NagR - UniProtKB: Q8EBJ8 regulon and binding site collection of Shewanella oneidensis MR-1


Sites are listed as curated.

AATGACAGCGTTGTCTTT
AATGACAACGCTGTCATT
AATGACAACGCTGTCATC
CATGACAGCGTTGTCATT
TTTGACAACGTTGTCTTT

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

AATGACAGCGTTGTCTTT
AATGACAGCGTTGTCATT
GATGACAGCGTTGTCATT
CATGACAGCGTTGTCATT
TTTGACAACGTTGTCTTT

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_004347.2 Q8EBJ8 not specified AATGACAGCGTTGTCTTT -[3655030:3655047] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) nagP (SO_3503)
    ... ... nagP
    981 21810205
    NC_004347.2 Q8EBJ8 not specified AATGACAACGCTGTCATT -[3659785:3659802] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) nagK (SO_3507) , nagB (SO_3506) , nagA (SO_3505) , nagX (SO_3504)
    ... ... nagK nagB nagA nagX
    981 21810205
    NC_004347.2 Q8EBJ8 not specified AATGACAACGCTGTCATC -[3663877:3663894] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) SO_3510 , hexB (SO_3509) , SO_4804
    ... ... SO_3510 hexB SO_4804
    981 21810205
    NC_004347.2 Q8EBJ8 not specified CATGACAGCGTTGTCATT -[3669783:3669800] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) SO_3514 , SO_3513 , SO_3512 , nagR (SO_3516)
    ... ... SO_3514 SO_3513 SO_3512 nagR
    981 21810205
    NC_004347.2 Q8EBJ8 not specified TTTGACAACGTTGTCTTT +[1112398:1112415] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) SO_1071 , gbpA (SO_1072)
    ... ... SO_1071 gbpA
    981 21810205

    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.

    AATGACAGCGTTGTCTTT
    AATGACAACGCTGTCATT
    AATGACAACGCTGTCATC
    CATGACAGCGTTGTCATT
    TTTGACAACGTTGTCTTT

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

    AATGACAGCGTTGTCTTT
    AATGACAGCGTTGTCATT
    GATGACAGCGTTGTCATT
    CATGACAGCGTTGTCATT
    TTTGACAACGTTGTCTTT
    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.