RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the PdhR regulatory interaction in pdhR 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 pdhR 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 sitespdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_sites.tab
Ortholog predicted binding sites graphpdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_sites.jpg
genespdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencepdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
OrthologspdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencespdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencespdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ sigpdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_sig.tab
Occ sig graphpdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_sig.jpg
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Occ freq graphpdhR_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_PdhR_occ_freq.jpg
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