title: Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family.
abstract: 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.
authors.affiliation: Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
authors.forename: Amy M
authors.initials: AM
authors.lastname: Wiles
authors.forename: Fred
authors.initials: F
authors.lastname: Naider
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Becker
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D016384:Consensus Sequence; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000378:metabolism; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000378:metabolism*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D021381:Protein Transport; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D001426:Bacterial Proteins; D026901:Membrane Transport Proteins; D009842:Oligopeptides