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Reaction Module

KEGG modules in the metabolic pathways represent tight functional units defined by a set of KO identifiers (K numbers) for the enzymes involved. Here another type of module is defined from purely chemical data without incorporating any enzyme data, i.e., from the analysis of chemical structure transformation patterns along the metabolic pathways. The newly introduced 'reaction module' is a conserved sequence of chemical structure transformation patterns defined by a set of Reaction Class identifiers (RC numbers).
ko/rc modules
Note that Reaction Class is like a reaction ortholog accommodating global structural differences of metabolites. Therefore, it is interesting to examine how well reaction modules (RC modules) defined by reaction orthologs correspond to KEGG modules (KO modules) defined by gene orthologs. This is shown in the following BRITE hierarchy file.
KEGG reaction modules


Carboxylic acid metabolism
2-Oxocarboxylic acid chain extension
RM0012-Oxocarboxylic acid chain extension by tricarboxylic acid pathway
2-Oxocarboxylic acid chain modification
RM002Carboxyl to amino conversion using protective N-acetyl group (basic amino acid synthesis)
RM032Carboxyl to amino conversion without using protective group
RM033Branched-chain addition (branched-chain amino acid synthesis)
RM030Glucosinolate synthesis
RG001 Reductive amination of 2-oxocarboxylic acid (aminotransferase reaction)
Fatty acid synthsis and degradation
RM018Beta oxidation in acyl-CoA degradation
RM020Fatty acid synthesis using acetyl-CoA (reversal of RM018)
RM021Fatty acid synthesis using malonyl-CoA
Acyl-CoA metabolism
RM019Acyl-CoA conversion via dicarboxylate semialdehyde
Reaction module variation
RM032 RM002 Carboxyl to amino conversion
RM020 RM021 Fatty acid synthesis
RM018 RM016 Beta oxidation
Reaction module combination
RM001+(RM002,RM032,RM033) Amino acid synthesis
RM001+RM030 Glucosinolate synthesis
Reaction module map
map01210 2-Oxocarboxylic acid metabolism
map01212 Fatty acid metabolism
map01230 Biosynthesis of amino acids
Aromatics degradation
Methyl to carboxyl conversion on aromatic ring (preprocessing module)
RM003Methyl to carboxyl conversion on aromatic ring
RM015Methyl to carboxyl conversion on aromatic ring, anaerobic
Dihydroxylation of aromatic ring
RM004Dihydroxylation of aromatic ring, type 1 (dioxygenase and dehydrogenase reactions)
RM005Dihydroxylation of aromatic ring, type 1a (dioxygenase and decarboxylating dehydrogenase reactions)
RG002Dihydroxylation of aromatic ring, type 1b (single dioxygenase reaction)
RM006Dihydroxylation of aromatic ring, type 2 (two monooxygenase reactions)
RM007Dihydroxylation of aromatic ring, type 3 (dealkylation and monooxygenase reactions)
Cleavage of aromatic ring
RM008Ortho-cleavage of dihydroxylated aromatic ring (beta-ketoadipate pathway)
RM009Meta-cleavage of dihydroxylated aromatic ring
RM013Ortho-cleavage of halogenated aromatic ring
RM016Ring cleavage via beta oxidation, anaerobic
RM017Ring cleavage via Baeyer-Villiger oxidation
Dihydroxylation and cleavage of aromatic ring
RM010Dihydroxylation and meta-cleavage of aromatic ring, type 1
RM011Dihydroxylation and meta-cleavage of aromatic ring, type 1b
RM012Dihydroxylation and meta-cleavage of aromatic ring, type 3a
RM014Ring removal from polycyclic aromatic ring
Reaction module comparison
RM003 RM015 Methyl to carboxyl conversion of aromatic ring
Reaction module combination
RM003+((RM004,RM005,RM006,RM007)+(RM008,RM009),RM010) Aromatics degradation
Reaction module map
map01220 Degradation of aromatic compounds
Other
Amino acid metabolism
RM025Conversion of amino acid moiety to carboxyl group (biogenic amine metabolism)
Nucleotide metabolism
RM024Pyrimidine degradation
Sugar metabolism
RM022Nucleotide sugar biosynthesis, type 1
RM023Nucleotide sugar biosynthesis, type 2
RM034Sugar degradation to aldehyde and pyruvate
Aromatics metabolism
RM027Hydroxylation and methylation motif
RM026Hydroxylation and decarboxylation motif
RM028Flavonoid synthesis
RM029Pterocarpan synthesis
RM031Oxime to acetate conversion

References
  1. Muto, A., Kotera, M., Tokimatsu, T., Nakagawa, Z., Goto, S., and Kanehisa, M.; Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J. Chem. Inf. Model. 53, 613-622 (2013). [pubmed] [pdf]
  2. Kanehisa, M.; Chemical and genomic evolution of enzyme-catalyzed reaction networks. FEBS Lett. 587, 2731-2737 (2013). [pubmed] [pdf]
  3. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014). [pubmed] [pdf]

Last updated: June 16, 2014
KEGG GenomeNet Kanehisa Laboratories