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Generated by SRI International Pathway Tools Version 25.0, Authors S Authors: Pallavi Subhraveti Ron Caspi Peter Midford 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_001431645Cyc: Stenotrophomonas panacihumi JCM 16536 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari molybdate spermidine ammonium phosphate putrescine RS01245 RS09040 RS02020 RS09210 RS06445 ModC RS13295 RS07950 RS10935 RS05290 CcmE RS10150 RS15175 CcmA TatC RS15730 PotA FliR FliN FliF RS16780 RS13205 RS11350 RS08505 RS08615 RS04655 HtpX MreD RodA RS11935 SecA Amt RS14010 RS09060 RS11475 FliJ FtsE Cls FtsY SecF RS04370 RS14605 RS03760 RS08055 RS10260 RS10235 RS11315 RarD RS07635 RS12840 RS06270 RS15230 MurJ RS07085 RS02925 FlhA RS06365 AmpE MgtE RS05150 RS17505 PstB spermidine molybdate ammonium putrescine phosphate RS11800 FliD Cofactor, Carrier, and Vitamin Biosynthesis Amino Acid Degradation Aromatic Compound Macromolecule Modification tRNA-uridine 2-thiolation NADH repair (prokaryotes) Degradation di-trans,octa-cis UDP-N-acetyl- ditrans,octacis- a peptidoglycan with UDP-N-acetyl-α-D- L-alanyl-γ-D- an N-terminal- an N-terminal- a peptidoglycan (R)-4-hydroxy- 4-hydroxy- a peptide with a [protein] and selenation (bacteria) ditrans,octacis- ditrans,octacis- phosphoenol an L-asparaginyl- [2Fe-2S] iron-sulfur Tetrapyrrole Biosynthesis L-valine degradation I -undecaprenyl α-D-muramoyl- undecaprenyldiphospho- (L-alanyl-γ-D-glutamyl- muramoyl-L-alanyl- undecaprenyldiphospho- undecaprenyldiphospho- glutamyl-meso- UDP-N-acetyl- a [glutamine- L-methionyl-L- L-methionyl-L- dimer (meso- 4-methyl-2- 4-methyl-2- an N-terminal C-terminal glu ubiquinol-8 biosynthesis ubiquinol-8 biosynthesis superpathway of tetrahydrofolate biosynthesis flavin biosynthesis I (bacteria and plants) superpathway of coenzyme A biosynthesis I (bacteria) NAD de novo biosynthesis superpathway of adenosylcobalamin salvage from cobinamide I adenosylcobalamin 2-methyladeninyl adenosylcobamide L-isoleucine degradation I L-leucine degradation I L-histidine degradation II L-phenylalanine catechol ATP dGDP pyruvate [tRNA Asn ] cluster biosynthesis phosphate L-alanyl-γ-D- N-acetyl-(N-acetyl-β-D- L-lysyl-D-alanyl-D- γ-D-glutamyl-meso- diaminopimelate α-D-muramate synthetase]- cysteinyl-[protein] threonyl-[protein] diaminopimelate oxoglutarate oxoglutarate L-methionine L-glutamate RS00630 FlgK (late decarboxylation) (early decarboxylation) II (from tryptophan) salvage from cobalamin biosynthesis from adenosylcobinamide-GDP NADH degradation degradation I (meta D-alanyl-D-alanine N-acetyl-(N- N-acetyl-(N- putative 4- putative 4- cys glutamyl-meso-2,6- glucosaminyl)muramoyl- alanine) pentapeptide 2,6-diaminopimelate L-tyrosine containing) 3-methyl-2- a 5,10- superpathway of heme b val I (aerobic) -cleavage pathway) acetylglucosaminyl) acetylglucosaminyl) hydroxy-4-methyl- hydroxy-4-methyl- L-cysteine desulfurase all-trans- cob(II)inamide heme b biosynthesis II Polyprenyl Biosynthesis ile his diaminopimeloyl- L-alanyl-γ-D-glutamyl-L- γ chorismate GTP oxobutanoate