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_001697945Cyc: Neisseria meningitidis M25476 Cellular Overview Connections between pathways are omitted for legibility. Anamika Kothari phosphate putrescine ammonium spermidine RS00335 TrkA NhaC RS04655 ExbB RS04440 RS03990 RS03595 HtpX RS08650 RS02780 RS02515 PotA FtsE YccS LolD RS06485 RS06395 RS00855 RS05985 YidC RS06405 RS11135 RS05880 RS00885 RS04430 RS01225 RS01595 RS02015 RS05870 RS07640 RS08060 RS08375 RS03165 RS03450 FxsA RS09655 RS09920 RS04565 RS04745 RS00175 RS05150 RS10910 RS09270 putrescine phosphate ammonium spermidine RS11000 RS00870 Fatty Acid and Polyprenyl Metabolic Regulator Lipid Degradation Cofactor, Prosthetic gln Aminoacyl-tRNA Charging glutaminyl-tRNA Biosynthesis Biosynthesis Group, Electron γ a {β-D-Gal-(1->4)-β-D- CMP-N-acetyl- 3-phenyl-2- L-alanyl- -D- a peptidoglycan a [protein]-L- biosynthesis via transamidation oleate β-oxidation Carrier Degradation β a [glutamine- a lipid II Fermentation mixed acid fermentation β -neuraminate tyr glutamyl-meso-2,6- dimer (meso- methionine octaprenyl Amine and Polyamine Biosynthesis ppGpp metabolism GlcNAc-(1->2)-[ -D- oxopropanoate ATP synthetase]- ATP pilin heme β diaminopimeloyl- UDP-N-acetyl- diaminopimelate biotin bifunctional RS11010 glu diphosphate Gal-(1->4)- -D-GlcNAc- L-tyrosine oleate degradation II (1->4)]-α-D-Man- D-alanine α-D-muramate containing) peptide- biosynthesis spermidine biosynthesis III pppGpp phosphoenolpyruvate spermidine (1->3)-[β-D-Gal-(1->4) aspartate/ methionine (2E,6E)-farnesyl putrescine fatty acid-- IPP biosynthesis I bifunctional (p)ppGpp protoheme -β-D-GlcNAc-(1->2)- tyrosine/aromatic bifunctional [glutamate- bifunctional biotin- (S)-S-oxide diphosphate biosynthesis I CoA ligase: UDP-N- arg SAM synthetase/guanosine- pyruvate kinase: pyk phosphoenolpyruvate [β-D-Gal-(1->4)-β-D- aminotransferase: -ammonia ligase]- -[acetyl-CoA- reductase RS00510 RS06990 A6M07_RS01120 acetylmuramate:L- gln 3',5'-bis(diphosphate) 3'- carboxylase: ppc GlcNAc-(1->6)]-α-D- A6M07_RS10215 adenylyl-L-tyrosine a N- carboxylase] MsrA/ an L-glutamyl- octaprenyl SAM arg (Z,Z)- alanyl-gamma-D- Gln pyrophosphohydrolase: Man-(1->6)]-β-D-Man- aspartate/ phosphorylase/ D-ala acetylglucosamine- ligase/type III peptide- [tRNA ] diphosphate biosynthetic arginine biosynthetic pyruvate oleoyl-CoA biliverdin-IX α glutamyl- meso- Asp-tRNA(Asn) A6M07_RS09935 guanosine 3'- (1->4)-β-D-GlcNAc- tyrosine/aromatic [glutamate-- -N-acetylmuramyl- a peptidoglycan pantothenate methionine synthase: ispB decarboxylase: speA arginine oxaloacetate diaminopimelate /Glu-tRNA(Gln) Asp-tRNA(Asn) bifunctional (p)ppGpp diphosphate 5'- acyl-CoA/acyl-ACP (1->4)-β-D-GlcNAc}- aminotransferase: ligase: mpl ammonia-ligase] (tetrapeptide) with D,D cross- D-ala kinase: (R)-S-oxide RS02305 /Glu-tRNA(Gln) decarboxylase: RS05905 amidotransferase: all-trans- agmatine dAdoMet synthetase/guanosine- triphosphate 3'- D-lactate dehydrogenase: N-Asn-[protein] A6M07_RS04810 adenylyltransferase: pyrophosphoryl- links (meso- A6M07_RS07890 reductase amidotransferase: speA guanosine-5'- A6M07_RS02285 glnE MsrB: msrAB gatB gatA gatC octaprenyl putrescine agmatine 3',5'-bis(diphosphate) 3'- diphosphatase: dehydrogenase: dld undecaprenol diaminopimelate gatB gatA gatC dAdoMet Aromatic Compound 3-(4- UDP-N-acetylmuramoyl- a protein-L- [+ 4 isozymes] diphosphate pyrophosphohydrolase: A6M07_RS10330 triphosphate,3'- acyl-CoA/acyl-ACP γ containing) a 5-phosphooxy- polyamine N-acetyllactosaminide L-alanyl- -D- biotinyl-5'- methionine- agmatinase: A6M07_RS10330 diphosphate (S)-malate dehydrogenase: Degradation hydroxyphenyl) phe a [glutamine L-glutamyl- aminopropyltransferase: (R)-lactate formate acetyl-CoA alpha-2,3- glutamyl-meso-2,6- adenylate (S)-S-oxide RS08345 ammonium spermidine speB phosphatase: ppx A6M07_RS01100 pyruvate synthetase]-O RS01135 [tRNA Gln ] A6M07_RS03135 fumarate hydratase: 4-hydroxyphenylacetate diaminopimeloyl- synthase: sialyltransferase: lst 4 (2E,9Z)- D-alanine -(5'-adenylyl) A6M07_RS06095 phosphate citrate (Si)- A6M07_RS10580 degradation Asp-tRNA(Asn) putrescine octadecenoyl-CoA -L-tyrosine 1 acetyltransferase: pta synthase: gltA class II fumarate (4-hydroxyphenyl) β β CMP /Glu-tRNA(Gln) N -(3-aminopropyl)agmatine [+ 2 isozymes] a { -D-Gal-(1->4)- - GTP ppGpp 2-methylcitrate hydratase: fumC acetate D-GlcNAc-(1->2)- RS05170 amidotransferase: CO H acetaldehyde 4-hydroxyphenylacetate RS07305 2 2 β β gatB gatA gatC acetyl phosphate synthase: prpC fumarate 3-monooxygenase, [ -D-Gal-(1->4)- -D- spermidine α alcohol (S)-3-hydroxy-(9Z) reductase GlcNAc-(1->4)]- -D- α acetate kinase: dehydrogenase citrate -octadecenoyl-CoA component: hpaC Man-(1->3)-[ -D-Sial- an L-glutaminyl- spermidine (3,4-dihydroxyphenyl) (2->3)-β-D-Gal-(1->4) Gln A6M07_RS09585 AdhP: adhP [tRNA ] bifunctional (p)ppGpp acetate -β-D-GlcNAc-(1->2)- RS07800 tRNA charging synthetase/guanosine- acetate kinase: bifunctional lys RS10890 lys GDP ethanol succinate [β-D-Gal-(1->4)-β-D- 3',5'-bis(diphosphate) 3'- A6M07_RS11075 aconitate hydratase pyrophosphokinase: 2/2-methylisocitrate 3-oxo-(9Z)- GlcNAc-(1->6)]-α-D- pyrophosphohydrolase: octadecenoyl-CoA gln Gln A6M07_RS10330 acetate Man-(1->6)]-β-D-Man- a tRNA A6M07_RS09935 dehydratase: acnB 2-hydroxy-5- asp ser Ala Arg Phe β tRNA asp ser a tRNA a tRNA ala arg a tRNA phe a tRNA carboxymethylmuconate (1->4)- -D-GlcNAc- RS08575 met RS08640 met elongator cis-aconitate β trp a tRNA Trp lys a tRNA Lys pro a tRNA Pro his a tRNA His thr a tRNA Thr ile a tRNA Ile tyr a tRNA Tyr leu a tRNA Leu met initiator tRNA Met met glu a tRNA glu cys a tRNA Cys gly a tRNA Gly bifunctional (p)ppGpp semialdehyde (1->4)- -D-GlcNAc}- tRNA Met glutamine-- synthetase/guanosine- N-Asn-[protein] val a tRNA Val bifunctional aspartate- serine- alanine- tRNA ligase/ arginine- phenylalanine- asn tRNA Asn 3',5'-bis(diphosphate) 3'- (7Z)-hexadecenoyl-CoA Macromolecule Modification aconitate hydratase trp RS08140 trp tryptophan- lysine- proline-- histidine- threonine- isoleucine- tyrosine- leucine-- methionine- methionine- glutamate-- cysteine-- -tRNA -tRNA -tRNA YqeY domain -tRNA glycine--tRNA -tRNA ligase: pyrophosphohydrolase: 2/2-methylisocitrate 6 a protein-L- RS08810 fusion protein: A6M07_RS10330 acyl-CoA/acyl-ACP 5-carboxymethyl-2- N -(3-methylbut- a [DNA]-3'- a 5'-phospho- (1S,2R)-1- a [glutamine queuosine at -tRNA -tRNA tRNA ligase: -tRNA -tRNA -tRNA -tRNA tRNA ligase: valine--tRNA ligase: -tRNA -tRNA tRNA ligase: tRNA ligase: ligase: ligase: ligase: ligase: ligase: glyQ A6M07_RS03790 a sulfurated NAD + H O a nucleoside tRNA-uridine 2-thiolation dehydratase: acnB dehydrogenase: 2-en-1-yl)- ser C-(indol-3- synthetase]-O 2 RNA glu position 34 methionine- ligase: trpS ligase: lysS A6M07_RS00820 ligase: hisS ligase: thrS ligase: ileS ligase: tyrS A6M07_RS05670 A6M07_RS06495 ligase: metG ligase: metG A6M07_RS07445 A6M07_RS07835 aspS serS alaS A6M07_RS10900 argS A6M07_RS08735 pheS GDP hydroxymuconate [sulfur carrier] hydroxyl [DNA] GTP triphosphate and selenation (bacteria) A6M07_RS02285 adenosine 37 yl)glycerol 4 -(5'-adenylyl) of a tRNA Asp (R)-S-oxide D-threo-isocitrate bifunctional an L-methionyl- acyl-CoA/acyl-ACP in tRNA 3-phosphate -L-tyrosine RS05375 an L-tryptophanyl- an L-lysyl- an L-prolyl- an L-histidyl- an L-threonyl- an L-isoleucyl- an L-tyrosyl- an L-leucyl- an L-valyl- an L-methionyl- an L-glutamyl- an L-cysteinyl- an L-aspartyl- an L-seryl- an L-alanyl- an L-glutaminyl- an L-arginyl- an L-phenylalanyl- an L-asparaginyl- DNA ligase: peptide- [elongator a glycyl-[tRNA Gly ] Aromatic Compound Biosynthesis cys NADP-dependent dehydrogenase: DNA- RS03665 [tRNA Trp ] [tRNA Lys ] [tRNA Pro ] [tRNA His ] [tRNA Thr ] [tRNA Ile ] [tRNA Tyr ] [tRNA Leu ] [tRNA Val ] [initiator tRNA Met ] [tRNA Glu ] [tRNA Cys ] [tRNA asp ] [tRNA ser ] [tRNA Ala ] [tRNA Gln ] [tRNA Arg ] [tRNA Phe ] [tRNA Asn ] A6M07_RS08035 GTPase tRNA methionine tRNA Met ] A6M07_RS01100 (3E,5R)-5-carboxy-2- tRNA (N6-isopentenyl tryptophan directed RNA isocitrate bifunctional [glutamate- ObgE: obgE glutamyl- (S)-S-oxide IscS subfamily oxohept-3-enedioate adenosine(37)-C2)- NAD- synthase polymerase chorismate biosynthesis I dehydrogenase: (2E,7Z)- -ammonia ligase]- [+ 6 isozymes] Q(34) reductase cysteine methylthiotransferase dependent subunit alpha: subunit 3-(4-hydroxyphenyl) A6M07_RS02720 hexadecenoyl-CoA adenylyl-L-tyrosine synthetase MsrA/ F0F1 ATP MiaB: miaB DNA ligase A6M07_RS04065 alpha: rpoA + + D-erythrose pyruvate biosynthesis desulfurase: phosphorylase/ GluQRS: peptide- H H RS09425 SohB 2-oxoglutarate succinate LigA: ligA tryptophan H + synthase 4-phosphate iscS [glutamate-- phosphate [+ 2 isozymes] gluQRS methionine peptidoglycan biosynthesis I Cell Structure Biosynthesis 3-deoxy-7- an [L-cysteine ATP biosynthesis (4Z)-2-oxohept- dehydrogenase, synthase GDP ammonia-ligase] (R)-S-oxide (meso-diaminopimelate containing) phosphoheptulonate tyr desulfurase]-S- (S)-3-hydroxy-(7Z) 4-enedioate hydrophobic subunit ADP-L-glycero-β- Carbohydrate Biosynthesis aspartate/ [DNA] NMN adenylyltransferase: glutamyl- reductase