KEGG   PATHWAY: vfi00020
Entry
vfi00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Aliivibrio fischeri ES114
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
vfi00020  Citrate cycle (TCA cycle)
vfi00020

Module
vfi_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:vfi00020]
vfi_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:vfi00020]
vfi_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:vfi00020]
vfi_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:vfi00020]
vfi_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:vfi00020]
Other DBs
GO: 0006099
Organism
Aliivibrio fischeri ES114 [GN:vfi]
Gene
VF_0818  gltA; citrate synthase [KO:K01647] [EC:2.3.3.1]
VF_2158  acnB; bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase [KO:K01682] [EC:4.2.1.3 4.2.1.99]
VF_1775  isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
VF_0823  sucA; 2-oxoglutarate decarboxylase, thiamin-requiring [KO:K00164] [EC:1.2.4.2]
VF_0824  sucB; dihydrolipoyltranssuccinase [KO:K00658] [EC:2.3.1.61]
VF_2178  lpd; lipoamide dehydrogenase, E3 component is part of three enzyme complexes [KO:K00382] [EC:1.8.1.4]
VF_2301  dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
VF_0826  sucD; succinyl-CoA synthetase, NAD(P)-binding, alpha subunit [KO:K01902] [EC:6.2.1.5]
VF_0825  sucC; succinyl-CoA synthetase, beta subunit [KO:K01903] [EC:6.2.1.5]
VF_0821  sdhA; succinate dehydrogenase, flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
VF_0822  sdhB; succinate dehydrogenase, Fe-S subunit [KO:K00240] [EC:1.3.5.1]
VF_0819  sdhC; succinate dehydrogenase, membrane subunit, binds cytochrome b556 [KO:K00241]
VF_0820  sdhD; succinate dehydrogenase, membrane subunit, binds cytochrome b556 [KO:K00242]
VF_2334  frdA; fumarate reductase (anaerobic) catalytic and NAD/flavoprotein subunit [KO:K00244] [EC:1.3.5.1]
VF_2335  frdB; fumarate reductase (anaerobic), Fe-S subunit [KO:K00245] [EC:1.3.5.1]
VF_2336  frdC; fumarate reductase (anaerobic), membrane anchor subunit [KO:K00246]
VF_2337  frdD; fumarate reductase (anaerobic), membrane anchor subunit [KO:K00247]
VF_1180  fumB; anaerobic class I fumarate hydratase (fumarase B) [KO:K01676] [EC:4.2.1.2]
VF_A0063  yggD; predicted DNA-binding transcriptional regulator [KO:K01774] [EC:4.2.1.2]
VF_0276  mdh; malate dehydrogenase, NAD(P)-binding [KO:K00024] [EC:1.1.1.37]
VF_2478  pck; phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
VF_2181  aceE; pyruvate dehydrogenase, decarboxylase component E1, thiamin-binding [KO:K00163] [EC:1.2.4.1]
VF_2179  aceF; pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 [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
vfi00010  Glycolysis / Gluconeogenesis
vfi00061  Fatty acid biosynthesis
vfi00071  Fatty acid degradation
vfi00190  Oxidative phosphorylation
vfi00220  Arginine biosynthesis
vfi00250  Alanine, aspartate and glutamate metabolism
vfi00280  Valine, leucine and isoleucine degradation
vfi00350  Tyrosine metabolism
vfi00470  D-Amino acid metabolism
vfi00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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