ColR - UniProtKB: Q88PE9 regulon and binding site collection of Pseudomonas putida KT2440


Sites are listed as curated.

TTCACGTTTTTTTCAC
TTCACACTTTTTTCAC
TTCACTATTTTTTCAC
TTGACGGTTTTTTCAC
CTAAGATTTTTTTGAC
TTCACGACTTTTTGAC
CCAACGTTTTTTTCAC

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

TTCACGTTTTTTTCAC
TTCACACTTTTTTCAC
TTCACTATTTTTTCAC
TTGACGGTTTTTTCAC
CTAAGATTTTTTTGAC
TTCACGACTTTTTGAC
CCAACGTTTTTTTCAC

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 Q88PE9 dimer TTCACGTTTTTTTCAC -[855941:855956] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) PP_0737 , murI (PP_0736)
    ... ... PP_0737 murI
    651 19445690
    NC_002947.3 Q88PE9 dimer TTCACACTTTTTTCAC +[4296097:4296112] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) gloA (PP_3766) , PP_3767
    ... ... gloA PP_3767
    651 19445690
    NC_002947.3 Q88PE9 dimer TTCACTATTTTTTCAC -[39037:39052] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) PP_0035 , PP_0034 , PP_0033 , PP_0036
    ... ... PP_0035 PP_0034 PP_0033 PP_0036
    651 19445690
    NC_002947.3 Q88PE9 dimer TTGACGGTTTTTTCAC -[1041401:1041416] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) PP_0900 , colR (PP_0901) , PP_0902 , PP_0903 , PP_0904 , PP_0905
    ... ... PP_0900 colR PP_0902 PP_0903 PP_0904 PP_0905
    651 19445690
    NC_002947.3 Q88PE9 dimer CTAAGATTTTTTTGAC +[2910678:2910693] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) PP_2561 , PP_2560 , hasE (PP_2559) , PP_2558
    ... ... PP_2561 PP_2560 hasE PP_2558
    651 19445690
    NC_002947.3 Q88PE9 dimer TTCACGACTTTTTGAC +[324501:324516] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) oprQ (PP_0268) , PP_0267
    ... ... oprQ PP_0267
    651 19445690
    NC_002947.3 Q88PE9 dimer CCAACGTTTTTTTCAC +[1043524:1043539] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) PP_0903 , PP_0904 , PP_0905
    ... ... PP_0903 PP_0904 PP_0905
    651 19445690

    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.

    TTCACGTTTTTTTCAC
    TTCACACTTTTTTCAC
    TTCACTATTTTTTCAC
    TTGACGGTTTTTTCAC
    CTAAGATTTTTTTGAC
    TTCACGACTTTTTGAC
    CCAACGTTTTTTTCAC

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

    TTCACGTTTTTTTCAC
    TTCACACTTTTTTCAC
    TTCACTATTTTTTCAC
    TTGACGGTTTTTTCAC
    CTAAGATTTTTTTGAC
    TTCACGACTTTTTGAC
    CCAACGTTTTTTTCAC
    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.