RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the CsgD regulatory interaction in nlpA 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 nlpA 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 sitesnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.tab
Ortholog predicted binding sites graphnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_sites.jpg
genesnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencenlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
OrthologsnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencesnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencesnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ signlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.tab
Occ sig graphnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_sig.jpg
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Occ freq graphnlpA_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_CsgD_occ_freq.jpg
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