Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting.

ABSTRACT:

Background

Although pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases.

Methods

To allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing re

SUBMITTER: McDermott JE 

PROVIDER: S-EPMC6557245 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature