0 C01582 KEGG - C01582 NCD GALACTOSE asn-L L-Asparagine C4H8N2O3 0 70-47-3 C00152 KEGG - C00152 Neutral MF = C4H8N2O3 SMP CHS Changed according to Genomatica JLR ASN thrp L-Threonine O-3-phosphate C4H8NO6P -2 C12147 AMF C12147 metacyc L-THREONINE-O-3-PHOSPHATE L-THREONINE-O-3-PHOSPHATE prpp 5-Phospho-alpha-D-ribose 1-diphosphate C5H8O14P3 -5 C00119 KEGG - C00119 Neutral MF = C5H13O14P3 SMP PRPP arbtn aerobactin minus Fe3 C22H33N4O13 -3 0 metacyc AEROBACTIN AEROBACTIN dgsn Deoxyguanosine C10H13N5O4 0 961-07-9 C00330 KEGG - C00330 Neutral Compound SMP CHS Checked N-groups JLR DEOXYGUANOSINE trnaglu tRNA (Glu) R 0 None C01641 KEGG - C01641 X = (C5H8O6PR)n Represent as uncharged species SMP; MF changed on May 7, 2002 CHS |GLT-tRNAs| gam D-Glucosamine C6H14NO5 1 3416-24-8 C00329 KEGG - C00329 Neutral Compound SMP CHS Changed according to Genomatica JLR GLUCOSAMINE trnaarg tRNA(Arg) R 0 C01636 KEGG - C01636 SMP |ARG-tRNAs| mlthf 5,10-Methylenetetrahydrofolate C20H21N7O6 -2 C00143 KEGG - C00143 Neutral MF = C20H23N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR METHYLENE-THF mso3 methanesulfonate CH3O3S -1 0 synmeta CPD-3746 CPD-3746 gmhep1p D-Glycero-D-manno-heptose 1-phosphate C7H13O10P -2 C07838 KEGG C07838 Neutral C7H15O10P D-BETA-D-HEPTOSE-1-P phaccoa Phenylacetyl-CoA C29H38N7O17P3S -4 C00582 KEGG - C00582 Neutral-C29H42N7O17P3S JLR CPD-207 ddcacoa Dodecanoyl-CoA (n-C12:0CoA) C33H54N7O17P3S -4 6244-92-4 C01832 KEGG - C01832 Neutral MF = C33H58N7O17P3S SMP synmeta LAUROYLCOA-CPD LAUROYLCOA-CPD ACP acyl carrier protein C11H21N2O7PRS -1 C00229 tv formula deducted by substraction the elemental compositon from (MalACP + CoA) - MalCoA checked with Neidhardt JLR needed to add an H, pka of thiol (-SH) is 9 to 12. JLR changed to include 4-phosphopantetheinyl moiety (see PMID 11867633) ACP hg2 Hg2+ Hg 2 C00703 KEGG - C00703 HG+2 anhgm3p N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide C34H52N6O19 -2 AMF other structure is unclear trnaasp tRNA(Asp) R 0 C01638 KEGG - C01638 SMP |ASP-tRNAs| trnaile tRNA(Ile) R 0 C01644 KEGG - C01644 SMP |ILE-tRNAs| pe_EC Phosphatidylethanolamine (ecoli) C1936H3748N50O400P50 0 C00350 tv org: Hpylori, Ecoli scaled up (50x) of ps with 2 ave fatty acids Checked N JLR L-1-PHOSPHATIDYL-ETHANOLAMINE stcoa Stearoyl-CoA (n-C18:0CoA) C39H66N7O17P3S -4 362-66-3 C00412 KEGG - C00412 NCD SMP (2/7/03) C18:0 + CoA synmeta STEAROYL-COA STEAROYL-COA anhm3p 1,6-anhydrous-N-Acetylmuramyl-tripeptide C26H39N5O14 -2 AMF unknown dmso Dimethyl sulfoxide C2H6OS 0 C11143 KEGG C11143 JLR DMSO murein4p4p two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain) C74H114N14O40 -4 AMF PMID: 9751644 has a good figure other structure is unclear scsertrna L-Selenocysteinyl-tRNA(Ser) C3H6NO2R 1 16561-29-8 C05173 KEGG - C05173 |Charged-SEC-tRNAs| dann 7,8-Diaminononanoate C9H21N2O2 1 C01037 KEGG - C01037 Neutral MF = C9H20N2O2 SMP CHS Changed according to Genomatica JLR DIAMINONONANOATE iasp Iminoaspartate C4H3NO4 -2 C05840 KEGG - C05840 Neutral MF = C4H5NO4 SMP Checked N-groups, agrees with ACD software, JLR Updated after checking with Pipeline Pilot, RM ==> C4H3NO4 -2 IMINOASPARTATE 3hhcoa (S)-3-Hydroxyhexanoyl-CoA C27H42N7O18P3S -4 C05268 KEGG - C05268 Neutral MF = C27H46N7O18P3S SMP synmeta OH-HEXANOYL-COA OH-HEXANOYL-COA 4r5au 4-(1-D-Ribitylamino)-5-aminouracil C9H16N4O6 0 C04732 KEGG - C04732 SMP Checked N-groups, agrees with ACD software, JLR AMINO-RIBOSYLAMINO-1H-3H-PYR-DIONE ugmda UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine C41H61N9O28P2 -4 C04882 KEGG - C04882 Neutral MF = C41H65N9O28P2 SMP Changed according to Genomatica JLR C1 h2o2 Hydrogen peroxide H2O2 0 7722-84-1 C00027 KEGG - C00027 Neutral Compound SMP CHS HYDROGEN-PEROXIDE sucgsa N2-Succinyl-L-glutamate 5-semialdehyde C9H11NO6 -2 2009-64-5 C05932 KEGG - C05932 Neutral: C9H13NO6 JLR Checked N-groups JLR N2-SUCCINYLGLUTAMIC-SEMIALDEHYDE cechddd cis-3-(3-carboxyethyl)-3,5-cyclohexadiene-1,2-diol C9H11O4 -1 No Kegg entry, see figure 1 PMID: 9603882 Neutral-C9H12O4 JLR CARBOXYETHYL-3-5-CYCLOHEXADIENE-1-2-DIOL synonym CARBOXYETHYL-3-5-CYCLOHEXADIENE-1-2-DIOL dhap Dihydroxyacetone phosphate C3H5O6P -2 57-04-5 C00111 KEGG - C00111 Neutral MF = C3H7O6P SMP CHS DIHYDROXY-ACETONE-PHOSPHATE gg4abut gamma-glutamyl-gamma aminobutyric acid C9H15O5N2 -1 MKA GAMMA-GLUTAMYL-GAMMA-AMINOBUTYRATE synonym GAMMA-GLUTAMYL-GAMMA-AMINOBUTYRATE ara5p D-Arabinose 5-phosphate C5H9O8P -2 C01112 KEGG - C01112 neutral MF = C5H11O8P SMP CHS JLR- had incorrect charge should be -2 ARABINOSE-5P gbbtn gamma-butyrobetaine C7H15NO2 0 No Kegg entry, it is in EcoCyc Compound is a zwitterion, + charge on N and - charge on O JLR Checked N-groups JLR GAMMA-BUTYROBETAINE 3hocoa (S)-3-Hydroxyoctanoyl-CoA C29H46N7O18P3S -4 C05266 KEGG - C05266 Neutral MF = C29H50N7O18P3S SMP fatty hdca Hexadecanoate (n-C16:0) C16H31O2 -1 57-10-3 C00249 KEGG - C00249 Neutral MF = C16H32O2 SMP CHS changed official name from Fatty acid (Palmitate, n-C16:0) to hexadecanoic acid; abbreviation chagned from fa8 to hdca; changed compound class from reviewed to fatty acid - NCD C16:0 PALMITATE acmanap N-Acetyl-D-mannosamine 6-phosphate C8H14NO9P -2 157296-99-6 C04257 KEGG - C04257 Neutral-C8H16NO9P JLR Checked N JLR N-ACETYL-D-MANNOSAMINE-6P dnad Deamino-NAD+ C21H24N6O15P2 -2 C00857 KEGG - C00857 Neutral MF = C21H27N6O15P2 SMP Checked N-groups JLR DEAMIDO-NAD synonym DEAMIDO-NAD dcdp dCDP C9H12N3O10P2 -3 None C00705 KEGG - C00705 Neutral MF = C9H15N3O10P2 SMP CHS DCDP udpg UDPglucose C15H22N2O17P2 -2 C00029 KEGG - C00029 Neutral MF = C15H24N2O17P2 SMP CHS UDP-GLUCOSE uamag UDP-N-acetylmuramoyl-L-alanyl-D-glutamate C28H39N5O23P2 -4 C00692 KEGG - C00692 Neutral MF = C28H43N5O23P2 SMP CHS Checked N-groups JLR UDP-AA-GLUTAMATE trnapro tRNA(Pro) R 0 C01649 KEGG - C01649 SMP |PRO-tRNAs| 12dgr_EC 1,2-Diacylglycerol (E.coli) C1836H3448O250 0 tv org: Hpylori, Ecoli 12dgr scaled up (50x) with 2 ave fatty acids. DIACYLGLYCEROL hack DIACYLGLYCEROL maltttr Maltotetraose C24H42O21 0 34612-38-9 C02052 KEGG - C02052 JLR MALTOTETRAOSE amet S-Adenosyl-L-methionine C15H23N6O5S 1 29908-03-0 C00019 KEGG - C00019 Neutral MF = C15H23N6O5S; neutral form has charge +1 - NCD SMP CHS Changed according to Genomatica JLR S-ADENOSYLMETHIONINE 4hba 4-Hydroxy-benzyl alcohol C7H8O2 0 tv 4-HYDROXY-BENZYL-ALCOHOL sbt6p D-Sorbitol 6-phosphate C6H13O9P -2 108392-12-7 C01096 KEGG - C01096 Neutral MF = C6H15O9P SMP CHS D-SORBITOL-6-P 6hmhpt 6-hydroxymethyl dihydropterin C7H9N5O2 0 JLR- Neidhardt pg 667; different from 2ahhmp because Ketone vs. OH group on nitrogen ring Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked - AMF AMINO-OH-HYDROXYMETHYL-DIHYDROPTERIDINE other typo fixed taur Taurine C2H7NO3S 0 107-35-7 C00245 KEGG - C00245 Neutral MF = C2H7NO3S SMP Changed according to Genomatica JLR TAURINE utp UTP C9H11N2O15P3 -4 63-39-8 C00075 KEGG - C00075 Neutral MF = C9H15N2O15P3 SMP CHS UTP 2omhmbl 2-Octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol C48H74O4 0 Neidhardt page 651 JLR unknown close is OCTAPRENYL-METHYL-METHOXY-BENZQ except it is quinone and lacks 5-OH pgp_EC Phosphatidylglycerophosphate (Ecoli) C1986H3698O650P100 -150 C03892 tv org: Ecoli scaled up (50x) of phosphatidylglycerophosphate with 2 ave fatty acid chain (C1686 H3148 O100) L-1-PHOSPHATIDYL-GLYCEROL-P class L-1-PHOSPHATIDYL-GLYCEROL-P coa Coenzyme A C21H32N7O16P3S -4 85-61-0 C00010 KEGG - C00010 Neutral MF = C21H36N7O16P3S SMP CHS Checked N JLR Note the H is attached to the S on the CoA CO-A trnalys tRNA(Lys) R 0 C01646 KEGG - C01646 SMP |LYS-tRNAs| gdp GDP C10H12N5O11P2 -3 146-91-8 C00035 KEGG - C00035 Neutral MF = C10H15N5O11P2 SMP CHS GDP cbi Cobinamide C48H72CoN11O8 0 1867-62-5 C05774 KEGG - C05774 Kegg shows C48H75CoN11O8 (removed 3H's from ring) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR Note: (Assumed that Co charge is +1 and no hydrogens are removed RM) this was not taken into account for this molecule H75 charge =0 8/2004 REDONE old values were C48H73CoN11O8 charge +5 (by JLR) COBINAMIDE cpgn-un coprogen unloaded (no Fe(III)) C35H52N6O13 -4 AMF unknown dad-5 5'-Deoxyadenosine C10H13N5O3 0 C05198 KEGG - C05198 Neutral Compound SMP CHS CH33ADO prfp 1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide C15H21N5O15P2 -4 C04896 KEGG - C04896 Neutral MF = C15H25N5O15P2 SMP CHS Checked N-groups, agrees with ACD software, JLR PHOSPHORIBOSYL-FORMIMINO-AICAR-P synonym PHOSPHORIBOSYL-FORMIMINO-AICAR-P ppal Propanal C3H6O 0 123-38-6 C00479 KEGG - C00479 Neutral Compound SMP CPD-665 ppap Propanoyl phosphate C3H5O5P -2 121-69-7 C02876 KEGG - C02876 Neutral: C3H7O5P JLR PROPIONYL-P 4hbz 4-Hydroxybenzoate C7H5O3 -1 99-96-7 C00156 KEGG - C00156 Neutral MF = C7H6O3 SMP CHS |4-hydroxybenzoate| thymd Thymidine C10H14N2O5 0 50-89-5 C00214 KEGG - C00214 Neutral Compound SMP CHS Checked N-groups JLR THYMIDINE skm Shikimate C7H9O5 -1 138-59-0 C00493 KEGG - C00493 Neutral MF = C7H10O5 SMP CHS SHIKIMATE