Zur - UniProtKB: Q4KKK3 regulon and binding site collection of Pseudomonas protegens Pf-5


Sites are listed as curated.

TTGTTATAATATAACAT
ATGTTATATTATAACAA
ATGTTATATTATAACAA
TTGTTATAATATAACAT
ATGTTATATTGTATCAA
ATGTGATCTTATAACAA
TTGTTATAAGATCACAT
ATGTTATATTGTTTCAA
ATGTTATTGTATAACGC
ATGATATGTTATTACAT
ATGTTACTTTATAACGC
TCGTTATATAGTAACGA

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

TTGTTATAATATAACAT
TTGTTATAATATAACAT
TTGTTATAATATAACAT
TTGTTATAATATAACAT
TTGATACAATATAACAT
TTGTTATAAGATCACAT
TTGTTATAAGATCACAT
TTGAAACAATATAACAT
GCGTTATACAATAACAT
ATGTAATAACATATCAT
GCGTTATAAAGTAACAT
TCGTTACTATATAACGA

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_004129.6 Q4KKK3 not specified TTGTTATAATATAACAT -[7012814:7012830] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_6174 , PFL_6173 , PFL_6172 , PFL_6171 , PFL_6175
    ... ... PFL_6174 PFL_6173 PFL_6172 PFL_6171 PFL_6175
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTATATTATAACAA +[7012814:7012830] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_6175 , PFL_6174 , PFL_6173 , PFL_6172 , PFL_6171
    ... ... PFL_6175 PFL_6174 PFL_6173 PFL_6172 PFL_6171
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTATATTATAACAA -[7014700:7014716] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) amiC (PFL_6176) , PFL_6177 , mntA (PFL_6178) , mntB (PFL_6179) , mntC (PFL_6180) , hisI2 (PFL_6181) , PFL_6182 , PFL_6183 , thrS_2 (PFL_6184)
    ... ... amiC PFL_6177 mntA mntB mntC hisI2 PFL_6182 PFL_6183 thrS_2
    776 22900619
    NC_004129.6 Q4KKK3 not specified TTGTTATAATATAACAT +[7014700:7014716] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_6177 , amiC (PFL_6176) , mntA (PFL_6178) , mntB (PFL_6179) , mntC (PFL_6180) , hisI2 (PFL_6181) , PFL_6182 , PFL_6183 , thrS_2 (PFL_6184)
    ... ... PFL_6177 amiC mntA mntB mntC hisI2 PFL_6182 PFL_6183 thrS_2
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTATATTGTATCAA +[5655550:5655566] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_4911 , PFL_4910 , PFL_4912
    ... ... PFL_4911 PFL_4910 PFL_4912
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTGATCTTATAACAA -[6308823:6308839] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_5527 , PFL_5528 , PFL_5529 , PFL_5530 , PFL_5531
    ... ... PFL_5527 PFL_5528 PFL_5529 PFL_5530 PFL_5531
    776 22900619
    NC_004129.6 Q4KKK3 not specified TTGTTATAAGATCACAT +[6308823:6308839] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_5528 , PFL_5527 , PFL_5529 , PFL_5530 , PFL_5531
    ... ... PFL_5528 PFL_5527 PFL_5529 PFL_5530 PFL_5531
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTATATTGTTTCAA -[1075045:1075061] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_0932 , PFL_0931
    ... ... PFL_0932 PFL_0931
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTATTGTATAACGC -[5639808:5639824] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) rpmE_1 (PFL_4896)
    ... ... rpmE_1
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGATATGTTATTACAT -[4404946:4404962] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) rpmJ (PFL_3806)
    ... ... rpmJ
    776 22900619
    NC_004129.6 Q4KKK3 not specified ATGTTACTTTATAACGC -[754736:754752] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_0646 , PFL_0645 , PFL_0644 , PFL_0643 , PFL_0642
    ... ... PFL_0646 PFL_0645 PFL_0644 PFL_0643 PFL_0642
    776 22900619
    NC_004129.6 Q4KKK3 not specified TCGTTATATAGTAACGA -[7033802:7033818] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) PFL_6194 , PFL_6193 , PFL_6192 , cadA_2 (PFL_6191) , PFL_6190 , PFL_6189 , PFL_6188 , PFL_6187 , PFL_6195 , PFL_6196 , PFL_6197 , PFL_6198 , PFL_6199 , cdsA_2 (PFL_6200)
    ... ... PFL_6194 PFL_6193 PFL_6192 cadA_2 PFL_6190 PFL_6189 PFL_6188 PFL_6187 PFL_6195 PFL_6196 PFL_6197 PFL_6198 PFL_6199 cdsA_2
    776 22900619

    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.

    TTGTTATAATATAACAT
    ATGTTATATTATAACAA
    ATGTTATATTATAACAA
    TTGTTATAATATAACAT
    ATGTTATATTGTATCAA
    ATGTGATCTTATAACAA
    TTGTTATAAGATCACAT
    ATGTTATATTGTTTCAA
    ATGTTATTGTATAACGC
    ATGATATGTTATTACAT
    ATGTTACTTTATAACGC
    TCGTTATATAGTAACGA

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

    TTGTTATAATATAACAT
    TTGTTATAATATAACAT
    TTGTTATAATATAACAT
    TTGTTATAATATAACAT
    TTGATACAATATAACAT
    TTGTTATAAGATCACAT
    TTGTTATAAGATCACAT
    TTGAAACAATATAACAT
    GCGTTATACAATAACAT
    ATGTAATAACATATCAT
    GCGTTATAAAGTAACAT
    TCGTTACTATATAACGA
    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.