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_000632515Cyc: Geobacillus stearothermophilus NUB3621 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari putrescine putrescine putrescine sn-glycerol spermidine 4-aminobutanoate 4-aminobutanoate 4-aminobutanoate ethanolamine spermidine spermidine spermidine uracil uracil 3-phosphate predicted predicted ABC ABC transporter transporter RS14525 RS13805 RS01110 RS05760 RS09950 RS06340 RS04510 RS01240 RS10530 of sn- of spermidine/ glycerol 3- putrescine phosphate putrescine putrescine uracil uracil spermidine 4-aminobutanoate 4-aminobutanoate 4-aminobutanoate ethanolamine spermidine spermidine putrescine spermidine sn-glycerol 3-phosphate Cofactor, Prosthetic Group, Electron Carrier, and Vitamin Biosynthesis Chlorinated Fatty Acid and Lipid Degradation Compound Degradation ditrans,octacis- a peptidoglycan UDP-N-acetyl- (1S,2R)-1- (2E,6Z,9Z,12Z,15Z,18Z) 3-(4- a peptidoglycan acetoacetyl-CoA hydrogenobyrinate cob(II)yrinate a,c- TCA cycle superpathway of glyoxylate bypass and TCA 4-chlorobenzoate undecaprenyldiphospho- with (L-alanyl-γ-D- α-D-muramoyl- di-trans,octa-cis a purine 2'- C-(indol-3- -tetracosahexaenoyl-CoA hydroxyphenyl) ser [2Fe-2S] iron-sulfur cluster biosynthesis 1,4-dihydroxy-2- siroheme biosynthesis NAD biosynthesis from 2- ubiquinol-8 biosynthesis adenosylcobalamin biosynthesis from cobyrinate a,c-diamide II N 10 -formyl-tetrahydrofolate biosynthesis thiamin diphosphate Aminoacyl-tRNA Charging fatty acid β-oxidation I with (L-alanyl- lipid II (meso ser diamide biosynthesis I acetone degradation N-acetyl-(N- glutamyl-meso-2,6- L-alanyl-γ-D- -undecaprenyl deoxyribonucleoside yl)glycerol enoyl-CoA 3-hydroxybutyryl- cobyrinic acid -3-hydroxy- naphthoate biosynthesis amino-3-carboxymuconate (prokaryotic) biosynthesis I (E. coli) γ-D-glutamyl-L- diaminopimelate purine nucleoside hydratase: serine (early cobalt insertion) degradation II acetylglucosaminyl) diaminopimeloyl- glutamyl-L- phospho-N-phosphate 3-phosphate tryptophan CoA a,c-diamide propanoyl-CoAenoyl-CoA semialdehyde cob(II)yrinate acetyl-CoA lysyl-D-alanyl- containing) phosphorylase: dehydratase: uroporphyrinogen-III all-trans- a tetrahydrofolate 2-[(2R,5Z)- tRNA charging a (3Z)-alk-3-enoyl-CoA (to acetoacetate) 4-chlorobenzoate muramoyl-L-alanyl- D-alanyl-D-alanine) peptidoglycan lysyl-D-alanine synthase H839_RS10635 dehydrogenase: synthase: uroporphyrinogen-III L-cysteine desulfurase chorismate aminocarboxymuconate a,c-diamide glutaminyl-tRNA gln D-alanine) peptidoglycan acetylmuramoyl- hydratase: H839_RS04660 siroheme synthase: 4-hydroxybenzoate octaprenyl 2-carboxy-4- 4-chlorobenzoate- γ-D-glutamyl-L-lysyl- pentapeptide glycosyltransferase: H839_RS09615 subunit beta: enoyl-CoA H839_RS10620 H839_RS04945 siroheme isochorismate semialdehyde arginine-- biosynthesis via isopropanol pentapeptide glycosyltransferase: pentapeptide H839_RS09480 serine cysteine H839_RS01450 diphosphate methylthiazol-5(2H dodecenoyl-CoA -CoA ligase: D-alanyl-D-alanine H839_RS01655 purine nucleoside H839_RS11320 hydratase: 3-hydroxybutyryl- synthase: synthase: tRNA ligase: transamidation isopropanol H839_RS01655 undecaprenyl-transferase: cobyrinic acid enoyl-CoA dehydratase: [+ 4 isozymes] 3-octaprenyl-4- )-ylidene]ethyl oxaloacetate peptidoglycan phosphorylase: H839_RS09480 H839_RS01450 desulfurase: H839_RS14605 H839_RS00590 D-isomerase: dehydrogenase: 4-chlorobenzoyl-H839_RS05955 diphospho-H839_RS04390N- tryptophan 3S-hydroxy- CoA a,c-diamide hydratase: precorrin-1 hydroxybenzoate methionine synthase: thiamine-phosphate citrate synthase: peptidoglycan a peptidoglycan α H839_RS11910 H839_RS04665 H839_RS10775 isochorismate quinolinate cob(I)yrinate phosphate glt H839_RS17290 H839_RS14125 a peptidoglycan glycosyltransferase: 2-deoxy- - synthase dehydrogenase: synthase: H839_RS10635 [+ 4 isozymes] H839_RS02865 pyrophosphorylase: arginine- H839_RS13965 coA glycosyltransferase: with (L-alanyl-γ-D- acetylmuramoyl- (6Z,9Z,12Z,15Z,18Z)- pyruvate [+ 4 isozymes] a,c-diamide glutamyl-tRNA Gln malate:quinone acetone with (L-alanyl- di-trans,octa-cisH839_RS14270 UMP γ D-ribose 1- a purine base subunit beta: H839_RS17290 H839_RS07325 4-coumaryl-CoA precorrin-1 uroporphyrinogen III thiE -tRNA di-trans,octa-cisH839_RS14270 glutamyl-meso-2,6- L-alanyl- -D- tetracosapentaenoyl-CoA (S)-3- 2-succinyl-5- nicotinate-nucleotide thiamin phosphate arg synthetase: oxidoreductase: γ-D-glutamyl-L- phosphate H839_RS06365 hydrogenobyrinate an S-sulfanyl-[L- methyltransferase: ATP:cob(I)alamin ligase: a (2E)-2-enoyl-CoA diaminopimeloyl- -undecaprenyl glutamyl-L- D-glyceraldehyde hydroxybutanoyl- uroporphyrinogen III enolpyruvyl- pyrophosphorylase: dihydrofolate reductase: H839_RS00045 H839_RS03370malate dehydrogenase: enoyl-CoA acetone -undecaprenyl a,c-diamide H839_RS07135 adenosyltransferase: argS an L-glutamyl- lysyl-D-alanyl- D-alanyl-D-alanine) diphosphate lysyl- D-alanine 3-phosphate trp CoA methyltransferase: cysteine desulfurase] 6-hydroxy-3- H839_RS13235 2-octaprenylphenol H839_RS01390 an L-arginyl- H839_RS13955 long-chain fatty hydratase: carboxylase diphosphate H839_RS11625 Gln 4-hydroxybenzoyl- D-alanine) [+ 3 isozymes] [tRNA Arg ] [tRNA ] acid--CoA ligase: H839_RS09480 pentapeptide H839_RS07135 scaffold protein cyclohexene- adenosyl- dihydrofolate reductase: (S)-malate citrate a 2,3,4-saturated 3-hydroxybutyryl- subunit beta: CoA pentapeptide citrate RS06700 citrate NaMN a tRNA Arg coenzyme A a 2,3,4-saturated (3R for iron-sulfur 1-carboxylate precorrin-2 H839_RS07495 glutamyl-tRNA fatty acidH839_RS05380 acyl-CoA enoyl-CoA CoA epimerase: H839_RS05270 [+ 3 isozymes] cobyrinate serine thiamin )-3-hydroxyacyl-CoA cluster assembly: synthase: nicotinate-nucleotide a,c-diamide amidotransferase: [+ 5 isozymes] dehydrogenase: hydratase: H839_RS17290 [+ 3 isozymes] a 7,8-dihydrofolate hydroxymethyltransferase: a 5-methyltetrahydrofolate diphosphate a nascent peptidoglycan ditrans,octacis- UDP-N-acetyl- 5'-deoxy-5'- (S)-2,3- a cis-delta9-3- precorrin-2 H839_RS15160 H839_RS14600 siroheme synthase: adenylyltransferase: 3-(all-trans gcv system: H839_RS04090 H839_RS01025 fumarate hydratase: malate synthase: aconitate hydratase: H839_RS00510 H839_RS10635 ADP-D-ribose OPC6-CoA acetyl-CoA (S)-4-amino-5- adenosyl- H839_RS17135 acetoacetate with (L-alanyl-γ-D- α-D-muramoyl- a myristoyl-[acp] hydroxyC28:1- an S-sulfanyl-[cysteine 2-succinyl-5- H839_RS01450 H839_RS12875 -octaprenyl) FMNH [+ 2 isozymes] H839_RS00850 H839_RS09845 a 2,3,4-saturated a 2,3,4-saturated (3S undecaprenyldiphospho- fluoroadenosine oxopentanoate dihydrodipicolinate glycerol RS05590 glycerol cys RS02485 cys cobyrate 2 H839_RS05535 [+ 11 isozymes] 4-hydroxybenzoate lipid II (meso trans,octacis ADP-ribose siroheme desulfurase]-[disordered- glutamyl-meso-2,6- N-acetyl-(N- L-alanyl-γ-D- purine nucleoside beta-ketoadipyl glutamate-1- dipicolinate enoyl-ACP [acp] 3-ketoacyl- enolpyruvyl-6-hydroxy- nicotinate adenine benzene-1,2-diol cysteinyl-tRNA an L-glutaminyl- fumarate hydratase: fatty acyl CoA )-3-hydroxyacyl-CoA diaminopimelate -decaprenyl synthase: synthase: cys 3-hydroxyacyl-CoA diaminopimeloyl- acetylglucosaminyl) glutamyl-meso-2,6- phosphorylase: pyrophosphatase: CoA thiolase: semialdehyde form scaffold sirohydrochlorin 3-demethylubiquinone- thymidylate synthase: synthetase: Gln synthase reductase: ACP 3-cyclohexene- dinucleotide H839_RS07330 adenosylcobalamin [tRNA ] H839_RS01565 dehydrogenase: containing) phosphate H839_RS06460 H839_RS01450 protein] complex 9 3-methyltransferase: H839_RS07490 fumarate cis-aconitate D-alanyl-D-alanine) peptidoglycan muramoyl-L-alanyl-γ- diaminopimeloyl- H839_RS09615 H839_RS10500 aminotransferase: subunit A: H839_RS03255 reductase: 1-carboxylate (R)-1-amino- salvage from cobalamin H839_RS00055 an L-cysteinyl- phospho-N- guanine RS17360 guanine cysteine siroheme synthase: NAD synthetase: aconitate hydratase: H839_RS17290 pentapeptide glycosyltransferase: D-isoglutaminyl-N-(β- D-alanyl-D-alanine purine nucleoside ADP-ribose beta-ketoadipyl H839_RS01790 cys RS10380 cys (1R,6R)-2- H839_RS08740 Cys acetyl-CoA glyoxylate acetylmuramoyl- H839_RS05110 enoyl-ACP fabG sirohydrochlorin desulfurase: 2-propanol O adenosylcobyrate [tRNA ] H839_RS05535 H839_RS01655 H839_RS01450 2-methoxy- Cys succinate dehydrogenase: beta-ketoadipyl phosphorylase: pyrophosphatase: CoA thiolase: succinyl-6- H839_RS13215 5,6-dimethylbenzimidazole cob(I)alamin a tRNA protocatechuate D-asparaginyl)-L-lysyl-peptidoglycan pentapeptide glutamate-1- dipicolinate reductase: [+ 5 isozymes] H839_RS10775 6-(all-trans- -2-phosphate a (6S)-5-formyltetrahydrofolate H839_RS13655 peptidoglycan H839_RS11945 a (9Z)-3- sirohydrochlorin hydroxy-2,4- sirohydrochlorin cob(I)alamin CoA thiolase: D-alanyl-D-alanineglycosyltransferase: transferase: H839_RS11910 H839_RS10615 semialdehyde synthase H839_RS01730 + adenosylcobinamide- 5,10- 5,10-methylene- Amine and Polyamine Biosynthesis isocitrate lyase: a nascent peptidoglycan decaprenyl- OPC8-3- oxooctacos- cobaltochelatase: [+ 4 isozymes] ferrochelatase: