HgtR - UniProtKB: Q747A3 regulon and binding site collection of Geobacter sulfurreducens PCA


Sites are listed as curated.

TTGTATACAGTATAC
AAATTGTATACAGTATACTAAA
GATTTGTATACTGTATACAAAA
AAATTGTATACAGTATACGCAA
TCCCTGTATACTGTATACAATA
AAATTGTATACAGTATCCATTT
CTTTTGTATACTGTATACAAAC
AAGTTGTATACAGTATGTGCTA
ATGCAGTATACTGTATGCGAAA
GTTTAGTATACAGTATACAGTA
CCGCCGTATACTGTATACACTT
AGATTGTATACAGTATGCGATC
ATAGTGCATACTGTATACACTT
TTATTGTATACAGTATACAGGG

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

AAATTGTATACAGTATACTAAAA
AAATTGTATACAGTATACTAAAA
GATTTGTATACTGTATACAAAAT
AAATTGTATACAGTATACGCAAG
TCCCTGTATACTGTATACAATAA
AAATTGTATACAGTATCCATTTC
AGTTTGTATACAGTATACAAAAG
AAGTTGTATACAGTATGTGCTAT
ATGCAGTATACTGTATGCGAAAA
ATACTGTATACTGTATACTAAAC
CCGCCGTATACTGTATACACTTA
AGATTGTATACAGTATGCGATCA
AAAGTGTATACAGTATGCACTAT
TCCCTGTATACTGTATACAATAA

