BOMP

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

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References in zbMATH (referenced in 4 articles )

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  1. Hu, Jing; Yan, Changhui: A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes (2008)
  2. Ou, Yu-Yen; Gromiha, M. Michael; Chen, Shu-An; Suwa, Makiko: TMBETADISC-RBF: discrimination of (\beta)-barrel membrane proteins using RBF networks and PSSM profiles (2008)
  3. Yan, Changhui; Hu, Jing; Wang, Yingfeng: Discrimination of outer membrane proteins with improved performance (2008) ioport
  4. Berven, Frode S.; Flikka, Kristian; Jensen, Harald B.; Eidhammer, Ingvar: BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of gram-negative bacteria. (2004) ioport