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 recently presented PRED-TMBB2 algoritmh , will serve as a powerful tool in terms of discrimination and classification of novel ß-barrel proteins and whole-proteome 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 / phmmer 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 can be downloaded in various formats (flat text, XML format or raw FASTA sequences). In the download page, the user may download the complete dataset of ß-barrel proteins, which is compiled following the regular updates of the PDBTM database, the OPM database and the list of membrane proteins of known 3D-structure from Stephen White's laboratory at UC Irvine.