Comprehensive functional identification of prokaryotic transmembrane proteins by binary topology pattern

摘要

The functions of more than one half of proteins in proteome are not annotated yet. The functions of transmembrane (TM) protein, which corresponds to one fourth in a proteome, is known only a little, because of difficulty in determining TM protein structure experimentally. Accordingly, a lot of efforts have been made in an attempt to predict TM topology which is considered to correspond to the fold in the case of globular protein. Because, it is known that TM protein function can be identified by its TM topology, at least roughly. We have developed a TM protein function identification method using the binary topology pattern based on the number of segments and loop length. The topology pattern is expressed as a sequence of "1", "0" and "*": "1" and"0" mean the long and short loop based on a defined threshold length, respectively, and "*" means the binary loop length is not defined. The topology pattern of a query TM protein is associated to a particular function when it corresponds to the topology pattern of a TM protein having a known function. In previous work, a common threshold length was used for all the loops. This time, we defined different threshold lengths for individual loops to improve identification accuracy. By using this method, weidentified comprehensively functions of putative TM proteins encoded within 39 microbial genomes, classifying the TM proteins into defined functional groups. We also compared the accuracy of our method in functional identification with one by BLAST.