PcaR - UniProtKB: Q88N41 regulon and binding site collection of Pseudomonas putida KT2440


Sites are listed as curated.

GTTCGATAATCGCAC
GTTCGATAATCGCAC
GCTCGCAGATCGCAC
GTTCGATAATCGCAC
GTTCGATAATCGCAC
GTTCGATAATCGCAC

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

GTTCGATAATCGCAC
GTTCGATAATCGCAC
GCTCGCAGATCGCAC
GTTCGATAATCGCAC
GTTCGATAATCGCAC
GTTCGATAATCGCAC

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_002947.3 Q88N41 dimer GTTCGATAATCGCAC +[1566274:1566288] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Premethylation interference footprinting (ECO:0005656) PP_1374 , pcaR (PP_1375)
    ... ... PP_1374 pcaR
    488 10231483
    NC_002947.3 Q88N41 dimer GTTCGATAATCGCAC +[4457195:4457209] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Premethylation interference footprinting (ECO:0005656) PP_3950 , pcaI (PP_3951) , pcaJ (PP_3952)
    ... ... PP_3950 pcaI pcaJ
    488 10231483
    NC_002947.3 Q88N41 dimer GCTCGCAGATCGCAC +[4457176:4457190] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Premethylation interference footprinting (ECO:0005656) PP_3950 , pcaI (PP_3951) , pcaJ (PP_3952)
    ... ... PP_3950 pcaI pcaJ
    488 10231483
    NC_002947.3 Q88N41 dimer GTTCGATAATCGCAC +[1566274:1566288] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details Random mutagenesis (ECO:0005530) - Experimental technique details Visual sequence inspection (nan) pcaR (PP_1375) , PP_1374
    ... ... pcaR PP_1374
    489 8083169
    NC_002947.3 Q88N41 dimer GTTCGATAATCGCAC +[1566274:1566288] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Primer Extension assay (ECO:0005657) - Experimental technique details Random mutagenesis (ECO:0005530) - Experimental technique details Visual sequence inspection (nan) pcaR (PP_1375) , PP_1374
    ... ... pcaR PP_1374
    489 8083169
    NC_002947.3 Q88N41 not specified GTTCGATAATCGCAC +[4457195:4457209] Experimental technique details Beta-gal reporter assay pcaI (PP_3951) , pcaJ (PP_3952) , PP_3950
    ... ... pcaI pcaJ PP_3950
    490 8376330

    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.

    GTTCGATAATCGCAC
    GTTCGATAATCGCAC
    GCTCGCAGATCGCAC
    GTTCGATAATCGCAC
    GTTCGATAATCGCAC
    GTTCGATAATCGCAC

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

    GTTCGATAATCGCAC
    GTTCGATAATCGCAC
    GCTCGCAGATCGCAC
    GTTCGATAATCGCAC
    GTTCGATAATCGCAC
    GTTCGATAATCGCAC
    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.