Predicting the metalloproteome of Deinococcus indicus DR1 through integrative structure and function annotation

Deinococcus indicus DR1, a rod-shaped bacterium isolated from the Dadri wetlands (Uttar Pradesh, India), tolerates ionizing radiation and arsenic. However, the molecular basis of its wider heavy-metal resilience remains unclear, particularly for 1017 of the 4128 proteins still annotated as hypothetical. The aim of this study is to perform a proteome-wide structural and functional survey to address this gap. All 4128 proteins were modeled with AlphaFold2, yielding very-high-confidence structures of predicted local distance difference test scores ≥ 90 for 2145 sequences. CATH and InterPro analysis assigned domains to 2735 proteins. Functions were predicted by combining DeepFRI (graph neural-network), MorphologFinder (Foldseek coupled with EggNOG-Mapper), and existing GenBank annotations. Structural classification revealed domains involved in arsenic resistance properties. Functional annotation identified metal binding proteins. Recurrent domain architectures that include P-loop NTPases, Rossmann folds, GNAT acetyl-transferases, and sensor modules point to coordinated redox regulation and efflux pathways. The integrated workflow suggests that more than 100 previously uncharacterized proteins are associated with diverse metal-related functions including metal binding, cofactor utilization, transport, and detoxification across chromium, cobalt, copper, iron, manganese, molybdenum, nickel, and zinc. This indicates the presence of additional metal-associated proteins beyond the known arsenic-resistance (ars) gene cluster. However, their functional roles require experimental validation. Twenty high-confidence metal-binding candidates were prioritized for experimental validation through expression, mutagenesis, and gene-knockout studies. All structural models, domain assignments, and query tools are available at https://deinococcus.in , providing a resource for future investigations of heavy-metal tolerance in this organism.