ChlamDB

ChlamDB provides comparative genomic data and analysis for the phylum Chlamydiae and related taxa within the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum by integrating 277 genomes to support annotation, ortholog detection, effector prediction, and domain/pathway analyses.

Key Features:

• Genomic Coverage: Integration of 277 genomes covering the entire Chlamydiae phylum and related PVC taxa.
• Data Integration: Linking of genomic entries to COG, KEGG orthologs, KEGG pathways and modules, Pfam, and InterPro identifiers.
• Comprehensive Annotations: Gene annotations sourced from UniProt (curated and automated), KEGG, COG, TCDB, STRING, and InterPro.
• Candidate Effector Identification: Application of four in silico methods to predict candidate effectors associated with the Type III secretion system (T3SS).
• Ortholog Detection and Comparative Genomics: Large-scale comparative analyses and identification of orthologs across all integrated genomes.
• Visualization and Analysis Outputs: Generation of phylogenetic relationships, transmembrane domain profiles, Pfam domain maps, gene neighborhood conservation, and taxonomic profiles as dynamic graphs.

Scientific Applications:

• Comparative genomics of Chlamydiae and PVC: Comparative analysis of genomes to study evolutionary relationships and functional conservation across the PVC superphylum.
• T3SS effector discovery: Prediction and prioritization of candidate Type III secretion system effectors for studies of bacterial pathogenic mechanisms.
• Functional annotation and pathway analysis: Use of integrated KEGG, Pfam, InterPro, and COG annotations to map genes to pathways, modules, and domain architectures.
• Transporter and interaction analysis: Investigation of transport proteins and protein-protein interaction contexts using TCDB and STRING annotations.
• Phylogeny and domain architecture studies: Assessment of phylogenetic relationships, transmembrane domain distribution, Pfam domain organization, and gene neighborhood conservation.

Methodology:

Integration of 277 genomes with annotations from UniProt, KEGG, COG, TCDB, STRING, and InterPro; identification of orthologs across genomes; application of four in silico methods for T3SS effector prediction; and dynamic generation of graphs for phylogeny, transmembrane domains, Pfam domains, gene neighborhood conservation, and taxonomic profiles.