RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the GadE regulatory interaction in hdeD 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 hdeD was scanned with the annotated matrix for GadE. 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 siteshdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_sites.tab
Ortholog predicted binding sites graphhdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_sites.jpg
geneshdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencehdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
OrthologshdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequenceshdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequenceshdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ sighdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_sig.tab
Occ sig graphhdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_sig.jpg
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Occ freq graphhdeD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_freq.jpg
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