Department of Biochemistry, Tulane University, New Orleans, LA 70112, USA.
Bioinformatics. 2012 Oct 1;28(19):2425-30. doi: 10.1093/bioinformatics/bts478. Epub 2012 Jul 27.
We previously reported the development of a highly accurate statistical algorithm for identifying β-barrel outer membrane proteins or transmembrane β-barrels (TMBBs), from genomic sequence data of Gram-negative bacteria (Freeman,T.C. and Wimley,W.C. (2010) Bioinformatics, 26, 1965-1974). We have now applied this identification algorithm to all available Gram-negative bacterial genomes (over 600 chromosomes) and have constructed a publicly available, searchable, up-to-date, database of all proteins in these genomes.
For each protein in the database, there is information on (i) β-barrel membrane protein probability for identification of β-barrels, (ii) β-strand and β-hairpin propensity for structure and topology prediction, (iii) signal sequence score because most TMBBs are secreted through the inner membrane translocon and, thus, have a signal sequence, and (iv) transmembrane α-helix predictions, for reducing false positive predictions. This information is sufficient for the accurate identification of most β-barrel membrane proteins in these genomes. In the database there are nearly 50 000 predicted TMBBs (out of 1.9 million total putative proteins). Of those, more than 15 000 are 'hypothetical' or 'putative' proteins, not previously identified as TMBBs. This wealth of genomic information is not available anywhere else.
The TMBB genomic database is available at http://beta-barrel.tulane.edu/.
我们之前报道了一种从革兰氏阴性菌基因组序列数据中识别β-桶外膜蛋白或跨膜β-桶（TMBB）的高度准确的统计算法的开发（Freeman，T.C.和 Wimley，W.C.（2010）生物信息学，26，1965-1974）。我们现在已经将这个识别算法应用于所有可用的革兰氏阴性细菌基因组（超过 600 个染色体），并构建了一个公共的、可搜索的、最新的、包含这些基因组中所有蛋白质的数据库。
对于数据库中的每个蛋白质，都有关于（i）β-桶膜蛋白识别β-桶的概率，（ii）β-链和β-发夹的结构和拓扑预测倾向，（iii）信号序列得分，因为大多数 TMBB 都是通过内膜转位器分泌的，因此有一个信号序列，（iv）跨膜α-螺旋预测，用于减少假阳性预测。这些信息足以准确识别这些基因组中的大多数β-桶膜蛋白。在数据库中，有近 50000 个预测的 TMBB（在 190 万个总假设蛋白中）。其中，超过 15000 个是“假设”或“假定”的蛋白质，以前没有被识别为 TMBB。基因组信息丰富，在其他地方无法获得。
TMBB 基因组数据库可在 http://beta-barrel.tulane.edu/ 获得。