methylenetetrahydrofolate trp cob(I)alamin 2-methyladenine biosynthesis from glutamate cysteine leu muramoyl-L-alanyl- - muramoyl-L-alanyl- UDP-N- type I methionyl type I methionyl 2-oxoglutarate 2-oxoglutarate type I methionyl 30S aminoacyl- 4-hydroxybenzoate octaprenyl GTP (oxygen-independent) catechol D-alanyl-D-alanine lysyl-D-alanyl-D-alanine β γ tryptophan 2,3- cob(I)yrinic acid a,c-diamide desulfurase: branched-chain branched-chain histidine phe UDP-N- D-isoglutaminyl-N-( - -D-isoglutaminyl- acetylmuramate:L- bifunctional [glutamate- aminopeptidase: aminopeptidase: pyruvate penicillin- aldolase: aldolase: aminopeptidase: ribosomal tRNA cysteine diphosphate branched-chain β 3-methyl-2-oxobutanoate dioxygenase: adenosyltransferase: cobO nicotinate-nucleotide-- glu polyisoprenoid biosynthesis (E. coli) ARC20_RS02445 amino acid amino acid ammonia- phenylalanine 4- phospho-N- acetylmuramoyl- D-asparaginyl)-L-lysyl- N-( -D-asparaginyl) alanyl-gamma-D- -ammonia ligase]- map map kinase: pyk binding ARC20_RS05905 ARC20_RS05905 map protein hydrolase: RS00650 FlgL desulfurase: GTP GTP uroporphyrinogen-III amino acid 4-hydroxybenzoate hydroxymethyltransferase: ARC20_RS10940 cob(I)yrinic acid a,c-diamide dimethylbenzimidazole glutamate- an [L-cysteine aminotransferase: aminotransferase: lyase: hutH monooxygenase: acetylmuramoyl- monofunctional tripeptide--D-alanyl- D-alanyl-D-alanine -L-lysyl-D-alanine glutamyl- meso- adenylyl-L-tyrosine type I methionyl type I methionyl protein type I methionyl S6--L- pth ARC20_RS02445 all-trans- cyclohydrolase cyclohydrolase N-Formyl-L- cob(II)alamin uroporphyrinogen (R)-NADHX aminotransferase: urocanate 4-carboxy-4- 4-carboxy-4- octaprenyltransferase: panB adenosyltransferase: phosphoribosyltransferase: -tRNA desulfurase]-S- ARC20_RS05925 ARC20_RS05925 ARC20_RS02715 HMS pentapeptide- biosynthetic D- alanine ligase: diaminopimelate phosphorylase/ aminopeptidase: aminopeptidase: 2: mrdA aminopeptidase: glutamate 4-hydroxybenzoate octaprenyl I FolE: folE II RibA: ribA kynurenine decarboxylase: IPP bifunctional ARC20_RS05925 4-methyl-2- tyr hydroxy-2- hydroxy-2- aminoacyl- an S-sulfanyl-[L- ubiA 2,5-diamino-6- ARC20_RS09900 cob(I)yrinic acid cobT sulfanyl-L-cysteine transferase: peptidoglycan ARC20_RS14040 ligase: mpl [glutamate-- map ligase: rimK diphosphate 7,8- asp an L-glutamyl-ligase: gltX ARC20_RS03955 ADP-dependent 3-methyl-2- oxopentanoate urocanate monofunctional monofunctional map pyruvate oxoadipate oxoadipate map tRNA cysteine desulfurase] (5-phospho-D- a,c-diamide (3S)-3-methyl-2- HmsH protein: ARC20_RS14035 transglycosylase: ammonia-ligase] dGTP dihydroneopterin Glu coproporphyrinogen III NAD(P)H-hydrate oxobutanoate hydratase: undecaprenyldiphospho- UMP biosynthetic biosynthetic a peptidoglycan hydrolase: RS11960 RS15645 2-dehydropantoate [corrinoid adenosyltranferase]-cob(II)inamide 2-methyladenine [tRNA ] oxopentanoate ARC20_RS17425 adenylyltransferase: aldolase/ aldolase/ 4-hydroxybenzoate 4-hydroxy-3- 3'-triphosphate ribosylamino) aspartate 1- adenosyltransferase: dehydratase/ ARC20_RS04155 