Evolutionary conservation in this RegulonDB version is limited to Gammaproteobacteria and to sigma70 promoters. The approach to assign evolutionary evidence to each RegulonDB promoter is based on i) conservation of the position of the promoter from the gene start [Huerta AM et al. MBE 2006], and ii) conservation of the promoter sequence recognized by the sigma70 factor (p < 0.0001). Target genomes were selected if 1) the sigma factor is conserved, and 2) the E. coli transcribed gene had orthologs in the target genome. Orthologs consisted of BLAST reciprocal best hits using soft masking and Smith-Waterman alignments as explained in [Moreno-Hagelsieb G. et al. 2008]. The evolutionary conservation of sigma70promoters is shown in the following table. The score of evolutionary conservation is calculated as the ratio of the number of orthologs with conserved promoters to the total number of orthologous genes of the downstream gene.
|Ortholog RNApol binding sites||pepDp3_E_coli_K12_MG1655_allGamma_ncbi_0001_s70_sites.tab|
|Ortholog RNApol binding sites graph||pepDp3_E_coli_K12_MG1655_allGamma_ncbi_0001_s70_sites.tab.png|