title: BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria.
abstract: This work describes the development of a program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral beta-barrel outer membrane protein. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane beta-strands. The precision of the predictions was found to be 80% with a recall of 88% when tested on the proteins with SwissProt annotated subcellular localization in Escherichia coli K 12 (788 sequences) and Salmonella typhimurium (366 sequences). When tested on the predicted proteome of E.coli, BOMP found 103 of a total of 4346 polypeptide sequences to be possible integral beta-barrel proteins. Of these, 36 were found by BLAST to lack similarity (E-value score < 1e-10) to proteins with annotated subcellular localization in SwissProt. BOMP predicted the content of integral beta-barrels per predicted proteome of 10 different bacteria to range from 1.8 to 3%. BOMP is available at http://www.bioinfo.no/tools/bomp.
authors.affiliation: Department of Molecular Biology, Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway.
authors.forename: Frode S
authors.initials: FS
authors.lastname: Berven
authors.forename: Kristian
authors.initials: K
authors.lastname: Flikka
authors.forename: Harald B
authors.initials: HB
authors.lastname: Jensen
authors.forename: Ingvar
authors.initials: I
authors.lastname: Eidhammer
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D006090:Gram-Negative Bacteria / Q000235:genetics*; D020407:Internet; D017433:Protein Structure, Secondary; D012486:Salmonella typhimurium / Q000235:genetics; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D001425:Bacterial Outer Membrane Proteins