title: Topological predictions for integral membrane permeases of the phosphoenolpyruvate:sugar phosphotransferase system.
abstract: We report bioinformatic analyses of the largest superfamily of integral membrane permeases of the bacterial phosphotransferase system (PTS), the Enzyme IIC constituents of the Glc superfamily. Phylogenetic analyses reveal that this superfamily consists of five equally distant families, the Glucose (Glc), beta-Glucoside (Bgl), Fructose (Fru), Mannitol (Mtl) and Lactose (Lac) families. Average hydropathy, amphipathicity and similarity plots were generated for these five families as well as for the entire superfamily. Charged residue distribution was analyzed, and the most conserved sequence motif, common to all five families, was identified. The results show that the members of all five families exhibit similar average hydropathy plots with regions of average amphipathicity and relative conservation also being similar. Evidence is presented suggesting that the Glucitol (Gut) family of Enzyme IIC constituents is a distant member of the Glc superfamily. Based on our analyses we offer a topological model that resembles, but differs in detail from the two previously proposed models.
authors.affiliation: Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA.
authors.forename: Thai X
authors.initials: TX
authors.lastname: Nguyen
authors.forename: Ming-Ren
authors.initials: MR
authors.lastname: Yen
authors.forename: Ravi D
authors.initials: RD
authors.lastname: Barabote
authors.forename: Milton H
authors.initials: MH
authors.lastname: Saier
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D016384:Consensus Sequence; D057927:Hydrophobic and Hydrophilic Interactions; D026901:Membrane Transport Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry*; D010802:Phylogeny; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D026901:Membrane Transport Proteins; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System