ß-barrel outer membrane proteins 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.
OMPdb is the most complete, up-to-date, collection of ß-barrel outer membrane proteins,
both prokaryotic and eukaryotic.
Each OMPdb family is characterised by a unique profile Hidden Markov Model (pHMM) and it includes
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.
OMPdb provides annotation for the transmembrane segments (using PRED-TMBB2)
and the presence of a signal peptide (using SignalP 5.0) in the protein sequence,
literature references and links to other public databases.
It also provides information regarding the existence of a 3D-structure of a given protein, if it is deposited in the
A list of protein entries with solved 3D-structure can also be found in the page of each family, when applicable.
The web interface of OMPdb offers the user the ability to browse the available data and to submit advanced queries
for text search within the database's protein entries or to use the
program of the HMMER suite in order to perform
protein or domain searches respectively.
The most recent 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.
||Dec 15, 2020
| Protein entries