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. Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. Mob3bCyc: Methylosinus trichosporium OB3b Cellular Overview Connections between pathways are omitted for legibility. Author: Katherine Rostkowski, Stanford University Aminoacyl- C1 Compound Utilization and Assimilation Amine and Polyamine Metabolic Regulator Detoxification tRNA Charging Biosynthesis Respiration respiration (anaerobic) Biosynthesis N-6-isopentenyl superpathway of C1 compounds oxidation to CO a reduced ammonium 2 a sulfurated 37 UQ a peptidoglycan O-phospho- L-glutamine ppGpp biosynthesis superoxide adenosine electron-transfer cys hydroxide glutathionylspermidine [sulfur carrier] L-homoserine biosynthesis II 2-phospho-D-glycerate radicals in tRNA flavoprotein nitrite biosynthesis (tRNA-dependent) methane reductase pppGpp degradation N-acetylmuramoyl- enolase: eno Electron- [NAD(P)H], glutathione spermidine glt superoxide Methane succinate L-alanine Cystathionine transferring- large subunit: Superoxide monooxygenase: dehydrogenase, amidase: gamma- flavoprotein MTRI02239 phosphoenolpyruvate dismutase: MTRI03541 hydrophobic MTRI03674 synthase: glutathionylspermidine dehydrogenase: an L-glutamyl- MTRI01611 membrane MTRI01910 nitrite synthase: MTRI00570 hydrogen MTRI00175 N-acetylmuramoyl- Gln methylamine methanol anchor protein: reductase [tRNA ] peroxide L-alanine pyruvate MTRI03869 Electron- [NAD(P)H], glutamyl-tRNA(Gln) kinase: pvtK amidase: glutathionylspermidine Catalase: transferring- small subunit: amidotransferase, MTRI03675 L-cystathionine GTP ppGpp Pyruvate MTRI00683 flavoprotein MTRI02240 B subunit: gatB oxaloacetate 2-methylthio- kinase: 5'-deoxyadenosine an unsulfurated dehydrogenase: nitrite [+ 2 isozymes] MTRI02411 O N-6-isopentyl met N-acetyl-D- 2 formaldehyde [sulfur carrier] MTRI00695 tRNA charging Nucleoside- adenosine- muramate Peptide an L-glutaminyl- diphosphate 37 tRNA Gln [tRNA ] kinase: pyruvate formaldehyde- an oxidized Phe Gly UQH gly 2 phe a tRNA a tRNA MTRI01595 (S)-malate activating electron-transfer enzyme: flavoprotein glt a tRNA glu fumarate MTRI03339 5,10- phenylalanyl-tRNA glycyl-tRNA GDP hydratase, [+ 2 isozymes] methylenetetrahydrofolate synthetase, alpha synthetase, beta class II: a [protein]-L- an N-modified a supercoiled Lys Trp Cys Thr Ile Met Leu Tyr ser asp His Val Ala Pro Arg Methylenetetrahydrofolate arachidoyl-CoA a lipid II lys a tRNA trp a tRNA cys a tRNA thr a tRNA ile a tRNA met a tRNA leu a tRNA tyr a tRNA ser a tRNA tRNA asp his a tRNA val a tRNA a tRNA ala pro a tRNA arg a tRNA acetyl-CoA formate 5,10-methylene- a malonyl-[acp] β-isoaspartate duplex DNA subunit: pheS subunit: glyS glutamyl-tRNA tRNA Asn gln Gln fumC_II aminoacyl-[tRNA] asn a tRNA tetrahydromethanopterin dehydrogenase Protein-L- replicative phenylalanyl-tRNA glycyl-tRNA synthetase: gltXb citrate (NADP(+)): MTRI03589 isoaspartate(D- fumarate Serine-type DNA lysyl-tRNA tryptophanyl-tRNA cysteinyl-tRNA threonyl-tRNA isoleucyl-tRNA methionyl-tRNA synthetase, beta leucyl-tRNA synthetase, alpha