Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family.

Amy M Wiles, Fred Naider, Jeffrey M Becker

Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.

Research in microbiology 2006 May

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Few polytopic membrane proteins have had their topology determined experimentally. Often, researchers turn to an algorithm to predict where the transmembrane domains might lie. Here we use a consensus method, using six different transmembrane domain prediction algorithms on six members of the oligopeptide transport family, all of which have been experimentally characterized. PSI-BLAST results indicate that the six chosen oligopeptide transport family members are distributed throughout most branches of the phylogram, suggesting that these members represent a broad view of the oligopeptide transport family. We combined the prediction algorithms with a multiple sequence alignment, and consensus transmembrane domains were assigned not only based on algorithmic output, but also based on conserved familial motifs found by analysis of the PSI-BLAST results. The consensus method combined with the "charge-difference rule" yields a model topology for the family containing 12 transmembrane domains with the N- and C-termini facing extracellular.

Citation

Amy M Wiles, Fred Naider, Jeffrey M Becker. Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family. Research in microbiology. 2006 May;157(4):395-406