title: Analysis of 58 Families of Holins Using a Novel Program, PhyST.
abstract: We have designed a freely accessible program, PhyST, which allows the automated characterization of any family of homologous proteins within the Transporter Classification Database. The program performs an NCBI-PSI-BLAST search and reports (1) the average protein sequence length with standard deviations, (2) the average predicted number of transmembrane segments, (3) the total number of homologues retrieved, (4) a quantitative list of all source phyla, and (5) potential fusion proteins of sizes considerably exceeding the average size of the proteins retrieved. We have applied this program to 58 families of holins, and the results are presented. The results show that holins are very rarely fused to other protein domains, suggesting that holins form transmembrane pores as homooligomers without the participation of other proteins or protein domains.
authors.affiliation: Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, Calif., USA.
authors.forename: Harikrishnan
authors.initials: H
authors.lastname: Kuppusamykrishnan
authors.forename: Larry M
authors.initials: LM
authors.lastname: Chau
authors.forename: Gabriel
authors.initials: G
authors.lastname: Moreno-Hagelsieb
authors.forename: Milton H
authors.initials: MH
authors.lastname: Saier
mesh_terms: D019295:Computational Biology / Q000379:methods*; D026901:Membrane Transport Proteins / Q000235:genetics* / Q000378:metabolism*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D026901:Membrane Transport Proteins