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_000971295Cyc: Devosia epidermidihirudinis E84 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari RS06150 RS12955 TrkD RS11615 RS15810 RS11365 RS11290 RS11165 RS07705 RS05785 RS03390 RS10640 CobD RS17455 RS14945 RS00945 RS00805 YejB RS02090 YajC RS13620 RS08710 CysA RS06300 RS14000 RS06930 RS13875 RS06915 RS06215 ArsB RS00420 RS05185 RS06210 SecY RS00490 RS13915 RS06260 RS14010 RS14120 RS08520 RS13535 RS13725 TatC SecA MacB RS16730 RS16965 RS03310 RS10470 RS02410 RS03365 RS00125 RS12050 RS07730 RS15485 RS12045 RS12185 RS15915 RS02770 RS12830 RS13080 RS06160 RS02150 Polyprenyl Biosynthesis Amino Acid Degradation Aminoacyl-tRNA Charging glutaminyl-tRNA gln Macromolecule Modification tRNA-uridine 2-thiolation ATP di-trans,octa-cis UDP-N-acetyl- ditrans,octacis- a peptidoglycan with ditrans,octacis- ditrans,octacis- a [glutamine (4R)-4-hydroxy- DNA with an N-terminal- biosynthesis via transamidation and selenation (bacteria) a [glutamine- an L-cysteinyl- di-trans,poly-cis biosynthesis L-leucine degradation I -undecaprenyl α-D-muramoyl- undecaprenyldiphospho- (L-alanyl-γ-D-glutamyl- undecaprenyldiphospho- undecaprenyldiphospho- synthetase]-O 2-oxoglutarate adenine:7,8- L-methionyl-L- 3',5'-ADP L-tyrosine degradation I L-histidine L-proline degradation I L-glutamate L-citrulline degradation ATP [tRNA Cys ] dGDP RS06245 RS15765 Alcohol Degradation phosphate γ β L-lysyl-D-alanyl-D- synthetase]- 4 -(5'-adenylyl) seryl-[protein] -undecaprenyl degradation VI phospho-N- L-alanyl- -D- N-acetyl-(N-acetyl- -D- N-acetyl-(N- N-acetyl-(N- dihydro-8- 3'(2'),5'- glu cys degradation II L-tyrosine class 1b phosphate biosynthesis acetylmuramoyl- glutamyl-meso-2,6- glucosaminyl)muramoyl- alanine) pentapeptide acetylglucosaminyl) acetylglucosaminyl) -L-tyrosine oxoguanine bisphosphate ADP leu (to pyruvate) bifunctional ribonucleoside- (2E,6E)-farnesyl pro glycerol and glycerophosphodiester degradation pentapeptide- diaminopimeloyl- L-alanyl-γ-D-glutamyl-L- muramoyl-L-alanyl-γ- muramoyl-L-alanyl- mismatch nucleotidase IPP cysteine F0F1 ATP branched-chain tyr his L-citrulline 4-hydroxy-2- type I methionyl aminoacyl-tRNA diphosphate diphosphate bifunctional glu transferase: D-alanyl-D-alanine lysyl-D-alanyl-D-alanine D-isoglutaminyl-N-(β- γ-D-isoglutaminyl- bifunctional [glutamine CysQ: desulfurase: synthase: amino acid aspartate/ ornithine bifunctional [glutamine oxoglutarate aminopeptidase: hydrolase: reductase: RS14015 FlgK gln proline glycerol WH87_RS16315 D-asparaginyl)-L-lysyl- N-(β-D-asparaginyl) synthetase] WH87_RS14290 sufS WH87_RS17935 aminotransferase: tyrosine/aromatic carbamoyltransferase: synthetase] aldolase/2- A/G-specific map WH87_RS13215 nrdF nrdE dehydrogenase/L- D-alanyl-D-alanine -L-lysyl-D-alanine adenylyltransferase/ an L-glutamyl- isoprenyl an [L-cysteine atpD WH87_RS11790 aminotransferase: argF monofunctional adenylyltransferase/ dehydro-3-deoxy- adenine type I methionyl aminoacyl-tRNA 3'(2'),5'- transferase: 4-methyl-2- 