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Generated by SRI International Pathway Tools Version 25.0 on Sat Jun 12, 2021 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_001746795Cyc: Piscirickettsia salmonis AY3800B Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari lipid II (meso diaminopimelate 2+ phosphate Mg containing) Co 2+ RS00065 RS15145 RS08855 RS08330 RS08105 RS07905 RS07160 RS06550 RS14225 RS05365 RS05005 FliQ RS13580 RS04095 RS03695 RS03315 RS03070 RS12345 TypA RS12050 RS01480 RS11100 RS11015 RS01215 RS10860 RS10620 RS08655 MurJ RS10415 RS10330 RS00450 RS10075 IcmP RS09985 RS09920 ApaG RS09870 RS00235 RS10015 RS10055 RS10080 RS10195 RS10405 RS10445 RS10515 RS10565 RS01040 RS01160 RS10950 FtsW RS01465 RS01705 RS02185 TolR RS02840 RS03190 RS03595 RS03945 RS04280 RS04650 RS13705 RS05285 RS05680 RS06165 RS06945 RS07480 RS10305 RS08640 MlaE RS09600 lipid II (meso Mg 2+ diaminopimelate phosphate Co 2+ containing) RS01875 RS09935 Macromolecule Modification glutaminyl-tRNA gln Aminoacyl-tRNA Charging 6 α L-alanyl-γ-D- tRNA-uridine 2-thiolation ATP biosynthesis Carbohydrate Degradation N -(3-methylbut- a nascent peptidoglycan UDP-N-acetyl- -D- a nascent UDP-N-acetyl- phosphoenol a nucleoside an L-cysteinyl- biosynthesis via transamidation a sulfurated γ a lipid II H O γ 2-en-1-yl)- with (L-alanyl- -D-glutamyl- muramoyl-L-alanyl- peptidoglycan glutamyl-meso- UDP-N-acetyl- α-D-muramoyl- 2 RNA -L-glutamyl- gly Cys and selenation (bacteria) [sulfur carrier] GTP dGDP pyruvate triphosphate ATP roseoflavin [tRNA ] RS02295 RS09970 Secondary Metabolite Biosynthesis adenosine 37 meso-2,6-diaminopimeloyl-D- γ-D-glutamyl-meso- (meso-DAP diaminopimelate α-D-muramate L-alanyl-γ-D- D-alanine ADP D-galactose degradation I (Leloir pathway) D-alanyl-D-alanine 5'-phosphate glu N-acetylneuraminate and in tRNA alanyl-D-alanine) pentapeptide 2,6-diaminopimelate containing) glutamyl-meso-2,6- cys F0F1 ATP synthase: penicillin- preQ biosynthesis N-acetylmannosamine UDP-N- diaminopimeloyl- DNA- glutathione aminoacyl- 0 AVM72_RS13010 atpB β-D-galactopyranose binding ribosome myo-inositol degradation I tRNA (N6-isopentenyl D-alanyl-D-alanine directed RNA bifunctional tRNA IscS subfamily atpE AVM72_RS13025 penicillin-binding UDP-N- endolytic acetylmuramate:L- protein biogenesis pyruvate synthase: biosynthesis N-acetylneuraminate adenosine(37)-C2)- polymerase riboflavin hydrolase: TolB RS10020 cysteine AVM72_RS13030 protein 2: mrdA acetylmuramoyl- transglycosylase alanyl-gamma-D- 2: mrdA GTPase kinase: pyk gshB GTP D-glucopyranose N-acetylneuraminate methylthiotransferase subunit kinase/FAD pth gln an L-glutamyl- desulfurase: AVM72_RS13035 atpG D-alanyl-D-alanine tripeptide--D-alanyl- MltG: mltG glutamyl- meso- penicillin- D-alanyl-D-alanine Der: der glutathione 6-phosphate lyase: MiaB: miaB omega: rpoZ synthetase: [tRNA Gln ] AVM72_RS02310 carboxypeptidase/ D- alanine ligase: lytic murein diaminopimelate binding [+ 3 isozymes] synthase: GTP cyclohydrolase I atpD AVM72_RS13050 α carboxypeptidase/ + + -D-galactopyranose AVM72_RS14570 