VKCDB

VKCDB provides a curated collection of voltage-gated potassium (K+) channel amino acid and corresponding nucleotide sequences to support phylogenetic, comparative genomic, and structural–functional analyses.

Key Features:

• Sequence collection: 2,063 full-length or nearly full-length unique channel entries comprising 477 Bacteria, 18 Archaea, and 1,568 Eukaryotes.
• Amino acid and nucleotide data: Parallel availability of amino acid sequences and their corresponding nucleotide sequences for each entry.
• Classification: Subfamily categorization performed using phylogenetic analysis and hidden Markov model (HMM) analyses to group sequences by evolutionary relationships and structural motifs.
• Validation and raw data: Public entries are filtered to retain sequences confirmed as likely voltage-gated K+ channels, while the raw dataset includes fragmentary, duplicated, obsolete, and non-channel sequences collected during acquisition.
• Entry types: Contains both complete entries and fragmentary entries that include core structural elements of voltage-gated K+ channels (VKCs).
• Automated updates: Database contents are refreshed on a quarterly schedule.
• Data export formats: Full database available as MySQL dump and XML dump.

Scientific Applications:

• Phylogenetic analysis: Reconstruction of evolutionary relationships among voltage-gated K+ channels across Bacteria, Archaea, and Eukaryotes.
• Comparative genomics and evolutionary studies: Cross-domain comparisons to investigate distribution, divergence, and lineage-specific features of K+ channels.
• Genomic and proteomic analyses: Use of paired nucleotide and amino acid sequences for sequence-based analyses, annotation, and comparative studies.
• Structural and functional investigations: Analysis of core structural elements and motifs of VKCs to inform hypotheses about channel structure–function relationships.

Methodology:

Classification is performed using phylogenetic analysis and hidden Markov model (HMM) analyses; the database is updated quarterly and provided as MySQL and XML dumps.