FNR - UniProtKB: P0A9E5 regulon and binding site collection of Escherichia coli str. K-12 substr. MG1655


Sites are listed as curated.

TTGATATGGATTAA
TTGATCCTGCTACA
ATCCTTGATGCAAAGCACT
TACTTTGAGCTACATCAAA
TTGATCCTGCTACA
TTGATAACGATCAA

Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

TCTATTGATATGGATTAATAAT
AACCTGTAGCAGGATCAAAAGA
TATAGTGCTTTGCATCAAGGAT
TACTTTGAGCTACATCAAAAAA
AACCTGTAGCAGGATCAAAAGA
TTAATTGATAACGATCAATGTT

For the selected transcription factor and species, the list of curated binding sites in the database are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation.

    Genome TF TF conformation Site sequence Site location Experimental techniques Gene regulation Curations PMIDs
    NC_000913.2 P0A9E5 dimer TTGATATGGATTAA +[1655979:1655992] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) ynfE (b1587) , ynfD (b1586)
    ... ... ynfE ynfD
    156 19251855
    NC_000913.2 P0A9E5 dimer TTGATCCTGCTACA -[2301653:2301666] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details In-vitro transcription (ECO:0001204) napC (b2202) , napB (b2203) , napH (b2204) , napG (b2205) , napA (b2206) , napD (b2207) , napF (b2208) , eco (b2209) , ccmH (b2194) , ccmG (b2195) , ccmF (b2196) , ccmE (b2197) , ccmD (b2198) , ccmC (b2199) , ccmB (b2200) , ccmA (b2201) , yojO (b4604)
    ... ... napC napB napH napG napA napD napF eco ccmH ccmG ccmF ccmE ccmD ccmC ccmB ccmA yojO
    377 9696769
    NC_000913.2 P0A9E5 dimer ATCCTTGATGCAAAGCACT -[4460886:4460904] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) nrdD (b4238) , treR (b4241) , treB (b4240) , treC (b4239)
    ... ... nrdD treR treB treC
    378 18683632
    NC_000913.2 P0A9E5 dimer TACTTTGAGCTACATCAAA -[4460917:4460935] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) nrdD (b4238) , treR (b4241) , treB (b4240) , treC (b4239)
    ... ... nrdD treR treB treC
    378 18683632
    NC_000913.2 P0A9E5 dimer TTGATCCTGCTACA -[2301653:2301666] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details In-vitro transcription (ECO:0001204) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) napF (b2208) , yojO (b4604) , napD (b2207) , napA (b2206) , napG (b2205) , napH (b2204) , napB (b2203) , napC (b2202) , ccmA (b2201) , ccmB (b2200) , ccmC (b2199) , ccmD (b2198) , ccmE (b2197) , ccmF (b2196) , ccmG (b2195) , ccmH (b2194) , eco (b2209)
    ... ... napF yojO napD napA napG napH napB napC ccmA ccmB ccmC ccmD ccmE ccmF ccmG ccmH eco
    178 16199562
    NC_000913.2 P0A9E5 dimer TTGATAACGATCAA -[1752701:1752714] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details qPCR [quantitative real-time] (ECO:0005660) ydhY (b1674) , ydhV (b1673) , ydhW (b1672) , ydhZ (b1675)
    ... ... ydhY ydhV ydhW ydhZ
    179 18227264

    All binding sites in split view are combined and a sequence logo is generated. Note that it may contain binding site sequences from different transcription factors and different species. To see individiual sequence logos and curation details go to split view.


    Sites are listed as curated.

    TTGATATGGATTAA
    TTGATCCTGCTACA
    ATCCTTGATGCAAAGCACT
    TACTTTGAGCTACATCAAA
    TTGATCCTGCTACA
    TTGATAACGATCAA

    Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

    TCTATTGATATGGATTAATAAT
    AACCTGTAGCAGGATCAAAAGA
    TATAGTGCTTTGCATCAAGGAT
    TACTTTGAGCTACATCAAAAAA
    AACCTGTAGCAGGATCAAAAGA
    TTAATTGATAACGATCAATGTT
    Download data in FASTA format.
    Download data in TSV (tab-separated-value) format. For each binding site, all sources of evidence (i.e. experimental techniques and publication information) are combined into one record.
    Download raw data in TSV format. All reported sites are exported individually.
    Download data in Attribute-Relation File Format (ARFF).
    Download Position-Specific-Frequency-Matrix of the motif in TRANSFAC format.
    Download Position-Specific-Frequency-Matrix of the motif in JASPAR format.
    Download Position-Specific-Frequency-Matrix of the motif in raw FASTA format. The matrix consists of four columns in the order A C G T.