BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9. doi: 10.1093/nar/gkh351.

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.

Publication types

  • Evaluation Study

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry*
  • Bacterial Outer Membrane Proteins / genetics
  • Escherichia coli / genetics
  • Genome, Bacterial
  • Gram-Negative Bacteria / genetics*
  • Internet
  • Protein Structure, Secondary
  • Salmonella typhimurium / genetics
  • Sequence Analysis, Protein
  • Software*
  • User-Computer Interface

Substances

  • Bacterial Outer Membrane Proteins