RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the CsgD regulatory interaction in yccT 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 yccT 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 sitesyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.tab
Ortholog predicted binding sites graphyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.jpg
genesyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequenceyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
OrthologsyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencesyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencesyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ sigyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.tab
Occ sig graphyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.jpg
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Occ freq graphyccT_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_freq.jpg
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