PhoB - UniProtKB: Q3K4G1 regulon and binding site collection of Pseudomonas fluorescens Pf0-1


Sites are listed as curated.

CTTTCATCCAATTGTCA
TTGTCATATTTCAGCCA
CTGCAACGAAAGCGTCA
GTGTCACACCCCTTTCA

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

CTTTCATCCAATTGTCAT
ATGGCTGAAATATGACAA
CTGCAACGAAAGCGTCAT
ATGAAAGGGGTGTGACAC

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_007492.2 Q3K4G1 not specified CTTTCATCCAATTGTCA -[6290672:6290688] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) Pfl01_5615
    ... ... Pfl01_5615
    751 16517638
    NC_007492.2 Q3K4G1 not specified TTGTCATATTTCAGCCA -[6290661:6290677] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) Pfl01_5615
    ... ... Pfl01_5615
    751 16517638
    NC_007492.2 Q3K4G1 not specified CTGCAACGAAAGCGTCA +[5823986:5824002] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) Pfl01_5179 , Pfl01_5180 , Pfl01_5181
    ... ... Pfl01_5179 Pfl01_5180 Pfl01_5181
    751 16517638
    NC_007492.2 Q3K4G1 not specified GTGTCACACCCCTTTCA +[936349:936365] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) Pfl01_0796
    ... ... Pfl01_0796
    751 16517638

    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.

    CTTTCATCCAATTGTCA
    TTGTCATATTTCAGCCA
    CTGCAACGAAAGCGTCA
    GTGTCACACCCCTTTCA

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

    CTTTCATCCAATTGTCAT
    ATGGCTGAAATATGACAA
    CTGCAACGAAAGCGTCAT
    ATGAAAGGGGTGTGACAC
    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.