Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems.

ABSTRACT: The type III secretion system is an essential component for virulence in many Gram-negative bacteria. Though components of the secretion system apparatus are conserved, its substrates--effector proteins--are not. We have used a novel computational approach to confidently identify new secreted effectors by integrating protein sequence-based features, including evolutionary measures such as the pattern of homologs in a range of other organisms, G+C content, amino acid composition, and the N-terminal 30 residues of the protein sequence. The method was trained on known effectors from the plant pathogen Pseudomonas syringae and validated on a set of effectors from the animal pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) after eliminating effectors with detectable sequence si

SUBMITTER: Samudrala R 

PROVIDER: S-EPMC2668754 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature