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Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways
journal contribution
posted on 2007-07-23, 00:00 authored by Mina Oh, Takuji Yamada, Masahiro Hattori, Susumu Goto, Minoru KanehisaThe roles of chemical compounds in biological systems are now systematically analyzed by high-throughput
experimental technologies. To automate the processing and interpretation of large-scale data it is necessary
to develop bioinformatics methods to extract information from the chemical structures of these small molecules
by considering the interactions and reactions involving proteins and other biological macromolecules. Here
we focus on metabolic compounds and present a knowledge-based approach for understanding reactivity
and metabolic fate in enzyme-catalyzed reactions in a given organism or group. We first constructed the
KEGG RPAIR database containing chemical structure alignments and structure transformation patterns,
called RDM patterns, for 7091 reactant pairs (substrate-product pairs) in 5734 known enzyme-catalyzed
reactions. A total of 2205 RDM patterns were then categorized based on the KEGG PATHWAY database.
The majority of RDM patterns were uniquely or preferentially found in specific classes of pathways, although
some RDM patterns, such as those involving phosphorylation, were ubiquitous. The xenobiotics biodegradation
pathways contained the most distinct RDM patterns, and we developed a scheme for predicting bacterial
biodegradation pathways given chemical structures of, for example, environmental compounds.