3-(4- urocanate glutamate gamma- carbamoyl phosphate [glutamine synthetase]- vitamin B12- [tRNA Gln ] imidazole desulfurase]-S- WH87_RS17945 WH87_RS17335 biosynthetic [glutamine synthetase]- phosphogluconate glycosylase: aminopeptidase: hydrolase: bisphosphate WH87_RS03710 oxopentanoate hydroxyphenyl) semialdehyde adenylyl-L-tyrosine adenylyl-L-tyrosine dependent glycerol sulfanyl-L-cysteine WH87_RS17950 urocanate a glycerophosphodiester peptidoglycan monofunctional monofunctional aldolase: eda WH87_RS00850 map WH87_RS12600 nucleotidase Asp-tRNA(Asn) pyruvate dehydrogenase (2S, 3S)-3- glutamine-hydrolyzing phosphorylase: ribonucleotide RS06295 RS15880 phosphate WH87_RS17955 glycerol undecaprenyldiphospho- UMP transglycosylase: biosynthetic biosynthetic phosphorylase: A/G-specific CysQ: cysQ /Glu-tRNA(Gln) di-trans,octa-cis hydratase: PutA: putA methylaspartate carbamoyl-phosphate WH87_RS06650 reductase: synthase: (S)-1-pyrroline- N-acetylmuramoyl-L- mtgA peptidoglycan peptidoglycan WH87_RS06650 amidotransferase: -undecaprenyl [+ 2 isozymes] WH87_RS11020 synthase small glycerophosphodiester adenine an N-terminal WH87_RS07555 hisF hisH alanyl-γ-D-glutamyl-meso transglycosylase: transglycosylase: Cys AMP a [TusA sulfur- ATP 3-methylbutanoyl- 4-imidazolone- 5-carboxylate phosphodiesterase: glycerol kinase glyoxylate pyruvate glycosylase: met L-seryl-[protein] cys a tRNA gatC gatA gatB diphosphate subunit: carA a [glutamine GDP [+ 6 isozymes] carrier protein]-S- CoA WH87_RS05735 -2,6-diaminopimeloyl- a peptidoglycan with di-trans,octa-cis mtgA mtgA a [glutamine- WH87_RS01205 a 5-phosphooxy- undecaprenyl- homogentisate 5-propanoate carbamoyl-phosphate GlpK: glpK sulfanyl-L-cysteine D-alanyl-D-alanine (L-alanyl-γ-D-glutamyl- -undecaprenyl synthetase]-O synthetase]- RS14110 L-glutamyl- diphosphate 4 ADP ammonium mesaconate synthase large -(5'-adenylyl) [tRNA Gln ] phosphatase: L-lysyl-D-alanyl-D- diphosphate a peptidoglycan di-trans,octa-cis a peptidoglycan di-trans,octa-cis L-tyrosine subunit: carB sn-glycerol 3-phosphate -L-tyrosine an apurinic site WH87_RS09520 L-glutamate-5- alanine) pentapeptide dimer (E. faeciums) -undecaprenyl dimer (E. faecium -undecaprenyl 3-methylcrotonyl- semialdehyde adenine within DNA Asp-tRNA(Asn) di-trans,octa-cis a [TusD sulfur- N-formimino- carbamate diphosphate , tetrapeptide) diphosphate CoA 4-maleyl- glycerol-3-phosphate /Glu-tRNA(Gln) -undecaprenyl carrier protein]-S- L-glutamate bifunctional RS08720 acetyl/propionyl/ acetoacetate dehydrogenase: amidotransferase: phosphate sulfanyl-L-cysteine proline methylcrotonyl- (S)-citramalate WH87_RS17270 gatC gatA gatB dehydrogenase/L- a ring-opened 7- a reduced ditrans,octacis- a mature a peptide with CoA carboxylase an N-modified a ribonucleoside an L-asparaginyl- UDP glutamate gamma- DHAP methylguanine adenosylcobinamide a purine ubiquinone-6 electron-transfer undecaprenyldiphospho- peptidoglycan leukotriene-D4 an N-terminal (n) aminoacyl-[tRNA] diphosphate [tRNA Asn ] dADP subunit alpha: citramalate