Escherichia coli transcription factor binding sites (TFBS)

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Escherichia coli transcription factor binding sites (TFBS)


Transcription Factor Binding Sites


L.A. McCue


Last Updated: 2002

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About Escherichia coli transcription factor binding sites (TFBS)

This site presents transcription factor binding site predictions[1] in the E. coli genome made by cross-species comparison (i.e. phylogenetic footprinting) using a Gibbs sampling algorithm for motif finding. Predictions were made upstream of 2086 E. coli genes; that is, all genes for which: 1) there was at least 50 bp upstream intergenic sequence, and 2) a probable ortholog was identified among the species used for comparison. The gene names and annotations used are those from the E. coli genome GenBank entry (U00096). Where available, correspondence of our predictions with experimentally verified binding sites or known repeats is presented. Regulons have been predicted by clustering these phylogenetic footprinted motifs.


The prediction page for each gene contains the following information.

  • The genome coordinates, orientation, gene type (CDS or RNA), gene name, EcoGene link, and annotation for the target gene, and also the genes immediately flanking the target gene.
  • The genome coordinates, source of information, transcription factor name, and annotation for known TF-binding sites that regulate the target gene.
  • A listing of the species for which a probable ortholog of the target gene was identified.
  • The predictions made for the target gene, separated into those predictions that were above our cutoff for statistical significance (p < 0.05), and those that were below the cutoff. For each prediction the following information is given: the Average MAP (maximum a posteriori probability) value, the genome coordinates (an "R" indicates that the sequence given is the reverse complement of that in the GenBank entry at those coordinates), the site sequence (plus 5 bp flanking), the transcription factor site type and overlap in bp (if site overlaps a known transcription factor binding site), the repeat name (if site overlaps a known repeat), a sequence logo if the motif model, a sequence logo of the aligned sites, a sequence alignment of the sites. For genes that are divergently transcribed, predictions were made for each gene separately and overlap with known sites is reported for all regulatory sites in that promoter region (sites that regulate the target gene and sites that regulate the divergently transcribed gene).
  • The critical MAP values for the target gene calculated for p = 0.01, p = 0.05, p = 0.1, and p = 0.2.

Using TFBS


Browse list of genes


Query by gene name

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content


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  1. McCue, LA et al. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res. 12 1523-32 PubMed

External Links

Escherichia coli transcription factor binding sites (TFBS)

Discussion of Escherichia coli transcription factor binding sites (TFBS) on other websites