BOMP:: a program to predict integral β-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
BOMP:: a program to predict integral β-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
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DOI：
10.1093/nar/gkh351
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Eidhammer, I
中科院分区：
文献类型：
--
作者：
Berven, FS;Flikka, K;Eidhammer, I
这项工作描述了一个程序的发展，该程序可以预测来自革兰氏阴性细菌的多肽序列是否是一个完整的β桶外膜蛋白。该程序被称为β -桶外膜蛋白预测器（BOMP），基于两个独立的组件来识别完整的β -桶蛋白。第一个成分是许多完整β -桶蛋白典型的c端模式。第二部分根据序列包含典型跨膜β -链氨基酸延伸的程度计算序列的整体β -桶分数。在大肠杆菌k12（788个序列）和鼠伤寒沙门氏菌（366个序列）中，用SwissProt标记的亚细胞定位蛋白进行测试，发现预测的精度为80%，召回率为88%。当对大肠杆菌预测的蛋白质组进行测试时，BOMP发现总共4346个多肽序列中的103个可能是完整的β -桶蛋白。其中，有36个通过BLAST发现与SwissProt中注释的亚细胞定位蛋白缺乏相似性（e值评分< 1e-10）。BOMP预测10种不同细菌蛋白质组的整体β桶含量在1.8 ~ 3%之间。BOMP的网址是http://www.bioinfo.no/tools/bomp。
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.