KEGG   PATHWAY: ger00020
Entry
ger00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Geomonas oryzisoli
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
ger00020  Citrate cycle (TCA cycle)
ger00020

Module
ger_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ger00020]
ger_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ger00020]
ger_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ger00020]
ger_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ger00020]
ger_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ger00020]
Other DBs
GO: 0006099
Organism
Geomonas oryzisoli [GN:ger]
Gene
KP004_11895  citrate (Si)-synthase [KO:K01647] [EC:2.3.3.1]
KP004_09785  acnA; aconitate hydratase AcnA [KO:K27802] [EC:4.2.1.3 4.2.1.99]
KP004_13565  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
KP004_06235  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
KP004_02815  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
KP004_02820  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
KP004_02825  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
KP004_05160  3-methyl-2-oxobutanoate dehydrogenase subunit VorB [KO:K00174] [EC:1.2.7.3 1.2.7.11]
KP004_06250  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
KP004_05165  2-oxoglutarate oxidoreductase [KO:K00175] [EC:1.2.7.3 1.2.7.11]
KP004_06255  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
KP004_05170  2-oxoacid:acceptor oxidoreductase family protein [KO:K00177] [EC:1.2.7.3]
KP004_06260  2-oxoacid:acceptor oxidoreductase family protein [KO:K00177] [EC:1.2.7.3]
KP004_05155  4Fe-4S binding protein [KO:K00176] [EC:1.2.7.3]
KP004_06245  4Fe-4S binding protein [KO:K00176] [EC:1.2.7.3]
KP004_04350  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
KP004_17795  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
KP004_04345  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
KP004_17790  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
KP004_03860  fumarate reductase/succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
KP004_03865  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
KP004_03855  succinate dehydrogenase cytochrome b subunit [KO:K00241]
KP004_01890  flavocytochrome c [KO:K26318] [EC:1.3.2.4]
KP004_19445  flavocytochrome c [KO:K26318] [EC:1.3.2.4]
KP004_01875  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
KP004_15845  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
KP004_06240  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
KP004_17690  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
KP004_02950  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
KP004_02955  phosphoenolpyruvate carboxykinase (GTP) [KO:K01596] [EC:4.1.1.32]
KP004_01500  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
KP004_10245  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
KP004_01505  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
KP004_10225  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
KP004_01510  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
KP004_10220  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
KP004_04360  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
KP004_19435  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
KP004_20615  nifJ; pyruvate:ferredoxin (flavodoxin) oxidoreductase [KO:K03737] [EC:1.2.7.1 1.2.7.-]
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
ger00010  Glycolysis / Gluconeogenesis
ger00053  Ascorbate and aldarate metabolism
ger00061  Fatty acid biosynthesis
ger00071  Fatty acid degradation
ger00190  Oxidative phosphorylation
ger00220  Arginine biosynthesis
ger00250  Alanine, aspartate and glutamate metabolism
ger00280  Valine, leucine and isoleucine degradation
ger00350  Tyrosine metabolism
ger00470  D-Amino acid metabolism
ger00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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