HrpL - UniProtKB: G3XDC4 regulon and binding site collection of Pseudomonas syringae pv. tomato str. DC3000


Sites are listed as curated.

TGGAACCAACTTGCACCTTCAACCACACA
TGGAACTGAAATCGATGCTCGACCACTTA
TGGAACCCGCTGGCATTGCATGCCACTCA
GGGAACCGGTCGCTGCGCTTTGCCACTCA

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

TGGAACCAACTTGCACCTTCAACCACACA
TGGAACTGAAATCGATGCTCGACCACTTA
TGGAACCCGCTGGCATTGCATGCCACTCA
GGGAACCGGTCGCTGCGCTTTGCCACTCA

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_004578.1 G3XDC4 not specified TGGAACCAACTTGCACCTTCAACCACACA +[1543415:1543443] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) hrpK1 (PSPTO_1405) , hopB1 (PSPTO_1406)
    ... ... hrpK1 hopB1
    1123 12207690
    NC_004578.1 G3XDC4 not specified TGGAACTGAAATCGATGCTCGACCACTTA -[1536876:1536904] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) hrpP (PSPTO_1398) , hrcU (PSPTO_1392) , hrpO (PSPTO_1399) , hrcQa (PSPTO_1397) , hrcQb (PSPTO_1396) , hrcR (PSPTO_1395) , hrcS (PSPTO_1394) , hrcT (PSPTO_1393)
    ... ... hrpP hrcU hrpO hrcQa hrcQb hrcR hrcS hrcT
    1123 12207690
    NC_004578.1 G3XDC4 not specified TGGAACCCGCTGGCATTGCATGCCACTCA -[1519572:1519600] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) avrE1 (PSPTO_1377) , hrpH (PSPTO_1378)
    ... ... avrE1 hrpH
    1123 12207690
    NC_004578.1 G3XDC4 not specified GGGAACCGGTCGCTGCGCTTTGCCACTCA -[1510787:1510815] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Northern blot (ECO:0005653) hrpW1 (PSPTO_1373) , shcM (PSPTO_1374) , hopM1 (PSPTO_1375) , shcE (PSPTO_1376)
    ... ... hrpW1 shcM hopM1 shcE
    1123 12207690

    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.

    TGGAACCAACTTGCACCTTCAACCACACA
    TGGAACTGAAATCGATGCTCGACCACTTA
    TGGAACCCGCTGGCATTGCATGCCACTCA
    GGGAACCGGTCGCTGCGCTTTGCCACTCA

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

    TGGAACCAACTTGCACCTTCAACCACACA
    TGGAACTGAAATCGATGCTCGACCACTTA
    TGGAACCCGCTGGCATTGCATGCCACTCA
    GGGAACCGGTCGCTGCGCTTTGCCACTCA
    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.