tyrosyl-tRNA seryl-tRNA aspartyl-tRNA histidyl-tRNA glutamyl-tRNA valyl-tRNA alanyl-tRNA prolyl-tRNA arginyl-tRNA synthase I: Aldehyde aspartate) O- 5,10- 3-oxoacyl-(acyl- D-Ala-D-Ala peptidyl- helicase: synthetase: lysSa synthetase: trpS synthetase: cysS synthetase: thrS synthetase: ileS synthetase: metG subunit: pheTb synthetase: leuS subunit: glyQ synthetase: tyrS synthetase: serS synthetase: aspSb synthetase: hisS1 synthetase: gltXb synthetase: valS synthetase: alaS synthetase: proS1 synthetase: argS MTRI00933 dehydrogenase methyltransferase: methenyltetrahydrofolate carrier-protein) carboxypeptidase: tRNA DnaB (NAD(+)): MTRI01436 CO H MTRI03744 5,10-methenyltetrahydromethanopterin S-hydroxymethylglutathione synthase III: fabH MTRI01604 hydrolase: ATP- citrate 2 2 an L-lysyl-[tRNA Lys ] an L-tryptophanyl-[tRNA Trp ] an L-cysteinyl-[tRNA Cys ] an L-threonyl-[tRNA Thr ] an L-isoleucyl-[tRNA Ile ] an L-methionyl-[elongator tRNA Met ] an L-phenylalanyl-[tRNA Phe ] an L-leucyl-[tRNA Leu ] a glycyl-[tRNA Gly ] an L-tyrosyl-[tRNA Tyr ] an L-seryl-[tRNA ser ] an L-aspartyl-[tRNA asp ] an L-histidyl-[tRNA His ] an L-glutamyl-[tRNA Glu ] an L-valyl-[tRNA Val ] an L-alanyl-[tRNA Ala ] an L-prolyl-[tRNA Pro ] an L-arginyl-[tRNA Arg ] an L-asparaginyl-[tRNA Asn ] an L-glutaminyl-[tRNA Gln ] 3-oxoacyl-(acyl- [+ 2 isozymes] protein-L- pth dependent aconitate succinate methenyltetrahydromethanopterin isoaspartate(D- DNA 10-formyl- carrier-protein) hydratase cyclohydrolase: MTRI03336 synthase III: fabH aspartate) O- helicase tetrahydrofolate a N- an N-modified 1: aco 5-formyl- methyltransferase: a tRNA RecQ: S-formylglutathione D-alanine acetylglucosamine- MTRI03956 amino acid tetrahydromethanopterin β recQ_fam cis-aconitate Formate-- -N-acetylmuramyl- a protein L- - a single Tetrapyrrole Biosynthesis coenzyme A tetrahydrofolate a 3-oxodocosanoyl-[acp] (tetrapeptide) isoaspartate stranded DNA Cofactor, Carrier, and Vitamin Biosynthesis aconitate ligase: MTRI03592 pyrophosphoryl- α-methyl ester tetrapyrrole biosynthesis I hydratase undecaprenol adenosylcobalamin biosynthesis II (late cobalt incorporation) superpathway of heme biosynthesis 1: aco adenosylcobalamin biosynthesis I (early cobalt insertion) biotin biosynthesis I superpathway of ubiquinol- ubiquinol-9 biosynthesis superpathway of pyridoxal 5'-phosphate biosynthesis and salvage adenosylcobalamin salvage from cobinamide I from uroporphyrinogen-III tetrapyrrole formate 8 biosynthesis (prokaryotic) (prokaryotic) biosynthesis II D-threo-isocitrate ditrans,octacis UDP-N- glt NAD + a nucleoside uroporphyrinogen-III D-erythrose- -undecaprenyl acetylmuramoyl- NADPH RNA citrate carbonic acid uroporphyrinogen-III malonyl-CoA all-trans- cobinamide glutamyl-tRNA uroporphyrinogen-III methanol triphosphate (2E,6E)-farnesyl isocitrate γ nonaprenyl 4-phosphate gly oxidation to phosphate L-alanyl- -D- diphosphate 4-hydroxybenzoate synthetase: gltXb dehydrogenase, chorismate diphosphate uroporphyrinogen 5-aminolevulinic formaldehyde II glutamyl-L-lysyl- glutamyl-tRNA NADP- CO NAD(P)(+) Citrate (pro-3S)- Carbonate