T346Hunter

T346Hunter identifies and localizes type III, type IV, and type VI secretion system (T3SS, T4SS, T6SS) clusters in bacterial chromosomes and plasmids to enable genomic characterization of bacterial virulence determinants and effector delivery systems.

Key Features:

• Secretion system detection: Predicts and localizes clusters of non-flagellar type III secretion system (NF-T3SS), type IV secretion system (T4SS), and type VI secretion system (T6SS) in bacterial genomes.
• HMM-based database: Uses a database constructed from hidden Markov model (HMM) protein profiles and representative sequences of secretion system components.
• Enriched-region searches: Performs comprehensive searches against the HMM/profile database to identify enriched genomic regions corresponding to secretion system clusters.
• Comparative dataset and visualization: Reports predicted clusters and provides visualization across approximately 1,700 bacterial chromosomes and plasmids for comparative analyses.
• Analysis of newly sequenced genomes: Applies predictions to newly sequenced bacterial genomes to identify potential virulence determinants and cluster localization.

Scientific Applications:

• Virulence determinant identification: Identification and cataloging of secretion system-encoded virulence determinants in bacterial genomes.
• Comparative genomics: Comparative analysis of secretion system distribution across ~1,700 chromosomes and plasmids.
• Effector translocation and host interaction studies: Studying mechanisms of effector translocation and bacterial interactions with eukaryotic hosts, with emphasis on NF-T3SS and T6SS.
• T4SS functional characterization: Characterizing T4SS-associated functions including conjugation and DNA uptake/release.
• Pathogenesis research support: Informing research into the molecular basis of bacterial pathogenesis and strategies to control bacterial-mediated diseases.

Methodology:

Database construction from hidden Markov model (HMM) protein profiles and representative sequences of secretion system components, and comprehensive searches of submitted bacterial genomic data against that database to detect enriched regions corresponding to T3SS, T4SS, and T6SS clusters.