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Genomics |
Center for Biological Sequence Analysis, Building 2081, and Section for Molecular Microbiology, Building 3012, BioCentrum-DTU, Technical University of Denmark, DK-2800 Lyngby, Denmark
Author for correspondence: Steen Knudsen. Tel: +45 45252480. Fax: +45 45931585. e-mail: steen{at}cbs.dtu.dk
A hidden Markov model of 
A RNA polymerase cofactor recognition sites in Bacillus subtilis, containing either the common or the extended -10 motifs, has been constructed based on experimentally verified A recognition sites. This work suggests that more information exists at the initiation site of transcription in both types of promoters than previously thought. When tested on the entire B. subtilis genome, the model predicts that approximately half of the A recognition sites are of the extended type. Some of the response-regulator aspartate phosphatases were among the predictions of promoters containing extended sites. The expression of rapA and rapB was confirmed by site-directed mutagenesis to depend on the extended -10 region.
Keywords: sigma factor, HMM, response regulator aspartate phosphatase, extended -10 region
Abbreviations: FP, false positive; HMM, hidden Markov model; RNAP, RNA polymerase; TP, true positive
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