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Generated by SRI International Pathway Tools Version 25.0, Authors S 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_000190595Cyc: Cellulophaga lytica DSM 7489 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari phosphate molybdate RS04350 RS08315 phosphate molybdate Macromolecule Modification tRNA-uridine 2-thiolation inosine 5'- Nucleoside and Nucleotide Degradation ditrans,octacis- a peptidoglycan with ditrans,octacis- a [bis(guanylyl an N-terminal- a [protein] and selenation (bacteria) phosphate guanosine ditrans,octacis- (4R)-4-hydroxy- an L-asparaginyl- an L-cysteinyl- Aminoacyl-tRNA Charging tRNA charging nucleotides undecaprenyldiphospho- (L-alanyl-γ-D-glutamyl- undecaprenyldiphospho- undecaprenyldiphospho- molybdopterin) cys L-methionyl-L- C-terminal glu degradation 2-oxoglutarate [tRNA Asn ] [tRNA Cys ] degradation III N-acetyl-(N-acetyl-β-D- L-lysyl-D-alanyl-D- N-acetyl-(N- N-acetyl-(N- cofactor cysteinyl-[protein] L-glutamate cys glucosaminyl)muramoyl- alanine) pentapeptide acetylglucosaminyl) acetylglucosaminyl) chaperone]- Phe IMP bifunctional phe a tRNA L-alanyl-γ-D-glutamyl-L- muramoyl-L-alanyl-γ- muramoyl-L-alanyl- L-cysteine cysteine IMP GMP type I methionyl 4-hydroxy-2- aminoacyl- aminoacyl- 30S lysyl-D-alanyl-D-alanine D-isoglutaminyl-N-(β- γ-D-isoglutaminyl- desulfurase: dehydrogenase: 5'/3'- aminopeptidase: oxoglutarate tRNA tRNA ribosomal nucleotidase D-asparaginyl)-L-lysyl- N-(β-D-asparaginyl) map phenylalanine- CELLY_RS00120 guaB cysteine aldolase/2- hydrolase: hydrolase: protein gln a tRNA Gln SurE: surE D-alanyl-D-alanine -L-lysyl-D-alanine -tRNA ligase XMP purine ribonucleosides degradation penicillin-binding desulfurase: type I methionyl dehydro-3-deoxy- arfB arfB S6--L- a tRNA Ala ala tRNA asp asp ser a tRNA ser cysteine guanosine subunit elongator protein 2: CELLY_RS07620 aminopeptidase: phosphogluconate aminoacyl-tRNA aminoacyl-tRNA glutamate his a tRNA His lys a tRNA Lys leu a tRNA Leu tyr a tRNA Tyr ile a tRNA Ile gly a tRNA Gly glu a tRNA glu trp a tRNA Trp met initiator tRNA Met met asn tRNA Asn arg a tRNA Arg cys a tRNA Cys pro a tRNA Pro thr a tRNA Thr desulfurase: alpha: pheS tRNA Met 5'/3'- CELLY_RS03925 penicillin-binding penicillin-binding cysteine map aldolase: hydrolase: hydrolase: ligase: rimK Val glutamine-- CELLY_RS07620 val a tRNA nucleotidase purine-nucleoside protein 2: protein 2: CELLY_RS08885 alanine- phenylalanine- tRNA ligase/ aspartate- serine- an [L-cysteine adenosine desulfurase: CELLY_RS11880 CELLY_RS08885 SurE: surE phosphorylase: a peptidoglycan with di-trans,octa-cis CELLY_RS03925 CELLY_RS03925 histidine-- lysine- -tRNA leucine-- tyrosine-- isoleucine-- glycine-- -tRNA ligase YqeY domain glutamate-- tryptophan- -tRNA methionine- methionine- -tRNA asparagine- arginine-- cysteine-- proline-- threonine- desulfurase]-S- CELLY_RS00120 an N-terminal L- a [protein] C- CELLY_RS04065 (L-alanyl-γ-D-glutamyl- -undecaprenyl α tRNA ligase: valine--tRNA ligase: -tRNA ligase: tRNA ligase: tRNA ligase: tRNA ligase: tRNA ligase: subunit beta: fusion protein: tRNA ligase: -tRNA ligase: -tRNA -tRNA ligase: -tRNA tRNA ligase: tRNA ligase: tRNA ligase: -tRNA sulfanyl-L-cysteine met cysteinyl-[protein] terminal -L- xanthosine L-lysyl-D-alanyl-D- diphosphate a peptidoglycan di-trans,octa-cis a peptidoglycan di-trans,octa-cis a [bis(guanylyl glyoxylate pyruvate tRNA Asn a tRNA Cys glutamate-α- CELLY_RS01540 CELLY_RS02920 ligase: lysS alaS CELLY_RS04560 CELLY_RS04990 CELLY_RS05395 CELLY_RS05525 CELLY_RS13435 CELLY_RS06660 CELLY_RS06670 ligase: trpS aspS ligase: metG ligase: metG serS ligase: asnS CELLY_RS10940 CELLY_RS11550 CELLY_RS11585 ligase: thrS guanine asn cys alanine) pentapeptide dimer (E. faeciums) -undecaprenyl dimer (E. faecium -undecaprenyl ala molybdopterin) L-glutamate an L-methionyl- diphosphate , tetrapeptide) diphosphate cofactor an L-histidyl- an L-valyl- an L-lysyl- an L-alanyl- an L-leucyl- an L-tyrosyl- an L-isoleucyl- an L-phenylalanyl- an L-glutaminyl- an L-glutamyl- an L-tryptophanyl- an L-aspartyl- an L-methionyl- an L-seryl- an L-asparaginyl- an L-arginyl- an L-cysteinyl- an L-prolyl- an L-threonyl- a [TusA sulfur- purine-nucleoside a glycyl-[tRNA Gly ] [elongator chaperone]-S- [tRNA His ] [tRNA Val ] [tRNA Lys ] [tRNA Ala ] [tRNA Leu ] [tRNA Tyr ] [tRNA Ile ] [tRNA Phe ] [tRNA Gln ] [tRNA Glu ] [tRNA Trp ] [tRNA asp ] [initiator tRNA Met ] [tRNA ser ] [tRNA Asn ] [tRNA Arg ] [tRNA Cys ] [tRNA Pro ] [tRNA Thr ] carrier protein]-S- phosphorylase: xanthosine adenosine inosine guanosine tRNA Met ] sulfanyl-L-cysteine CELLY_RS04065 sulfanyl-L-cysteine xanthine xanthine purine-nucleoside purine-nucleoside purine-nucleoside purine-nucleoside a mature peptidoglycan a methylated sn-glycero-3- an N-terminal- 6-O-trans- an N-terminal- a peptide with an N-modified a [protein]-L- a [TusD sulfur- phosphorylase: phosphorylase: phosphorylase: phosphorylase: (meso-diaminopimelate 2-oxoglutarate nucleobase phospho-N- L-methionyl-L- methoxy-mycolyl- L-methionyl-L- an N-terminal aminoacyl-[tRNA] methionine carrier protein]-S- CELLY_RS04065 CELLY_RS04065 CELLY_RS04065 CELLY_RS04065 containing) within DNA (arachidonoyl) threonyl-[protein] trehalose 6- alanyl-[protein] L-methionine peptide- sulfanyl-L-cysteine ethanolamine phosphatebifunctional methionine α-D-ribose- (S)-S-oxide urate urate endolytic alpha-ketoglutarate- aminoacyl- type I methionyl alpha,alpha- type I methionyl type I methionyl [2Fe-2S] iron-sulfur Cofactor, Carrier, and Vitamin Biosynthesis 1-phosphate dependent reductase superpathway of tetrahydrofolate biosynthesis superpathway of coenzyme A biosynthesis I (bacteria) superpathway of thiamine diphosphate biosynthesis I thiamine diphosphate transglycosylase glycerophosphoryl tRNA aminopeptidase: trehalose- aminopeptidase: aminopeptidase: cluster biosynthesis UTP and CTP dephosphorylation I C1 Compound Utilization MsrA: msrA biosynthesis II (Bacillus) a [TusE sulfur MltG: mltG dioxygenase AlkB: diester hydrolase: map phosphate map map Metabolic Regulator Biosynthesis and Assimilation CELLY_RS08110 synthase (UDP- peptide- 3-methyl-2- a 5,10- a