Background: Molecular pathology and biochemistry have significantly advanced the precision of infectious disease diagnostics, enabling rapid and accurate pathogen identification through techniques like PCR and next-generation sequencing. Homology modeling is a key computational tool in understanding protein structures, identifying drug targets, and aiding in therapeutic design. Objective: This study aimed to perform sequence and structural analysis of the CRISPR-associated protein STY3065 from Salmonella typhi using homology modeling to gain insights into its structural integrity and functional roles. Material: The genomic sequence of Salmonella typhi CT18 was obtained from the Comprehensive Microbial Resource (CMR). InterProScan was used to predict protein functions, and BLAST identified a homologous template from E. coli K 12 (PDB ID: 3NKD). Structural modeling was performed using Modeler 9.10, and the model's quality was assessed through ProCheck and ProSA. Results: The homology model of CRISPR-associated protein STY3065 showed 94% sequence identity and 100% query coverage with the template. The model consisted of 10 alpha-helical structures and 7 beta sheets, indicating good protein flexibility. Ramachandran plot analysis showed 91.1% of residues in the most favored regions, confirming high structural quality. ProSA energy calculations indicated a stable model. Conclusion: The study successfully generated a reliable 3D model of the CRISPR-associated protein STY3065, providing valuable structural insights. These findings highlight the potential of homology modeling in advancing our understanding of microbial proteins and aiding in the development of targeted therapies for infectious diseases.