A Consensus Transmembrane Topology Prediction Method of High-Reliability

It has been revealed that the function of transmembrane (TM) proteins (20-30% in most genomes [1]) can be classified and identified with the information of its TM topologies, i.e., the number of TM segments (TMSs), the position of TMS and the orientation of the TMS to the membrane lipid bilayer [6]. Therefore, developing the TM topology prediction method with high reliability is critical task for the elucidation of TM protein functions. Although many TM topology prediction methods have been proposed, the prediction accuracies of these methods are still not high enough, i.e., at most 50-60% as to whole TM topology [3]. In this study, we propose a new consensus approach (ConPred elite) with reliabilities of 0.98 and 0.95 for prokaryotic and eukaryotic TM protein sequences, respectively, by combining the results from five currently used TM topology prediction methods. We applied this method to TM proteins extracted from 87 prokaryotic and 12 eukaryotic proteomes.