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Generated by SRI International Pathway Tools Version 25.0 on Sun Authors: Pallavi Subhraveti Ron Caspi Quang Ong Peter D Karp An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Ingrid Keseler Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Gcf_000204315Cyc: gamma proteobacterium IMCC3088 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari ammonium ammonium hydrogencarbonate RS01670 RS06240 RS03760 ammonium ammonium hydrogencarbonate Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Cofactor, Prosthetic Group, Electron Carrier Degradation a 3-methyl- D-ribulose a 2'- a [protein] (2Z,4E)-2-amino- (2Z,4E)-2-amino- 1498 N 6 -dimethylallyladenosine 37 a sulfurated a (7Z)-hexadec- a (4Z)-hexadec- an N-modified an L-asparaginyl- a uracil ubiquinol-8 biosynthesis (prokaryotic) a malonyl-[acp] branched 2,3,4- a malonyl-[acp] 5-phosphate deoxyribonucleoside C-terminal Glu 5-methyl-muconate 6-oxohexa- met DMAPP pyridoxal 5'-phosphate biosynthesis I NAD thioredoxin pathway 6-hydroxymethyl-dihydropterin tetrapyrrole biosynthesis superpathway of heme biosynthesis menaquinol-7 biosynthesis di-trans,poly-cis-undecaprenyl vitamin B degradation in tRNA [sulfur carrier] 7-enoyl-[acp] 4-enoyl-[acp] aminoacyl-[tRNA] [tRNA Asn ] in 16S rRNA 6 saturated fatty acid 3,4-dihydroxy- 5'-diphosphate 16S rRNA all-trans- phosphorylation and from uroporphyrinogen-III phosphate biosynthesis L-valine degradation I Amino Acid Degradation succinate beta-ketoacyl-[acyl- long-chain-fatty- beta-ketoacyl-[acyl- aminoacyl-tRNA ribonucleotide- L-glutamate ribosomal protein S6 semialdehyde aminoacyl-tRNA 2,4-dienoate bifunctional 4-hydroxy- diphosphate biosynthesis I I (from glutamate) all-trans- Metabolic Regulator Biosynthesis 2-butanone-4- 2-hydroxymuconic 2-hydroxymuconic (uracil(1498)-N(3))- 4-hydroxybenzoate octaprenyl D-erythrose transhydrogenation an oxidized 2-carboxy-1,4- Macromolecule Modification protein S-nitrosylation and denitrosylation dehydrogenase, carrier-protein] acid--CoA ligase: carrier-protein] hydrolase: diphosphate modification protein: semialdehyde hydrolase: semialdehyde ornithine 3-methylbut- 4-phosphate uroporphyrinogen-III heptaprenyl (2E,6E)-farnesyl L-leucine degradation I pyridoxamine phosphate synthase: methyltransferase: diphosphate + IPP hydrophobic membrane synthase I: IMCC3088_RS11970 synthase II: IMCC3088_RS06635 reductase subunit beta: IMCC3088_RS13660 IMCC3088_RS06635 acetyltransferase/ 2-enyl 4-hydroxybenzoate NAD thioredoxin Glu naphthoquinol diphosphate diphosphate ppGpp biosynthesis IMCC3088_RS13260 dehydrogenase: dehydrogenase: IMCC3088_RS09280 erythrose 4- GTP di-trans,poly-cis- a [protein]- val anchor protein: IMCC3088_RS00415 [+ 15 isozymes] IMCC3088_RS05200 IMCC3088_RS00495 N-acetylglutamate diphosphate octaprenyltransferase: NAD(+) mannosylglycerate pyridoxine a 3-methyl- aminoacyl-tRNA ribosomal protein S6 IMCC3088_RS04110 aminoacyl-tRNA IMCC3088_RS04110 phosphate GTP cyclohydrolase glutamate-tRNA ligase: uroporphyrinogen decaprenylcistransferase: L-cysteine pyridoxamine-pyruvate IMCC3088_RS11580 [+ 3 isozymes] 3,4-dihydroxy- 16S rRNA synthase: argJ reductase: 3-octaprenyl-4-ubiA kinase: ppnK demethylmenaquinol-7 biosynthesis I leu beta-ketoacyl synthase: branched a (6Z)-3- hydrolase: ribonucleotide- modification protein: 2-hydroxymuconic hydrolase: 2-hydroxymuconic dehydrogenase: I FolE: IMCC3088_RS03005 decarboxylase: hemE di-trans,octa-cisIMCC3088_RS00885 pppGpp branched chain amino aminotransferase: diphosphate AMP 2-butanone-4- (uracil(1498)-N(3))- ispH + thioredoxin- branched chain amino tRNA-2-methylthio-N(6)- IMCC3088_RS00975a (9Z)-3-oxo- 2,3,4-saturated acyl-carrier protein oxooctadec- IMCC3088_RS11140 diphosphate reductase a [protein] C-IMCC3088_RS12635 IMCC3088_RS11140 amino-acid N- (E)-4-hydroxy-3- hydroxybenzoate NADP an L-glutamyl- (p)ppGpp synthetase: relA α acid aminotransferase: an uncharged semialdehyde semialdehyde gapA IMCC3088_RS14110 bifunctional -undecaprenyl GDP- -D-mannose IMCC3088_RS05385 an N-modified phosphate synthase: Asn methyltransferase: disulfide reductase: [tRNA Glu ] guanosine-5'-triphosphate, acid aminotransferase: dimethylallyladenosine acyl-carrier protein octadec-9- fatty acyl-CoA 6-enoyl-[acp] subunit alpha: terminal α-L- dehydrogenase: tRNA asn dehydrogenase: acetyltransferase: methylbut-2-en- 3-polyprenyl-4- coproporphyrinogen III demethylmenaquinone diphosphate bifunctional (p)ppGpp IMCC3088_RS01185 amino acid tRNA IMCC3088_RS00960 IMCC3088_RS03230 4-phospho- NAD(P)(+) IMCC3088_RS04935 GTP 3'-diphosphate a [protein] 3- IMCC3088_RS01185 synthase MiaB: enoyl-[acp] IMCC3088_RS00500 glutamate-α- an N 3 - IMCC3088_RS01205 1-yl diphosphate hydroxybenzoate synthetase II/ guanosine- branched chain amino L-isoleucine degradation I 1-deoxy-L- IMCC3088_RS04180 IMCC3088_RS04180 D-erythronate cyclohydrolase glutamyl-tRNA methyltransferase/2- undecaprenyl- nitrosothio- a ribonucleoside (2Z,4E)-2-amino- (2Z,4E)-2- 1498 N α -acetyl-L- transhydrogenase: pyrophosphatase: α branched chain amino pyridoxal IMCC3088_RS112752-methylthio-N 6 - glycero-tetrulose formate L-glutamate methyluracil decarboxylase: 7,8- reductase: radical SAM protein: methoxy-6-polyprenyl- diphosphatase: 3',5'-bis pyrophosphate 3'- guanosine 3'-diphosphate 2-O-( -D-mannosyl) acid aminotransferase: an unsulfurated diphosphate 5-methyl-muconate aminomuconate methionine erythronate- IMCC3088_RS02595 I FolE: folE IMCC3088_RS02910 L-alanine 37 in 16S rRNA IMCC3088_RS13435 dihydroneopterin pyrophosphohydrolase: -3-phosphoglycerate IMCC3088_RS03040 acid aminotransferase: met 5'-deoxyadenosine dimethylallyladenosine 4-phosphate 4-phosphate a reduced IMCC3088_RS11105 IMCC3088_RS08045 1,4-benzoquinol IMCC3088_RS02400 5'-triphosphate 3'- ile 3-oxoacyl-[acyl- [sulfur carrier] [+ 3 isozymes] 3'-triphosphate IMCC3088_RS12820 4-methyl-2- IMCC3088_RS03040 in tRNA 3-octaprenyl-4- dehydrogenase: thioredoxin (S)-4-amino-5- methylase: ubiE di-trans,octa-cis- diphosphatase: mannosyl-3- 3-methyl-2- branched chain amino carrier-protein] hydroxybenzoate protoporphyrinogen IX IMCC3088_RS12820 phosphoglycerate oxopentanoate IMCC3088_RS14065 NADPH oxopentanoate protoporphyrinogen IX undecaprenyl phosphate oxobutanoate acid aminotransferase: reductase: fabG carboxy-lyase: menaquinol-7 phosphatase: 4-methyl-2- 2-methoxy-6-all trans- 2 glutamate-1- a [protein]- 3-methyl-2- IMCC3088_RS01185 2-amino-6-[1-hydroxyethyl]- a (3Z)-dec- N - 4-bromodiphenyl (2R,3S)-3- (3R)-3-hydroxy-2-oxo-4 S-nitrosoglutathione 4-pyridoxolactone an octanoyl-[acp] heptaprenyl-2-methoxy- ADP-D-ribose DMKH2-13 oxaloacetate IPP IMCC3088_RS07505 7,8- semialdehyde IMCC3088_RS07775 L-cysteine oxobutanoate oxopentanoate 7-methyl-7,8-dihydropterin a malonyl-[acp] a palmitoleoyl-[acp] a malonyl-[acp] a lignoceroyl-[acp] an arachidoyl-[acp] succinylglutamate ether isopropylmalate phosphonooxybutanoate N 10 -formyl-tetrahydrofolate biosynthesis branched chain amino 2-amino-4-hydroxy-6- 3-enoyl-[acp] 1,4-benzoquinol ADP-ribose biphenyl 2,3- dihydroneopterin aminotransferase: 2-O-(α-D-mannosyl) dehydrogenase: dehydrogenase: beta-ketoacyl-[acyl- beta-ketoacyl-[acyl- beta-ketoacyl-[acyl- beta-ketoacyl-[acyl- bifunctional beta-ketoacyl-[acyl- succinylglutamate bifunctional 3-isopropylmalate oxaloacetate 4-hydroxy- 2-octaprenylphenol 3-phosphoserine/ GTP ppGpp S-(hydroxymethyl) acid aminotransferase: hydroxymethyldihydropteridine pyrophosphatase: dioxygenase: 3'-phosphate IMCC3088_RS03445 -D-glycerate IMCC3088_RS11560 IMCC3088_RS11555 carrier-protein] carrier-protein] carrier-protein] synthase carrier-protein] synthase demethylmenaquinone carrier-protein] desuccinylase: demethylmenaquinone dehydratase decarboxylase 3-methylbut- phosphohydroxythreonine acyl carrier protein metabolism glutathione IMCC3088_RS03040 pyrophosphokinase: IMCC3088_RS04800 IMCC3088_RS11175 2-octaprenylphenol a tetrahydrofolate bis(guanylyl molybdenum (S)-3-methyl-2- synthase I: synthase II: I: IMCC3088_RS00415 I: IMCC3088_RS00415 methyltransferase/2- synthase I: IMCC3088_RS13655 methyltransferase/2- large subunit: subunit beta: 2-enyl aminotransferase: protoporphyrin IX dehydrogenase: isovaleryl-CoA IMCC3088_RS08555 hydroxylase: 5-aminolevulinate cofactor) biosynthesis isobutanoyl-CoA oxopentanoate IMCC3088_RS00415 IMCC3088_RS05200 beta-ketoacyl synthase: beta-ketoacyl synthase: methoxy-6-polyprenyl- IMCC3088_RS00415 ADP-ribose succinylglutamate methoxy-6-polyprenyl- biphenyl 2,3- IMCC3088_RS05370 IMCC3088_RS13605 diphosphate IMCC3088_RS03135 an acyl- IMCC3088_RS07020 4-pyridoxate IMCC3088_RS07635 ferrochelatase: MoO - nucleoside- bifunctional (p)ppGpp isovaleryl-CoA 3-methyl-2- 2-amino-4-hydroxy-6- beta-ketoacyl synthase: [+ 3 isozymes] IMCC3088_RS00975 IMCC3088_RS00975 1,4-benzoquinol beta-ketoacyl synthase: pyrophosphatase: desuccinylase/ 1,4-benzoquinol dioxygenase: 3-isopropylmalate oxaloacetate reductase: 7,8- delta-aminolevulinic 2 carrier protein S-(hydroxymethyl) isobutyryl-CoA:FAD an (11Z)-3- 3-(all-trans 4-phospho- hemH molybdopterin molybdopterin diphosphate kinase: synthetase II/ guanosine- dehydrogenase: oxopentanoate hydroxymethyldihydropteridine IMCC3088_RS00975 methylase: ubiE IMCC3088_RS00975 nudF aspartoacylase: methylase: ubiE IMCC3088_RS11420
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