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_000421485Cyc: Desulfurobacterium sp. TC5-1 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari Na + phosphate OadA PstB Na + phosphate Aromatic Compound Other Biosynthesis C1 Compound Utilization Carboxylate Tetrapyrrole Biosynthesis and Assimilation glutaminyl-tRNA gln Aminoacyl-tRNA Charging Biosynthesis Degradation a nascent peptidoglycan a peptidoglycan (1S,2R)-1- DNA combined biosynthesis via transamidation Polyprenyl Biosynthesis Macromolecule Modification 3-[(1-carboxyvinyl) H O D-glycero-β-D- a [glutamine- a nucleoside 8-amino-7- tetrapyrrole biosynthesis reductive TCA cycle I γ γ C-(indol-3- diphosphate 2 H O with exogenous Amine and Polyamine Biosynthesis chorismate biosynthesis acetate with (L-alanyl- -D- with (L-alanyl- -D- oxy]benzoate SAM ser ATP 2 ATP RNA ATP roseoflavin oxononanoate manno-heptose GTP synthetase]- triphosphate from 3-dehydroquinate I (from glutamate) conversion glutamyl-meso-2,6- glutamyl-meso-2,6- yl)glycerol 5'-phosphate DNA to form a glu trans, trans-farnesyl biosynthesis III tRNA-uridine 2-thiolation and selenation (bacteria) 3-phosphate 1-phosphate L-tyrosine recombinational spermidine biosynthesis III di-trans,poly-cis geranyl diphosphate 2-oxoglutarate to acetyl-CoA diaminopimeloyl- diaminopimeloyl-D- spermidine biosynthesis I putrescine diphosphate 3-dehydroquinate D-alanyl-D-alanine) alanine) tetrapeptide aminofutalosine RdgB/HAM1 family DNA- junctionHolliday -undecaprenyl biosynthesis pimelate glu acetate elongation biosynthesis I biosynthesis type I 3- 6-carboxyhexanoate- glutamate-- pentapeptide synthase tryptophan non-canonical D-glycero-beta-D- [glutamate-- directed RNA riboflavin junction phosphate biosynthesis cys acetate- factor 4: lepA SAM dehydroquinate -CoA ligase: tRNA ligase: MqnE: mqnE synthase purine NTP manno-heptose ammonia-ligase] polymerase: biosynthesis resolvase SAM IPP (2E,6E)-farnesyl IPP -CoA [+ 5 isozymes] resolution of dehydratase: aroD H153_RS09535 H153_RS0103970 aminofutalosine subunit pyrophosphatase: 1-phosphate adenylyltransferase: rpoB rpoC protein RuvX: ruvX an L-glutamyl- arg diphosphate an L-glutamyl- ligase: acs penicillin-binding recombinational S-adenosylmethionine di-trans,poly-cis- prenyltransferase: 3-dehydroshikimate pimeloyl-CoA synthase beta: trpB rdgB adenylyltransferase: H153_RS0104125 RibF: ribF F0F1 ATP Gln Glu NADP-dependent protein 2: [+ 2 isozymes] junction + + [tRNA ] S-adenosylmethionine H153_RS0107220 [tRNA ] acetyl-CoA + H H decarboxylase: decaprenylcistransferase: MqnE: mqnE tryptophan synthase inorganic rfaE2 phosphate H synthase gln decarboxylase: geranyl shikimate 8-amino-7- isocitrate dehydrogenase: H153_RS0101440 GDP formation of two Asp-tRNA(Asn) H153_RS0105370 arg DMAPP di-trans,octa-cisuppS glutamyl-tRNA an [L-cysteine desulfurase]- subunit alpha: diphosphatase: a [glutamine roseoflavin H153_RS0105370 agmatine diphosphate dehydrogenase: oxononanoate H153_RS0104890 intact strands /Glu-tRNA(Gln) S-adenosylmethionine -undecaprenyl reductase: S-sulfanyl-L-cysteine 6-amino-6- H153_RS0105850 H153_RS0102540 ADP-D-glycero-β- synthetase]-O RNA adenine imidazole S-adenosylmethionine prenyltransferase: H153_RS0108200 synthase: bioF a nascent peptidoglycan amidotransferase decarboxylase: diphosphate H153_RS09080 deoxyfutalosine met D-manno-heptose 4 -(5'-adenylyl) dinucleotide V-type ATP glycerol agmatinase: with D,D cross-links D-ala H + H + subunit GatB: gatB decarboxylase: H153_RS0107220 undecaprenyl- (8S)-8-amino-7- succinyl-CoA D-threo-isocitrate D-glyceraldehyde synthase phosphate H153_RS0108635 speB shikimate (S)-4-amino-5- (meso-diaminopimelate -L-tyrosine H153_RS0108635 diphosphate oxononanoate 3-phosphate trp + Asp-tRNA(Asn) synthase geranyl oxopentanoate containing) phosphate H dAdoMet agmatine phosphatase: shikimate kinase: a [TusA sulfur-carrier protein]- /Glu-tRNA(Gln) subunit putrescine dAdoMet putrescine diphosphate glutamate-1- H153_RS0102190 H153_RS0105455 S-sulfanyl-L-cysteine amidotransferase: semialdehyde + F0F1 ATP + HisF: hisF prenyltransferase: di-trans,octa-cis H H gatA gatC polyamine 2,1- synthase [+ 9 isozymes] H153_RS0107220 -undecaprenyl shikimate 3- a mature peptidoglycan a [DNA]-3'- a 5'-phospho- a mature a 5-phosphooxy- aminopropyltransferase: polyamine aminomutase: NAD + a D-tryptophanyl- a D-tyrosyl- an L-aspartyl- phosphate phosphate aconitate hydratase: (meso-diaminopimelate hydroxyl [DNA] peptidoglycan Trp Tyr a protein a protein L-glutamyl- aminopropyltransferase: hypoxanthine (n) [tRNA ] [tRNA ] Asn ATP ammonium speE (2E,6E)-farnesyl hemL H153_RS0101165 [tRNA ] Gln 3-phosphoshikimate 1- a [TusD sulfur-carrier protein]- containing) PRPP (meso-DAP biotin ATP-dependent [tRNA ] speE diphosphate ADP-forming succinate- Asp-tRNA(Asn) ATP- carboxyvinyltransferase: S-sulfanyl-L-cysteine containing) /Glu-tRNA(Gln) Clp protease dependent N 1 -(3-aminopropyl) 5-aminolevulinate -CoA ligase: sucC sucD DNA Asp-tRNA(Asn) aroA endolytic ligase D-tyrosyl-tRNA(Tyr) D-tyrosyl-tRNA(Tyr) amidotransferase ATP-binding protease agmatine spermidine 5-enolpyruvoyl- biotin--[acetyl-CoA- /Glu-tRNA(Gln) porphobilinogen succinate cis-aconitate transglycosylase hypoxanthine (NAD(+)) endolytic deacylase: deacylase: subunit GatB: gatB subunit ClpX: clpX subunit shikimate 3- H153_RS0106960 H153_RS0106960 carboxylase] ligase: amidotransferase synthase: hemB a [TusE sulfur carrier MltG: mltG phosphoribosyltransferase: hpt LigA: ligA transglycosylase Asp-tRNA(Asn) ATP-dependent HslV: hslV phosphate 34 H153_RS0104580 subunit GatB: gatB a uridine in tRNA succinate dehydrogenase/ [+ 3 isozymes] MltG: mltG /Glu-tRNA(Gln) Clp endopeptidase a peptide chorismate porphobilinogen protein]-S-sulfanylcysteine Asp-tRNA(Asn) fumarate reductase [+ 3 isozymes] amidotransferase: proteolytic spermidine synthase: Trp Tyr /Glu-tRNA(Gln) tRNA 2-thiouridine(34) iron-sulfur subunit: a mature peptidoglycan a mature peptidoglycan [DNA] NMN D-tryptophan a tRNA D-tyrosine a tRNA gatA gatC biotinyl-5'- subunit ClpP: