A database of ß-barrel outer membrane proteins
from Gram-negative bacteria
Introduction

ß-barrel outer membrane proteins from Gram-negative bacteria are implicated in a broad range of functions crucial for their survival. Such functions include passive nutrient uptake, active transport of large molecules, protein secretion as well as adhesion to host cells, through which bacteria expose their virulence activity. These proteins differ from typical membrane proteins (like the ones found in inner membranes) in that their membrane-spanning regions are formed by amphipathic beta strands instead of alpha helices. Their biological importance together with the inadequate annotation and classification found in public databases, urges the need for intensive studies and accurate data collection regarding ß-barrel proteins.

Information included in OMPdb consists of sequence data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. We also offer information regarding the existence of a 3D-structure of a given protein, if it is deposited in the PDB database. A list of protein entries with solved 3D-structure can be also found in each family entry page, when applicable. We chose to include in OMPdb only protein sequences having a length of at least 120 amino-acids and a coverage of at least 70% in the respective pHMM of the family they belong to.

Along with the database, a collection of profile Hidden Markov Models that were shown to be characteristic for ß-barrel outer membrane proteins was also compiled. This set, when used in combination with our previously developed algorithms (PRED-TMBB, MCMBB and ConBBPRED) will serve as a powerful tool in matters of discrimination and classification of novel ß-barrel proteins and whole-genome analyses.

The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for text search within the database's protein entries or to use the BLAST and hmmscan program of the HMMER suite in order to perform protein or domain searches respectively. The most up-to-date version of the database (as well as all previous versions) can be downloaded in various formats (flat text, XML format or raw FASTA sequences).

Database statistics

Database version 45.0
Revision date Jul 9, 2014
Protein entries 579,382
Families 91
Uniprot release 2014_7
Pfam release 27.0
HMMER version 3.1b1
BLAST version 2.2.26

Contact information

Database administration kostas.tsirigosscilifelab.se
Scientific questions pbagoscompgen.org

Jump to family entry


If you use OMPdb in your research, please cite the respective paper:

Tsirigos KD, Bagos PG and Hamodrakas SJ.
OMPdb: A database of ß-barrel outer membrane proteins from Gram negative bacteria.
Nucl. Acids Res. (2011) 39(suppl 1): D324-D331 (Database Issue)   [PMID: 20952406]

University of Athens
Faculty of Biology
Biophysics & Bioinformatics Laboratory