SEQUENCE ALIGNMENT AND STRUCTURAL MODELING OF THE LAMB GLYCOPORIN FAMILY

lamB gene segments were obtained from Yersinia enterocolitica and Vibr io parahaemolyticus by the CR and the DNA sequence determined. The ded uced polypeptide sequences showed high similarity to six other LamB-re lated proteins and all contained typical signature sequences present i n all members of the family but not other proteins. The aligned amino acid sequences permitted derivation of a model of LamB folding across the bacterial outer membrane using an approach successfully applied in the identification of structural features in other porins (Ferenci,T. (1994) Mel. Microbiol. 14:188-189). The alignment-based model differs from previous LamB structure predictions and is also more complex tha n that found for OmpF-related porins; more than 16 conserved stretches of amino acid sequence potentially corresponded to membrane-spanning segments. (C) 1995 Academic Press, Inc.