KEGG   PATHWAY: vdb00020
Entry
vdb00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Vibrio diabolicus
Description
The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data, many organisms seem to lack genes for the full cycle [MD:M00009], but contain genes for specific segments [MD:M00010 M00011].
Class
Metabolism; Carbohydrate metabolism
Pathway map
vdb00020  Citrate cycle (TCA cycle)
vdb00020

Module
vdb_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vdb00020]
vdb_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vdb00020]
vdb_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vdb00020]
vdb_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vdb00020]
vdb_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vdb00020]
Other DBs
GO: 0006099
Organism
Vibrio diabolicus [GN:vdb]
Gene
AL552_12600  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
AL552_21130  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
AL552_13450  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
AL552_12625  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
AL552_12630  dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
AL552_21225  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
AL552_22615  dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
AL552_05700  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
AL552_12640  succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
AL552_12635  succinyl-CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
AL552_12615  succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
AL552_12620  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
AL552_12605  succinate dehydrogenase cytochrome b556 subunit [KO:K00241]
AL552_12610  sdhD; succinate dehydrogenase, hydrophobic membrane anchor protein [KO:K00242]
AL552_23085  frdA; fumarate reductase (quinol) flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
AL552_23090  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00245] [EC:1.3.5.1]
AL552_23095  fumarate reductase subunit FrdC [KO:K00246]
AL552_23100  fumarate reductase subunit D [KO:K00247]
AL552_18075  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
AL552_23230  aspA; aspartate ammonia-lyase [KO:K01679] [EC:4.2.1.2]
AL552_00890  transcriptional regulator [KO:K01774] [EC:4.2.1.2]
AL552_10040  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
AL552_08920  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
AL552_21235  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
AL552_21230  aceF; pyruvate dehydrogenase complex dihydrolipoyllysine-residue acetyltransferase [KO:K00627] [EC:2.3.1.12]
Compound
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00036  Oxaloacetate
C00042  Succinate
C00068  Thiamin diphosphate
C00074  Phosphoenolpyruvate
C00091  Succinyl-CoA
C00122  Fumarate
C00149  (S)-Malate
C00158  Citrate
C00311  Isocitrate
C00417  cis-Aconitate
C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate
C05379  Oxalosuccinate
C05381  3-Carboxy-1-hydroxypropyl-ThPP
C15972  Enzyme N6-(lipoyl)lysine
C15973  Enzyme N6-(dihydrolipoyl)lysine
C16254  [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
Reference
  Authors
Nishizuka Y (ed).
  Title
[Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1980)
Reference
  Authors
Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
  Title
[Cellular Functions and Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1997)
Reference
  Authors
Michal G.
  Title
Biochemical Pathways
  Journal
Wiley (1999)
Related
pathway
vdb00010  Glycolysis / Gluconeogenesis
vdb00053  Ascorbate and aldarate metabolism
vdb00061  Fatty acid biosynthesis
vdb00071  Fatty acid degradation
vdb00190  Oxidative phosphorylation
vdb00220  Arginine biosynthesis
vdb00250  Alanine, aspartate and glutamate metabolism
vdb00280  Valine, leucine and isoleucine degradation
vdb00350  Tyrosine metabolism
vdb00470  D-Amino acid metabolism
vdb00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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