BOMP: a program to predict integral ß-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
Department of Molecular Biology, 1 Computational Biology Unit, Bergen Centre for Computational Science and 2 Department of Informatics, University of Bergen, 5020 Bergen, Norway
* To whom correspondence should be addressed. Tel: +47 55584032; Fax: +47 55584199; Email: flikka{at}ii.uib.no
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received December 18, 2003; Revised and Accepted February 18, 2004
This work describes the development of a program that predicts whether or not a polypeptide sequence from a Gram-negative bacterium is an integral ß-barrel outer membrane protein. The program, called the ß-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral ß-barrel proteins. The first component is a C-terminal pattern typical of many integral ß-barrel proteins. The second component calculates an integral ß-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane ß-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 ß-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 ß-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.
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