| Research Abstract |
We first collected experimentally-characterized transmembrane topology models from literatures and constructed them into a database(TMBDB). By using this, we evaluated the performances of several published transmembrane topology prediction methods, and we developed a consensus prediction method(ConPred) which is a combination of some of the proposed methods. By applying ConPred to TM proteomes from 99 completed genomes(88 prokaryotic and 12 eukaryotic), we obtained 52,686 TM protein sequences with reliable TM topologies and analysed the TM topologies of them in detail with respect to their relation to the function. From this analysis, it was revealed that the function of TM protein is closely related to its TM topology, and each functional group pfTM proteins has its own specific TM topology pattern expressed as a binary topology patter. The genome-scale functional classification and identification of GPCRs were also earned out, by applying the binary topology pattern method, and many novel GPCR genes were found by our study. We also investigated die TM topology evolution by internal gene duplication, through the internal sequence similarity comparison within a single sequences.
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