Systematic Analysis of Enzyme-Catalyzed Reaction Patterns and Prediction of Microbial Biodegradation Pathways

• DOI: 10.1021/ci700006f
• Publication Date: 2007-05-23T09:45:21Z
• Authors: Mina Oh; Takuji Yamada; Masahiro Hattori; Susumu Goto; Minoru Kanehisa
• Keywords: RDM; KEGG; Metabolic pathway; Biotransformation

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