N-acetylmuramoyl-L- mtgA UDP-N-acetyl-α-D- peptidoglycan peptidoglycan UDP-N-acetyl- with D,D cross- D-ala a [protein] C- arfB adenosylcobinamide- ribotide phosphate oxygen-independent (2Z)-2- glnE an N-terminal L- an N-terminal L- oxaloacetate oxaloacetate octaprenyltransferase: octaprenylbenzoate pyrimidin- 2-dehydropantoate decarboxylase: cobO glutamyl-tRNA a [TusA sulfur- NAD(P)H-hydrate 4-imidazolone- alanyl-γ-D-glutamyl-meso muramoyl-L-alanyl- transglycosylase: transglycosylase: α-D-muramoyl- met met links (meso- met a peptide terminal α-L- GDP coproporphyrinogen hydroxypenta- cysteinyl-[protein] threonyl-[protein] decarboxylase: decarboxylase: ubiA 4(3H)-one 2-reductase: panE ARC20_RS06285 L-kynurenine cob(I)yrinic acid reductase: carrier protein]-S- epimerase: 3-methylbutanoyl- 5-propanoate -2,6-diaminopimeloyl- a peptidoglycan with di-trans,octa-cis γ-D-glutamyl-meso- mtgA mtgA L-alanyl-γ-D- diaminopimelate glutamate-α- an S-sulfanyl-[cysteine bifunctional ARC20_RS15810 III oxidase: hemN DMAPP L-glutamine 2,4-dienoate ligK ligK a,c-diamide sulfanyl-L-cysteine ARC20_RS11045 CoA D-alanyl-D-alanine (L-alanyl-γ-D-glutamyl- -undecaprenyl 2,6-diaminopimeloyl- glutamyl-meso-2,6- a [glutamine containing) L-glutamate Asn desulfurase]-[disordered- 7,8- β (S)-NADHX isobutanoyl-CoA (2S)-2- imidazolonepropionase: pyruvate pyruvate asn tRNA RS08440 4-hydroxy-3- diaminohydroxyphosphoribosylaminopyrimidine (R)-pantoate -alanine adenosyltransferase: adenosylcobinamide- (S)-4-amino-5- isovaleryl-CoA degradation II 2-keto-4- diphosphate D-alanyl-D-alanine diaminopimelate synthetase]-O form scaffold dihydroneopterin [corrinoid adenosyltranferase]-cob(I)inamide protoporphyrinogen IX methylbutanoyl-CoA ARC20_RS04170 L-lysyl-D-alanyl-D- a peptidoglycan di-trans,octa-cis a peptidoglycan di-trans,octa-cis octaprenylbenzoate deaminase/5-amino-6-(5-phosphoribosylamino) GDP oxopentanoate pentenoate 4 -(5'-adenylyl) 2-octaprenylphenol 3'-phosphate ARC20_RS09900 bifunctional dehydrogenase: alanine) pentapeptide dimer (E. faeciums) -undecaprenyl dimer (E. faecium -undecaprenyl protein] complex uracil reductase RibD: ribD cob(I)yrinic acid a,c-diamide ribazoletransferase: gln hydratase: -L-tyrosine 4-hydroxy-3- cob(II)alamin- glutamate-1- a [TusD sulfur- ADP-dependent ARC20_RS13130 N-formimino- diphosphate , tetrapeptide) diphosphate 5-amino-6-(5- pantoate--beta- 3-hydroxy- adenosyltransferase: cobO ARC20_RS12250 glutamate ARC20_RS02615 octaprenylbenzoate 2-polyprenylphenol [corrinoid semialdehyde geranyl carrier protein]-S- NAD(P)H-hydrate 3-methylcrotonyl- L-glutamate phospho-D- alanine ligase: L-kynurenine synthase large 2-keto-4- RS05960 5-hydroxylase: ubiH 6-hydroxylase: ubiB cob(I)yrinic acid a,c-diamide adenosyltranferase] 2,1- diphosphate methylacrylyl-CoA (E)-2- CoA 6 ribosylamino)uracil ARC20_RS06290 Coα-[α-(2- sulfanyl-L-cysteine dehydratase/ formimidoylglutamate a ring-opened 7- an O - ditrans,octacis- a [glutamine (3E)-5-chloro-2- an N-terminal- an N-terminal- L-alanyl-γ-D- a [cysteine desulfurase]- 3,4-dihydroxy-
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