title: Multiple sequence alignment of protein families showing low sequence homology: a methodological approach using database pattern-matching discriminators for G-protein-linked receptors.
abstract: A multiple alignment has been constructed, containing 37 sequences from related families of membrane-bound receptors believed to share the same structural framework as rhodopsin. Sequence homology within families was high (occasionally greater than 90%), but homology between them was generally low (20% or less). Database pattern-scanning methods were therefore used to construct a set of discriminators to aid both the task of alignment and the identification of distantly related sequences showing similar rhodopsin-like transmembrane helices. The results indicate that these discriminators are uniquely able to identify each of the transmembrane helices without major cross-reaction with similar regions in unrelated integral membrane proteins. This ability engenders more accurate alignments of the sequences and facilitates structural analysis and model building of the receptors.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Leeds, U.K.
authors.forename: T K
authors.initials: TK
authors.lastname: Attwood
authors.forename: E E
authors.initials: EE
authors.lastname: Eliopoulos
authors.forename: J B
authors.initials: JB
authors.lastname: Findlay
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D019204:GTP-Binding Proteins / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011956:Receptors, Cell Surface / Q000235:genetics*; D012243:Rhodopsin / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D011956:Receptors, Cell Surface; D012243:Rhodopsin; D019204:GTP-Binding Proteins