Enzyme Nomenclature
KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number) of the IUBMB/IUPAC biochemical nomenclature committee.
KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG LIGAND relational database with additional annotation of reaction and organism information.
KEGG REACTION Database
KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the KEGG metabolic pathways.
Each reaction is identified by the R number, such as R00259 for the acetylation of L-glutamate.
Reactions are linked to ortholog groups of enzymes as defined by the KEGG ORTHOLOGY database, enabling integrated analysis genomic (enzyme genes) and chemical (compound pairs) information.
Reactant Pair
KEGG RPAIR is a collection of chemical structure transformation patterns for substrate-product pairs (reactant pairs) in KEGG REACTION.
In general, a reaction consists of multiple reactant pairs, and the one that appears on the KEGG metabolic pathway is called the main pair, such as A04458 for the above acetylation reaction.
KEGG Atom Types
In order to distinguish functional groups and microenvironments of atoms, atomic species of C, N, O, S, and P are classified into 68 types, called KEGG atom types. They were first introduced for detecting biochemical similarities by graph-based chemical structure comparison (see reference).
|
|
RDM Pattern
(Example) RDM pattern for A04458
The RDM pattern is defined as KEGG atom type changes at the reaction center (R), the difference region (D), and the matched region (M) for each reactant pair. It characterizes chemical structure transformation patterns associated with enzymatic reactions (see reference).
Reaction Prediction
The RDM patterns are the basis for predicting reaction types given a pair (or pairs) of chemical compound structures in e-zyme software.
Furthermore, based on the observation that specific RDM patterns are uniquely or preferentially found in specific categories of KEGG metabolic pathways, new software is being developed for predicting metabolic fate of a given chemical compound (see reference).
|
|
