KEGG   PATHWAY: lpak00020
Entry
lpak00020                   Pathway                                
Name
Citrate cycle (TCA cycle) - Lysinibacillus pakistanensis
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
lpak00020  Citrate cycle (TCA cycle)
lpak00020

Module
lpak_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:lpak00020]
lpak_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:lpak00020]
lpak_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:lpak00020]
lpak_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:lpak00020]
lpak_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:lpak00020]
Other DBs
GO: 0006099
Organism
Lysinibacillus pakistanensis [GN:lpak]
Gene
GDS87_17955  citZ; citrate synthase [KO:K01647] [EC:2.3.3.1]
GDS87_13055  acnA; aconitate hydratase AcnA [KO:K01681] [EC:4.2.1.3]
GDS87_17950  NADP-dependent isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
GDS87_12130  2-oxoglutarate dehydrogenase E1 component [KO:K00164] [EC:1.2.4.2]
GDS87_12135  odhB; 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase [KO:K00658] [EC:2.3.1.61]
GDS87_04000  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GDS87_23980  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GDS87_04450  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GDS87_15095  lpdA; dihydrolipoyl dehydrogenase [KO:K00382] [EC:1.8.1.4]
GDS87_05745  2-oxoacid:acceptor oxidoreductase subunit alpha [KO:K00174] [EC:1.2.7.3 1.2.7.11]
GDS87_05750  2-oxoacid:ferredoxin oxidoreductase subunit beta [KO:K00175] [EC:1.2.7.3 1.2.7.11]
GDS87_05275  sucD; succinate--CoA ligase subunit alpha [KO:K01902] [EC:6.2.1.5]
GDS87_05270  sucC; ADP-forming succinate--CoA ligase subunit beta [KO:K01903] [EC:6.2.1.5]
GDS87_02025  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
GDS87_08090  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
GDS87_21950  succinate CoA transferase [KO:K18118] [EC:2.8.3.18]
GDS87_17600  sdhA; succinate dehydrogenase flavoprotein subunit [KO:K00239] [EC:1.3.5.1]
GDS87_17595  sdhB; succinate dehydrogenase iron-sulfur subunit [KO:K00240] [EC:1.3.5.1]
GDS87_17605  succinate dehydrogenase [KO:K00241]
GDS87_20835  fumarate hydratase [KO:K01676] [EC:4.2.1.2]
GDS87_10120  fumC; class II fumarate hydratase [KO:K01679] [EC:4.2.1.2]
GDS87_08640  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
GDS87_17945  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
GDS87_09970  mdh; malate dehydrogenase [KO:K00024] [EC:1.1.1.37]
GDS87_24050  malate:quinone oxidoreductase [KO:K00116] [EC:1.1.5.4]
GDS87_04555  pyc; pyruvate carboxylase [KO:K01958] [EC:6.4.1.1]
GDS87_18475  pckA; phosphoenolpyruvate carboxykinase (ATP) [KO:K01610] [EC:4.1.1.49]
GDS87_04435  pdhA; pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha [KO:K00161] [EC:1.2.4.1]
GDS87_04440  alpha-ketoacid dehydrogenase subunit beta [KO:K00162] [EC:1.2.4.1]
GDS87_23985  2-oxo acid dehydrogenase subunit E2 [KO:K00627] [EC:2.3.1.12]
GDS87_04445  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
lpak00010  Glycolysis / Gluconeogenesis
lpak00061  Fatty acid biosynthesis
lpak00062  Fatty acid elongation
lpak00071  Fatty acid degradation
lpak00190  Oxidative phosphorylation
lpak00220  Arginine biosynthesis
lpak00250  Alanine, aspartate and glutamate metabolism
lpak00280  Valine, leucine and isoleucine degradation
lpak00350  Tyrosine metabolism
lpak00470  D-Amino acid metabolism
lpak00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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