uagmda Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine C87H139N7O23P2 -4 C05897 KEGG - C05897 Neutral MF = C87H143N7O23P2 SMP Changed according to Genomatica JLR unknown very similar to C4 , but with additional carboxyl hphhlipa heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H231N2O60P3 -8 AMF unknown pant-R (R)-Pantoate C6H11O4 -1 470-29-1 C00522 KEGG - C00522 Neutral MF = C6H12O4 SMP CHS L-PANTOATE fc1p L-Fuculose 1-phosphate C6H11O8P -2 None C01099 KEGG - C01099 Neutral MF = C6H13O8P SMP NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR FUCULOSE-1P 2dhglcn 2-Dehydro-D-gluconate C6H9O7 -1 C00629 KEGG - C00629 Neutral-C6H10O7 JLR CPD-377 LalaDglu L-alanine-D-glutamate C8H13N2O5 -1 AMF unknown op4en 2-Oxopent-4-enoate C5H5O3 -1 C00596 KEGG - C00596 Neutral-C5H6O3 JLR OXOPENTENOATE acmum N-Acetylmuramate C11H18NO8 -1 61633-75-8 C02713 KEGG - C02713 JLR Checked N-Groups NACMUR rdmbzi N1-(alpha-D-ribosyl)-5,6-dimethylbenzimidazole C14H18N2O4 0 C05775 KEGG - C05775 SMP JLR Checked N-groups JLR ALPHA-RIBAZOLE sucarg N2-Succinyl-L-arginine C10H17N4O5 -1 1758-80-1 C03296 KEGG - C03296 Neutral:C10H18N4O5 JLR Checked N-groups JLR CPD-421 trnaval tRNA(Val) R 0 C01653 KEGG - C01653 SMP |VAL-tRNAs| ttdca tetradecanoate (n-C14:0) C14H27O2 -1 544-63-8 C06424 KEGG C06424 Neutral MF = C14H28O2 SMP saturated fatty acid, 14 carbons changed compound class from peptides to fatty acid - NCD fatty ttdcea tetradecenoate (n-C14:1) C14H25O2 -1 monounsaturated fatty acid, 14 carbons NCD fatty dadp dADP C10H12N5O9P2 -3 None C00206 KEGG - C00206 Neutral MF = C10H15N5O9P2 SMP CHS DADP ap4a P1,P4-Bis(5'-adenosyl) tetraphosphate C20H24N10O19P4 -4 C01260 Kegg- C01260 Neutral-C20H28N10O19P4 JLR ADENOSYL-P4 so4 Sulfate O4S -2 7664-93-9 C00059 KEGG - C00059 Neutral MF = H2O4S (sulfuric acid) SMP CHS SULFATE fuc1p-L L-Fucose 1-phosphate C6H11O8P -2 526-31-8 C02985 KEGG - C02985 Neutral-C6H13O8P JLR synmeta CPD-488 CPD-488 amp AMP C10H12N5O7P -2 61-19-8 C00020 KEGG - C00020 Neutral MF = C10H14N5O7P SMP CHS AMP kdo2lipid4L KDO(2)-lipid IV(A) with laurate C96H170N2O38P2 -6 C06251 C06251 NH page 1043 Neutral-C96H176N2O38P2 JLR KDO2-LAUROYL-LIPID-IVA hack KDO2-LAUROYL-LIPID-IVA pram 5-Phospho-beta-D-ribosylamine C5H11NO7P -1 C03090 KEGG - C03090 Neutral MF = C5H12NO7P SMP CHS Changed according to Genomatica JLR 5-P-BETA-D-RIBOSYL-AMINE pran N-(5-Phospho-D-ribosyl)anthranilate C12H13NO9P -3 None C04302 KEGG - C04302 Neutral MF = C12H16NO9P SMP CHS Checked N-groups JLR |N-(5-PHOSPHORIBOSYL)-ANTHRANILATE| synonym |N-(5-PHOSPHORIBOSYL)-ANTHRANILATE| acmana N-Acetyl-D-mannosamine C8H15NO6 0 3615-17-6 C00645 KEGG - C00645 Neutral Compound SMP Checked N-groups JLR N-ACETYL-D-MANNOSAMINE cpg_EC cyclopropane phosphatidylglycerol (Ecoli) C2036H3848O500P50 -50 tv org: Ecoli scaled up (50x) of phosphatidylglycerol with an ave fatty acid of C1686 H3148 O100 fatty tyrtrna L-Tyrosyl-tRNA(Tyr) C9H10NO2R 1 C02839 KEGG - C02839 SMP adjusted for Genomatica's change to aa - NCD |Charged-TYR-tRNAs| his-L L-Histidine C6H9N3O2 0 71-00-1 C00135 KEGG - C00135 Neutral MF = C6H9N3O2 SMP CHS Changed according to Genomatica JLR HIS dgdp dGDP C10H12N5O10P2 -3 C00361 KEGG - C00361 Neutral MF=C10H15N5O10P2 CHS DGDP rhcys S-Ribosyl-L-homocysteine C9H17NO6S 0 37558-16-0 C03539 KEGG - C03539 Neutral-C9H17NO6S JLR Checked N-groups JLR CPD-561 o16a4colipa (O16 antigen)x4 core oligosaccharide lipid A C312H523N6O200P4 -11 AMF unknown lac-L L-Lactate C3H5O3 -1 79-33-4 C00186 KEGG - C00186 Neutral MF = C3H6O3 SMP CHS L-LACTATE galct-D D-Galactarate C6H8O8 -2 526-99-8 C00879 KEGG - C00879 Neutral-C6H10O8 JLR D-GALACTARATE sucglu N2-Succinyl-L-glutamate C9H10NO7 -3 2009-64-5 C05931 KEGG - C05931 Neutral: C9H13NO7 JLR Checked N-groups JLR N2-SUCCINYLGLUTAMATE orn Ornithine C5H13N2O2 1 70-26-8 C01602 KEGG - C01602 Neutral MF = C5H12N2O2 SMP CHS Checked N-groups JLR L-ORNITHINE pc_EC Phosphatidylcholine (E.coli) C2086H4048N50O400P50 0 C00157 Scaled up by 50, really is 50 molecules or phosphatidylcholine. Scale was used so that the elements were whole numbers. JLR PHOSPHATIDYLCHOLINE hack PHOSPHATIDYLCHOLINE gicolipa glucosyl-inner core oligosaccharide lipid A C151H261N2O79P4 -11 AMF other structure is unclear 3ig3p C'-(3-Indolyl)-glycerol 3-phosphate C11H12NO6P -2 C03506 KEGG - C03506 Neutral MF = C11H14NO6P SMP Checked N-groups JLR INDOLE-3-GLYCEROL-P synonym INDOLE-3-GLYCEROL-P mmet S-Methyl-L-methionine C6H14NO2S 1 4289-98-9 C03172 KEGG - C03172 NCD changed to protonated form, added charge - NCD CPD-397 btnso d-biotin d-sulfoxide C10H15N2O4S -1 Not in Kegg (see PMID 10747793, figure 1) Neutral- C10H16N2O4S JLR Checked N-groups JLR CPD-722 pser-L O-Phospho-L-serine C3H6NO6P -2 407-41-0 C01005 KEGG - C01005 Neutral MF = C3H8NO6P SMP Changed according to Genomatica JLR 3-P-SERINE 2mecdp 2-C-methyl-D-erythritol 2,4-cyclodiphosphate C5H10O9P2 -2 C11453 KEGG ID- C11453 Neutral MF = C5H12O9P2 SMP 2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE 1pyr5c 1-Pyrroline-5-carboxylate C5H6NO2 -1 C03912 KEGG - C03912 Neutral MF = C5H7NO2 SMP CHS Checked N-groups JLR,NCD |l-delta(1)-pyrroline_5-carboxylate| acglu N-Acetyl-L-glutamate C7H9NO5 -2 1188-37-0 C00624 KEGG - C00624 Neutral MF = C7H11NO5 SMP CHS Checked N-groups JLR ACETYL-GLU 34hpp 3-(4-Hydroxyphenyl)pyruvate C9H7O4 -1 C01179 KEGG - C01179 Neutral MF = C9H8O4 SMP CHS metacyc 3-4-HYDROXYPHENYLPYRUVATE 3-4-HYDROXYPHENYLPYRUVATE dcyt Deoxycytidine C9H13N3O4 0 951-77-9 C00881 KEGG - C00881 Neutral Compound SMP CHS Checked N-groups JLR DEOXYCYTIDINE 25aics (S)-2-[5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate C13H15N4O12P -4 C04823 KEGG - C04823 Neutral MF = C13H19N4O12P SMP CHS Checked N-groups JLR P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE synonym P-RIBOSYL-4-SUCCCARB-AMINOIMIDAZOLE udpgal UDPgalactose C15H22N2O17P2 -2 C00052 KEGG - C00052 Neutral MF = C15H24N2O17P2 SMP CHS UDP-GLACTOSE thr-D D-Threonine C4H9NO3 0 632-20-2 C00820 KEGG - C00820 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR D-THREONINE murein3p3p two linked disacharide tripeptide murein units (uncrosslinked, middle of chain) C68H104N12O38 -4 AMF PMID: 9751644 has a good figure unknown crn L-Carnitine C7H15NO3 0 44985-71-9 C00318 KEGG - C00318 At neutral pH, this compound is neutral due to positive on nitrogen and negative charge on carboxyl ends. SMP Checked N-groups JLR CARNITINE uacgam UDP-N-acetyl-D-glucosamine C17H25N3O17P2 -2 C00043 KEGG - C00043 KEGG glycan: G10610 Neutral MF = C17H27N3O17P2 SMP CHS Checked N-groups JLR UDP-N-ACETYL-D-GLUCOSAMINE uacmam UDP-N-acetyl-D-mannosamine C17H25N3O17P2 -2 C01170 KEGG - C01170 Neutral MF = C17H27N3O17P2 SMP CHS Kegg Picture is missing the N on the 2-C of the sugar Checked N-groups JLR UDP-MANNAC alac-S (S)-2-Acetolactate C5H7O4 -1 C06010 KEGG - C06010 (C00900 Deleted) Neutral MF = C5H8O4 SMP CHS 2-ACETO-LACTATE hack 2-ACETO-LACTATE icit Isocitrate C6H5O7 -3 30810-51-6 C00311 KEGG - C00311 Neutral MF = C6H8O7 SMP CHS |threo-d(s)-iso-citrate| 2h3oppan 2-Hydroxy-3-oxopropanoate C3H3O4 -1 C01146 KEGG - C01146 Neutral-C3H4O4 JLR TARTRONATE-S-ALD ura Uracil C4H4N2O2 0 66-22-8 C00106 KEGG - C00106 Neutral Compound SMP CHS URACIL udpLa4n uridine 5''-diphospho-{beta}-4-deoxy-4-amino-L-arabinose C14H22N3O15P2 -1 AMF UDP-4-AMINO-4-DEOXY-L-ARABINOSE synonym UDP-4-AMINO-4-DEOXY-L-ARABINOSE mg2 magnesium Mg 2 C00305 KEGG - C00305 SMP MG+2 15dap 1,5-Diaminopentane C5H16N2 2 462-94-2 C01672 KEGG - C01672 Neutral Compound SMP CHS Changed according to Genomatica JLR CADAVERINE synonym CADAVERINE palmACP Palmitoyl-ACP (n-C16:0ACP) C27H51N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty pnto-R (R)-Pantothenate C9H16NO5 -1 79-83-4 C00864 Deleted KEGG - C00864 KEGG - C02349 Neutral MF = C9H17NO5 SMP CHS Checked N-groups JLR PANTOTHENATE arab-L L-Arabinose C5H10O5 0 147-81-9 C00259 KEGG - C00259 Neutral Compound SMP CHS L-ARABINOSE class L-ARABINOSE dmbzid 5,6-Dimethylbenzimidazole C9H10N2 0 582-60-5 C03114 KEGG - C03114 SMP JLR Checked N-groups JLR DIMETHYLBENZIMIDAZOLE 2dda7p 2-Dehydro-3-deoxy-D-arabino-heptonate 7-phosphate C7H10O10P -3 C04691 KEGG - C04691 Neutral MF = C7H13O10P SMP CHS 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-P gmhep7p D-Glycero-D-manno-heptose 7-phosphate C7H13O10P -2 C07836 Kegg C07836 Neutral-C7H15O10P JLR other could be D-ALPHABETA-D-HEPTOSE-7-PHOSPHATE but what is the alpha beta ?? apoACP apoprotein [acyl carrier protein] RHO 0 JLR ACP-MONOMER synonym ACP-MONOMER arbt6p Arbutin 6-phosphate C12H15O10P -2 C06187 KEGG - C06187 Neutral MF = C12H17O10P SMP CPD-1162 zn2 Zinc Zn 2 7440-66-6 C00038 KEGG - C00038 ZN+2 thr-L L-Threonine C4H9NO3 0 72-19-5 C00188 KEGG - C00188 Neutral MF = C4H9NO3 SMP CHS Changed according to Genomatica JLR THR sertrna L-Seryl-tRNA(Ser) C3H6NO2R 1 C02553 KEGG - C02553 SMP adjusted for Genomatica's change to aa - NCD |Charged-SER-tRNAs| eig3p D-erythro-1-(Imidazol-4-yl)glycerol 3-phosphate C6H9N2O6P -2 C04666 KEGG - C04666 