Tsirigos Konstantinos D, Bagos Pantelis G, Hamodrakas Stavros J
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens 15701, Greece.
Nucleic Acids Res. 2011 Jan;39(Database issue):D324-31. doi: 10.1093/nar/gkq863. Epub 2010 Oct 15.
We describe here OMPdb, which is currently the most complete and comprehensive collection of integral β-barrel outer membrane proteins from Gram-negative bacteria. The database currently contains 69,354 proteins, which are classified into 85 families, based mainly on structural and functional criteria. Although OMPdb follows the annotation scheme of Pfam, many of the families included in the database were not previously described or annotated in other publicly available databases. There are also cross-references to other databases, references to the literature and annotation for sequence features, like transmembrane segments and signal peptides. Furthermore, via the web interface, the user can not only browse the available data, but submit advanced text searches and run BLAST queries against the database protein sequences or domain searches against the collection of profile Hidden Markov Models that represent each family's domain organization as well. The database is freely accessible for academic users at http://bioinformatics.biol.uoa.gr/OMPdb and we expect it to be useful for genome-wide analyses, comparative genomics as well as for providing training and test sets for predictive algorithms regarding transmembrane β-barrels.
我们在此介绍OMPdb，它是目前来自革兰氏阴性菌的完整且全面的整合β桶状外膜蛋白集合。该数据库目前包含69354种蛋白质，主要基于结构和功能标准分为85个家族。尽管OMPdb遵循Pfam的注释方案，但数据库中包含的许多家族此前在其他公开可用数据库中未被描述或注释。此外，还有与其他数据库的交叉引用、文献引用以及序列特征（如跨膜片段和信号肽）的注释。此外，通过网络界面，用户不仅可以浏览现有数据，还可以提交高级文本搜索，并针对数据库蛋白质序列运行BLAST查询，或针对代表每个家族结构域组织的轮廓隐马尔可夫模型集合进行结构域搜索。学术用户可通过http://bioinformatics.biol.uoa.gr/OMPdb免费访问该数据库，我们预计它将有助于全基因组分析、比较基因组学，以及为跨膜β桶预测算法提供训练和测试集。