uridine 34 in tRNA carrier protein]-S UTP [+ 2 isozymes] phosphodiesterase: arfB type I methionyl type I methionyl type I methionyl L-cysteine desulfurase cys methionine GTP oxobutanoate methylenetetrahydrofolate HMP-PP -sulfanylcysteine D-ribose 5- formaldehyde oxidation alpha-ketoglutarate- CELLY_RS04240 aminoacyl-tRNA aminopeptidase: forming)/trehalose- aminopeptidase: aminopeptidase: thiamine trehalose biosynthesis I pyrimidine deoxyribonucleotides dependent phosphatase: (S)-S-oxide ppGpp metabolism phosphate CTP synthase: VII (THF pathway) a mature peptidoglycan a mature peptidoglycan glycerophosphodiester hydrolase: map map map cysteine cysteine phosphate tRNA 2- dephosphorylation dioxygenase AlkB: trehalose- CELLY_RS12785 reductase 3-methyl-2-oxobutanoate CELLY_RS01085 with (L-alanyl-γ-D- strand (non- phosphodiesterase: CELLY_RS08885 desulfurase: GTP desulfurase: D-glucopyranose nucleoside triphosphate CELLY_RS14395 trans-methoxy- MsrA: msrA hydroxymethyltransferase: synthase: UDP-α-D-glucose thiouridine(34) formaldehyde glutamyl-meso-2,6- reducing terminus) CELLY_RS02790 CELLY_RS00120 cyclohydrolase CELLY_RS00120 6-phosphate pppGpp pyrophosphohydrolase: UDP an N-terminal L- mono-mycolate an N-terminal L- a protein-L- panB CELLY_RS09390 synthase CTP diaminopimeloyl-D- cysteine I FolE: folE cysteine mazG met threonyl-[protein] met alanyl-[protein] met a peptide methionine- asp thiamine MnmA: mnmA a nucleobase an N-modified an uncharged [+ 3 isozymes] bifunctional (p)ppGpp alanine) tetrapeptide formaldehyde succinate (S)-S-oxide desulfurase: desulfurase: bifunctional nucleotide a 5,10- within DNA sn-glycerol amino acid tRNA 7,8- 2-dehydropantoate phosphate synthetase/guanosine- anandamide CELLY_RS07620 CELLY_RS07620 alpha,alpha- guanosine 3'- 34 pyrophosphohydrolase: dihydroneopterin aspartate 1- synthase: 3',5'-bis(diphosphate) 3'- a 2-thiouridine UMP methylenetetrahydrofolate 3-phosphate an [L-cysteine trehalose- diphosphate 5'- CELLY_RS10010 an S-sulfanyl-[L- 3'-triphosphate decarboxylase: thiE cytidylyl molybdenum in tRNA CDP bifunctional 5,10- 2-dehydropantoate desulfurase]-S- pyrophosphohydrolase: triphosphate 3'- dCTP dCMP 5'/3'- cysteine desulfurase] flavin biosynthesis I (bacteria and plants) CELLY_RS05305 thiamine cofactor sulfurylation phosphate tRNA uridine-5- methylenetetrahydrofolate 2-reductase: ilvC sulfanyl-L-cysteine CELLY_RS01370 diphosphatase: nucleotidase ditrans,octacis- a [ThiI sulfur- 6-O-trans-keto- an N-terminal- (3R,5S)-3- phosphate synthase (UDP- carboxymethylaminomethyl(34) succinate cysteine cytidylyl molybdenum dehydrogenase/5,10- a 5,10- a uridine 34 a ferrocytochrome stearoyl-CoA H O mycolyl-trehalose β-alanine forming)/trehalose- CELLY_RS01370 dUTP diphosphatase: dut SurE: surE gly undecaprenyldiphospho- carrier protein]- cys 2 L-methionyl-L- semialdehyde hydroxy-1- (R)-pantoate desulfurase: thiamine- synthesis GTPase MnmE: mnmE methenyltetrahydrofolate b GTP a [ThiS sulfur- cofactor (trioxo) methylenetetrahydrofolate in tRNA 5 L-cysteine
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