Neutral MF = C6H11N2O6P SMP CHS Checked N-groups JLR D-ERYTHRO-IMIDAZOLE-GLYCEROL-P anhm 1,6-anhydrous-N-Acetylmuramate C11H16NO7 -1 AMF CPD0-882 hack CPD0-882 dctp dCTP C9H12N3O13P3 -4 2056-98-6 C00458 KEGG - C00458 Neutral MF = C9H16N3O13P3 SMP CHS DCTP hxcoa Hexanoyl-CoA C27H42N7O17P3S -4 C05270 KEGG - C05270 Neutral MF = C27H46N7O18P3S SMP metacyc HEXANOYL-COA HEXANOYL-COA sheme Siroheme C42H36FeN4O16 -8 C00748 KEGG - C00748 Neutral MF = C42H46FeN4O16 Chemfinder formula is incorrect SMP CHS Checked N-groups, removed H from two N's in ring, JLR SIROHEME 4ahmmp 4-Amino-5-hydroxymethyl-2-methylpyrimidine C6H9N3O 0 73-67-6 C01279 KEGG - C01279 Neutral SMP CHS Checked N-groups JLR HMP adn Adenosine C10H13N5O4 0 58-61-7 C00212 KEGG - C00212 Neutral Compound SMP CHS Checked N-groups JLR ADENOSINE nad Nicotinamide adenine dinucleotide C21H26N7O14P2 -1 53-84-9 C00003 KEGG - C00003 Neutral MF = C21H28N7O14P2 (Charge +1) SMP CHS Checked N-groups JLR (agrees with ACD software) NAD 2pg D-Glycerate 2-phosphate C3H4O7P -3 C00631 KEGG - C00631 Neutral MF = C3H7O7P SMP CHS 2-PG trnaasn tRNA(Asn) R 0 C01637 KEGG - C01637 SMP |ASN-tRNAs| fe2 Fe2+ Fe 2 None C00023 KEGG - C00023 Neutral Compound SMP CHS FE+2 uaccg UDP-N-acetyl-3-O-(1-carboxyvinyl)-D-glucosamine C20H26N3O19P2 -3 C04631 KEGG - C04631 Neutral MF = C20H29N3O19P2 SMP CHS Checked N-groups JLR UDP-ACETYL-CARBOXYVINYL-GLUCOSAMINE acorn N2-Acetyl-L-ornithine C7H14N2O3 0 None C00437 KEGG - C00437 Neutral MF = C7H14N2O3 SMP CHS Changed according to Genomatica JLR N-ALPHA-ACETYLORNITHINE gtp GTP C10H12N5O14P3 -4 86-01-1 C00044 KEGG - C00044 Neutral MF = C10H16N5O14P3 SMP CHS GTP glc-D D-Glucose C6H12O6 0 50-99-7 C00031 KEGG - C00031 Deleted KEGG - C00267 (alpha-D-Glucose) Deleted KEGG - C00221 (beta-D-Glucose) L-glucose is abbreviated as glc-L SMP CHS GLC fprica 5-Formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide C10H13N4O9P -2 C04734 KEGG - C04734 Neutral MF = C10H15N4O9P SMP Checked N-groups JLR PHOSPHORIBOSYL-FORMAMIDO-CARBOXAMIDE synonym PHOSPHORIBOSYL-FORMAMIDO-CARBOXAMIDE udpglcur UDP-D-glucuronate C15H19N2O18P2 -3 C00167 KEGG - C00167 Neutral-C15H22N2O18P2 JLR Checked N-groups JLR UDP-GLUCURONATE 4mop 4-Methyl-2-oxopentanoate C6H9O3 -1 C00233 KEGG - C00233 Neutral MF = C6H10O3 SMP CHS 2K-4CH3-PENTANOATE val-L L-Valine C5H11NO2 0 72-18-4 C00183 KEGG - C00183 Neutral MF = C5H11NO2 SMP CHS Changed according to Genomatica JLR VAL suc6p Sucrose 6-phosphate C12H21O14P -2 C02591 KEGG - C02591 Neutral MF = C12H23O14P SMP CHS synmeta SUCROSE-6P SUCROSE-6P gagicolipa galactosyl-glucosyl-inner core oligosaccharide lipid A C157H271N2O84P4 -11 AMF other structure is unclear 3c4mop 3-Carboxy-4-methyl-2-oxopentanoate C7H8O5 -2 C04236 KEGG - C04236 Neutral MF = C7H10O5 SMP unknown sucsal Succinic semialdehyde C4H5O3 -1 692-29-5 C00232 KEGG - C00232 Neutral MF = C4H6O3 SMP CHS SUCC-S-ALD dudp dUDP C9H11N2O11P2 -3 C01346 KEGG - C01346 Neutral MF = C9H14N2O11P2 SMP CHS DUDP fldox flavodoxin (oxidized) X 0 121-69-7 C02869 KEGG - C02869 OX-FLAVODOXIN class OX-FLAVODOXIN pa_EC phosphatidate (E.coli) C1836H3398O400P50 -100 C00416 tv org: Hpylori, Ecoli phosphatidate (50x scaled up) with 2 ave fatty acids JLR- needs to be -100 charge L-PHOSPHATIDATE class L-PHOSPHATIDATE fatty o2- Superoxide anion O2 -1 C00704 KEGG - C00704 JLR SUPER-OXIDE synonym SUPER-OXIDE histd L-Histidinol C6H12N3O 1 None C00860 KEGG - C00860 Neutral Compound SMP CHS Changed according to Genomatica JLR HISTIDINOL 3ohcoa 3-Oxohexanoyl-CoA C27H40N7O18P3S -4 5096-70-8 C05269 KEGG - C05269 Neutral MF = C27H44N7O18P3S SMP synmeta K-HEXANOYL-COA K-HEXANOYL-COA pmcoa Pimeloyl-CoA C28H41N7O19P3S -5 C01063 KEGG - C01063 Neutral MF = C28H46N7O19P3S SMP CHS 6-CARBOXYHEXANOYL-COA cdpea CDPethanolamine C11H19N4O11P2 -1 C00570 KEGG - C00570 Neutral MF = C11H20N4O11P2 SMP CHS Checked N-groups JLR metacyc CDP-ETHANOLAMINE CDP-ETHANOLAMINE trnamet tRNA(Met) R 0 C01647 KEGG - C01647 SMP |MET-tRNAs| ser-D D-Serine C3H7NO3 0 312-84-5 C00740 KEGG - C00740 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR D-SERINE pppg9 Protoporphyrinogen IX C34H38N4O4 -2 C01079 KEGG - C01079 Neutral MF = C34H40N4O4 SMP Checked N-groups JLR PROTOPORPHYRINOGEN fmnh2 Reduced FMN C17H21N4O9P -2 67-63-0 KEGG - C01847 Neutral-C17H23N4O9P JLR FMNH2 synonym FMNH2 mmcoa-R (R)-Methylmalonyl-CoA C25H35N7O19P3S -5 C01213 KEGG - C01213 Neutral MF = C25H40N7O19P3S SMP Checked N-groups JLR METHYL-MALONYL-COA tsul Thiosulfate O3S2 -2 C00320 KEGG - C00320 Neutral MF = H2O3S2 SMP S2O3 ethso3 ethanesulfonate C2H5O3S -1 AMF unknown 3oocoa 3-Oxooctanoyl-CoA C29H44N7O18P3S -4 C05267 KEGG - C05267 Neutral MF = C29H48N7O18P3S SMP fatty malttr Maltotriose C18H32O16 0 1109-28-0 C01835 KEGG - C01835 JLR MALTOTRIOSE alaala D-Alanyl-D-alanine C6H12N2O3 0 923-16-0 C00993 KEGG - C00993 Neutral MF = C6H12N2O3 SMP CHS Changed according to Genomatica JLR D-ALA-D-ALA 4adcho 4-amino-4-deoxychorismate C10H10NO5 -1 C11355 KEGG - C11355 MM Neutral MF = C10H11NO5 SMP Note: NH pg 667 has metab drawn incorrectly should be carboxylic not methyl group (pka of N group around 9,using ACD software) Checked N-groups JLR 4-AMINO-4-DEOXYCHORISMATE cyst-L L-Cystathionine C7H14N2O4S 0 56-88-2 C02291 KEGG - C02291 Neutral MF = C7H14N2O4S SMP CHS Changed according to Genomatica JLR L-CYSTATHIONINE 3htdcoa (S)-3-Hydroxytetradecanoyl-CoA C35H58N7O18P3S -4 C05260 KEGG - C05260 Neutral MF = C35H62N7O18P3S SMP fatty nmn NMN C11H14N2O8P -1 1094-61-7 C00455 KEGG - C00455 Correct MF = C11H16N2O8P KEGG MF = C11H15N2O8P with charge +1 SMP Checked N-groups JLR NICOTINAMIDE_NUCLEOTIDE datp dATP C10H12N5O12P3 -4 1927-31-7 C00131 KEGG - C00131 Neutral MF = C10H16N5O12P3 SMP CHS DATP 3hddcoa (S)-3-Hydroxydodecanoyl-CoA C33H54N7O18P3S -4 C05262 KEGG - C05262 Neutral MF = C33H58N7O18P3S SMP fatty ser-L L-Serine C3H7NO3 0 56-45-1 C00065 KEGG - C00065 Neutral MF = C3H7NO3 SMP CHS Changed according to Genomatica JLR SER trnathr tRNA(Thr) R 0 C01651 KEGG - C01651 SMP |THR-tRNAs| quln Quinolinate C7H3NO4 -2 89-00-9 C03722 KEGG - C03722 Neutral MF = C7H5NO4 SMP CHS Checked N-groups JLR QUINOLINATE dhcinnm 2,3-dihydroxicinnamic acid C9H7O4 -1 No Kegg entry see figure 1 PMID: 9603882 Neutral-C9H8O4 JLR other unknown but close, but spelling error etoh Ethanol C2H6O 0 64-17-5 C00469 KEGG - C00469 Neutral Compound SMP CHS ETOH glutrna L-Glutamyl-tRNA(Glu) C5H7NO3R 0 None C02987 KEGG - C02987 X = (C5H8O6PR)n Represent as neutral SMP; MF changed on May 7, 2002 CHS Changed according to Genomatica JLR |Charged-GLT-tRNAs| cpppg3 Coproporphyrinogen III C36H40N4O8 -4 2624-63-7 C03263 KEGG - C03263 Deleted C02667 (Coproporphyrinogen) Neutral MF = C36H44N4O8 SMP CHS Checked N-groups JLR COPROPORPHYRINOGEN_III tma trimethylamine C3H10N 1 75-50-3 C00565 KEGG - C00565 pKa=9.8 Checked N-groups JLR TRIMETHYLAMINE xylu-L L-Xylulose C5H10O5 0 527-50-4 C00312 KEGG - C00312 Neutral Compound SMP CHS L-XYLULOSE dgtp dGTP C10H12N5O13P3 -4 2564-35-4 C00286 KEGG - C00286 Neutral MF = C10H16N5O13P3 SMP CHS DGTP 2p4c2me 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H22N3O17P3 -4 No KEGG Entry Neutral MF = C14H26N3O17P3 SMP Checked N-groups JLR 2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET LalaDgluMdap L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate C15H25N4O8 -1 AMF unknown sucbz o-Succinylbenzoate C11H8O5 -2 C02730 KEGG - C02730 Neutral MF = C11H10O5 SMP CHS O-SUCCINYLBENZOATE pydx Pyridoxal C8H9NO3 0 66-72-8 C00250 KEGG - C00250 Neutral Compound SMP CHS Checked N-groups JLR PYRIDOXAL all6p D-Allose 6-phosphate C6H11O9P -2 147-94-4 C02962 KEGG - C02962 D-ALLOSE-6-PHOSPHATE 2me4p 2-C-methyl-D-erythritol 4-phosphate C5H11O7P -2 C11434 KEGG C11434 Neutral MF = C5H13O7P SMP 2-C-METHYL-D-ERYTHRITOL-4-PHOSPHATE aps Adenosine 5'-phosphosulfate C10H12N5O10PS -2 C00224 KEGG - C00224 Neutral MF = C10H14N5O10PS SMP CHS Checked N-groups JLR APS synonym APS cyan Hydrogen cyanide CHN 0 57-12-5 C01326 KEGG - C01326 JLR pKa of H attached to C is 9.3 Checked N-groups JLR HCN btal Butanal C4H8O 0 123-72-8 C01412 KEGG - C01412 Neutral Compound SMP BUTANAL acyllpp_EC acyl-lipoprotein (E. coli) XC843H1524O50 0 AMF generic acyllipoprotein unknown histrna L-Histidyl-tRNA(His) C6H8N3OR 1 C02988 KEGG - C02988 SMP adjusted for Genomatica's change to aa - NCD |Charged-HIS-tRNAs| nadh Nicotinamide adenine dinucleotide - reduced C21H27N7O14P2 -2 53-84-9 C00004 KEGG - C00004 Neutral MF = C21H29N7O14P2 SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR NADH fruur D-Fructuronate C6H9O7 -1 669-90-9 C00905 KEGG - C00905 Neutral MF = C6H10O7 SMP CHS FRUCTURONATE uaagmda Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala C95H152N8O28P2 -4 C05898 KEGG - C05898 Neutral MF = C95H156N8O28P2 SMP Changed according to Genomatica JLR C6 synonym C6 prlp 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide C15H21N5O15P2 -4 C04916 KEGG - C04916 Neutral MF = C15H25N5O15P2 SMP CHS Checked N-groups, agrees with ACD