VKCDB is a comprehensive sequence database of voltage-gated potassium channels (VKCs) from Eukaryotes, Bacteria and Archaea, designed to serve as a resource for research on VKC evolution and structure/function relationships. Protein sequences, corresponding nucleic acid sequences of open reading frames, references, information on the organisms of origin of each channel and functional data are stored in this database. The current version (v 2) has been significantly expanded and updated since the release of v1 in 2003.
VKCDB will allow you to browse and search using different annotation criteria, and search against the protein and nucleotide sequences in VKCDB with VKCDB BLAST. Displayed entries can be selected to download as multiple protein and/or nucleotide sequences in FASTA format for further analyses. Several computational tools are being developed to help guide structure function analysis of voltage-gated potassium channels and other protein families in general.
VKCDB currently stores 4279 entries, including some "unknown proteins" annotated by automatic genome annotation projects which share a high degree of sequence similarity with voltage-gated potassium channels, but also some entries that are clearly not VKCs, but rather similar to protein domains that have been fused to one or more VKCs in some organisms. VKCDB was initially populated using automatic parsing of BLASTP search outputs from larger databases; updates are based on the results of Hidden Markov Model searches of the GENBANK non-redundant protein database using HMMER. Entries were checked manually for redundancy, sequence conflicts, and isoforms. Manual curation, based on visual inspection of the length of the sequence and on p hylogenetic analysis, was used to identify 1391 unique VKC sequences that cover a major portion of the full channel length.
The web interface only retrieves entries that cover a significant proportion of the core structure of VKCs (the voltage sensor and pore regions), and does not retrieve a number of entries that were identified by manual inspection as non-VKC prote ins. If you wish to look at small fragmentary sequences and/or non-channel sequences that have been retrieved during population of the database, the entire database is available for download in XML format or as a SQL dump file.
VKCDB is a part of an ongoing project on the structure/function relationships in VKCs in the laboratory of Dr. Warren J. Gallin at the University of Alberta, Canada.