Predicting enzyme subclass by functional domain composition and pseudo amino acid composition.
As a continuous effort to use the sequence approach to identify enzymatic function at a deeper level, investigations are extended from the main enzyme classes (Protein Sci. 2004, 13, 2857-2863) to their subclasses. This is indispensable if we wish to understand the molecular mechanism of an enzyme at a deeper level. For each of the 6 main enzyme classes (i.e., oxidoreductase, transferase, hydrolase, lyase, isomerase, and ligase), a subclass training dataset is constructed. To reduce homologous bias, a stringent cutoff was imposed that all the entries included in the datasets have less than 40% sequence identity to each other. To catch the core feature that is intimately related to the biological function, the sample of a protein is represented by hybridizing the functional domain composition and pseudo amino acid composition. On the basis of such a hybridization representation, the FunD-PseAA predictor is established. It is demonstrated by the jackknife cross-validation tests that the overall success rate in identifying the 21 subclasses of oxidoreductases is above 86%, and the corresponding rates in identifying the subclasses of the other 5 main enzyme classes are 94-97%. The high success rates imply that the FunD-PseAA predictor may become a useful tool in bioinformatics and proteomics of the post-genomic era.
Cai
Yu-Dong
YD
Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Chou
Kuo-Chen
KC
D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D002965:Classification; D019295:Computational Biology / Q000379:methods*; D004798:Enzymes / Q000737:chemistry / Q000145:classification*; D010088:Oxidoreductases / Q000145:classification; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods
D004798:Enzymes; D010088:Oxidoreductases