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_002939.5 Q747A3 not specified TTGTATACAGTATAC +[1191975:1191989] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) gltA (GSU1106) , GSU1105 , GSU1104 , GSU1103 , GSU1107 , GSU1108
    ... ... gltA GSU1105 GSU1104 GSU1103 GSU1107 GSU1108
    455 19939938
    NC_002939.5 Q747A3 not specified AAATTGTATACAGTATACTAAA +[1191972:1191993] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) gltA (GSU1106) , GSU1105 , GSU1104 , GSU1103 , GSU1107 , GSU1108
    ... ... gltA GSU1105 GSU1104 GSU1103 GSU1107 GSU1108
    456 19939938
    NC_002939.5 Q747A3 not specified GATTTGTATACTGTATACAAAA +[123503:123524] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) atpG (GSU0112) , GSU0107 , GSU0106 , atpX (GSU0108) , atpF (GSU0109) , atpH (GSU0110) , atpA (GSU0111) , atpD (GSU0113) , atpC (GSU0114) , pdxA (GSU0115) , GSU0116 , GSU0117
    ... ... atpG GSU0107 GSU0106 atpX atpF atpH atpA atpD atpC pdxA GSU0116 GSU0117
    456 19939938
    NC_002939.5 Q747A3 not specified AAATTGTATACAGTATACGCAA +[367755:367776] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) nuoA-1 (GSU0338) , hemL (GSU0337) , atpZ (GSU0336) , atpI (GSU0335) , atpB (GSU0334) , atpE (GSU0333) , pepA (GSU0332) , degP (GSU0331) , nuoB (GSU0339) , nuoC (GSU0340) , nuoD (GSU0341) , nuoE-1 (GSU0342) , nuoF-1 (GSU0343) , nuoG-1 (GSU0344) , nuoH-1 (GSU0345) , nuoI-1 (GSU0346) , nuoJ-1 (GSU0347) , nuoK-1 (GSU0348) , nuoL-1 (GSU0349) , nuoM-1 (GSU0350) , nuoN-1 (GSU0351) , prx-3 (GSU0352) , yqaA (GSU0353) , GSU0354 , GSU0355
    ... ... nuoA-1 hemL atpZ atpI atpB atpE pepA degP nuoB nuoC nuoD nuoE-1 nuoF-1 nuoG-1 nuoH-1 nuoI-1 nuoJ-1 nuoK-1 nuoL-1 nuoM-1 nuoN-1 prx-3 yqaA GSU0354 GSU0355
    456 19939938
    NC_002939.5 Q747A3 not specified TCCCTGTATACTGTATACAATA -[3704539:3704560] Experimental technique details EMSA (ECO:0001807) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) GSU3370 , GSU3371 , cls-2 (GSU3372)
    ... ... GSU3370 GSU3371 cls-2
    456 19939938
    NC_002939.5 Q747A3 not specified AAATTGTATACAGTATCCATTT +[1822569:1822590] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) acnB (GSU1660) , hisS (GSU1659) , GSU1658 , GSU1657 , GSU1661 , GSU1662
    ... ... acnB hisS GSU1658 GSU1657 GSU1661 GSU1662
    457 19939938
    NC_002939.5 Q747A3 not specified CTTTTGTATACTGTATACAAAC +[1606339:1606360] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) icd (GSU1465) , GSU1464 , aspS (GSU1463) , mdh (GSU1466)
    ... ... icd GSU1464 aspS mdh
    457 19939938
    NC_002939.5 Q747A3 not specified AAGTTGTATACAGTATGTGCTA +[1609868:1609889] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) korD (GSU1467) , korA (GSU1468) , korB (GSU1469) , korC (GSU1470) , mdh (GSU1466) , icd (GSU1465)
    ... ... korD korA korB korC mdh icd
    457 19939938
    NC_002939.5 Q747A3 not specified ATGCAGTATACTGTATGCGAAA +[521301:521322] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) ato-1 (GSU0490) , comM (GSU0489) , trxB (GSU0488) , rhlE-1 (GSU0491)
    ... ... ato-1 comM trxB rhlE-1
    457 19939938
    NC_002939.5 Q747A3 not specified GTTTAGTATACAGTATACAGTA +[1281609:1281630] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) frdC (GSU1176) , frdA (GSU1177) , frdB (GSU1178) , tgt-1 (GSU1175) , mazG (GSU1174)
    ... ... frdC frdA frdB tgt-1 mazG
    457 19939938
    NC_002939.5 Q747A3 not specified CCGCCGTATACTGTATACACTT -[1076351:1076372] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) fumB (GSU0994) , GSU0993 , GSU0992 , GSU0991 , GSU0990 , GSU0989 , GSU0988 , GSU0987 , GSU0986 , GSU0985 , GSU0996 , mutM (GSU0997) , dnaB (GSU0998) , lpxA-2 (GSU0999) , GSU1000
    ... ... fumB GSU0993 GSU0992 GSU0991 GSU0990 GSU0989 GSU0988 GSU0987 GSU0986 GSU0985 GSU0996 mutM dnaB lpxA-2 GSU1000
    457 19939938
    NC_002939.5 Q747A3 not specified AGATTGTATACAGTATGCGATC +[417288:417309] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) GSU0385 , GSU0384 , GSU0383 , GSU0382 , GSU0381 , lipA (GSU0380) , lplA (GSU0379) , gcvP2 (GSU0378) , gcvP1 (GSU0377) , gcvH-1 (GSU0376) , gcvT (GSU0375) , hypA (GSU0374) , GSU0386 , uppP (GSU0387)
    ... ... GSU0385 GSU0384 GSU0383 GSU0382 GSU0381 lipA lplA gcvP2 gcvP1 gcvH-1 gcvT hypA GSU0386 uppP
    457 19939938
    NC_002939.5 Q747A3 not specified ATAGTGCATACTGTATACACTT -[544290:544311] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) sfrB (GSU0510) , sfrA (GSU0509) , yceG (GSU0508) , plsY (GSU0507) , GSU0506 , GSU0505 , GSU0504 , crcB (GSU0503) , GSU0502 , yfiO (GSU0501) , typA (GSU0500) , GSU0511 , GSU0512 , GSU0513 , GSU0514
    ... ... sfrB sfrA yceG plsY GSU0506 GSU0505 GSU0504 crcB GSU0502 yfiO typA GSU0511 GSU0512 GSU0513 GSU0514
    457 19939938
    NC_002939.5 Q747A3 not specified TTATTGTATACAGTATACAGGG +[3704538:3704559] Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) GSU3370 , GSU3371 , cls-2 (GSU3372)
    ... ... GSU3370 GSU3371 cls-2
    457 19939938

    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.

    TTGTATACAGTATAC
    AAATTGTATACAGTATACTAAA
    GATTTGTATACTGTATACAAAA
    AAATTGTATACAGTATACGCAA
    TCCCTGTATACTGTATACAATA
    AAATTGTATACAGTATCCATTT
    CTTTTGTATACTGTATACAAAC
    AAGTTGTATACAGTATGTGCTA
    ATGCAGTATACTGTATGCGAAA
    GTTTAGTATACAGTATACAGTA
    CCGCCGTATACTGTATACACTT
    AGATTGTATACAGTATGCGATC
    ATAGTGCATACTGTATACACTT
    TTATTGTATACAGTATACAGGG

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

    AAATTGTATACAGTATACTAAAA
    AAATTGTATACAGTATACTAAAA
    GATTTGTATACTGTATACAAAAT
    AAATTGTATACAGTATACGCAAG
    TCCCTGTATACTGTATACAATAA
    AAATTGTATACAGTATCCATTTC
    AGTTTGTATACAGTATACAAAAG
    AAGTTGTATACAGTATGTGCTAT
    ATGCAGTATACTGTATGCGAAAA
    ATACTGTATACTGTATACTAAAC
    CCGCCGTATACTGTATACACTTA
    AGATTGTATACAGTATGCGATCA
    AAAGTGTATACAGTATGCACTAT
    TCCCTGTATACTGTATACAATAA
    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.