In Silico Structural and Functional Characterization of Hypothetical Protein WP_000477209.1 from Hypervirulent Klebsiella aerogenes G7 Reveals a Potential Epigenetic Regulator

Hypothetical proteins (HPs) represent a substantial portion of prokaryotic genomes and may play critical roles in virulence, antibiotic resistance, and epigenetic regulation. Klebsiella aerogenes strain G7, a hypervirulent and multidrug-resistant isolate belonging to the ST93 lineage, contains numerous uncharacterized proteins that could serve as potential therapeutic targets. In this analysis, we performed a comprehensive in silico analysis of the structural and functional characteristics of the hypothetical protein WP_000477209.1, selected from a pool of 472 HPs based on its conserved domain architecture and predicted functional relevance. We evaluated its physicochemical properties, subcellular localization, and structural features using tools such as ProtParam, CELLO, InterProScan, HHpred, PSIPRED, and YASARA. The 294-amino-acid protein was predicted to be a stable, hydrophilic cytoplasmic protein, with a molecular weight of 30.87 kDa and a theoretical pI of 8.98. Domain analysis indicated the presence of a DpnI_C superfamily domain, associated with Dam-replacing endonucleases that are involved in DNA methylation and restriction-modification systems. Homology modeling produced a high-confidence tertiary structure, with 93.2% of residues located in favored regions of the Ramachandran plot, corroborated by strong QMEAN and Verify3D scores. PrankWeb identified four potential ligand-binding sites, and VICMpred suggested possible virulence-associated functions. Our findings suggest that WP_000477209.1 likely acts as an epigenetic regulator and stands out as a promising candidate for further experimental validation and drug discovery. This analysis enhances the functional annotation of the K. aerogenes G7 proteome and emphasizes the significance of characterizing hypothetical proteins in pathogenic bacteria.