Genome-wide Functional Classification/identification of Prokaryotic Transmembrane Proteins Based On Transmembrane Topology Similarity

摘要

Functions of transmembrane (TM) proteins holding 20-30% [1] in individual proteomes are difficult to be inferred comprehensively based on only sequence similarity, which is partly because TM protein sequences of known function are lacking. Recent studies, however, revealed that TM protein functions are closely correlated to their TM topologies, i.e., the number of TM segments (TMSs), positions of TMSs and the N-tail location [5]. In this study, we propose a new method for the comprehensive classification/identification of TM protein functions by single-linkage clustering based on TM topology similarity. Applying this method to TM protein sequences predicted from 87 sequenced prokaryotic genomes, it was realized that TM topology- information improved functional classification/identification greatly.