LexA - UniProtKB: Q87KN2 regulon and binding site collection of Vibrio parahaemolyticus RIMD 2210633


Sites are listed as curated.

TTACTGGATATACTCACAGTTA
TAACTGTATAAAAAGACAGGTG
ATACTGTTGATTCATACAGTGT
TACCTGTATATAAATACAGTAT
AAACTGTATAAATGAACAGTAA
TTCCTGTACAAAAACACAGCTC
GGGCTGGATGAATAAACAGGGG
ATGCTGTATGTGTATACAGTAG
ATACTGTATATAAAAACAGTAT
ACCTGTATAAATAAACAGAC

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

TAACTGTGAGTATATCCAGTAA
TAACTGTATAAAAAGACAGGTG
ACACTGTATGAATCAACAGTAT
TACCTGTATATAAATACAGTAT
AAACTGTATAAATGAACAGTAA
GAGCTGTGTTTTTGTACAGGAA
GGGCTGGATGAATAAACAGGGG
ATGCTGTATGTGTATACAGTAG
ATACTGTATATAAAAACAGTAT
CACCTGTATAAATAAACAGACT

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 Q87KN2 dimer TTACTGGATATACTCACAGTTA -[3150341:3150362] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP2945 , VP2946
    ... ... VP2945 VP2946
    1 22305460
    NC_004603.1 Q87KN2 dimer TAACTGTATAAAAAGACAGGTG -[3150321:3150342] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP2945 , VP2946
    ... ... VP2945 VP2946
    1 22305460
    NC_004603.1 Q87KN2 dimer ATACTGTTGATTCATACAGTGT +[2694441:2694462] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) recA (VP2550) , VP2551
    ... ... recA VP2551
    1 22305460
    NC_004603.1 Q87KN2 dimer TACCTGTATATAAATACAGTAT -[2132041:2132062] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP2033 , VP2034 , VP2035 , VP2036
    ... ... VP2033 VP2034 VP2035 VP2036
    1 22305460
    NC_004603.1 Q87KN2 dimer AAACTGTATAAATGAACAGTAA +[2260931:2260952] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP2149 , VP2147 , VP2148 , VP2146 , VP2150
    ... ... VP2149 VP2147 VP2148 VP2146 VP2150
    1 22305460
    NC_004603.1 Q87KN2 dimer TTCCTGTACAAAAACACAGCTC -[170660:170681] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP0157 , VP0158
    ... ... VP0157 VP0158
    1 22305460
    NC_004603.1 Q87KN2 dimer GGGCTGGATGAATAAACAGGGG +[535829:535850] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP0518 , VP0517 , VP0519
    ... ... VP0518 VP0517 VP0519
    1 22305460
    NC_004603.1 Q87KN2 dimer ATGCTGTATGTGTATACAGTAG +[1339300:1339321] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP1264 , VP1265
    ... ... VP1264 VP1265
    1 22305460
    NC_004603.1 Q87KN2 dimer ATACTGTATATAAAAACAGTAT -[1534638:1534659] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) VP1427 , VP1428 , VP1429
    ... ... VP1427 VP1428 VP1429
    1 22305460
    NC_004603.1 Q87KN2 dimer ACCTGTATAAATAAACAGAC +[1948250:1948269] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) VP1865
    ... ... VP1865
    664 21529368

    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.

    TTACTGGATATACTCACAGTTA
    TAACTGTATAAAAAGACAGGTG
    ATACTGTTGATTCATACAGTGT
    TACCTGTATATAAATACAGTAT
    AAACTGTATAAATGAACAGTAA
    TTCCTGTACAAAAACACAGCTC
    GGGCTGGATGAATAAACAGGGG
    ATGCTGTATGTGTATACAGTAG
    ATACTGTATATAAAAACAGTAT
    ACCTGTATAAATAAACAGAC

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

    TAACTGTGAGTATATCCAGTAA
    TAACTGTATAAAAAGACAGGTG
    ACACTGTATGAATCAACAGTAT
    TACCTGTATATAAATACAGTAT
    AAACTGTATAAATGAACAGTAA
    GAGCTGTGTTTTTGTACAGGAA
    GGGCTGGATGAATAAACAGGGG
    ATGCTGTATGTGTATACAGTAG
    ATACTGTATATAAAAACAGTAT
    CACCTGTATAAATAAACAGACT
    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.