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_000753795Cyc: Shewanella mangrovi YQH10 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari molybdate phosphate phosphate PstC RS04785 RS08110 FtsX GspE RS18465 FliL RS02695 RS05740 ModC RsxB RS12030 SohB FliG FliM FliQ FlhF RS02410 RS02250 RS10010 RS15620 LptG RS01680 RS01605 MurJ RS02400 RS01330 RS11775 RS06520 RS11750 RS08505 FlhB RS00580 RS09545 LptC CrcB RS06405 RS14070 RS14040 FliG RS08485 RS08495 RS00745 RS15365 RS01080 MotA RS11785 RS09655 CcmD RS19200 YajC BrnQ TrkA ArsB RS02180 RS05465 NrfE FlhB FliO FliJ FliF TolR RS10365 ZipA RS06935 RS05785 RS12390 GspL RS03340 RS03595 RS06070 RS07340 RS16385 UbiB PstB PstB molybdate phosphate phosphate LolA RS14075 6 Tetrapyrrole Biosynthesis N -(3-methylbut- ditrans,octacis- a peptidoglycan with 3-phenyl-2- ditrans,octacis- ditrans,octacis- a [bis(guanylyl UDP-N-acetyl- (4R)-4-hydroxy- a [protein]-L- a [protein]-L- a [protein] Cofactor, Carrier, and Vitamin Biosynthesis a sulfurated a lipid II MoO - a uracil in DNA a nucleoside 5 an L-asparaginyl- NADPH NAD + biotin biosynthesis I Fermentation 2-en-1-yl)- undecaprenyldiphospho- (L-alanyl-γ-D-glutamyl- tyr undecaprenyldiphospho- undecaprenyldiphospho- molybdopterin) cys α-D-muramoyl- 2 RNA glutamate-O C-terminal glu superpathway of menaquinol-8 biosynthesis I acyl carrier guanylyl molybdenum ubiquinol-8 biosynthesis NADP flavin biosynthesis I (bacteria and plants) FeMo cofactor biosynthesis molybdenum cofactor biosynthesis tetrahydromonapterin mixed acid fermentation [sulfur carrier] oxopropanoate 2-oxoglutarate ATP triphosphate methionine [tRNA Asn ] ubiquinol-8 biosynthesis superpathway of heme b biosynthesis from uroporphyrinogen-III superpathway of pyrimidine Nucleoside and Nucleotide Degradation adenosine 37 N-acetyl-(N-acetyl-β-D- L-lysyl-D-alanyl-D- N-acetyl-(N- N-acetyl-(N- cofactor L-alanyl-γ-D- molybdopterin -methyl-ester peptide- L-glutamate LptA FliD protein activation cofactor biosynthesis (late decarboxylation) biosynthesis biosynthesis superpathway of purine deoxyribonucleosides degradation (early decarboxylation) tetrapyrrole biosynthesis siroheme biosynthesis deoxyribonucleosides degradation in tRNA glucosaminyl)muramoyl- alanine) pentapeptide acetylglucosaminyl) acetylglucosaminyl) chaperone]- glutamyl-meso-2,6- cofactor methionine a malonyl-[acp] MoO - a [4Fe-4S] iron- I (from glutamate) phosphoenolpyruvate penicillin- bifunctional uracil-DNA chorismate an apo acyl- all-trans- 2 chorismate + molybdate L-alanyl-γ-D-glutamyl-L- aspartate/ muramoyl-L-alanyl-γ- muramoyl-L-alanyl-γ-D- L-cysteine diaminopimeloyl- DNA- (S)-S-oxide malonyl-ACP O- molybdopterin NAD GTP sulfur cluster uroporphyrinogen-III 2'-deoxycytidine binding 4-hydroxy-2- glycosylase: chemotaxis 30S aminoacyl- carrier protein 4-hydroxybenzoate octaprenyl NAD(+) uroporphyrinogen-III tRNA (N6-isopentenyl lysyl-D-alanyl-D-alanine tyrosine/aromatic D-isoglutaminyl-N-(β- isoglutaminyl-L-lysyl- D-alanyl-D-alanine molybdenum cofactor directed RNA