HexR - UniProtKB: Q8EE97 regulon and binding site collection of Shewanella oneidensis MR-1


Sites are listed as curated.

TTGTTATAAAACTACAT
TTGAAATTAAACTCCAA
TTGTAATATTGCTACAG
TGGTAATTAAGTTACAA
TGGTAATTTTACTACCA
CTCTAATAAAATTACAG
CTGTTGTTATATTACAA
TTGTAACTTTACTACAT
TAGTAATAAAATTACAA
CTGTAACAAAATTACTA
TTGTAAGAAAATTACAA
TTGTAATTTTTTTACAT
CTGTAAATTTTTTACAG

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

TTGTTATAAAACTACAT
TTGAAATTAAACTCCAA
TTGTAATATTGCTACAG
TGGTAATTAAGTTACAA
TGGTAATTTTACTACCA
CTGTAATTTTATTAGAG
TTGTAATATAACAACAG
TTGTAACTTTACTACAT
TAGTAATAAAATTACAA
TAGTAATTTTGTTACAG
TTGTAATTTTCTTACAA
TTGTAATTTTTTTACAT
CTGTAAATTTTTTACAG

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 Q8EE97 not specified TTGTTATAAAACTACAT +[928748:928764] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) nqrA (SO_0902) , nqrB (SO_0903) , nqrC (SO_0904) , nqrD (SO_0905) , nqrE (SO_0906) , nqrF (SO_0907) , SO_0900 , SO_0899 , SO_0898
    ... ... nqrA nqrB nqrC nqrD nqrE nqrF SO_0900 SO_0899 SO_0898
    984 21849503
    NC_004347.2 Q8EE97 not specified TTGAAATTAAACTCCAA +[1260774:1260790] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) SO_1214
    ... ... SO_1214
    984 21849503
    NC_004347.2 Q8EE97 not specified TTGTAATATTGCTACAG +[1264666:1264682] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) deoA (SO_1218) , deoB (SO_1219) , deoD (SO_1221)
    ... ... deoA deoB deoD
    984 21849503
    NC_004347.2 Q8EE97 not specified TGGTAATTAAGTTACAA +[2001966:2001982] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) gnd (SO_1902)
    ... ... gnd
    984 21849503
    NC_004347.2 Q8EE97 not specified TGGTAATTTTACTACCA -[2453840:2453856] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) gapA (SO_2345)
    ... ... gapA
    984 21849503
    NC_004347.2 Q8EE97 not specified CTCTAATAAAATTACAG +[2454934:2454950] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) gapB (SO_2347) , SO_2346
    ... ... gapB SO_2346
    984 21849503
    NC_004347.2 Q8EE97 not specified CTGTTGTTATATTACAA -[2612650:2612666] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) zwf (SO_2489) , pgl (SO_2488) , edd (SO_2487) , eda (SO_2486) , hexR (SO_2490)
    ... ... zwf pgl edd eda hexR
    984 21849503
    NC_004347.2 Q8EE97 not specified TTGTAACTTTACTACAT +[2613863:2613879] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) pykA (SO_2491)
    ... ... pykA
    984 21849503
    NC_004347.2 Q8EE97 not specified TAGTAATAAAATTACAA -[2782333:2782349] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) ppsA (SO_2644) , SO_2643 , SO_2642 , SO_2640 , ydiA (SO_2645)
    ... ... ppsA SO_2643 SO_2642 SO_2640 ydiA
    984 21849503
    NC_004347.2 Q8EE97 not specified CTGTAACAAAATTACTA +[2913730:2913746] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) cdd (SO_2791)
    ... ... cdd
    984 21849503
    NC_004347.2 Q8EE97 not specified TTGTAAGAAAATTACAA +[3696432:3696448] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) xfp (SO_3542) , SO_3541 , SO_3540 , tnpA (SO_3543)
    ... ... xfp SO_3541 SO_3540 tnpA
    984 21849503
    NC_004347.2 Q8EE97 not specified TTGTAATTTTTTTACAT +[3703006:3703022] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Fluorescence anisotropy (ECO:0005632) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) talB (SO_3546) , pgi (SO_3547)
    ... ... talB pgi
    984 21849503
    NC_004347.2 Q8EE97 not specified CTGTAAATTTTTTACAG -[4755365:4755381] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) SO_4557 , SO_4558
    ... ... SO_4557 SO_4558
    984 21849503

    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.

    TTGTTATAAAACTACAT
    TTGAAATTAAACTCCAA
    TTGTAATATTGCTACAG
    TGGTAATTAAGTTACAA
    TGGTAATTTTACTACCA
    CTCTAATAAAATTACAG
    CTGTTGTTATATTACAA
    TTGTAACTTTACTACAT
    TAGTAATAAAATTACAA
    CTGTAACAAAATTACTA
    TTGTAAGAAAATTACAA
    TTGTAATTTTTTTACAT
    CTGTAAATTTTTTACAG

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

    TTGTTATAAAACTACAT
    TTGAAATTAAACTCCAA
    TTGTAATATTGCTACAG
    TGGTAATTAAGTTACAA
    TGGTAATTTTACTACCA
    CTGTAATTTTATTAGAG
    TTGTAATATAACAACAG
    TTGTAACTTTACTACAT
    TAGTAATAAAATTACAA
    TAGTAATTTTGTTACAG
    TTGTAATTTTCTTACAA
    TTGTAATTTTTTTACAT
    CTGTAAATTTTTTACAG
    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.