Sigma 28 promoter prediction in members of the Gammaproteobacteria

Abstract

A two-step approach was used to predict σ28 promoter sequences in a number of Gammaproteobacteria. Putative promoters were initially identified upstream of motility and chemotaxis genes in test species based on their similarity to the Escherichia coli σ28 promoter consensus. These sequences were then used to generate position specific score matrices that were used iteratively during whole-genome analyses. The consistent identification of promoter sequences upstream of orthologous genes suggested that the predictions were biologically relevant. © 2007 Federation of European Microbiological Societies.