software, JLR PHOSPHORIBULOSYL-FORMIMINO-AICAR-P synonym PHOSPHORIBULOSYL-FORMIMINO-AICAR-P 3c3hmp 3-Carboxy-3-hydroxy-4-methylpentanoate C7H10O5 -2 C02504 KEGG - C02504 Neutral MF = C7H12O5 SMP CHS 3-CARBOXY-3-HYDROXY-ISOCAPROATE ditp dITP C10H11N4O13P3 -4 66701-25-5 C01345 KEGG - C01345 Neutral MF = C10H15N4O13P3 SMP CHS DITP nadp Nicotinamide adenine dinucleotide phosphate C21H25N7O17P3 -3 53-59-8 C00006 KEGG - C00006 Original KEGG MF = C21H29N7O17P3 (+1) SMP CHS Checked N-groups JLR NADP bglycogen branching glycogen C6H10O5 0 AMF unknown sl26da N-Succinyl-LL-2,6-diaminoheptanedioate C11H16N2O7 -2 C04421 KEGG - C04421 Neutral MF = C11H18N2O7 SMP CHS Changed according to Genomatica JLR |n-succinylll-2,6-diaminopimelate| 3oodcoa 3-Oxooctadecanoyl-CoA C39H64N7O18P3S -4 SMP (2/7/03) fatty 14glucan 1,4-alpha-D-glucan C36H62O31 0 AMF made up formula to match malthx, the highest carbon maltodextrin that is transported in the model |1-4-alpha-D-Glucan| protrna L-Prolyl-tRNA(Pro) C5H8NOR 1 C02702 KEGG - C02702 SMP adjusted for Genomatica's change to aa - NCD |Charged-PRO-tRNAs| 3amp 3'-AMP C10H12N5O7P -2 84-21-9 C01367 MKA AMF metacyc CPD-3706 CPD-3706 murein5p3p two linked disacharide pentapeptide and tripeptide murein units (uncrosslinked, middle of chain) C74H114N14O40 -4 AMF PMID: 9751644 has a good figure other structure is unclear lac-D D-Lactate C3H5O3 -1 10326-41-7 C00256 KEGG - C00256 Neutral MF = C3H6O3 SMP CHS D-LACTATE gsn Guanosine C10H13N5O5 0 118-00-3 C00387 KEGG - C00387 Neutral Compound SMP CHS Checked N-groups JLR GUANOSINE uppg3 Uroporphyrinogen III C40H36N4O16 -8 1976-85-8 C01051 KEGG - C01051 Neutral MF = C40H44N4O16 SMP CHS Checked N-groups JLR UROPORPHYRINOGEN-III man1p D-Mannose 1-phosphate C6H11O9P -2 C03812 KEGG - C03812 Neutral MF = C6H13O9P SMP CHS MANNOSE-1P pro-L L-Proline C5H9NO2 0 147-85-3 C00148 KEGG - C00148 Neutral MF = C5H9NO2 SMP CHS Changed according to Genomatica JLR PRO micit methylisocitrate C7H7O7 -3 20298-95-7 C04593 KEGG - C04593 Neutral-C7H10O7 JLR CPD-618 man6p D-Mannose 6-phosphate C6H11O9P -2 None C00275 KEGG - C00275 Neutral MF = C6H13O9P SMP CHS MANNOSE-6P u3aga UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine C31H51N3O19P2 -2 C04738 KEGG - C04738 Neutral MF = C31H53N3O19P2 SMP CHS Checked N-groups JLR UDP-OHMYR-ACETYLGLUCOSAMINE acglc-D 6-Acetyl-D-glucose C8H14O7 0 107-85-7 C02655 KEGG - C02655 AMF metacyc CPD-522 CPD-522 glyc-R (R)-Glycerate C3H5O4 -1 473-81-4 C00258 KEGG - C00258 Neutral MF = C3H6O4 SMP CHS GLYCERATE 3gmp 3'-GMP C10H12N5O8P -2 497-76-7 C06193 KEGG - C06193 AMF metacyc CPD-3708 CPD-3708 trnaphe tRNA(Phe) R 0 C01648 KEGG - C01648 SMP |PHE-tRNAs| acac Acetoacetate C4H5O3 -1 541-50-4 C00164 KEGG - C00164 NCD 3-KETOBUTYRATE idon-L L-Idonate C6H11O7 -1 1114-17-6 C00770 KEGG - C00770 Neutral-C6H12O7 JLR L-IDONATE dutp dUTP C9H11N2O14P3 -4 C00460 KEGG - C00460 Neutral MF = C9H15N2O14P3 SMP CHS DUTP fcl-L L-fuculose C6H12O5 0 C01721 KEGG - C01721 Neutral Compound SMP CHS NOTE Kegg Picture is incorrect, C=O should be on C2 not C1 (should be five member ring) JLR L-FUCULOSE feenter Fe-enterobactin C30H27FeN3O15 3 90-02-8 C06230 KEGG - C06230 FERRIC-ENTEROBACTIN-COMPLEX hack FERRIC-ENTEROBACTIN-COMPLEX dtbt Dethiobiotin C10H17N2O3 -1 C01909 KEGG - C01909 Neutral MF = C10H18N2O3 SMP CHS Checked N-groups JLR DETHIOBIOTIN unagamuf Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose C79H126N3O22P2 -3 No Kegg entry Neutral-C79H129N3O22P2 JLR Checked N-groups JLR C55-PP-GLCNAC-MANNACA-FUC4NAC synonym C55-PP-GLCNAC-MANNACA-FUC4NAC arbtn-fe3 Aerobactin C22H33FeN4O13 0 61-33-6 C05554 KEGG - C05554 AMF is a siderophore - Fe-scavenging molecule. requires secretion and re-uptake pathways other not in ecocyc, because on plasmid. could be under |Ferric-Hydroxamate-Complexes| gmhep17bp D-Glycero-D-manno-heptose 1,7-bisphosphate C7H12O13P2 -4 C11472 Kegg C11472 Neutral- C7H16O13P2 JLR D-BETA-D-HEPTOSE-17-DIPHOSPHATE hack D-BETA-D-HEPTOSE-17-DIPHOSPHATE lipidA 2,3,2'3'-Tetrakis(beta-hydroxymyristoyl)-D-glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate C68H126N2O23P2 -4 None Neutral MF = C68H130N2O23P2 SMP CHS JLR- similar to C04919 but phosphate is on a different oxygen(see NH pg 1043). Changed to -4 charge LIPID-IV-A synonym LIPID-IV-A h H+ H 1 12408-02-5 C00080 KEGG - C00080 PROTON 3cmp 3'-cmp C9H12N3O8P -2 C05822 MKA AMF synmeta CPD-3711 CPD-3711 5aizc 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate C9H11N3O9P -3 C04751 KEGG - C04751 Neutral MF = C9H14N3O9P SMP CHS Checked N-groups JLR PHOSPHORIBOSYL-CARBOXY-AMINOIMIDAZOLE lpp lipoprotein X 0 6244-92-4 C01834 KEGG - C01834 AMF generic lipoprotein for acyl transfering unknown betald Betaine aldehyde C5H12NO 1 C00576 KEGG - C00576 JLR Checked N-groups JLR BETAINE_ALDEHYDE iletrna L-Isoleucyl-tRNA(Ile) C6H12NOR 1 C03127 KEGG - C03127 SMP adjusted for Genomatica's change to aa - NCD |Charged-ILE-tRNAs| btcoa Butanoyl-CoA C25H38N7O17P3S -4 C00136 KEGG - C00136 Neutral MF = C25H42N7O17P3S SMP metacyc BUTYRYL-COA BUTYRYL-COA ap5a P1,P5-Bis(5'-adenosyl) pentaphosphate C20H24N10O22P5 -5 4637-56-3 C04058 KEGG - C04058 Neutral-C20H29N10O22P5 JLR unknown succoa Succinyl-CoA C25H35N7O19P3S -5 604-98-8 C00091 KEGG - C00091 Neutral MF = C25H40N7O19P3S SMP CHS checked N groups - NCD SUC-COA g3p Glyceraldehyde 3-phosphate C3H5O6P -2 142-10-9 C00661 KEGG - C00661 Neutral MF = C3H7O6P SMP CHS JLR (deleted duplicate entry, Dglyad3p. g3p should be KEGG- C00118) GAP 2dh3dgal6p 2-Dehydro-3-deoxy-D-galactonate 6-phosphate C6H8O9P -3 C01286 KEGG - C01286 Neutral-C6H11O9P JLR DEHYDRO-DEOXY-GALACTONATE-PHOSPHATE succ Succinate C4H4O4 -2 110-15-6 C00042 KEGG - C00042 Neutral MF = C4H6O4 SMP CHS SUC tmao Trimethylamine N-oxide C3H9NO 0 1184-78-7 C01104 KEGG - C01104 Zwitter ion, pKa =4.65 Checked N-groups JLR TRIMENTHLAMINE-N-O valtrna L-Valyl-tRNA(Val) C5H10NOR 1 C02554 KEGG - C02554 SMP adjusted for Genomatica's change to aa - NCD |Charged-VAL-tRNAs| 5aprbu 5-Amino-6-(5'-phosphoribitylamino)uracil C9H15N4O9P -2 C04454 KEGG - C04454 Neutral MF = C9H17N4O9P SMP Checked N-groups NCD, JLR CPD-1086 ru5p-D D-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C00199 KEGG - C00199 Neutral MF = C5H11O8P Error in Chemfinder molecular formula SMP CHS RIBULOSE-5P cinnm trans-Cinnamate C9H7O2 -1 140-10-3 C00423 KEGG - C00423 Neutral-C9H8O2 JLR metacyc CPD-674 CPD-674 thdp 2,3,4,5-Tetrahydrodipicolinate C7H7NO4 -2 52-52-8 C03972 KEGG - C03972 Neutral MF = C7H9NO4 SMP CHS Checked N-groups JLR DELTA{1}-PIPERIDEINE-2-6-DICARBOXYLATE synonym DELTA{1}-PIPERIDEINE-2-6-DICARBOXYLATE nicrnt Nicotinate D-ribonucleotide C11H12NO9P -2 C01185 KEGG - C01185 Neutral MF = C11H15NO9P SMP Checked N-groups JLR NICOTINATE_NUCLEOTIDE sucr Sucrose C12H22O11 0 57-50-1 C00089 KEGG - C00089 SUCROSE udpgalfur UDP-D-galacto-1,4-furanose C15H22N2O17P2 -2 638-23-3 C03733 KEGG - C03733 Neutral-C15H24N2O17P2 JLR Checked N-groups JLR UDP-D-GALACTO-14-FURANOSE phe-L L-Phenylalanine C9H11NO2 0 63-91-2 C00079 KEGG - C00079 Neutral MF = C9H11NO2 SMP CHS Changed according to Genomatica JLR PHE xan Xanthine C5H4N4O2 0 69-89-6 C00385 KEGG - C00385 Neutral Compound SMP CHS Checked N-groups JLR XANTHINE db4p 3,4-dihydroxy-2-butanone 4-phosphate C4H7O6P -2 No KEGG Entry Neutral MF = C4H9O6P SMP DIHYDROXY-BUTANONE-P adocbip Adenosyl cobinamide phosphate C58H83CoN16O14P -1 7625-23-2 C06509 KEGG - C06509 Kegg shows C58H88CoN16O14P (removed 3 H's from the ring and 2 from the phosphate group) JLR before charge was +1 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C58H84CoN16O14P charge +4 (by JLR) ADENOSYLCOBINAMIDE-P ichor Isochorismate C10H8O6 -2 C00885 KEGG - C00885 Neutral MF = C10H10O6 SMP CHS ISOCHORISMATE gggagicolipa glucosyl-glucosyl-galactosyl-glucosyl-inner core oligosaccharide lipid A C169H291N2O94P4 -11 AMF other structure is unclear glcur D-Glucuronate C6H9O7 -1 12/03/6556 C00191 KEGG - C00191 Neutral MF = C6H10O7 SMP CHS GLUCURONATE galt1p Galactitol 1-phosphate C6H13O9P -2 C06311 KEGG- C06311 Neutral MF = C6H15O9P JLR GALACTITOL-1-PHOSPHATE pap Adenosine 3',5'-bisphosphate C10H11N5O10P2 -4 1053-73-2 C00054 KEGG - C00054 Neutral MF = C10H15N5O10P2 SMP CHS PAP acanth N-Acetylanthranilate C9H8NO3 -1 89-52-1 C06332 KEGG - C06332 AMF synmeta N-ACETYLANTHRANILATE N-ACETYLANTHRANILATE hdd2coa trans-Hexadec-2-enoyl-CoA C37H60N7O17P3S -4 C05272 KEGG - C05272 Neutral MF = C37H64N7O17P3S SMP 1 degree of unsaturation fatty 2shchc 2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate C11H10O6 -2 C05817 KEGG - C05817 Neutral MF = C11H12O6 SMP CHS SUCCINYL-OH-CYCLOHEXADIENE-COOH xtp XTP C10H11N4O15P3 -4 C00700 KEGG - C00700 IT XTP hlipa heptosyl-kdo2-lipidA C117H208N2O45P2 -6 AMF unknown LPS biosynthesis murein4p3p two linked disacharide tetrapeptide and tripeptide murein units (uncrosslinked, middle of chain) C71H109N13O39 -4 AMF PMID: 9751644 has a good figure other structure is unclear aragund O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C71H115N1O17P2 -2 AMF unknown chol Choline C5H14NO 1 62-49-7 C00114 KEGG - C00114 SMP Checked N-groups JLR CHOLINE g1p D-Glucose 1-phosphate C6H11O9P -2 59-56-3 C00103 KEGG - C00103 Neutral MF = C6H13O9P SMP CHS GLC-1-P indole Indole C8H7N 0 120-72-9 C00463 KEGG - C00463 Checked N-groups JLR INDOLE 23dhbzs 2,3-dihydroxybenzoylserine C10H10NO6 -1 AMF 23-DIHYDROXYBENZOYLSERINE-MULTIMERS s7p Sedoheptulose 7-phosphate C7H13O10P -2 None C00281 KEGG - C00281 Neutral MF = C7H15O10P SMP CHS D-SEDOHEPTULOSE-7-P chor chorismate C10H8O6 -2 55508-12-8 C00251 KEGG - C00251 Neutral MF = C10H10O6 SMP CHS CHORISMATE 5apru 5-Amino-6-(5'-phosphoribosylamino)uracil C9H13N4O9P -2 C01268 KEGG - C01268 Neutral MF = C9H15N4O9P SMP Checked N-groups JLR, NCD CPD-602 3hdcoa (S)-3-Hydroxydecanoyl-CoA C31H50N7O18P3S -4 C05264 KEGG - C05264 Neutral MF = C31H54N7O18P3S SMP fatty malthp Maltoheptaose C42H72O36 0 Not in Kegg JLR unknown 23dappa 2,3-diaminopropionate C3H9N2O2 1 C06393 MKA L- and D- forms not distinguished here CPD-1782 man6pglyc 2(alpha-D-Mannosyl-6-phosphate)-D-glycerate C9H14O12P -3 JLR- not in Kegg The same as manglyc but with a phosphate group on the 6th carbon of the mannose moiety unknown we have the phosphate on the glycerate group after PTS transport 2mahmp 2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphate C6H8N3O7P2 -3 745-65-3 C04752 KEGG - C04752 Neutral MF = C6H11N3O7P2 SMP Checked N-groups JLR AMINO-HYDROXYMETHYL-METHYLPYRIMIDINE-PP but Butyrate (n-C4:0) C4H7O2 -1 107-92-6 C00246 KEGG - C00246 Neutral MF = C4H8O2 SMP changed compound class from peptides - NCD BUTYRIC_ACID synonym BUTYRIC_ACID 2ohph 2-Octaprenyl-6-hydroxyphenol C46H70O2 0 C05811 KEGG - C05811 SMP CHS 2-OCTAPRENYL-6-HYDROXYPHENOL arg-L L-Arginine C6H15N4O2 1 74-79-3 C00062 KEGG - C00062 Neutral MF = C6H14N4O2 SMP CHS Changed according to Genomatica JLR ARG all-D D-Allose C6H12O6 0 2595-97-3 C01487 KEGG - C01487 JLR ALLOSE crn-D D-Carnitine C7H15NO3 0 C00487 KEGG - C00487 AMF D-CARNITINE fe3 Fe3+ Fe 3 None Neutral Compound SMP CHS FE+3 na1 Sodium Na 1 7440-23-5 C01330 KEGG - C01330 SMP CHS NA+ 26dap-M meso-2,6-Diaminoheptanedioate C7H14N2O4 0 None C00680 KEGG - C00680 Neutral MF = C7H14N2O4 SMP CHS Changed according to Genomatica JLR MESO-DIAMINOPIMELATE argsuc N(omega)-(L-Arginino)succinate C10H17N4O6 -1 None C03406 KEGG - C03406 Neutral MF = C10H18N4O6 SMP CHS Changed according to Genomatica JLR pKa = 9.58 nitrogen group L-ARGININO-SUCCINATE hack L-ARGININO-SUCCINATE alltn Allantoin C4H6N4O3 0 97-59-6 C01551 KEGG - C01551 Neutral Compound SMP CHS Checked N-groups JLR ALLANTOIN acmum6p N-acetylmuramate 6-phosphate C11H17NO11P -3 Not in KEGG see PMID 15060041 JLR AMF CPD0-881 occoa Octanoyl-CoA (n-C8:0CoA) C29H46N7O17P3S -4 C01944 KEGG - C01944 Neutral MF = C29H50N7O17P3S SMP metacyc CPD-196 CPD-196 acACP Acetyl-ACP C13H23N2O8PRS -1 tv Neidhardt JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) ACETYL-ACP ddca Dodecanoate (n-C12:0) C12H23O2 -1 143-07-7 C02679 KEGG - C02679 Neutral MF = C12H24O2 SMP saturated fatty acid, 12 carbons changed compound class from peptides to fatty acid - NCD synmeta DODECANOATE DODECANOATE malt6p Maltose 6'-phosphate C12H21O14P -2 None C02995 KEGG - C02995 Neutral MF = C12H23O14P SMP CHS metacyc CPD-1244 CPD-1244 12ppd-S (S)-Propane-1,2-diol C3H8O2 0 4254-14-2 C02917 KEGG - C02917 SMP CHS other is this the same as |PROPANE-1,2-DIOL| ??? selnp Selenophosphate H2O3PSe -1 16561-29-8 C05172 KEGG - C05172 Neutral H3O3PSe JLR SEPO3 thym Thymine C5H6N2O2 0 65-71-4 C00178 KEGG - C00178 Neutral Compound SMP CHS THYMINE cu Cu+ Cu 1 C00070 CU+ 2pglyc 2-Phosphoglycolate C2H2O6P -3 C00988 KEGG - C00988 Neutral MF = C2H5O6P SMP CHS CPD-67 murein4px4p two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain) C74H112N14O39 -4 AMF PMID: 9751644 has a good figure unknown g3pc sn-Glycero-3-phosphocholine C8H20NO6P 0 C00670 KEGG - C00670 Normally has a + charge (C8H21NO6P) JLR L-1-GLYCERO-PHOSPHORYLCHOLINE g3pe sn-Glycero-3-phosphoethanolamine C5H14NO6P 0 C01233 KEGG - C01233 Neutral-C5H14NO6P JLR Checked N JLR synmeta L-1-GLYCEROPHOSPHORYLETHANOL-AMINE L-1-GLYCEROPHOSPHORYLETHANOL-AMINE g3pg Glycerophosphoglycerol C6H14O8P -1 11034-93-8 C03274 KEGG - C03274 Neutral-C6H15O8P JLR unknown pydxn Pyridoxine C8H11NO3 0 65-23-6 C00314 KEGG - C00314 Neutral Compound SMP CHS Checked N-groups JLR PYRIDOXINE g3pi sn-Glycero-3-phospho-1-inositol C9H18O11P -1 C01225 KEGG - C01225 Neutral-C9H19O11P JLR metacyc CPD-541 CPD-541 fgam N2-Formyl-N1-(5-phospho-D-ribosyl)glycinamide C8H13N2O9P -2 C04376 KEGG - C04376 Neutral MF = C8H15N2O9P SMP CHS Checked N-groups JLR 5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE synonym 5-P-RIBOSYL-N-FORMYLGLYCINEAMIDE 2obut 2-Oxobutanoate C4H5O3 -1 600-18-0 C00109 KEGG - C00109 Neutral MF = C4H6O3 SMP CHS NCD 2-OXOBUTANOATE 2cpr5p 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate C12H13NO9P -3 C01302 KEGG - C01302 Neutral MF = C12H16NO9P SMP Checked N-groups JLR CARBOXYPHENYLAMINO-DEOXYRIBULOSE-P malt Maltose C12H22O11 0 69-79-4 C00208 KEGG - C00208 Neutral Compound SMP CHS MALTOSE murein5px3p two disacharide linked murein units, pentapeptide corsslinked tripeptide (A2pm->A2pm) (middle of chain) C74H112N14O39 -4 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslink is between A2pm->A2pm other murein recycling stuff met-D D-Methionine C5H10NO2S 0 348-67-4 C00855 KEGG - C00855 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR CPD-218 minohp myo-Inositol hexakisphosphate C6H6O24P6 -12 C01204 KEGG - C01204 JLR MI-HEXAKISPHOSPHATE 3odcoa 3-Oxodecanoyl-CoA C31H48N7O18P3S -4 C05265 KEGG - C05265 Neutral MF = C31H52N7O18P3S SMP fatty ahdt 2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate C9H12N5O13P3 -4 C04895 KEGG - C04895 Neutral MF = C9H16N5O13P3 SMP Checked N-groups, ACD software indicates a N is protonated, JLR Pipeline Pilot indicates that this N is not protonated. JLR DIHYDRONEOPTERIN-P3 rib-D D-Ribose C5H10O5 0 50-69-1 C00121 KEGG - C00121 Neutral Compound SMP CHS RIBOSE g3ps Glycerophosphoserine C6H13NO8P -1 No Kegg entry Neutral-C6H14NO8P JLR Checked N JLR unknown metsox-S-L L-Methionine-S-Sulfoxide C5H11NO3S 0 C02989 KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR Kegg C02989 L-METHIONINE_SULFOXIDE metsox-R-L L-methionine-R-sulfoxide C5H11NO3S 0 MKA KEGG - C02989 Neutral MF = C5H11NO3S SMP Checked N-groups, JLR other metacyc has S-version kdo2lipid4 KDO(2)-lipid IV(A) C84H148N2O37P2 -6 C06025 KEGG C06025 Neutral C84H154N2O37P2 JLR - NH page 1043 KDO2-LIPID-IVA pep Phosphoenolpyruvate C3H2O6P -3 138-08-9 C00074 KEGG - C00074 Neutral MF = C3H5O6P SMP CHS PHOSPHO-ENOL-PYRUVATE glycogen glycogen C6H10O5 0 C00182 KEGG- C00182 |6-alpha-D--1-4-alpha-D-Glucano--Glucan| cdp CDP C9H12N3O11P2 -3 63-38-7 C00112 KEGG - C00112 Neutral MF = C9H15N3O11P2 SMP CHS CDP q8 Ubiquinone-8 C49H74O4 0 1339-63-5 C00399 KEGG C00399 Formula- C14H18O4(C5H8)n , where n=7 for q8 JLR UBIQUINONE-8 dca Decanoate (n-C10:0) C10H19O2 -1 334-48-5 C01571 KEGG - C01571 Neutral MF = C10H20O2 SMP saturated fatty acid, 10 carbons changed compound class from peptide to fatty acid - NCD synmeta CPD-3617 CPD-3617 mi1p-D 1D-myo-Inositol 1-phosphate C6H11O9P -2 C01177 Kegg C01177 Neutral-C6H13O9P JLR D-MYO-INOSITOL-1-MONOPHOSPHATE synonym D-MYO-INOSITOL-1-MONOPHOSPHATE alltt Allantoate C4H7N4O4 -1 99-16-1 C00499 KEGG - C00499 Neutral MF = C4H8N4O4 SMP CHS Checked N-groups JLR ALLANTOATE tcynt Thiocyanate CNS -1 463-56-9 C01755 KEGG - C01755 Neutral-CHNS JLR Checked N-groups JLR HSCN ag silver Ag 1 7440-22-4 C06710 KEGG - C06710 CPD-1485 met-L L-Methionine C5H11NO2S 0 63-68-3 C00073 KEGG - C00073 Neutral MF = C5H11NO2S SMP CHS Changed according to Genomatica JLR MET hx2coa trans-Hex-2-enoyl-CoA C27H40N7O17P3S -4 C05271 KEGG - C05271 Neutral MF = C27H44N7O17P3S SMP fatty aacoa Acetoacetyl-CoA C25H36N7O18P3S -4 1420-36-6 C00332 KEGG - C00332 Neutral MF = C25H40N7O18P3S SMP CHS ACETOACETYL-COA 3ump 3'-UMP C9H11N2O9P -2 35170-03-7 C01368 KEGG - C01368 AMF metacyc CPD-3724 CPD-3724 orot Orotate C5H3N2O4 -1 65-86-1 C00295 KEGG - C00295 Neutral MF = C5H4N2O4 SMP CHS Checked N-groups JLR OROTATE 4abutn 4-Aminobutanal C4H10NO 1 C00555 KEGG - C00555 Neutral Compound SMP CHS Changed according to Genomatica JLR 4-AMINO-BUTYRALDEHYDE akg 2-Oxoglutarate C5H4O5 -2 328-50-7 C00026 KEGG - C00026 Neutral MF = C5H6O5 SMP CHS 2-KETOGLUTARATE dtmp dTMP C10H13N2O8P -2 365-07-1 C00364 KEGG - C00364 Neutral MF = C10H15N2O8P Thymine is normally found as a deoxyriboside SMP CHS TMP cenchddd cis-3-(3-carboxyethenyl)-3,5-cyclohexadiene-1,2-diol C9H9O4 -1 No KEGG entry see Figure 1in PMID: 9603882 Neutral-C9H10O4 JLR unknown isetac Isethionic acid C2H5O4S -1 107-36-8 C05123 KEGG - C05123 SAB charged following taurine's charge metacyc CPD-3745 CPD-3745 gtspmd Glutathionylspermidine C17H36N6O5S 2 08/06/7783 C05730 KEGG - C05730 Neutral-C17H34N6O5S JLR Checked N-groups JLR GLUTATHIONYLSPERMIDINE dtdp4addg dTDP-4-amino-4,6-dideoxy-D-glucose C16H26N3O14P2 -1 157296-99-6 C04268 KEGG - C04268 Neutral-C16H25N3O14P2 JLR Checked N-groups JLR metacyc CPD-472 CPD-472 ac Acetate C2H3O2 -1 64-19-7 C00033 KEGG - C00033 Neutral MF = C2H4O2 SMP CHS ACET 2dhp 2-Dehydropantoate C6H9O4 -1 C00966 KEGG - C00966 Neutral MF = C6H10O4 SMP CHS 2-DEHYDROPANTOATE unaga Undecaprenyl diphospho N-acetyl-glucosamine C63H103NO12P2 -2 Not in Kegg Neutral-C63H105NO12P2 JLR Checked N-groups GLCNAC-PP-LIPID synonym GLCNAC-PP-LIPID glytrna Glycyl-tRNA(Gly) C2H4NOR 1 C02412 KEGG - C02412 SMP adjusted for Genomatica's change to aa - NCD |Charged-GLY-tRNAs| udpacgal UDP-N-acetyl-D-galactosamine C17H25N3O17P2 -2 None C00203 KEGG - C00203 changed to proper charge - NCD metacyc UDP-N-ACETYL-GALACTOSAMINE UDP-N-ACETYL-GALACTOSAMINE asp-L L-Aspartate C4H6NO4 -1 56-84-8 C00049 KEGG - C00049 Neutral MF = C4H7NO4 SMP CHS Changed according to Genomatica JLR L-ASPARTATE paps 3'-Phosphoadenylyl sulfate C10H11N5O13P2S -4 482-67-7 C00053 KEGG - C00053 Neutral MF = C10H15N5O13P2S SMP Checked N-groups JLR PAPS tdeACP Tetradecenoyl-ACP (n-C14:1ACP) C25H45N2O8PRS -1 tv JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty ade Adenine C5H5N5 0 73-24-5 C00147 KEGG - C00147 Neutral Compound SMP CHS ADENINE f6p D-Fructose 6-phosphate C6H11O9P -2 643-13-0 C00085 KEGG - C00085 Neutral MF = C6H13O9P SMP CHS FRUCTOSE-6P 2ombzl 2-Octaprenyl-6-methoxy-1,4-benzoquinol C47H72O3 0 Neidhardt page 651 JLR other we use the quinone compounds in our Coenzyme Q biosynthesis pathway lipidAds Lipid A Disaccharide C68H127N2O20P -2 C04932 tv Kegg C04932 BISOHMYR-GLC mql8 Menaquinol 8 C51H74O2 0 C05819 KEGG - C05819 General Formula = C16H18O2(C5H8)n; n = 7 for mql7 SMP REDUCED-MENAQUINONE synonym REDUCED-MENAQUINONE trnasecys tRNA(SeCys) R 0 0 |Charged-SEC-tRNAs| hack |Charged-SEC-tRNAs| camp cAMP C10H11N5O6P -1 C00575 Kegg C00575 Neutral-C10H12N5O6P JLR CAMP ptrc Putrescine C4H14N2 2 110-60-1 C00134 KEGG - C00134 Neutral Compound SMP CHS Changed according to Genomatica JLR PUTRESCINE rbl-L L-Ribulose C5H10O5 0 488-84-6 C00508 KEGG - C00508 Neutral Compound SMP CHS L-RIBULOSE dtdp4d6dm dTDP-4-dehydro-6-deoxy-L-mannose C16H22N2O15P2 -2 C00688 KEGG - C00688 Neutral-C16H24N2O15P2 JLR Checked N-groups JLR DTDP-DEOH-DEOXY-MANNOSE tre6p alpha,alpha'-Trehalose 6-phosphate C12H21O14P -2 4484-88-2 C00689 KEGG - C00689 Neutral MF = C12H23O14P SMP CHS TREHALOSE-6P eca4und (enterobacterial common antigen)x3 undecaprenyl-diphosphate C151H234N12O67P2 -6 AMF fatty eca3und (enterobacterial common antigen)x3 undecaprenyl-diphosphate C127H198N9O52P2 -5 AMF other structure is unclear 23dhmp (R)-2,3-Dihydroxy-3-methylpentanoate C6H11O4 -1 C06007 KEGG - C06007 (C04104 Deleted) Neutral MF = C6H12O4 SMP CHS 1-KETO-2-METHYLVALERATE cbp Carbamoyl phosphate CH2NO5P -2 C00169 KEGG - C00169 Neutral MF = CH4NO5P SMP CHS Checked N-groups JLR CARBAMOYL-P 3psme 5-O-(1-Carboxyvinyl)-3-phosphoshikimate C10H9O10P -4 C01269 KEGG - C01269 Neutral MF = C10H13O10P SMP 3-ENOLPYRUVYL-SHIKIMATE-5P trnacys tRNA(Cys) R 0 C01639 KEGG - C01639 SMP |CYS-tRNAs| gcald Glycolaldehyde C2H4O2 0 C00266 KEGG - C00266 SMP CHS GLYCOLALDEHYDE agdpcbi Adenosine-GDP-cobinamide C68H95CoN21O21P2 -1 7625-23-2 C06510 KEGG - C06510 Kegg shows C68H100CoN21O21P2 (removed 3 H's from ring and 2 from phosphate groups) JLR before charge was +1 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C68H96CoN21O21P2 charge +4 (by JLR) ADENOSYLCOBINAMIDE-GDP synonym ADENOSYLCOBINAMIDE-GDP pphn Prephenate C10H8O6 -2 126-49-8 C00254 KEGG - C00254 Neutral MF = C10H10O6 SMP CHS PREPHENATE 23ddhb 2,3-Dihydro-2,3-dihydroxybenzoate C7H7O4 -1 C04171 KEGG - C04171 Neutral MF = C7H8O4 SMP CHS DIHYDRO-DIOH-BENZOATE fe3dcit Fe(III)dicitrate C12H10FeO14 -3 90-02-8 C06229 KEGG - C06229 AMF- not sure if any h complexed with iron or carboxyls FERRIC-CITRATE-COMPLEX synonym FERRIC-CITRATE-COMPLEX eca2und (enterobacterial common antigen)x2 undecaprenyl-diphosphate C103H162N6O37P2 -4 AMF unknown dc2coa trans-Dec-2-enoyl-CoA C31H48N7O17P3S -4 C05275 KEGG - C05275 Neutral MF = C31H52N7O17P3S SMP T2-DECENOYL-COA synonym T2-DECENOYL-COA lgt-S (R)-S-Lactoylglutathione C13H20N3O8S -1 59-85-8 C03451 KEGG - C03451 Neutral MF = C13H21N3O8S SMP CHS Changed according to Genomatica JLR S-LACTOYL-GLUTATHIONE hpyr Hydroxypyruvate C3H3O4 -1 1113-60-6 C00168 KEGG - C00168 Neutral MF = C3H4O4 SMP CHS OH-PYR dhnpt Dihydroneopterin C9H13N5O4 0 C04874 KEGG - C04874 SMP CHS Checked N-groups, ACD software indicates N should be protonated JLR Pipeline Pilot indicates this N is not charged JLR checked - AMF DIHYDRO-NEO-PTERIN 23doguln 2,3-Dioxo-L-gulonate C6H7O7 -1 583-08-4 C05409 KEGG - C05409 Neutral-C6H8O7 JLR |2,3-diketo-l-gulonate| synonym |2,3-diketo-l-gulonate| 3c2hmp 3-Carboxy-2-hydroxy-4-methylpentanoate C7H10O5 -2 C04411 KEGG - C04411 Neutral MF = C7H12O5 SMP CHS 2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE glcur1p D-Glucuronate 1-phosphate C6H8O10P -3 583-08-4 C05385 KEGG - C05385 NCD metacyc CPD-510 CPD-510 glucys gamma-L-Glutamyl-L-cysteine C8H13N2O5S -1 686-58-8 C00669 KEGG - C00669 Neutral MF = C8H14N2O5S SMP CHS Changed according to Genomatica JLR L-GAMMA-GLUTAMYLCYSTEINE dad-2 Deoxyadenosine C10H13N5O3 0 958-09-8 C00559 KEGG - C00559 Neutral Compound SMP CHS Checked N-groups JLR DEOXYADENOSINE cd2 Cadmium Cd 2 C01413 KEGG - C01413 SMP (02/16/03) CD+2 adpglc ADPglucose C16H23N5O15P2 -2 C00498 KEGG - C00498 Neutral MF = C16H25N5O15P2 SMP CHS ADP-D-GLUCOSE dmpp Dimethylallyl diphosphate C5H9O7P2 -3 358-71-4 C00235 KEGG - C00235 Neutral MF = C5H12O7P2 SMP CHS CPD-4211 2dr1p 2-Deoxy-D-ribose 1-phosphate C5H9O7P -2 C00672 KEGG - C00672 Neutral MF = C5H11O7P SMP CHS DEOXY-RIBOSE-1P hmgth hydroxymethylglutathione C11H18N3O7S -1 AMF S-HYDROXYMETHYLGLUTATHIONE 3hmrsACP R-3-hydroxy-myristoyl-ACP C25H47N2O9PRS -1 Based on NH page 1040 and 615 JLR JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) 3-OHMYRISTOYL-ACP aconm E-3-carboxy-2-pentenedioate 6-methyl ester C7H6O6 -2 Not in Kegg (see PMID 11329290, figure 1) Neutral-C7H8O6 JLR MONOMETHYL-ESTER-OF-TRANS-ACONITATE synonym MONOMETHYL-ESTER-OF-TRANS-ACONITATE 2dr5p 2-Deoxy-D-ribose 5-phosphate C5H9O7P -2 102916-66-5 C00673 KEGG - C00673 Neutral MF = C5H11O7P SMP CHS DEOXY-RIBOSE-5P rbt Ribitol C5H12O5 0 488-81-3 C00474 KEGG - C00474 SMP RIBITOL leutrna L-Leucyl-tRNA(Leu) C6H12NOR 1 C02047 KEGG -C02047 SMP adjusted for Genomatica's change to aa - NCD |Charged-LEU-tRNAs| aacald Aminoacetaldehyde C2H6NO 1 452-86-8 C06735 KEGG - C06735 Checked N JLR CPD-1772 colipa core oligosaccharide lipid A C176H303N2O100P4 -11 AMF other structure is unclear nh4 Ammonium H4N 1 66701-25-5 C01342 KEGG - C01342 Charged Compound Diiferentiate Ammonia from Ammonium SMP CHS Checked N-groups JLR AMMONIUM 5caiz 5-phosphoribosyl-5-carboxyaminoimidazole C9H11N3O9P -3 JLR - could not find the metabolite in KEGG. Metabolite is in Neidhardt," Escherichia coli and Salmonella cellular and molecular biology" 2nd edition, page 563. Used in E. coli purine biosynthesis Checked N-groups JLR CPD0-181 synonym CPD0-181 fldrd flavodoxin (reduced) XH2 0 358-71-4 C02745 KEGG - C02745 RED-FLAVODOXIN class RED-FLAVODOXIN Sfglutth S-Formylglutathione C11H16N3O7S -1 C01031 KEGG - C01031 NCD changed to protonated form, added +1 charge - NCD CPD-548 adocbi Adenosyl cobinamide C58H84CoN16O11 1 7625-23-2 C06508 KEGG - C06508 (removed 3 H's from the ring) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 Redone old values were C58H85CoN16O11 with +6 charge (by JLR) ADENOSYLCOBINAMIDE accoa Acetyl-CoA C23H34N7O17P3S -4 72-89-9 C00024 KEGG - C00024 Neutral MF = C23H38N7O17P3S SMP CHS ACETYL-COA trdrd Reduced thioredoxin XH2 0 C00342 KEGG - C00342 SMP RED-THIOREDOXIN-MONOMER o16a3und (O16 antigen)x3 undecaprenyl diphosphate C157H255N3O82P2 -2 AMF other structure is unclear malACP Malonyl-[acyl-carrier protein] C14H22N2O10PRS -2 None C01209 KEGG - C01209 Error in KEGG: ACP attached to Malonyl via a S, NOT Oxygen. Checked with Neidhardt (tv) Neutral MF = C3H3O3R (S)R = [acyl-carrier protein] SMP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) MALONYL-ACP dopa Dopamine C8H12NO2 1 51-61-6 C03758 KEGG - C03758 SAB metacyc DOPAMINE DOPAMINE anth Anthranilate C7H6NO2 -1 118-92-3 C00108 KEGG - C00108 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR ANTHRANILATE dd2coa trans-Dodec-2-enoyl-CoA C33H52N7O17P3S -4 C03221 KEGG - C03221 Neutral MF = C33H56N7O17P3S SMP fatty agpe_EC acyl-glycerophosphoethanolamine (E.coli) C1093H2224O350N50P50 0 1-acyl and 2-acyl are treated the same for simplicity Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 agpe_EC is really one molecule of agpe. JLR Checked N JLR 2-ACYL-GPE hack 2-ACYL-GPE agpc_EC acyl-glycerophosphocholine C1243H2524N50O350P50 0 Scaled up by 50, really is 50 molecules or phosphatidylcholine. Scale was used so that the elements were whole numbers. JLR PHOSPHATIDYLCHOLINE class PHOSPHATIDYLCHOLINE 