YodB - UniProtKB: O34844 regulon and binding site collection of Bacillus subtilis subsp. subtilis str. 168


Sites are listed as curated.

TACTTGACGTAAACA
TACTATTTGTAAGTA
TACATTTAGTAAGCT
TACTTTTTTATAGTA

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

TACTTGACGTAAACA
TACTATTTGTAAGTA
TACATTTAGTAAGCT
TACTATAAAAAAGTA

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_000964.3 O34844 not specified TACTTGACGTAAACA +[897512:897526] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details MALDI-TOF Mass Spectrometry (ECO:0005527) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Western blot (quantitative) expression analysis (ECO:0000279) catE (BSU08240) , catD (BSU08230) , yfiF (BSU08250)
    ... ... catE catD yfiF
    1085 20639328
    NC_000964.3 O34844 not specified TACTATTTGTAAGTA -[2097006:2097020] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) yocJ (BSU19230)
    ... ... yocJ
    1085 20639328
    NC_000964.3 O34844 not specified TACATTTAGTAAGCT +[2127749:2127763] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) yodC (BSU19550) , yodB (BSU19540)
    ... ... yodC yodB
    1085 20639328
    NC_000964.3 O34844 not specified TACTTTTTTATAGTA +[1227593:1227607] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) spxA (BSU11500)
    ... ... spxA
    1085 20639328

    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.

    TACTTGACGTAAACA
    TACTATTTGTAAGTA
    TACATTTAGTAAGCT
    TACTTTTTTATAGTA

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

    TACTTGACGTAAACA
    TACTATTTGTAAGTA
    TACATTTAGTAAGCT
    TACTATAAAAAAGTA
    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.