PathFams: statistical detection of pathogen-associated protein domains.

Autor: Lobb B; Department of Biology, University of Waterloo, Waterloo, Ontario, Canada., Tremblay BJ; Department of Biology, University of Waterloo, Waterloo, Ontario, Canada., Moreno-Hagelsieb G; Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada., Doxey AC; Department of Biology, University of Waterloo, Waterloo, Ontario, Canada. acdoxey@uwaterloo.ca.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2021 Sep 14; Vol. 22 (1), pp. 663. Date of Electronic Publication: 2021 Sep 14.
DOI: 10.1186/s12864-021-07982-8
Abstrakt: Background: A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal.
Results: To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within the Pfam database, and scored them based on their overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, relative abundance in metagenomic datasets, and other factors.
Conclusions: We identify pathogen-associated domain families, candidate virulence factors in the human gut, and eukaryotic-like mimicry domains with likely roles in virulence. Furthermore, we provide an interactive database called PathFams to allow users to explore pathogen-associated domains as well as identify pathogen-associated domains and domain architectures in user-uploaded sequences of interest. PathFams is freely available at https://pathfams.uwaterloo.ca .
(© 2021. The Author(s).)
Databáze: MEDLINE
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