PathFams

PathFams identifies pathogen-associated protein domain families to detect potential virulence factors in bacterial genomes by analyzing Pfam domain distributions and abundances.

Key Features:

• Pfam domain coverage: Leverages domain family annotations from the Pfam database for analysis.
• Domain family count: Evaluates 17,929 protein domain families.
• Overrepresentation scoring: Scores domains by overrepresentation in pathogenic versus non-pathogenic species.
• Taxonomic distribution analysis: Assesses taxonomic distribution of domain families across species.
• Metagenomic abundance scoring: Measures relative abundance of domain families within metagenomic datasets.
• Pathogen-associated domain identification: Identifies domain families associated with pathogenic organisms.
• Human gut candidate virulence factors: Detects candidate virulence factor domains specific to the human gut.
• Eukaryotic-like mimicry detection: Identifies eukaryotic-like mimicry domains likely involved in virulence mechanisms.
• Analysis of uncharacterized proteins: Targets proteins of unknown function by characterizing their domain content.
• Domain architecture identification in sequences: Identifies pathogen-associated domains and domain architectures within input sequences.

Scientific Applications:

• Microbial pathogenesis studies: Supports investigation of molecular mechanisms used by bacterial pathogens to infect hosts.
• Virulence factor discovery: Enables identification of candidate virulence factors for further experimental validation.
• Metagenomic surveillance: Facilitates detection of pathogen-associated domains and their abundance in metagenomic datasets.
• Functional annotation: Aids annotation of uncharacterized proteins in pathogenic bacteria via domain-based inference.
• Host–pathogen interaction research: Assists study of eukaryotic-like mimicry domains relevant to virulence mechanisms.
• Antimicrobial target identification: Informs selection of molecular targets for development of antimicrobial strategies.

Methodology:

PathFams evaluates 17,929 Pfam protein domain families and scores them by overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, and relative abundance in metagenomic datasets to identify pathogen-associated domain families, human gut candidate virulence factors, and eukaryotic-like mimicry domains.