KEGG   PATHWAY: gim00020
Entry
gim00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Gimesia benthica
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
gim00020  Citrate cycle (TCA cycle)
gim00020

Module
gim_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:gim00020]
gim_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:gim00020]
gim_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:gim00020]
gim_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:gim00020]
Other DBs
GO: 0006099
Organism
Gimesia benthica [GN:gim]
Gene
F1728_21405  citrate synthase [KO:K01647] [EC:2.3.3.1]
F1728_17315  citrate synthase [KO:K01647] [EC:2.3.3.1]
F1728_08670  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
F1728_23930  aconitate hydratase [KO:K01681] [EC:4.2.1.3]
F1728_14240  isocitrate/isopropylmalate dehydrogenase family protein [KO:K00030] [EC:1.1.1.41]
F1728_26350  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
F1728_22605  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
F1728_22600  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
F1728_28310  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
F1728_17620  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
F1728_17625  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
F1728_08080  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
F1728_08085  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
F1728_08395  fumarate reductase/succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
F1728_08390  succinate dehydrogenase/fumarate reductase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
F1728_08400  succinate dehydrogenase cytochrome b subunit [KO:K00241]
F1728_12925  class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
F1728_28295  malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
F1728_21610  pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
F1728_04050  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
F1728_28320  aceE; pyruvate dehydrogenase (acetyl-transferring), homodimeric type [KO:K00163] [EC:1.2.4.1]
F1728_28315  biotin/lipoyl-binding protein [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
gim00010  Glycolysis / Gluconeogenesis
gim00053  Ascorbate and aldarate metabolism
gim00061  Fatty acid biosynthesis
gim00071  Fatty acid degradation
gim00190  Oxidative phosphorylation
gim00220  Arginine biosynthesis
gim00250  Alanine, aspartate and glutamate metabolism
gim00280  Valine, leucine and isoleucine degradation
gim00350  Tyrosine metabolism
gim00470  D-Amino acid metabolism
gim00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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