Abstract
BackgroundThe family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins. They help maintain and regulate the potassium ion-based component of the membrane potential and are thus central to many critical physiological processes. VKCDB (Voltage-gated potassium [K] Channel DataBase) is a database of structural and functional data on these channels. It is designed as a resource for research on the molecular basis of voltage-gated potassium channel function.DescriptionVoltage-gated potassium channel sequences were identified by using BLASTP to search GENBANK and SWISSPROT. Annotations for all voltage-gated potassium channels were selectively parsed and integrated into VKCDB. Electrophysiological and pharmacological data for the channels were collected from published journal articles. Transmembrane domain predictions by TMHMM and PHD are included for each VKCDB entry. Multiple sequence alignments of conserved domains of channels of the four Kv families and the KCNQ family are also included. Currently VKCDB contains 346 channel entries. It can be browsed and searched using a set of functionally relevant categories. Protein sequences can also be searched using a local BLAST engine.ConclusionsVKCDB is a resource for comparative studies of voltage-gated potassium channels. The methods used to construct VKCDB are general; they can be used to create specialized databases for other protein families. VKCDB is accessible at .
Highlights
The family of voltage-gated potassium channels comprises a functionally diverse group of membrane proteins
VKCDB is a resource for comparative studies of voltage-gated potassium channels
Voltage-gated potassium channels (VKCs) are intrinsic membrane proteins that respond to changes in the transmembrane electrical field by altering conformation and selectively allowing potassium ions to pass through the membrane [3]
Summary
VKCDB contains structural and functional data and related multiple alignments for voltage-gated potassium channels in a single database. As a small, customized protein family database, VKCDB is a useful and convenient resource for research on VKCs. As our understanding of VKCs increases, more annotations and applications will be added to enrich VKCDB so that it can continue to serve as a main resource for structural and functional studies of VKCs. VKCDB is freely accessible at http://vkcdb.biology.ual berta.ca. BL carried out the design of the database schema and the building of the MySQL database. He built the web interface and related CGIs, and wrote code to populate, implement and update VKCDB, manually checked each. WJG conceived of the study, and participated in the design, building, data checking and analyses
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