ArcA - UniProtKB: Q8EAB9 regulon and binding site collection of Shewanella oneidensis MR-1


Sites are listed as curated.

GTGAACAGAATGTTA
TTTAAAAATATGTTA
GTAATTTAAATGTTA
GTTAACAAAGCGATA
GTTAATAAAATGTTT
GTTACTTTATTGTTA
GTTAAATAATTGTTA
GTTAATAAAATGTTT
GTTAATTTGATGTTA
GTTAAGTAATTGTAA
GTTAATTAAATGTCA
GTTGAAAAAATGTAA
GTTATTCAAATGTAA
GTTAATTAAATTATA
GTAAATTAATTGTTA
GTTAACTCAATGTTA
GTTAATTAATTGTTG
GTAAAATCGATGTTA
GTTAATTGATTGTAA
GTTAAAAAAATGTGA

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

GTGAACAGAATGTTA
TTTAAAAATATGTTA
GTAATTTAAATGTTA
GTTAACAAAGCGATA
GTTAATAAAATGTTT
GTTACTTTATTGTTA
GTTAAATAATTGTTA
GTTAATAAAATGTTT
GTTAATTTGATGTTA
GTTAAGTAATTGTAA
GTTAATTAAATGTCA
GTTGAAAAAATGTAA
GTTATTCAAATGTAA
GTTAATTAAATTATA
GTAAATTAATTGTTA
GTTAACTCAATGTTA
GTTAATTAATTGTTG
GTAAAATCGATGTTA
GTTAATTGATTGTAA
GTTAAAAAAATGTGA

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 Q8EAB9 not specified GTGAACAGAATGTTA +[265599:265613] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) ccmF (SO_0266) , ccmI (SO_0265) , ccmG (SO_0267) , ccmH (SO_0268) , SO_0269
    ... ... ccmF ccmI ccmG ccmH SO_0269
    1015 18221523
    NC_004347.2 Q8EAB9 not specified TTTAAAAATATGTTA -[773146:773160] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) aroG (SO_0756)
    ... ... aroG
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTAATTTAAATGTTA +[895586:895600] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) csgB (SO_0866) , csgA (SO_0865) , SO_0867
    ... ... csgB csgA SO_0867
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAACAAAGCGATA -[1359486:1359500] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) aqpZ (SO_1307) , SO_1309
    ... ... aqpZ SO_1309
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATAAAATGTTT -[1487965:1487979] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) dmsE (SO_1427) , dmsF (SO_1428) , dmsA (SO_1429) , dmsB (SO_1430) , dmsG (SO_1431) , dmsH (SO_1432)
    ... ... dmsE dmsF dmsA dmsB dmsG dmsH
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTACTTTATTGTTA -[1703646:1703660] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) ptsG (SO_1623) , SO_1621 , yqcA (SO_1622) , purU (SO_1624)
    ... ... ptsG SO_1621 yqcA purU
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAAATAATTGTTA -[1749992:1750006] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) SO_1661
    ... ... SO_1661
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATAAAATGTTT +[1897728:1897742] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) pspF (SO_1806) , sapA (SO_1805) , sapB (SO_1804) , sapC (SO_1803) , sapD (SO_1802) , sapF (SO_1801) , fabV (SO_1800) , pspA (SO_1807) , pspB (SO_1808) , pspC (SO_1809) , ycjX (SO_1810) , ycjF (SO_1811)
    ... ... pspF sapA sapB sapC sapD sapF fabV pspA pspB pspC ycjX ycjF
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATTTGATGTTA +[1912473:1912487] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) SO_1821 , polB (SO_1820) , dinG (SO_1819) , SO_1818 , SO_1817 , SO_1816 , SO_1815 , comFB (SO_1814)
    ... ... SO_1821 polB dinG SO_1818 SO_1817 SO_1816 SO_1815 comFB
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAAGTAATTGTAA -[2047012:2047026] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) SO_1944 , SO_1942
    ... ... SO_1944 SO_1942
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATTAAATGTCA -[2198141:2198155] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) hyaA (SO_2099) , hyaB (SO_2098) , hyaC (SO_2097) , hyaD (SO_2096) , hyaE (SO_2095) , hypF (SO_2094) , SO_2100 , SO_2101 , SO_2102
    ... ... hyaA hyaB hyaC hyaD hyaE hypF SO_2100 SO_2101 SO_2102
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTGAAAAAATGTAA +[2825742:2825756] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) astB (SO_2706) , topA (SO_2705)
    ... ... astB topA
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTATTCAAATGTAA -[2844528:2844542] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) cctA (SO_2727)
    ... ... cctA
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATTAAATTATA -[3224817:3224831] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) SO_3099 , SO_3100
    ... ... SO_3099 SO_3100
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTAAATTAATTGTTA -[3233415:3233429] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) sapSH (SO_3106)
    ... ... sapSH
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAACTCAATGTTA +[3659763:3659777] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) nagK (SO_3507) , nagB (SO_3506) , nagA (SO_3505) , nagX (SO_3504)
    ... ... nagK nagB nagA nagX
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATTAATTGTTG -[3727321:3727335] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) cpdB (SO_3565) , dcp (SO_3564)
    ... ... cpdB dcp
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTAAAATCGATGTTA +[3811652:3811666] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) SO_3659 , SO_3657
    ... ... SO_3659 SO_3657
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAATTGATTGTAA -[4000620:4000634] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) sfcA (SO_3855)
    ... ... sfcA
    1015 18221523
    NC_004347.2 Q8EAB9 not specified GTTAAAAAAATGTGA -[4424606:4424620] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) argA (SO_4245) , SO_4244
    ... ... argA SO_4244
    1015 18221523

    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.

    GTGAACAGAATGTTA
    TTTAAAAATATGTTA
    GTAATTTAAATGTTA
    GTTAACAAAGCGATA
    GTTAATAAAATGTTT
    GTTACTTTATTGTTA
    GTTAAATAATTGTTA
    GTTAATAAAATGTTT
    GTTAATTTGATGTTA
    GTTAAGTAATTGTAA
    GTTAATTAAATGTCA
    GTTGAAAAAATGTAA
    GTTATTCAAATGTAA
    GTTAATTAAATTATA
    GTAAATTAATTGTTA
    GTTAACTCAATGTTA
    GTTAATTAATTGTTG
    GTAAAATCGATGTTA
    GTTAATTGATTGTAA
    GTTAAAAAAATGTGA

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

    GTGAACAGAATGTTA
    TTTAAAAATATGTTA
    GTAATTTAAATGTTA
    GTTAACAAAGCGATA
    GTTAATAAAATGTTT
    GTTACTTTATTGTTA
    GTTAAATAATTGTTA
    GTTAATAAAATGTTT
    GTTAATTTGATGTTA
    GTTAAGTAATTGTAA
    GTTAATTAAATGTCA
    GTTGAAAAAATGTAA
    GTTATTCAAATGTAA
    GTTAATTAAATTATA
    GTAAATTAATTGTTA
    GTTAACTCAATGTTA
    GTTAATTAATTGTTG
    GTAAAATCGATGTTA
    GTTAATTGATTGTAA
    GTTAAAAAAATGTGA
    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.