clpP aroC hydroxymethylbilane IMP AMP an L-asparaginyl- amidotransferase: synthase MnmA: mnmA H153_RS0102310 aconitate hydratase: with (L-alanyl-γ-D- strand (non- a mature GlcNAc-1,6- adenylate a peptide synthase: hemC Asn gatA gatC glutamyl-meso-2,6- reducing terminus) peptidoglycan anhMurNAc- [tRNA ] chorismate succinate dehydrogenase/ H153_RS0101165 (n) diaminopimeloyl-D- (meso-DAP L-Ala-γ-D-Glu- preuroporphyrinogen a 2-thiouridine 34 in tRNA fumarate reductase an L-glutaminyl- iron-sulfur subunit: alanine) tetrapeptide containing) DAP-D-Ala uroporphyrinogen- [tRNA Gln ] tRNA uridine-5- fumarate H153_RS09370 citrate III synthase: carboxymethylaminomethyl(34) a DNA containing an N-terminal- an N-terminal- H153_RS0102575 a peptide with a an L-glutamyl- 34 synthesis GTPase MnmE: mnmE a 5,10-gly a uridine 34 phenylacetate an apurinic/ L-methionyl-L- L-methionyl-L- a cytidine lys 5-MTR-1-P tRNA charging ATP Gln methylenetetrahydrofolate in tRNA a tRNA precursor apyrimidinic site leader sequence threonyl-[protein] [tRNA ] alanyl-[protein] in tRNA Ile2 uroporphyrinogen-III tRNA uridine-5- fumarate hydratase: CTP Asp-tRNA(Asn) S-methyl-5- carboxymethylaminomethyl(34) ATP-citrate synthase thioribose-1- H153_RS0106030 phenylacetate--CoA /Glu-tRNA(Gln) gly a tRNA Gly phe a tRNA Phe thr a tRNA Thr trp a tRNA Trp tRNA asp asp arg a tRNA Arg glu a tRNA glu his a tRNA His elongator tRNA Met met initiator tRNA Met met cys a tRNA Cys ile a tRNA Ile tyr a tRNA Tyr synthesis enzyme MnmG: mnmG subunit beta protein tRNA uridine-5- endonuclease signal type I methionyl amidotransferase type I methionyl tRNA phosphate 1: H153_RS0104880 ligase: H153_RS0106385 CCA tRNA ser a tRNA ser leu a tRNA Leu pro a tRNA Pro val a tRNA Val a tRNA Ala ala lys a tRNA Lys a 5-carboxymethylaminomethyl- carboxymethylaminomethyl(34) III domain- peptidase aminopeptidase: subunit GatB: gatB aminopeptidase: lysidine(34) isomerase: asn tRNA Asn gln a tRNA Gln phenylacetate--CoA nucleotidyltransferase: 2-thiouridine 34 in tRNA synthesis GTPase MnmE: mnmE containing protein: I: lepB map map synthetase S-methyl-5-mtnA glycine--tRNA ligase: phenylalanine-- threonine- tryptophan- aspartate- arginine-- glutamate-- histidine-- methionine- methionine- cysteine-- isoleucine- tyrosine-- ligase: H153_RS0106390 H153_RS0100780 Asp-tRNA(Asn) tRNA uridine-5- H153_RS0106175 /Glu-tRNA(Gln) TilS: tilS thio-D-ribulose H153_RS0106250 tRNA ligase: pheS serine--tRNA -tRNA -tRNA -tRNA tRNA ligase: tRNA ligase: tRNA ligase: -tRNA -tRNA tRNA ligase: leucine--tRNA ligase: proline--tRNA ligase: valine--tRNA ligase: -tRNA alanine--tRNA tRNA ligase: lysine--tRNA carboxymethylaminomethyl(34) endonuclease III: an N-terminal L- amidotransferase: an N-terminal L- 1-phosphate H153_RS0106255 H153_RS0104070 ligase: serS ligase: thrS ligase: trpS ligase: aspS H153_RS0102985 H153_RS0103970 H153_RS0103985 ligase: metG ligase: metG H153_RS0105890 H153_RS0106945 H153_RS0107305 H153_RS0107530 ligase: ileS ligase: alaS H153_RS0108330 ligase: lysS (S)-malate