RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the PdhR regulatory interaction in ndh orthologous genes

In general an interaction is conserved if there is a significant overrepresentation of TFBSs in the set of orthologous promoters of the target gene. The set of orthologous promoter for ndh was scanned with the annotated matrix for PdhR. In order to avoid bias due to an excessive representation of close genomes (i.e. several E. coli genomes) we masked the regulatory sequences that were too similar. Overrepresentation is calculated based on the binomial distribution, comparing the observed scores vs. the expected ones for the masked sequence set.


Ortholog predicted binding sitesndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_sites.tab
Ortholog predicted binding sites graphndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_sites.jpg
genesndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencendh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
Orthologsndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencesndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencesndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ signdh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_sig.tab
Occ sig graphndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_sig.jpg
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Occ freq graphndh_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_freq.jpg
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