reductase methyltransferase isochorismate holo-ACP cofactor molybdenum cofactor molybdenum GTP 2'-deoxyguanosine protein oxoglutarate ung response ribosomal tRNA diphosphate kinase: glu uroporphyrin-III pyruvate kinase: pyk phosphoenolpyruvate cytidine adenosine(37)-C2)- aminotransferase: D-asparaginyl)-L-lysyl- (glycyl) -D-alanyl-D-alanine guanylyltransferase: polymerase: regulator protein- MsrA: msrA BioC: bioC synthase: synthase: guanylyltransferase: ABC GTP uroporphyrinogen 5 cysteine 2: mrdA aldolase/2- protein hydrolase: RS14185 RS06560 a malonyl-[acp] nadK bifunctional molybdopterin methyltransferase: carboxylase: ppc 2'-deoxyadenosine methylthiotransferase HR45_RS02745 D-alanyl-D-alanine mobA uracil-DNA rpoC rpoB HR45_RS08935 HR45_RS07245 4-hydroxybenzoate guanylyl mobA all-trans- transporter cyclohydrolase decarboxylase: hemE glutamate-- deaminase: monofunctional desulfurase penicillin- D-alanyl-D-alanine dehydro-3-deoxy- glutamate bifunctional S6--L- pth methyl ester a holo acyl- + 3,4-dihydroxy- MiaB: miaB glycosylase: + molybdenum NADP a NifB protein I FolE: folE tRNA ligase: gltX HR45_RS12620 cdd thymidine biosynthetic aspartate/ monofunctional [+ 3 isozymes] methylesterase: methionine glutamate NADH NADP carrier protein octaprenyltransferase: 4-hydroxybenzoate octaprenyl 2-butanone-4- ATP-binding molybdopterin 7,8-dihydroneopterin pyruvate NifS: nifS binding carboxypeptidase/ phosphogluconate ung aminoacyl- beta-ketoacyl- isochorismate coproporphyrinogen III Glu [+ 2 isozymes] pyrimidine/purine succinate tyrosine/aromatic adenylyl HR45_RS13515 sulfoxide ubiA cofactor diphosphate with a K-cluster protein adenylyltransferase: 3'-triphosphate an L-glutamyl-[tRNA ] oxaloacetate peptidoglycan monofunctional biosynthetic [+ 2 isozymes] protein D-alanyl-D-alanine- aldolase: eda ligase: rimK tRNA ACP synthase phosphate synthase/ precorrin-1 2'-deoxyuridine pyrimidine/purine adenosine nucleoside dehydrogenase, aminotransferase: molybdenum reductase ModC: modC mog transglycosylase: biosynthetic peptidoglycan 2: mrdA endopeptidase: dacB hydrolase: I: fabB 2-succinyl-6- GTP cyclohydrolase dihydroneopterin malate nucleoside deaminase: phosphorylase: hydrophobic HR45_RS10860 cofactor an apyrimidinic uracil RNA B/A protein: RS01160 FlgL 4-hydroxy-3- 4-hydroxybenzoate oxygen-independent oxygen-dependent glutamyl-tRNA uroporphyrin-III formate C- mtgA peptidoglycan transglycosylase: a [bis(guanylyl α a [protein] C- arfB hydroxy-2, 4- II: HR45_RS18030 molybdopterin triphosphate 2'- dehydrogenase: phosphorylase: add HR45_RS08435 membrane anchor D-alanyl-D-alanine site in DNA MeOH a [protein]- - HR45_RS04300 beta-ketoacyl- octaprenylbenzoate octaprenyltransferase: molybdate coproporphyrinogen coproporphyrinogen reductase: hemA methyltransferase: acetyltransferase: pflB transglycosylase: mtgA ala molybdopterin) glyoxylate pyruvate terminal α-L- cyclohexadiene- GTP cyclohydrolase adenine dinucleotide epimerase: folX HR45_RS11295 HR45_RS08435 purine-nucleoside protein: sdhD 3-(4- carboxypeptidase/ a N- L-glutamate a protein-L- ACP synthase UbiD family ubiA a NifB protein III oxidase: hemN oxidase: hemF HR45_RS12620 a peptidoglycan with di-trans,octa-cis mtgA cofactor D-alanyl-D-alanine- methionine- glutamate-α- 1-carboxylate II: ribA 7,8-dihydromonapterin (R)-lactate [+ 2 isozymes] thymidine pyrimidine/purine phosphorylase: hydroxyphenyl) phe D-ala acetylglucosamine- II: fabF with an L-cluster (S)-4-amino-5-oxopentanoate 6 (L-alanyl-γ-D-glutamyl- -undecaprenyl a peptidoglycan di-trans,octa-cis chaperone]-S- L-glutamate Asn synthase: menH decarboxylase: bifunctional triphosphate [+ 2 isozymes] formate acetyl-CoA nucleoside 2'-deoxyinosine deoD N -(3-methylbut- pyruvate endopeptidase: dacB -N-acetylmuramyl- (S)-S-oxide asn tRNA RS01350 FlgK 4-hydroxy-3- 2,5-diamino-6-(5-phospho-D- phosphorylase: 5'-deoxyadenosine an unsulfurated L-lysyl-D-alanyl-D- diphosphate di-trans,octa-cis dimer (S. aureus) -undecaprenyl sulfanyl-L-cysteine a 3-oxoglutaryl- HR45_RS00530 nitrogenase molybdopterin- protoporphyrinogen IX protoporphyrinogen IX glutamate-1- (S)-malate pyrimidine/purine phosphorylase: 2-en-1-yl)-2- met a peptidoglycan (tetrapeptide) 2-succinyl-5- octaprenylbenzoate ribosylamino)pyrimidin-4(3H)-one phosphopantothenate biosynthesis I precorrin-2 deoA [sulfur carrier] alanine) pentapeptide -undecaprenyl diphosphate [acp] methyl ester 4-hydroxy-3- iron- guanine dinucleotide semialdehyde 2,1- nucleoside HR45_RS08435 (methylsulfanyl) dimer (E. faeciums) UDP-N- pyrophosphoryl- enolpyruvyl- 4-hydroxy-3- bifunctional 37 polyprenylbenzoate phosphate bifunctional 2-methylcitrate fumarate hydratase: phosphorylase: thymine adenosine diphosphate D-ala acetylmuramoyl- undecaprenol 3-oxoacyl- 6-hydroxy-3- octaprenylbenzoate diaminohydroxyphosphoribosylaminopyrimidine molybdenum biosynthesis 2-methyladeninyl adenosylcobamide aminomutase: hemL bifunctional purine-nucleoside pyrimidine/purine decarboxylase: ubiD D-threo-7,8- menaquinone- menaquinone- acetyltransferase: pta acetaldehyde- synthase: prpC HR45_RS03200 HR45_RS08435 purine nucleotides degradation II (aerobic) in tRNA L-alanyl-γ-D- ACP cyclohexene- 5-hydroxylase: ubiH deaminase/5-amino-6-(5-phosphoribosylamino) cofactor adaptor protein biosynthesis from adenosylcobinamide-GDP 3-methyl-2-oxobutanoate precorrin-2 phosphorylase: nucleoside superpathway of D-ribulose 5-phosphate pyridoxal 5'-phosphate biosynthesis I dihydroneopterin dependent dependent 5-aminolevulinate CoA/alcohol citrate synthase: [+ 2 isozymes] glutamyl-meso-2,6- RS06585 FliD reductase 1-carboxylic- 3,4-dihydroxy- uracil reductase RibD: ribD biosynthesis MobB/molybdopterin dehydrogenase/ CO H uridine deoD phosphorylase: 2-octaprenylphenol demethylmenaquinol-8 biosynthesis I 3-methyl-2-oxobutanoate protoporphyrinogen IX protoporphyrinogen IX 2 2 dehydrogenase: adhE FabG: fabG protein molybdotransferase sirohydrochlorin HR45_RS05150 fumarate phosphorylase: HR45_RS08435 diaminopimeloyl- acid synthase: 5-all-trans- bifunctional 5-amino-6-(5-phospho-