BSepDB: a database of bacterial selenoprotein genes and proteins

BACKGROUND: Selenoproteins represent a structurally and functionally distinct class of proteins that contribute to cellular antioxidant defense and a wide range of other essential biological processes in specific organisms. They contain the 21st amino acid selenocysteine (Sec) in their active sites, which is encoded by an in-frame UGA stop codon through a translational reprogramming mechanism. Due to the dual functionality of the UGA codon, selenoprotein genes are frequently misidentified and misannotated in genomic databases, especially in bacteria where selenoproteins exhibit greater complexity and diversity compared to their eukaryotic counterparts. Thus, a comprehensive resource is urgently required to enable accurate identification of selenoprotein genes across diverse bacterial genomes. RESULTS: We have developed BSepDB, a specialized database dedicated to systematic curation of bacterial selenoprotein genes and proteins, providing an exhaustive resource for the research community. The current version (BSepDB v. 1.0) encompasses over 57,000 selenoprotein entries derived from 16,621 bacterial species, representing the largest and most taxonomically diverse repository of bacterial selenoproteins to date. To facilitate intuitive data exploration, BSepDB offers multiple user-friendly interfaces, such as interactive browsing and search tools, an integrated BLAST search function, and options for bulk data download. Additionally, the curated entries in BSepDB are cross-referenced with established genomic databases (e.g., GenBank and RefSeq) to improve the accuracy of selenoprotein annotations in large-scale genomic projects. CONCLUSIONS: BSepDB serves as a valuable resource for researchers investigating selenium utilization and the functional diversity of selenoproteins in bacteria. The database is freely available at https://bsepdb.metalbioinfolab.net.