4mpetz 4-Methyl-5-(2-phosphoethyl)-thiazole C6H8NO4PS -2 C04327 KEGG - C04327 Neutral MF = C6H10NO4PS SMP CHS Checked N-groups JLR THZ-P imp IMP C10H11N4O8P -2 131-99-7 C00130 KEGG - C00130 Neutral MF = C10H13N4O8P SMP CHS Checked N-groups JLR IMP agpg_EC acyl-glycerophosphoglycerol (E.coli) C1143H2224O450P50 -50 1-acyl and 2-acyl are treated the same for simplicity Molecular formula is 50 times the actual molecular formula to get whole numbers, so 0.02 agpg_EC is really one molecule of agpg. JLR fatty ctp CTP C9H12N3O14P3 -4 65-47-4 C00063 KEGG - C00063 Neutral MF = C9H16N3O14P3 SMP CHS CTP tartr-L L-tartrate C4H4O6 -2 87-69-4 C00898 KEGG - C00898 Neutral-C4H6O6 JLR TARTRATE 2ddg6p 2-Dehydro-3-deoxy-D-gluconate 6-phosphate C6H8O9P -3 C04442 KEGG - C04442 Neutral MF = C6H11O9P SMP CHS 2-KETO-3-DEOXY-6-P-GLUCONATE 3dhsk 3-Dehydroshikimate C7H7O5 -1 10457-99-5 C02637 KEGG - C02637 Neutral MF = C7H8O5 SMP CHS 3-DEHYDRO-SHIKIMATE fald Formaldehyde CH2O 0 50-00-0 C00067 KEGG - C00067 Neutral Compound SMP CHS FORMALDEHYDE mnl1p D-Mannitol 1-phosphate C6H13O9P -2 C00644 KEGG - C00644 Neutral MF = C6H15O9P SMP MANNITOL-1P 5aop 5-Amino-4-oxopentanoate C5H9NO3 0 106-60-5 C00430 KEGG - C00430 Neutral MF = C5H9NO3 SMP CHS Changed according to Genomatica JLR 5-AMINO-LEVULINATE synonym 5-AMINO-LEVULINATE tre Trehalose C12H22O11 0 99-20-7 C01083 KEGG - C01083 Neutral Compound SMP TREHALOSE 3oddcoa 3-Oxododecanoyl-CoA C33H52N7O18P3S -4 C05263 KEGG - C05263 Neutral MF = C33H56N7O18P3S SMP fatty trnatyr tRNA(Tyr) R 0 C00787 KEGG - C00787 SMP |TYR-tRNAs| Nmtrp N-Methyltryptophan C12H14N2O2 0 526-31-8 C02983 KEGG - C02983 N-METHYLTRYPTOPHAN udpLa4fn uridine 5''-diphospho-{beta}-4-deoxy-4-formamido-L-arabinose C15H21N3O16P2 -2 AMF UDP-L-ARA4-FORMYL-N hack UDP-L-ARA4-FORMYL-N adphep-L,D ADP-L-glycero-D-manno-heptose C17H25N5O16P2 -2 C06398 Kegg- C06398 Neutral-C17H27N5O16P2 JLR Checked N JLR ADP-L-GLYCERO-D-MANNO-HEPTOSE rml L-Rhamnulose C6H12O5 0 C00861 KEGG - C00861 SMP RHAMNULOSE q8h2 Ubiquinol-8 C49H76O4 0 C00390 KEGG C00390 JLR UBIQUINOL-8 prbatp 1-(5-Phosphoribosyl)-ATP C15H19N5O20P4 -6 C02739 KEGG - C02739 Neutral MF = C15H25N5O20P4 SMP CHS PHOSPHORIBOSYL-ATP synonym PHOSPHORIBOSYL-ATP air 5-amino-1-(5-phospho-D-ribosyl)imidazole C8H12N3O7P -2 25635-88-5 C03373 KEGG - C03373 Neutral MF = C8H14N3O7P SMP CHS Checked N-groups JLR 5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE synonym 5-PHOSPHORIBOSYL-5-AMINOIMIDAZOLE agm Agmatine C5H16N4 2 306-60-5 C00179 KEGG - C00179 Neutral Compound SMP CHS Changed according to Genomatica JLR AGMATHINE tagdp-D D-Tagatose 1,6-biphosphate C6H10O12P2 -4 C03785 KEGG - C03785 Neutral MF = C6H14O12P2 NCD TAGATOSE-1-6-DIPHOSPHATE hack TAGATOSE-1-6-DIPHOSPHATE n8aspmd N8-Acetylspermidine C9H23N3O 2 34450-15-2 C01029 KEGG - C01029 JLR Checked N-groups JLR metacyc CPD-3462 CPD-3462 feoxam ferroxamine C25H46FeN6O8 1 C07597 AMF unknown ohpb 2-Oxo-3-hydroxy-4-phosphobutanoate C4H4O8P -3 C06054 KEGG - C06054 Neutral-C4H7O8P JLR 3OH-4P-OH-ALPHA-KETOBUTYRATE synonym 3OH-4P-OH-ALPHA-KETOBUTYRATE phhlipa phospho-heptosyl-heptosyl-kdo2-lipidA C124H219N2O54P3 -8 AMF unknown adphep-D,D ADP-D-glycero-D-manno-heptose C17H25N5O16P2 -2 119-61-9 C06397 KEGG - C06397 Neutral-C17H27N5016P2 JLR Checked N JLR ADP-D-GLYCERO-D-MANNO-HEPTOSE acald Acetaldehyde C2H4O 0 75-07-0 C00084 KEGG - C00084 Neutral Compound SMP CHS ACETALD malthx Maltohexaose C36H62O31 0 34620-77-4 C01936 KEGG - C01936 JLR metacyc MALTOHEXAOSE MALTOHEXAOSE 2dhguln 2-Dehydro-L-gulonate C6H9O7 -1 No Kegg entry Neutral- C6H10O7 JLR CPD-377 synonym CPD-377 tag6p-D D-Tagatose 6-phosphate C6H11O9P -2 C01097 KEGG - C01097 Neutral MF=C6H13O9P JLR TAGATOSE-6-PHOSPHATE asptrna L-Aspartyl-tRNA(Asp) C4H5NO3R 0 C02984 KEGG - C02984 SMP |Charged-ASP-tRNAs| pmtcoa Palmitoyl-CoA (n-C16:0CoA) C37H62N7O17P3S -4 C00154 KEGG - C00154 Neutral MF = C37H66N7O17P3S SMP changed compound class from peptides to fatty acids - NCD C16:0 - C16H31O2 (charge -1) CoA - C21H32N7O16P3S (charge -4) NJ PALMITYL-COA synonym PALMITYL-COA crnDcoa D-carnitinyl-CoA C28H46N8O18P3S -3 AMF D-CARNITINYL-COA phthr O-Phospho-4-hydroxy-L-threonine C4H8NO7P -2 C06055 KEGG - C06055 NCD Checked N-groups JLR PHOSPHO-HYDROXY-THREONINE synonym PHOSPHO-HYDROXY-THREONINE xu5p-D D-Xylulose 5-phosphate C5H9O8P -2 None C00231 KEGG - C00231 Neutral MF = C5H11O8P SMP CHS XYLULOSE-5-PHOSPHATE methf 5,10-Methenyltetrahydrofolate C20H20N7O6 -1 C00445 KEGG - C00445 Merged with C04270 Neutral MF = C20H22N7O6 netural form has +1 charge -NCD SMP CHS Checked N-groups, agrees with ACD software, NCD, JLR Agrees with pipeline pilot |5,10-methenyl-thf| rml1p L-Rhamnulose 1-phosphate C6H11O8P -2 C01131 KEGG - C01131 Neutral MF = C6H13O8P SMP RHAMNULOSE-1P lcts Lactose C12H22O11 0 63-42-3 C00243 KEGG - C00243 Neutral Compound SMP CHS LACTOSE o2 O2 O2 0 7782-44-7 C00007 KEGG - C00007 SMP CHS OXYGEN-MOLECULE 2dmmql8 2-Demethylmenaquinol 8 C50H72O2 0 JLR unknown acg5p N-Acetyl-L-glutamyl 5-phosphate C7H9NO8P -3 C04133 KEGG - C04133 Neutral MF = C7H12NO8P SMP CHS Checked N-groups JLR N-ACETYL-GLUTAMYL-P synonym N-ACETYL-GLUTAMYL-P aicar 5-Amino-1-(5-Phospho-D-ribosyl)imidazole-4-carboxamide C9H13N4O8P -2 3031-94-5 C04677 KEGG - C04677 Neutral MF = C9H15N4O8P SMP CHS Checked N-groups JLR AICAR hack AICAR murein5px4px4p three disacharide linked murein units (pentapeptide corsslinked tetrapeptide (A2pm->D-ala) tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) C114H172N22O59 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala other structure is unclear n2o Nitrous oxide N2O 0 10024-97-2 C00887 KEGG - C00887 SMP CHS NITROUS-OXIDE N1aspmd N1-Acetylspermidine C9H23N3O 2 34450-16-3 C00612 KEGG - C00612 JLR capitalized N at beginning of abbrev -NCD Checked N-groups JLR metacyc CPD-568 CPD-568 2ahbut (S)-2-Aceto-2-hydroxybutanoate C6H9O4 -1 C06006 KEGG - C06006 (C00659 Deleted) Neutral MF = C6H10O4 SMP CHS 2-ACETO-2-HYDROXY-BUTYRATE hack 2-ACETO-2-HYDROXY-BUTYRATE ump UMP C9H11N2O9P -2 58-97-9 C00105 KEGG - C00105 Neutral MF = C9H13N2O9P SMP CHS UMP 2oph 2-Octaprenylphenol C46H70O 0 C05810 KEGG - C05810 SMP CHS 2-OCTAPRENYLPHENOL murein4px4px4p three disacharide linked murein units (tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain) C111H167N21O58 -6 AMF PMID: 9751644 has a good figure basic 2 unit crosslinked murein chain from the middle of a murein chain The murein crosslinks are between A2pm->D-ala other murein recycling stuff lystrna L-Lysine-tRNA (Lys) C6H14N2OR 2 C01931 KEGG - C01931 SMP adjusted for Genomatica's change to aa - NCD |Charged-LYS-tRNAs| synonym |Charged-LYS-tRNAs| acon-T trans-Aconitate C6H3O6 -3 4023-65-8 C02341 KEGG - C02341 Neutral MF = C6H6O6 SMP CHS CPD-225 cys-L L-Cysteine C3H7NO2S 0 52-90-4 C00097 KEGG - C00097 Neutral MF = C3H7NO2S SMP CHS Changed according to Genomatica JLR CYS ppi Diphosphate HO7P2 -3 09/03/2466 C00013 KEGG - C00013 Neutral MF = H4O7P2 SMP CHS Formula changed to HO7P2 (Charge -3) on Feb-26-2002 PPI adp ADP C10H12N5O10P2 -3 20398-34-9 C00008 KEGG - C00008 Neutral MF = C10H15N5O10P2 SMP CHS ADP 5mta 5-Methylthioadenosine C11H15N5O3S 0 2457-80-9 C00170 KEGG - C00170 Neutral MF = C11H15N5O3S SMP CHS Checked N-groups JLR 5-METHYLTHIOADENOSINE pacald Phenylacetaldehyde C8H8O 0 122-78-1 C00601 KEGG - C00601 JLR PHENYLACETALDEHYDE 2aobut L-2-Amino-3-oxobutanoate C4H7NO3 0 C03508 KEGG - C03508 (C03214 Deleted) Neutral MF = C4H7NO3 SMP CHS Checked N-groups JLR AMINO-OXOBUT 3hhdcoa (S)-3-Hydroxyhexadecanoyl-CoA C37H62N7O18P3S -4 C05258 KEGG - C05258 Neutral MF = C37H66N7O18P3S SMP fatty frdp Farnesyl diphosphate C15H25O7P2 -3 13058-04-3 C00448 KEGG - C00448 Neutral MF = C15H28O7P2 SMP FARNESYL-PP k potassium K 1 C00238 KEGG - C00238 K+ clpn_EC Cardiolipin (Ecoli) C3822H7096O850P100 -100 C05980 KEGG - C05980 JLR- really represents 50 cardiolipin molecules, based on composition of fatty acids in E.coli (0.04 C14:0, 0.1 C14:1, 0.72 C16:0, 0.14 C16:1, 1.0 C18:1) CARDIOLIPIN hack CARDIOLIPIN ru5p-L L-Ribulose 5-phosphate C5H9O8P -2 4151-19-3 C01101 KEGG - C01101 Neutral MF = C5H11O8P SMP L-RIBULOSE-5-P acgam6p N-Acetyl-D-glucosamine 6-phosphate C8H14NO9P -2 102029-88-9 C00357 KEGG - C00357 Neutral MF = C8H16NO9P SMP CHS Checked N-groups JLR N-ACETYL-D-GLUCOSAMINE-6-P 2tpr3dpcoa 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA C26H40N7O26P5S -6 AMF 2-5-TRIPHOSPHORIBOSYL-3-DEPHOSPHO- trnatrp tRNA(Trp) R 0 C01652 KEGG - C01652 SMP |TRP-tRNAs| 4abz 4-Aminobenzoate C7H6NO2 -1 150-13-0 C00568 KEGG - C00568 Neutral MF = C7H7NO2 SMP CHS Checked N-groups JLR P-AMINO-BENZOATE udpLa4o UDP-4-keto-pyranose C14H18N2O16P2 -2 AMF 5-BETA-L-THREO-PENTAPYRANOSYL-4-ULOSE- synonym 5-BETA-L-THREO-PENTAPYRANOSYL-4-ULOSE- 5mdru1p 5-Methylthio-5-deoxy-D-ribulose 1-phosphate C6H11O7PS -2 C04582 KEGG - C04582 Neutral MF = C6H13O7PS SMP CHS metacyc CPD-1063 CPD-1063 dhna 1,4-Dihydroxy-2-naphthoate C11H7O4 -1 C03657 KEGG - C03657 Neutral MF = C11H8O4 SMP CHS