Computer analysis of regulatory signals in complete bacterial genomes. LexA and DinR binding sites

The method for recognition of transcription regulatory patterns using a com bination of statistical analysis of operators and homology analysis of regu lated genes was applied to the SOS regulons of Escherichia coli, Haemophilu s influenzae, and Bacillus subtilis. New members of these regulons were fou nd. It is demonstrated that recognition of the Cheo boxes by the regulatory protein DinR in B. subtilis is often cooperative and the mutual positionin g of the operators is consistent with the geometry of the double helix.