CO in DNA ribonucleoside class 1b an L-glutaminyl- a [TusE sulfur 4-fumaryl- N-formyl- semialdehyde 2 flavoprotein N-acetyl-(N- (meso-DAP class 1b L-methionine RS08785 Gln WH87_RS09940 synthase: 5'-triphosphate ribonucleoside- class 1b [tRNA ] acetoacetate L-glutamate dehydrogenase acetylglucosaminyl) containing) 34 carrier protein]-S ribonucleoside- diphosphate tRNA charging a uridine in tRNA 3-methylglutaconyl- PutA: putA WH87_RS06470 electron transfer muramoyl-L-alanyl-γ-D- membrane ribonucleoside- -sulfanylcysteine fumarylacetoacetate N-formylglutamate bifunctional DNA- aminoacyl-tRNA diphosphate aminoacyl-tRNA type I methionyl reductase: CoA bifunctional flavoprotein- isoglutaminyl-L-lysyl- dipeptidase: diphosphate hydrolase: amidohydrolase: Aldehyde Degradation formamidopyrimidine lytic hydrolase: reductase: hydrolase: aminopeptidase: nrdF nrdE glu adenosylcobinamide ubiquinone (glycyl) -D-alanyl-D-alanine WH87_RS15310 reductase: glu tRNA 2- WH87_RS10765 acetate pyruvate glycosylase/ 5 WH87_RS13215 nrdF nrdE WH87_RS13215 map glu a tRNA WH87_RS02550 kinase/ transglycosylase membrane vitamin B12- nrdF nrdE RS08845 Gly thiouridine(34) DNA-(apurinic oxidoreductase: gly a tRNA fumarylacetoacetate glycine cleavage methylglyoxal degradation I adenosylcobinamide- domain-containing aminoacyl-tRNA dipeptidase: vitamin B12- aminoacyl-tRNA type I methionyl dependent synthase glu or apyrimidinic WH87_RS00785 vitamin B12- phe a tRNA Phe tRNA asp asp ser a tRNA ser a tRNA Ala ala hydrolase: phosphate monofunctional protein: hydrolase: WH87_RS07805 dependent hydrolase: aminopeptidase: ribonucleotide elongator glutamate-- MnmA: mnmA HMG-CoA a [glycine-cleavage site) lyase: mutM electron transfer dependent met initiator tRNA Met met arg a tRNA Arg val a tRNA Val cys a tRNA Cys pro a tRNA Pro tyr a tRNA Tyr trp a tRNA Trp thr a tRNA Thr lys a tRNA Lys his a tRNA His ile a tRNA Ile leu a tRNA Leu WH87_RS11965 guanylyltransferase: biosynthetic WH87_RS10055 WH87_RS12600 ribonucleotide WH87_RS12600 map reductase: tRNA Met tRNA ligase: complex H protein] N 6 methylglyoxal flavoprotein- ribonucleotide glycine-- cobU peptidoglycan [+ 4 isozymes] reductase: WH87_RS07555 Asn Gln 34 L-methionine degradation lactoylglutathione reductase: RS13625 phenylalanine- asn tRNA gln a tRNA aspartate- WH87_RS03665 serine- tRNA ligase alanine- a 2-thiouridine fumarate -[(R)-lipoyl]-L-lysine glycine cleavage system a [DNA]- 2,6-diamino-4- ubiquinone transglycosylase: WH87_RS07555 I (to L-homocysteine) a 5'-phospho- adenosyl- leukotriene-E4 gly a 2'- WH87_RS07555 in tRNA lyase: 4-oxo-2-pentenal oxidoreductase: an N-modified an uncharged Asn dUDP -tRNA ligase: -tRNA methionine-- methionine-- glutamate-- -tRNA arginine-- valine-- cysteine-- proline-- tyrosine-- tryptophan- threonine- subunit beta: -tRNA lysine-- histidine-- isoleucine-- leucine-- aminomethyltransferase nucleotide- [DNA] hydroxy-5-(N-methyl) mtgA a mature GlcNAc-1,6- deoxyribonucleoside asn tRNA met a peptide tRNA uridine-5- glycine cleavage