ToxT - UniProtKB: A5F384 regulon and binding site collection of Vibrio cholerae O395


Sites are listed as curated.

CATTTTTTGCTGT
TATTTTTTTAATA
AATTTTTAAAAAT
CATTTTGTTAAAT
AATTTTAAGTTAA
TGTTTTTTTAATG
TGTTTTTTTAAAT
GATTTTTGATTTT
GATTTTTGATTTT
GATTTTTGATTTT
GATTTCAAATAAT

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

CATTTTTTGCTGTG
TATTTTTTTAATAA
AATTTTTAAAAATA
CATTTTGTTAAATT
AATTTTAAGTTAAT
TGTTTTTTTAATGC
TGTTTTTTTAAATC
TGATTTTTGATTTT
TGATTTTTGATTTT
TGATTTTTGATTTT
TATTATTTGAAATC

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_009457.1 A5F384 monomer CATTTTTTGCTGT -[381056:381068] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details Site directed mutagenesis (ECO:0005667) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351)
    ... ... tcpA tcpH tcpP
    46 16553883
    NC_009457.1 A5F384 monomer TATTTTTTTAATA -[381036:381048] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details Site directed mutagenesis (ECO:0005667) tcpA (VC0395_A0353) , tcpH (VC0395_A0352) , tcpP (VC0395_A0351)
    ... ... tcpA tcpH tcpP
    46 16553883
    NC_009457.1 A5F384 monomer AATTTTTAAAAAT +[397023:397035] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details Site directed mutagenesis (ECO:0005667) acfA (VC0395_A0368) , VC0395_A0369 , tagE-1 (VC0395_A0367) , VC0395_A0370
    ... ... acfA VC0395_A0369 tagE-1 VC0395_A0370
    47 15853890
    NC_009457.1 A5F384 monomer CATTTTGTTAAAT -[397038:397050] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details Site directed mutagenesis (ECO:0005667) acfA (VC0395_A0368) , VC0395_A0369 , tagE-1 (VC0395_A0367) , VC0395_A0370
    ... ... acfA VC0395_A0369 tagE-1 VC0395_A0370
    47 15853890
    NC_009457.1 A5F384 monomer AATTTTAAGTTAA +[367626:367638] Experimental technique details Beta-gal reporter assay - Experimental technique details Site directed mutagenesis (ECO:0005667) tagA (VC0395_A0345) , aldA-1 (VC0395_A0344)
    ... ... tagA aldA-1
    48 16291662
    NC_009457.1 A5F384 monomer TGTTTTTTTAATG -[367648:367660] Experimental technique details Beta-gal reporter assay - Experimental technique details Site directed mutagenesis (ECO:0005667) tagA (VC0395_A0345) , aldA-1 (VC0395_A0344)
    ... ... tagA aldA-1
    48 16291662
    NC_009457.1 A5F384 monomer TGTTTTTTTAAAT -[367588:367600] Experimental technique details Beta-gal reporter assay - Experimental technique details Site directed mutagenesis (ECO:0005667) aldA-1 (VC0395_A0344) , VC0395_A0343 , tagA (VC0395_A0345)
    ... ... aldA-1 VC0395_A0343 tagA
    48 16291662
    NC_009456.1 A5F384 monomer GATTTTTGATTTT +[566250:566262] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details In-vitro transcription (ECO:0001204) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508)
    ... ... ctxA zot ace VC0395_0509 cep
    49 11849541
    NC_009456.1 A5F384 monomer GATTTTTGATTTT +[566250:566262] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details In-vitro transcription (ECO:0001204) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508)
    ... ... ctxA zot ace VC0395_0509 cep
    49 11849541
    NC_009456.1 A5F384 monomer GATTTTTGATTTT +[566278:566290] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    543 22821976
    NC_009456.1 A5F384 monomer GATTTCAAATAAT +[566292:566304] Experimental technique details Beta-gal reporter assay - Experimental technique details Copper-phenanthroline footprinting (ECO:0005626) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) ctxA (VC0395_0512) , zot (VC0395_0511) , ace (VC0395_0510) , VC0395_0509 , cep (VC0395_0508) , rstB2 (VC0395_0507) , rstA1 (VC0395_0506) , VC0395_0505
    ... ... ctxA zot ace VC0395_0509 cep rstB2 rstA1 VC0395_0505
    543 22821976

    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.

    CATTTTTTGCTGT
    TATTTTTTTAATA
    AATTTTTAAAAAT
    CATTTTGTTAAAT
    AATTTTAAGTTAA
    TGTTTTTTTAATG
    TGTTTTTTTAAAT
    GATTTTTGATTTT
    GATTTTTGATTTT
    GATTTTTGATTTT
    GATTTCAAATAAT

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

    CATTTTTTGCTGTG
    TATTTTTTTAATAA
    AATTTTTAAAAATA
    CATTTTGTTAAATT
    AATTTTAAGTTAAT
    TGTTTTTTTAATGC
    TGTTTTTTTAAATC
    TGATTTTTGATTTT
    TGATTTTTGATTTT
    TGATTTTTGATTTT
    TATTATTTGAAATC
    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.