RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the CsgD regulatory interaction in pepD 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 pepD was scanned with the annotated matrix for CsgD. 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 sitespepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.tab
Ortholog predicted binding sites graphpepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.jpg
genespepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencepepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
OrthologspepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencespepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencespepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ sigpepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.tab
Occ sig graphpepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.jpg
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Occ freq graphpepD_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_freq.jpg
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