Sigma A recognition sites in the Bacillus subtilis genome

A hidden Markov model of sigma (A) RNA polymerase cofactor recognition site s in Bacillus subtilis, containing either the common or the extended -10 mo tifs, has been constructed based on experimentally verified sigma (A) recog nition sites. This work suggests that more information exists at the initia tion site of transcription in both types of promoters than previously thoug ht. When tested on the entire B. subtilis genome, the model predicts that a pproximately half of the sigma (A) recognition sites are of the extended ty pe. Some of the response-regulator aspartate phosphatases were among the pr edictions of promoters containing extended sites. The expression of rapA an d rapB was confirmed by site-directed mutagenesis to depend on the extended -10 region.