malonyl-CoA decarboxylase: hemE acid synthase: 2 D-alanyl-D-alanine DNA- synthetase: gltXb dependent: idh1 methanol transhydrogenase lyase: MTRI03467 dehydratase: methyl ester 4-hydroxybenzoate an L-glutamyl-[tRNA Glu ] MTRI02263 phospho-N- directed RNA precorrin-1 erythronate- (AB-specific) Citrate (pro-3S)- MTRI03466 precorrin-1 polyprenyl adenosylcobinamide coproporphyrinogen III 5-amino-levulinate acetylmuramoyl- polymerase, all-trans- 4-phosphate 2-oxoglutarate : MTRI03418 lyase: MTRI03584 [+ 3 isozymes] transferase: ubiA pentapeptide- beta' subunit: 4-hydroxybenzoate octaprenyl Porphobilinogen formaldehyde transferase: mraY NAD(P)(+) MTRI02623 diphosphate oxygen-independent synthase: formaldehyde assimilation I (serine pathway) nonaprenyl-4- transhydrogenase [+ 3 isozymes] a 3-oxoglutaryl- coproporphyrinogen MTRI01637 N-acetylmuramoyl-L- acetate oxaloacetate CO H O (AB-specific) 2 2 precorrin-2 [acp] methyl ester 4-hydroxybenzoate hydroxybenzoate 2-oxo-3-hydroxy-4- adenosyl-cobinamide glutamate-1-semialdehyde III oxidase: MTRI02338 γ UMP precorrin-2 aerobic respiration (alternative oxidase pathway) formaldehyde alanyl- -D-glutamyl-L- : MTRI03420 polyprenyl phosphobutanoate phosphate nicotinate protoporphyrinogen IX porphobilinogen Nucleoside 5,6-dimethylbenzimidazole oxygen-independent lysyl- D-alanyl-D-alanine- precorrin-2 C20- transferase: ubiA mononucleotide and Nucleotide RNA Adenosylcobinamide- coproporphyrinogen diphosphoundecaprenol methyltransferase: UbiA porphobilinogen NAD + Degradation phosphate III oxidase: hemN NADH NADP + cobI_cbiL a (3R)-3- prenyltransferase: 2-nonaprenylphenol deaminase: hemC adenosine hydroxyglutaryl- 4-phospho- guanylyltransferase: 5-amino-levulinate UQH 5,10- MTRI00242 2 nucleotides precorrin-3A cobalt-precorrin-2 MTRI01382 methylenetetrahydrofolate [acp] methyl ester hydroxy-L-threonine protoporphyrinogen IX hydroxymethylbilane degradation II Porphobilinogen N-acetylmuramoyl-L- a protein with a (3R,11Z)-3- precorrin-3B 3-octaprenyl-4- 4-hydroxythreonine- adenosylcobinamide- α-ribazole-5'-phosphate coenzyme A biosynthesis synthase: Uroporphyrinogen gly Glycine a malonyl-[acp] a palmitoleoyl-[acp] alanyl-D-isoglutaminyl- reduced L- hydroxyoctadec- synthase: hydroxybenzoate 3-(all-trans- 4-phosphate GDP AMP ATP a glutamine MTRI01637 III synthase hydroxymethyltransferase: L-lysyl-(glycyl) - cysteine residuesDSBA 11-enoyl-[acp] MTRI04055 a (2E)- nonaprenyl) dehydrogenase: D-4'- 5 synthetase beta- D-glyceraldehyde- HEM4: MTRI00590 MTRI00618 D-alanyl-D-alanine- cobalt-precorrin-3 enoylglutaryl- benzene-1,2-diol pyruvate pdxA phosphopantothenate porphobilinogen NADH-ubiquinone oxidoreductase: hydroxyacyl- 3-phosphate 3-oxoacyl- diphosphoundecaprenyl- MTRI00875 precorrin-3B [acp] methyl ester (2S)-2-amino-3-oxo-4- protoporphyrin IX uroporphyrinogen-III oxidoreductase (acyl-carrier- Uroporphyrin-III R-4'- porphobilinogen [acyl-carrier- N-acetylglucosamine [Glutamate-- DSBA protein) precorrin-3B C17- 2-octaprenylphenol phosphonooxybutanoate adenosylcobalamin chain 4L: adenosine C/tetrapyrrole