Berven Frode S, Flikka Kristian, Jensen Harald B, Eidhammer Ingvar
Department of Molecular Biology, Bergen Centre for Computational Science, University of Bergen, 5020 Bergen, Norway.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9. doi: 10.1093/nar/gkh351.
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.
这项工作描述了一个程序的开发，该程序可预测革兰氏阴性细菌的多肽序列是否为完整的β-桶状外膜蛋白。这个名为β-桶状外膜蛋白预测器（BOMP）的程序基于两个独立的组件来识别完整的β-桶状蛋白。第一个组件是许多完整β-桶状蛋白典型的C端模式。第二个组件根据序列中包含跨膜β-链典型氨基酸片段的程度来计算该序列的完整β-桶状得分。当在具有瑞士蛋白质数据库（SwissProt）注释的大肠杆菌K12（788个序列）和鼠伤寒沙门氏菌（366个序列）亚细胞定位的蛋白质上进行测试时，发现预测的精度为80%，召回率为88%。当在大肠杆菌的预测蛋白质组上进行测试时，BOMP在总共4346个多肽序列中发现103个可能是完整的β-桶状蛋白。其中，通过BLAST发现有36个与瑞士蛋白质数据库中注释了亚细胞定位的蛋白质缺乏相似性（E值得分<1e - 10）。BOMP预测10种不同细菌的每个预测蛋白质组中完整β-桶状蛋白的含量范围为1.8%至3%。可通过http://www.bioinfo.no/tools/bomp获取BOMP。
