Anr - UniProtKB: Q88F34 regulon and binding site collection of Pseudomonas putida KT2440


Sites are listed as curated.

TTGATCCAGATCAA
TTGAGGCCTATCAA
TTGATCTGGGTCAA
TCGTTCCAGATCAA
TTGATCCCCGTCAA

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

TTGATCCAGATCAA
TTGAGGCCTATCAA
TTGACCCAGATCAA
TCGTTCCAGATCAA
TTGATCCCCGTCAA

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 Q88F34 not specified TTGATCCAGATCAA +[949728:949741] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) cyoB (PP_0813) , cyoA (PP_0812) , cyoC (PP_0814) , cyoD (PP_0815) , cyoE-2 (PP_0816) , cyoups2 (PP_0811) , cyoups1 (PP_0810)
    ... ... cyoB cyoA cyoC cyoD cyoE-2 cyoups2 cyoups1
    719 18341582
    NC_002947.3 Q88F34 not specified TTGAGGCCTATCAA +[949767:949780] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) cyoA (PP_0812) , cyoB (PP_0813) , cyoC (PP_0814) , cyoD (PP_0815) , cyoE-2 (PP_0816) , cyoups1 (PP_0810) , cyoups2 (PP_0811)
    ... ... cyoA cyoB cyoC cyoD cyoE-2 cyoups1 cyoups2
    719 18341582
    NC_002947.3 Q88F34 not specified TTGATCTGGGTCAA -[5276839:5276852] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) cioA (PP_4651) , cioB (PP_4650) , PP_4649 , PP_4652
    ... ... cioA cioB PP_4649 PP_4652
    719 18341582
    NC_002947.3 Q88F34 not specified TCGTTCCAGATCAA -[5276825:5276838] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) cioA (PP_4651) , cioB (PP_4650) , PP_4649 , PP_4652
    ... ... cioA cioB PP_4649 PP_4652
    719 18341582
    NC_002947.3 Q88F34 not specified TTGATCCCCGTCAA +[4835903:4835916] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) ccoN-1 (PP_4250) , ccoO-1 (PP_4251) , ccoQ-1 (PP_4252) , ccoP-1 (PP_4253) , PP_4249
    ... ... ccoN-1 ccoO-1 ccoQ-1 ccoP-1 PP_4249
    719 18341582

    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.

    TTGATCCAGATCAA
    TTGAGGCCTATCAA
    TTGATCTGGGTCAA
    TCGTTCCAGATCAA
    TTGATCCCCGTCAA

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

    TTGATCCAGATCAA
    TTGAGGCCTATCAA
    TTGACCCAGATCAA
    TCGTTCCAGATCAA
    TTGATCCCCGTCAA
    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.