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_000020585Cyc: Alteromonas mediterranea DE Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari pro pro L-fucose GlnK RS01880 FucP RS01650 RS01915 PutP PutP L-fucose pro pro RS01595 Aminoacyl-tRNA Charging Amino Acid Degradation N 6 -(3-methylbut- a nascent peptidoglycan a peptidoglycan UDP-N-acetyl-α-D- a nascent DNA with adenine:7,8- (4R)-4-hydroxy- a peptidoglycan a [protein]-L- queuosine at an [amino-group a sulfurated + a nucleoside an L-asparaginyl- tRNA charging L-valine degradation I 2-en-1-yl)- γ γ muramoyl-L-alanyl- NADPH NAD a [glutamine- dihydro-8- dimer (meso- glutamate-O 5 Fermentation mixed acid fermentation L-isoleucine degradation I Alcohol Degradation with (L-alanyl- -D- with (L-alanyl- -D- peptidoglycan ATP 2-oxoglutarate RNA glu position 34 Asn carrier protein]- L-leucine degradation I L-threonine degradation I L-arginine degradation [sulfur carrier] 37 synthetase]- triphosphate [tRNA ] adenosine glutamyl-meso-2,6- glutamyl-meso-2,6- γ-D-glutamyl-meso- (meso-DAP oxoguanine mismatch diaminopimelate -methyl-ester of a tRNA Asp C-terminal-γ- II (AST pathway) D-alanyl-D-alanine L-tyrosine in tRNA diaminopimeloyl- diaminopimeloyl-D- 2,6-diaminopimelate containing) containing) (L-glutamate 5- Phe Gly Trp Arg asp Asn Thr Gln Met Met Cys Ile Pro His Tyr Val phosphoenolpyruvate val phe a tRNA gly a tRNA trp a tRNA arg a tRNA tRNA asp asn tRNA thr a tRNA gln a tRNA elongator tRNA met initiator tRNA met cys a tRNA ile a tRNA pro a tRNA his a tRNA tyr a tRNA val a tRNA ile glycerol and glycerophosphodiester degradation alanine) tetrapeptide NAD(P)(+) bifunctional N-acetyl- leu thr D-alanyl-D-alanine) A/G-specific DNA- chemotaxis tRNA aminoacyl- semialdehyde-2- a tRNA Ala ala lys a tRNA Lys leu a tRNA Leu ser a tRNA ser arg tRNA (N6-isopentenyl transhydrogenase 4-hydroxy-2- gamma- glu pentapeptide bifunctional [glutamate- adenine directed RNA yl)-L-glutamate glu a tRNA branched-chain branched-chain serine/threonine UDP-N- membrane-bound oxoglutarate penicillin- response glutamyl- tRNA phosphoenolpyruvate branched-chain arginine N- glycerol adenosine(37)-C2)- (Re/Si-specific): -ammonia ligase]- polymerase glutamyl- glycine-- arginine- threonine- glutamine- methionine- methionine- isoleucine- proline-- histidine- valine-- pyruvate kinase: pyk amino acid amino acid dehydratase: acetylmuramoyl- lytic murein glycosylase: binding regulator protein- Q(34) hydrolase: phenylalanine- tryptophan- aspartate- asparagine- cysteine-- tyrosine-- carboxylase: ppc amino acid succinyltransferase: a glycerophosphodiester methylthiotransferase MADE_RS18895 aldolase/2- phosphate aminotransferase: aminotransferase: MADE_RS16755 penicillin- tripeptide--D- transglycosylase adenylyl-L-tyrosine mutY protein subunit glutamate synthetase pth -tRNA ligase: tRNA ligase: -tRNA alanine--tRNA -tRNA lysine--tRNA -tRNA -tRNA -tRNA leucine--tRNA -tRNA serine--tRNA -tRNA -tRNA tRNA ligase: -tRNA tRNA ligase: -tRNA tRNA ligase: tRNA ligase: (2Z)-2-aminobut- astA MiaB: miaB MADE_RS18900 dehydro-3-deoxy- an [amino-groupreductase: aminotransferase: N 2 -succinyl- alanyl-D- alanine phosphorylase/ 2: mrdA omega: rpoZ pheS pheT glyS glyQ ligase: trpS ligase: alaS ligase: argS ligase: lysS ligase: aspS ligase: asnS ligase: thrS ligase: leuS ligase: glnS ligase: serS ligase: metG ligase: metG MADE_RS11920 ligase: ileS MADE_RS13080 ligase: hisS MADE_RS15540 MADE_RS15745 MADE_RS02090 4-methyl-2-MADE_RS02090 2-enoate binding MltF: mltF phosphogluconate methylesterase: GluQRS: aminoacyl- carrier protein]- pyruvate MADE_RS02090 succinate MADE_RS18905 [glutamate-- argC oxaloacetate oxopentanoate L-arginine glycerophosphodiester protein ligase: murF [+ 3 isozymes] an apurinic site aldolase: eda [+ 3 isozymes] MADE_RS05550 gluQRS tRNA C-terminal-γ- 3-methyl-2-oxobutanoate (3S)-3-methyl-2- glycerol phosphodiesterase: dehydrogenase, 2: mrdA Si-specific NAD(P)(+) ammonia-ligase] an L-phenylalanyl- an L-tryptophanyl- an L-asparaginyl- an L-glutaminyl- an L-methionyl- an L-methionyl- N-succinylarginine adenine within DNA a peptidoglycan chemotaxis hydrolase: (5-phospho- a glycyl-[tRNA Gly ] an L-alanyl-[tRNA Ala ] an L-arginyl-[tRNA Arg ] an L-lysyl-[tRNA Lys ] an L-aspartyl-[tRNA asp ] an L-threonyl-[tRNA Thr ] an L-leucyl-[tRNA Leu ] an L-seryl-[tRNA ser ] an L-cysteinyl-[tRNA Cys ] an L-isoleucyl-[tRNA Ile ] an L-prolyl-[tRNA Pro ] an L-histidyl-[tRNA His ] an L-tyrosyl-[tRNA Tyr ] an L-valyl-[tRNA Val ] an L-glutamyl-[tRNA Glu ] D-lactate malate oxopentanoate MADE_RS02600 hydrophobic transhydrogenase: adenylyltransferase: Phe Trp Asn [tRNA Gln ] Met Met dihydrolase: astB UDP-N-acetyl-α-D- a mature a nascent with D,D cross- D-ala response glutamyl- arfB L-glutamyl)- [tRNA ] [tRNA ] [tRNA ] [elongator tRNA ] [initiator tRNA ] dehydrogenase: dld dehydrogenase: mdh membrane anchor sthA glnE RNA nitrite nitrite 2 glycerol kinase glycerophosphodiester muramoyl-L-alanyl- pyruvate links (meso- queuosine at L-glutamate RS07525 2-iminobutanoate N -succinyl- protein: sdhD a nascent peptidoglycan peptidoglycan peptidoglycan glyoxylate regulator protein- formate formate D-lactate malate 3-methylbutanoyl- phosphodiesterase: glpQ γ diaminopimelate L-ornithine GlpK: glpK with D,D cross-links D-ala -D-glutamyl-meso- with (L-alanyl- (meso-DAP glutamate position 34 dehydrogenase: Asp dehydrogenase: dld formate acetyl-CoA CoA 6 a [glutamine containing) Asn isobutanoyl-CoA (2S)-2- succinylornithine N -(3-methylbut- (meso-diaminopimelate 2,6-diaminopimeloyl- γ-D-glutamyl- containing) with NADH NADP + methylesterase: of a tRNA asn tRNA MADE_RS17745 an unsulfurated synthetase]-O isovaleryl-CoA methylbutanoyl-CoA transaminase: 5'-deoxyadenosine 2-en-1-yl)-2- met containing) D-alanyl-D-alanine meso-2,6- GlcNAc terminus MADE_RS01975 nitrite nitrite dehydrogenase: sn-glycerol 3-phosphate [sulfur carrier] 4 -(5'-adenylyl) RS12470 (R)-lactate phosphate citrate synthase: (S)-malate MADE_RS02370 (methylsulfanyl) diaminopimeloyl- formate formate 2-oxobutanoate 37 -L-tyrosine MADE_RS08235 N 2 -succinyl- adenosine D-alanine) acetyltransferase: pta MADE_RS09575 glycerol-3-phosphate a [protein]-α- Amino Acid Biosynthesis fumarate hydratase: isovaleryl-CoA L-glutamate 5- in tRNA tetrapeptide MeOH superpathway of L- L-histidine biosynthesis superpathway of L-methionine 2-methylcitrate dehydrogenase: glpD L-glutamate L-lysine biosynthesis I L-cysteine biosynthesis I superpathway superpathway of L-serine CO H acetaldehyde MADE_RS09970 methylacrylyl-CoA dehydrogenase: (E)-2- semialdehyde isoleucine biosynthesis I 2 2 synthase: prpC biosynthesis (by sulfhydrylation) of L-threonine and glycine biosynthesis I acetyl phosphate class II fumarate MADE_RS13905 methylcrotonoyl-CoA ethanol fatty acid succinylglutamate- DHAP oxaloacetate PRPP biosynthesis hydratase: fatty acid an inactive α-Kdo-(2->4)- a reduced L-alanyl-γ-D- a [bis(guanylyl 2445 UDP-N-acetyl- a peptidoglycan α ε an insertion ser Metabolic Regulator Biosynthesis oxidation 3-methylcrotonyl- propanoyl-CoA semialdehyde a guanine N ,N -diacetyl-lysyl- an L-cysteinyl- asp oxaloacetate 3-phospho-D-glycerate acetate kinase: dehydrogenase: citrate MADE_RS15625 a reduced α ubiquinone-6 a protein with glutathione α 3',5'-ADP aspartate/ CoA oxidation dehydrogenase: ribonucleoside SAM -Kdo-(2->6)- a palmitoleoyl-[acp] electron-transfer glutamyl-meso-2,6- molybdopterin) cys in 23S rRNA -D-muramoyl- D-glt dimer (E. faeciums) D-alanyl-D-alanine sequence Cys a metal a metal ATP lysine-sensitive oxaloacetate MADE_RS15225 complex subunit Degradation/ flavodoxin a disulfide bond ATP [tRNA ] tyrosine/aromatic phosphoglycerate MADE_RS07260 complex triphosphate lipid IV (E. coli) flavoprotein diaminopimeloyl- UDP-N-acetyl- cofactor bifunctional L-alanine element IS30 biotin cation cation aspartate/ serine O- aspartate/ acetyl/propionyl/ phosphate astD A DDE-type 3'(2'),5'- phosphoribosyltransferase: aspartokinase dehydrogenase: serA ppGpp metabolism aconitate hydratase fumarate alpha FadJ: fadJ Utilization/ α RS17025 aminotransferase: glycine betaine subunit alpha 2 reductase D-alanine -D-muramate chaperone]- 23S rRNA tyrosine/aromatic acetyltransferase: tyrosine/aromatic ethanol AcnA: acnA methylcrotonyl- propionyltransferase: pta N - penicillin- penicillin- integrase/ bisphosphate hisG 3: lysC 3-phosphooxypyruvate acetate (S)-3-hydroxy- Assimilation - Other electron transfer L-cysteine acetate acetate MADE_RS11050 aminotransferase: cysE aminotransferase: biosynthesis I (Gram- CoA carboxylase FadJ: fadJ succinylglutamate LpxL/LpxP glutathione- (guanine(2069)-N(7) UDP-N- binding transposase/ aminoacyl- nucleotidase bifunctional pppGpp [+ 2 isozymes] isobutanoyl-CoA propanoyl acrylonitrile flavoprotein- binding asp β MADE_RS11050 MADE_RS11050 negative bacteria) (2S,3S)-3-hydroxy-2- anaerobic family Kdo(2)- UDP-N- dependent )-methyltransferase acetylmuramoyl- protein recombinase: bifunctional biotin- tRNA CysQ: cysQ 1-(5-phospho- -D-ribosyl)-ATP serine O- 3-phosphoserine/ bifunctional GTP subunit alpha: phosphate