DIHYDROXYNAPHTHOATE trnagln tRNA(Gln) R 0 C01640 KEGG - C01640 SMP |GLN-tRNAs| cbasp N-Carbamoyl-L-aspartate C5H6N2O5 -2 C00438 KEGG - C00438 Neutral MF = C5H8N2O5 SMP CHS Checked N-groups JLR CARBAMYUL-L-ASPARTATE uLa4fn undecaprenyl phosphate-4-amino-4-formyl-L-arabinose C61H99N1O8P1 -1 AMF CPD0-888 hack CPD0-888 mobd Molybdate MoO4 -2 C06232 KEGG - C06232 Neutral MF = H2MoO4 SMP CPD-3 5mtr 5-Methylthio-D-ribose C6H12O4S 0 C03089 KEGG - C03089 Neutral Compound SMP CHS metacyc CPD-560 CPD-560 dcacoa Decanoyl-CoA (n-C10:0CoA) C31H50N7O17P3S -4 C05274 KEGG - C05274 Neutral MF = C31H54N7O17P3S SMP fatty tym Tyramine C8H12NO 1 51-67-2 C00483 KEGG - C00483 AMF metacyc TYRAMINE TYRAMINE kdo2lipid4p KDO(2)-lipid IV(A) with palmitoleoyl C100H176N2O38P2 -6 see PMID 10092655 Neutral-C100H182N2O38P2 JLR KDO2-PALMITOLEOYL-LIPID-IVA hack KDO2-PALMITOLEOYL-LIPID-IVA kdo 3-Deoxy-D-manno-2-octulosonate C8H13O8 -1 C01187 KEGG - C01187 Neutral MF = C8H14O8 SMP CHS KDO hack KDO xyl-D D-Xylose C5H10O5 0 58-86-6 C00181 KEGG - C00181 Neutral Compound SMP CHS XYLOSE leu-L L-Leucine C6H13NO2 0 61-90-5 C00123 KEGG - C00123 Neutral MF = C6H13NO2 SMP CHS Changed according to Genomatica JLR LEU mmcoa-S (S)-Methylmalonyl-CoA C25H35N7O19P3S -5 C00683 KEGG - C00683 Neutral MF = C25H40N7O19P3S SMP CHS Checked N-groups JLR D-METHYL-MALONYL-COA ins Inosine C10H12N4O5 0 58-63-9 C00294 KEGG - C00294 Neutral Compound SMP CHS Checked N-groups JLR INOSINE csn Cytosine C4H5N3O 0 71-30-7 C00380 KEGG - C00380 Neutral Compound SMP CHS CYTOSINE trptrna L-Tryptophanyl-tRNA(Trp) C11H11N2OR 1 C03512 KEGG - C03512 SMP adjusted for Genomatica's change to aa - NCD |Charged-TRP-tRNAs| 4abut 4-Aminobutanoate C4H9NO2 0 56-12-2 C00334 KEGG - C00334 Neutral MF = C4H9NO2 SMP CHS Changed according to Genomatica JLR 4-AMINO-BUTYRATE 10fthf 10-Formyltetrahydrofolate C20H21N7O7 -2 692-29-5 C00234 KEGG - C00234 Neutral MF = C20H23N7O7 SMP CHS checked N groups - NCD Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR 10-FORMYL-THF oxur Oxalureate C3H3N2O4 -1 585-05-7 C00802 KEGG - C00802 Checked Protonation state JLR CPD-389 h2 H2 H2 0 1333-74-0 C00282 KEGG - C00282 HYDROGEN-MOLECULE ppcoa Propanoyl-CoA C24H36N7O17P3S -4 317-66-8 C00100 KEGG - C00100 Neutral MF = C24H40N7O17P3S SMP CHS NCD PROPIONYL-COA peamn Phenethylamine C8H12N 1 64-04-0 C05332 KEGG - C05332 JLR Checked N-groups JLR PHENYLETHYLAMINE synonym PHENYLETHYLAMINE 3pg 3-Phospho-D-glycerate C3H4O7P -3 C00197 KEGG - C00197 Neutral MF = C3H7O7P Deleted C00597 SMP CHS G3P hdcea Hexadecenoate (n-C16:1) C16H29O2 -1 KEGG - C08362 Neutral MF = C16H30O2 SMP monounsaturated fatty acid, 16 carbons changed name from Fatty acid (n-C16:1) to hexadecenoic acid; changed abbreviation from fa7 to hdcea; changed compound class from peptides to fatty acid - NCD updated names, added KEGG entry PALMITATE hack PALMITATE bbtcoa gamma-butyrobetainyl-CoA C28H46N8O17P3S -3 No Kegg Entry gamma-butyrobetaine with a CoA attached +1 charge on butyrobetaine -4 charge on CoA JLR Checked N-groups JLR GAMMA-BUTYROBETAINYL-COA glyc2p Glycerol 2-phosphate C3H7O6P -2 3249-68-1 C02979 KEGG - C02979 AMF metacyc CPD-536 CPD-536 phphhlipa phospho-heptosyl-phospho-heptosyl-heptosyl-kdo2-lipidA C131H230N2O63P4 -10 AMF unknown udcpp Undecaprenyl phosphate C55H89O4P -2 C00348 KEGG - C00348 Neutral MF = C55H91O4P SMP CHS UNDECAPRENYL-P enlipa phosphoethanolamine KDO(2)-lipid (A) C112H202N3O42P3 -6 AMF PHOSPHATIDYLETHANOLAMINE-KDO2 hack PHOSPHATIDYLETHANOLAMINE-KDO2 34dhpac 3,4-Dihydroxyphenylacetaldehyde C8H8O3 0 145-14-2 C04043 KEGG - C04043 SAB 34-DIHYDROXYPHENYLACETALDEHYDE ni2 nickel Ni 2 C00291 KEGG - C00291 NI+2 hemeO Heme O C49H56FeN4O5 -2 No KEGG Entry Neutral MF = C49H58FeN4O5 SMP Note Neidhardt picture (pg 734) is incorrect Checked N-groups, JLR HEME_O 4c2me 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol C14H23N3O14P2 -2 C11435 KEGG C11435 Neutral MF = C14H25N3O14P2 SMP Checked N-groups JLR 4-CYTIDINE-5-DIPHOSPHO-2-C xu5p-L L-Xylulose 5-phosphate C5H9O8P -2 None C03291 KEGG - C03291 Neutral MF = C5H11O8P Different from xu5p-D (C00231): Change abbv from xu5p to x5p-L SMP CHS L-XYLULOSE-5-P manglyc 2(alpha-D-Mannosyl)-D-glycerate C9H15O9 -1 C11544 KEGG C11544 2-O-ALPHA-MANNOSYL-D-GLYCERATE synonym 2-O-ALPHA-MANNOSYL-D-GLYCERATE cys-D D-Cysteine C3H7NO2S 0 921-01-7 C00793 KEGG - C00793 JLR Changed according to Genomatica JLR D-CYSTEINE acgal1p N-Acetyl-D-galactosamine 1-phosphate C8H14NO9P -2 not in KEGG NCD unknown rbt5p D-Ribitol 5-phosphate C5H11O8P -2 C01068 KEGG - C01068 Neutral MF = C5H13O8P SMP metacyc CPD-372 CPD-372 ascb-L L-Ascorbate C6H8O6 0 50-81-7 C00072 KEGG - C00072 JLR ASCORBATE sbt-D D-Sorbitol C6H14O6 0 50-70-4 C00794 KEGG - C00794 Neutral Compound SMP CHS SORBITOL hcys-L L-Homocysteine C4H9NO2S 0 6027-13-0 C00155 KEGG - C00155 Deleted C05330 Neutral MF = C4H9NO2S SMP CHS Changed according to Genomatica JLR HOMO-CYS allul6p Allulose 6-phosphate C6H11O9P -2 No KEGG entry see allulose and PMID 9401019 JLR synmeta D-ALLULOSE-6-PHOSPHATE D-ALLULOSE-6-PHOSPHATE no2 Nitrite NO2 -1 7697-37-2 C00088 KEGG - C00088 Neutral MF = HNO2 SMP CHS Checked N-groups JLR NITRITE thf 5,6,7,8-Tetrahydrofolate C19H21N7O6 -2 135-16-0 C00101 KEGG - C00101 Merged with C03041 Neutral MF = C19H23N7O6 SMP CHS Checked N-groups, added +1 charge and proton based on ACD software, NCD, JLR Pipeline Pilot indicates this N is not charged JLR THF gthox Oxidized glutathione C20H30N6O12S2 -2 C00127 KEGG - C00127 Neutral MF = C20H32N6O12S2 SMP CHS Changed according to Genomatica JLR OXIDIZED-GLUTATHIONE 3dhgulnp 3-keto-L-gulonate-6-phosphate C6H8O10P -3 No Kegg entry Neutral-C6H11O10P JLR CPD-2343 trp-L L-Tryptophan C11H12N2O2 0 73-22-3 C00078 KEGG - C00078 Neutral MF = C11H12N2O2 SMP CHS Changed according to Genomatica JLR TRP octdp all-trans-Octaprenyl diphosphate C40H65O7P2 -3 C04146 KEGG - C04146 Neutral MF = C40H68O7P2 SMP OCTAPRENYL-DIPHOSPHATE pdx5p Pyridoxine 5'-phosphate C8H10NO6P -2 447-05-2 C00627 KEGG - C00627 Neutral MF = C8H12NO6P SMP CHS Checked N-groups JLR PYRIDOXINE-5P thrtrna L-Threonyl-tRNA(Thr) C4H8NO2R 1 C02992 KEGG - C02992 SMP adjusted for Genomatica's change to aa - NCD |Charged-THR-tRNAs| phetrna L-Phenylalanyl-tRNA(Phe) C9H10NOR 1 C03511 KEGG - C03511 SMP adjusted for Genomatica's change to aa - NCD |Charged-PHE-tRNAs| crncoa L-Carnitinyl-CoA C28H46N8O18P3S -3 No Kegg Entry Carnitine with a CoA attached +1 charge on carnitine -4 charge on CoA JLR Checked N-groups JLR L-CARNITINYL-COA acg5sa N-Acetyl-L-glutamate 5-semialdehyde C7H10NO4 -1 None C01250 KEGG - C01250 Neutral MF = C7H11NO4 SMP CHS Checked N-groups JLR N-ACETYLGLUTAMATE_SEMIALDEHYDE adocbl Adenosylcobalamin C72H100CoN18O17P 0 13870-90-1 C00194 KEGG - C00194 Kegg shows C72H105CoN18O17P (removed 3 H from ring, 1H from phosphate group, 1H from ribazole group) JLR before charge was +3 (no charge on Co was taken into account). New charge from assuming Co with 6 ligands has a +3 charge--5=+2 or 4=+1) JLR ADD H and a +1 charge for N in ring JLR 8/2004 REDONE old values were C72H101CoN18O17P charge +7 (by JLR) ADENOSYLCOBALAMIN tyrp Phosphotyrosine C9H10NO6P -2 7625-23-2 C06501 KEGG - C06501 synmeta CPD-3728 CPD-3728 ocACP Octanoyl-ACP (n-C8:0ACP) C19H35N2O8PRS -1 JLR- saturated fatty acid with 8 carbons attached to ACP JLR changed to fix ACP(used to be just R, now C11H20N2O7PRS) fatty ppgpp Guanosine 3',5'-bis(diphosphate) C10H11N5O17P4 -6 C01228 KEGG - C01228 Neutral MF = C10H17N5O17P4 SMP GUANOSINE-5DP-3DP for Formate CH1O2 -1 64-18-6 C00058 KEGG - C00058 Neutral MF = CH2O2 SMP CHS FORMATE 8aonn 8-Amino-7-oxononanoate C9H17NO3 0 C01092 KEGG - C01092 Neutral MF = C9H17NO3 SMP CHS Changed according to Genomatica JLR 8-AMINO-7-OXONONANOATE ppbng Porphobilinogen C10H13N2O4 -1 487-90-1 C00931 KEGG - C00931 Neutral MF = C10H14N2O4 SMP Changed according to Genomatica JLR PORPHOBILINOGEN gmp GMP C10H12N5O8P -2 85-32-5 C00144 KEGG - C00144 Neutral = C10H14N5O8P SMP CHS GMP gp4g P1,P4-Bis(5'-guanosyl) tetraphosphate C20H24N10O21P4 -4 C01261 Kegg- C01261 Neutral-C20H28N10O21P4 JLR synmeta CPD-609 CPD-609 acmalt Acetyl-maltose C14H24O12 0 C02130 KEGG - C02130 Neutral Compound SMP ACETYLMALTOSE atp ATP C10H12N5O13P3 -4 56-65-5 C00002 KEGG - C00002 Neutral MF = C10H16N5O13P3 SMP CHS ATP gfgaragund galactofuranosyl-glucosyl-O-acetyl-rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate C83H135N1O27P2 -2 AMF unknown anhm4p 1,6-anhydrous-N-Acetylmuramyl-tetrapeptide C29H44N6O15 -2 AMF unknown hkndd 2-Hydroxy-6-oxonona-2,4-diene-1,9-dioate C9H8O6 -2 53-42-9 C04479 KEGG - C04479 Neutral-C9H10O6 JLR Changed to -2 charge CPD-157 other got merged in the meantime aact Aminoacetone C3H8NO 1 298-08-8 C01888 KEGG - C01888 Neutral Compound SMP Checked N-groups JLR AMINO-ACETONE trnaleu tRNA(Leu) R 0 C01645 KEGG - C01645 SMP |LEU-tRNAs| acnam N-Acetylneuraminate C11H18NO9 -1 131-48-6 C00270 KEGG - C00270 Neutral MF = C11H19NO9 SMP CHS Checked N-groups JLR N-ACETYLNEURAMINATE