BOMP: A program to predict integral β-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 β-barrel outer membrane protein. The program, called the β-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral β-barrel proteins. The first component is a C-terminal pattern typical of many integral β -barrel proteins. The second component calculates an integral β -barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane β -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 β-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 β-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. © Oxford University Press 2004; all rights reserved.