AphA - UniProtKB: Q87L53 regulon and binding site collection of Vibrio parahaemolyticus RIMD 2210633


Sites are listed as curated.

GTATTCCACTTCATGCTTAT
ATATGCACCATTACACTCAT
CAATGTAACAAGTGGCATAT

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

GTATTCCACTTCATGCTTAT
ATATGCACCATTACACTCAT
ATATGCCACTTGTTACATTG

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_004603.1 Q87L53 dimer GTATTCCACTTCATGCTTAT +[2929670:2929689] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Primer Extension assay (ECO:0005657) VP2762 , VP2761 , metF (VP2763)
    ... ... VP2762 VP2761 metF
    506 22984476
    NC_004603.1 Q87L53 dimer ATATGCACCATTACACTCAT +[2653116:2653135] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Primer Extension assay (ECO:0005657) VP2516 , VP2515 , VP2514 , VP2517
    ... ... VP2516 VP2515 VP2514 VP2517
    507 22984476
    NC_004605.1 Q87L53 dimer CAATGTAACAAGTGGCATAT +[200434:200453] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Primer Extension assay (ECO:0005657) VPA0199 , VPA0198 , VPA0197 , VPA0196 , VPA0195 , VPA0200
    ... ... VPA0199 VPA0198 VPA0197 VPA0196 VPA0195 VPA0200
    508 22984476

    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.

    GTATTCCACTTCATGCTTAT
    ATATGCACCATTACACTCAT
    CAATGTAACAAGTGGCATAT

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

    GTATTCCACTTCATGCTTAT
    ATATGCACCATTACACTCAT
    ATATGCCACTTGTTACATTG
    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.