PhcA - UniProtKB: P52698 regulon and binding site collection of Ralstonia solanacearum GMI1000


Sites are listed as curated.

ATGAGGTTCACGCAT
TTAAAAAATCTTGAT
TTAAAAAATCTTGA

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

GTAACAATGCGTGAACCTCAT
TTAAAAAATCTTGATTCTCTT
TTAAAAAATCTTGATTCTCTT

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_003296.1 P52698 not specified ATGAGGTTCACGCAT +[1080147:1080161] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) RS_RS21185 , RS_RS21190 , RS_RS21195
    ... ... RS_RS21185 RS_RS21190 RS_RS21195
    1124 19060134
    NC_003296.1 P52698 not specified TTAAAAAATCTTGAT -[1265422:1265436] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) RS_RS21960 , RS_RS21955 , RS_RS21950 , RS_RS21965
    ... ... RS_RS21960 RS_RS21955 RS_RS21950 RS_RS21965
    1124 19060134
    NC_003296.1 P52698 not specified TTAAAAAATCTTGA -[1265423:1265436] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) RS_RS21960 , RS_RS21955 , RS_RS21950 , RS_RS21965
    ... ... RS_RS21960 RS_RS21955 RS_RS21950 RS_RS21965
    1125 9573161

    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.

    ATGAGGTTCACGCAT
    TTAAAAAATCTTGAT
    TTAAAAAATCTTGA

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

    GTAACAATGCGTGAACCTCAT
    TTAAAAAATCTTGATTCTCTT
    TTAAAAAATCTTGATTCTCTT
    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.