succinate AVM72_RS12905 ligase: mpl [+ 3 isozymes] ribF H RS04195 H Asp-tRNA(Asn) FolE2: AVM72_RS07325 cysteine N-acetyl-D- D-alanyl-D-alanine- transglycosylase protein D-alanyl-D-alanine- pyruvate gshB Asp-tRNA(Asn) dehydrogenase, Cys /Glu-tRNA(Gln) 7,8-dihydroneopterin 3'-triphosphate ATP mannosamine endopeptidase: dacB B: mltB 2: mrdA dGTP cys a tRNA RS04215 RS10085 /Glu-tRNA(Gln) desulfurase: galactokinase: endopeptidase: dacB H + amidotransferase: Ins(3)P hydrophobic α phosphate roseoflavin N-acetylmannosamine UDP-N-acetyl- -D- UDP-N-acetyl- GDP + + amidotransferase: AVM72_RS04815 AVM72_RS01485 membrane anchor D-alanyl-D-alanine RNA adenine H RS05225 H gatB gatA gatC 6-carboxytetrahydropterin an [L-cysteine kinase: muramoyl-L-alanyl- α-D-muramoyl- norophthalmate gatB gatA gatC inositol protein: sdhD a nascent peptidoglycan a mature a nascent carboxypeptidase/ a N- dinucleotide [+ 5 isozymes] synthase: AVM72_RS00325 desulfurase]-S- AVM72_RS14560 γ γ-D-glutamyl-meso- L-alanyl-γ-D- a 5-phosphooxy- monophosphatase: α-D-galactose 1-phosphate UDP-α-D-glucose with (L-alanyl- -D-glutamyl- D-ala peptidoglycan peptidoglycan D-alanyl-D-alanine- D-ala acetylglucosamine- 6-carboxytetrahydropterin sulfanyl-L-cysteine N-acetyl-D- 6 2,6-diaminopimeloyl- glutamyl-meso-2,6- RS13570 RS10100 L-glutamyl- AVM72_RS02300 N -(3-methylbut- meso-2,6-diaminopimeloyl- with (L-alanyl- (meso-DAP endopeptidase: dacB -N-acetylmuramyl- + F0F1 ATP + ammonium an unsulfurated H H [tRNA Gln ] synthase: AVM72_RS11575 mannosamine 5'-deoxyadenosine 2-en-1-yl)-2- met D-alanine) tetrapeptide D-alanyl-D-alanine γ-D-glutamyl- containing) with diaminopimelate (tetrapeptide) synthase myo-inositol 6-phosphate [sulfur carrier] GlcNAc terminus 6-carboxy-5,6,7,8-tetrahydropterin (methylsulfanyl) meso-2,6- UDP-N- pyrophosphoryl- putative N- 37 Asp-tRNA(Asn) a [TusA sulfur- adenosine diaminopimeloyl- D-ala acetylmuramoyl- undecaprenol acetylmannosamine- /Glu-tRNA(Gln) carrier protein]-S- in tRNA D-alanine) L-alanyl-γ-D- RS00095 RS04955 RS00660 7-carboxy-7-deazaguanine 6-phosphate amidotransferase: sulfanyl-L-cysteine tetrapeptide glutamyl-meso-2,6- synthase QueE: queE 2-epimerase: gatB gatA gatC sulfurtransferase diaminopimeloyl- RS09795 AVM72_RS14555 7-carboxy-7-deazaguanine complex: tusD D-alanine tusC TusB N-acetyl-D- an L-glutaminyl- tRNA charging glucosamine RS05750 RS10465 Gln 7-cyano-7-deazaguanine a [TusD sulfur- RS09620 [tRNA ] γ α synthase: AVM72_RS02645 carrier protein]-S- 6-phosphate a nascent peptidoglycan a peptidoglycan a peptidoglycan dimer (meso N-acetyl-muramoyl-(L- L-alanyl- -D- a [bis(guanylyl UDP-N-acetyl- phosphoenol an [apo BCAA N-acetyl- - menadione NADH H + a [glutamine- RS09660 sulfanyl-L-cysteine α with (L-alanyl-γ-D- with (L-alanyl-γ-D- -diaminopimelate containing) alanyl-γ-D-glutamyl-L- glutamyl-meso-2,6- molybdopterin) cys α-D-muramoyl- D-glt dehydrogenase ala UDP-N-acetyl- D-muramoyl- ser a tRNA sec glu a tRNA glu 7-cyano-7-deazaguanine 2-deoxy- -D-ribose 1- ATP dADP pyruvate synthetase]- 6 α synthase QueC: queC TusD:TusE phosphate degradation glutamyl-meso-2,6- glutamyl-meso-2,6- lysyl-D-alanyl-D-alanine) diaminopimeloyl- UDP-N-acetyl- cofactor L-alanine E2 protein] N -D-muramate L-alanine(1-) sulfurtransferase: diaminopimeloyl- diaminopimeloyl-D- D-alanine α-D-muramate chaperone]- L-tyrosine -dihydrolipoyl- ser Ala asp α penicillin-binding RS05755 RS01630 ser a tRNA a tRNA ala tRNA asp preQ AVM72_RS08485 2-deoxy- -D- NADH-quinone dihydrolipoyl RS09540 glutamate- elongator 0 D-alanyl-D-alanine) alanine) tetrapeptide penicillin-binding L-cysteine L-lysine 1,6-anhydro-N- lys a tRNA Lys tyr a tRNA Tyr his a tRNA His pro a tRNA Pro cys a tRNA Cys met initiator tRNA Met met leu a tRNA Leu arg a tRNA Arg trp a tRNA Trp asn tRNA Asn thr a tRNA Thr ile a tRNA Ile gly a tRNA Gly phe a tRNA Phe a [TusE sulfur UDP-glucose-- ribose 1-phosphate protein 2: mrdA oxidoreductase: UDP-N- dehydrogenase: UDP-N- serine- -tRNA tRNA Met UDP-glucose pentapeptide protein 2: mrdA bifunctional [glutamate- acetylmuramyl- RS09545 Val hexose-1-phosphate D-alanyl-D-alanine UDP-N- acetylmuramoyl- pyruvate acetylmuramate- -tRNA val a tRNA 34 carrier protein]-S 4-epimerase phosphopentomutase: nuoN nuoK lpdA ligase: gltX gln Gln a uridine in tRNA acetylmuramate:L- -ammonia ligase]- L-alanine-- kinase: pyk -L-alanine L-alanine ligase: serine- alanine- aspartate- a tRNA -sulfanylcysteine uridylyltransferase: GalE: galE carboxypeptidase/ D-alanyl-D-alanine AVM72_RS11705 cysteine dihydrolipoyl Metabolic Regulator AVM72_RS03725 alanyl-gamma-D- adenylyl-L-tyrosine D-glutamate ligase: murC amidase serS lysine- tyrosine-- histidine- glutamate-- proline-- -tRNA -tRNA -tRNA cysteine-- methionine- methionine- leucine-- arginine-- tryptophan- asparagine- threonine- isoleucine- glycine--tRNA phenylalanine- AVM72_RS01490 penicillin-binding D-alanyl-D-alanine- carboxypeptidase/ nuoI nuoH desulfurase: dehydrogenase: RS06705 RS12280 Biosynthesis α-D-glucopyranose 2-deoxy-D-ribose glutamyl- meso- phosphorylase/ ligase: murD an [apo BCAA AmpD: ampD -tRNA tRNA ligase: -tRNA tRNA ligase: tRNA ligase: valine--tRNA ligase: ligase: ligase: ligase: tRNA ligase: -tRNA -tRNA tRNA ligase: tRNA ligase: -tRNA -tRNA -tRNA -tRNA ligase: glyQ -tRNA ligase: tRNA 2- UDP-α-D-galactose protein 2: endopeptidase: dacB D-alanyl-D-alanine- AVM72_RS11720 AVM72_RS04815 AVM72_RS04655 RS09385 1-phosphate 5-phosphate diaminopimelate [glutamate-- dehydrogenase RS09335 ligase: lysS AVM72_RS00285 ligase: hisS AVM72_RS05810 AVM72_RS02545 AVM72_RS03075 serS alaS aspS AVM72_RS05805 ligase: metG ligase: metG AVM72_RS11000 AVM72_RS11060 ligase: trpS ligase: asnS ligase: thrS ligase: ileS AVM72_RS12570 pheS pheT ppGpp metabolism thiouridine(34) AVM72_RS12915 endopeptidase: dacB nuoF IscS subfamily pyruvate UDP-N-acetyl- ligase: mpl ammonia-ligase] dATP E2 protein] N 6 α N-acetyl-D- an L-seryl- synthase [+ 3 isozymes] a peptidoglycan with AVM72_RS11735 cysteine UDP-N-acetyl- -D-muramoyl- sec an L-methionyl- phosphomannomutase/ deoxyribose- adenylyltransferase: -lipoyl-L-lysine [tRNA ] an L-lysyl- an L-tyrosyl- an
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