ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability.

ConPred II (http://bioinfo.si.hirosaki-u.

Internal gene duplication in the evolution of prokaryotic transmembrane proteins.

We investigated the evolution of transmembrane (TM) topology by detecting partial sequence repeats in TM protein sequences and analyzing them in detail. A total of 377 sequences that seem to have evolved by internal gene duplication events were found among 38,124 predicted TM protein sequences (except for single-spannings) from 87 prokaryotic genomes. Various types of internal duplication patterns were identified in these sequences.