Comprehensive analysis of transmembrane topologies in prokaryotic genomes

We analysed comprehensively transmembrane (TM) topologies of TM proteins of 50 selected prokaryotic genomes, by discriminating between TM and soluble proteins by using SOSUI, then detecting and removing signal peptides by applying 'DetecSig', and finally predicting TM topologies by employing 'ConPred'. Estimated fraction of TM proteins in proteome averaged over the 50 genomes is approximately 22%. About 13% of TM proteins were predicted to have a signal peptide, and the fraction of soluble proteins with signal peptide (secretory proteins) ranges from 8 to 18% for most majority of the genomes. The N(in)-type TM proteins with 2-, 4-, 6- and 12-tms (number of transmembrane segments) are predominant among multi-spanning TM proteins, and correspondingly, significantly higher fractions of N(out)-type TM proteins with 1-, 3-, 5- and 11-tms have a signal peptide. It is also found that the TM proteins with signal peptide tend to have a long N-tail loop. The averaged sequence length of TM proteins increases linearly with the increase of the number of TM segments, with the increasing rate of about 35 residues, suggesting a possibility that TM topologies might have been evolved by the 'internal gene duplication' mechanism. Datasets of TM topologies predicted in this study are available at http://bioinfo.si.hirosaki-u.ac.jp/ approximately TMPinGS/.