RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the GadE regulatory interaction in gnd 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 gnd 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 sitesgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_sites.tab
Ortholog predicted binding sites graphgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_sites.jpg
genesgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencegnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
Orthologsgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencesgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencesgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ siggnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_sig.tab
Occ sig graphgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_sig.jpg
(Click on image below)
Occ freq graphgnd_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_GadE_occ_freq.jpg
(Click on image below)
RegulonDB