LexA - UniProtKB: A0A0H3NC35 regulon and binding site collection of Peptoclostridium difficile R20291


Sites are listed as curated.

AGGAACAAATGTTTGC
GAGAACAAATGTTTGT
TAGAACATAAGTTTTT
AGGAACTAATGTTCGA
CAGAACAGTAGTTCCA
TAGAACATAAAAATTT
TTGAACTTTAGTTTCT
AAGAACATCTGAAAAG
CAGAACTATTATTTTA
ATGAACTTAGGTTTCT
ATGAACTATTGTTTTA
TGGAACTTTGGTTCAG
GTGAACCAATGTTTGA
TGGAACTTTAGTTCTA
AAAAACACCCGTTCTG
AAGAACTAAAGTTCCT

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

AGGAACAAATGTTTGC
GAGAACAAATGTTTGT
AAAAACTTATGTTCTA
AGGAACTAATGTTCGA
TGGAACTACTGTTCTG
AAATTTTTATGTTCTA
AGAAACTAAAGTTCAA
AAGAACATCTGAAAAG
CAGAACTATTATTTTA
AGAAACCTAAGTTCAT
ATGAACTATTGTTTTA
TGGAACTTTGGTTCAG
GTGAACCAATGTTTGA
TGGAACTTTAGTTCTA
AAAAACACCCGTTCTG
AGGAACTTTAGTTCTT

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_013316.1 A0A0H3NC35 dimer AGGAACAAATGTTTGC -[2168608:2168623] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance dinR (CDR20291_1854)
    ... ... dinR
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer GAGAACAAATGTTTGT +[1395928:1395943] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance recA (CDR20291_1169)
    ... ... recA
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer TAGAACATAAGTTTTT -[3187647:3187662] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance ruvC (CDR20291_2696) , ruvA (CDR20291_2695) , ruvB (CDR20291_2694)
    ... ... ruvC ruvA ruvB
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer AGGAACTAATGTTCGA -[3863557:3863572] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance uvrB (CDR20291_3234) , uvrA (CDR20291_3233)
    ... ... uvrB uvrA
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer CAGAACAGTAGTTCCA +[3710720:3710735] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance sspB (CDR20291_3107) , CDR20291_3106 , CDR20291_3108
    ... ... sspB CDR20291_3106 CDR20291_3108
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer TAGAACATAAAAATTT +[953590:953605] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_0782 , CDR20291_0781 , oppB (CDR20291_0783) , oppC (CDR20291_0784) , oppA (CDR20291_0785) , oppD (CDR20291_0786) , oppF (CDR20291_0787)
    ... ... CDR20291_0782 CDR20291_0781 oppB oppC oppA oppD oppF
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer TTGAACTTTAGTTTCT +[4183519:4183534] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_3533 , soj (CDR20291_3532) , spo0J (CDR20291_3531) , CDR20291_3530
    ... ... CDR20291_3533 soj spo0J CDR20291_3530
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer AAGAACATCTGAAAAG +[2694006:2694021] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_2298
    ... ... CDR20291_2298
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer CAGAACTATTATTTTA -[3732293:3732308] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_3125 , CDR20291_3124 , CDR20291_3123
    ... ... CDR20291_3125 CDR20291_3124 CDR20291_3123
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer ATGAACTTAGGTTTCT +[113808:113823] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance rplF (CDR20291_0082) , rplR (CDR20291_0083) , rpsE (CDR20291_0084) , rpmD (CDR20291_0085) , rplO (CDR20291_0086) , prlA (CDR20291_0087) , adk (CDR20291_0088) , map1 (CDR20291_0089) , CDR20291_0090 , infA (CDR20291_0091) , rpmJ (CDR20291_0092)
    ... ... rplF rplR rpsE rpmD rplO prlA adk map1 CDR20291_0090 infA rpmJ
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer ATGAACTATTGTTTTA +[93864:93879] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance rpoB (CDR20291_0060) , rpoC (CDR20291_0061)
    ... ... rpoB rpoC
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer TGGAACTTTGGTTCAG +[1076101:1076116] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance potB (CDR20291_0881) , potC (CDR20291_0882) , potD (CDR20291_0883)
    ... ... potB potC potD
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer GTGAACCAATGTTTGA -[715455:715470] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance tcdA (CDR20291_0584)
    ... ... tcdA
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer TGGAACTTTAGTTCTA +[3181958:3181973] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_2690 , CDR20291_2689
    ... ... CDR20291_2690 CDR20291_2689
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer AAAAACACCCGTTCTG +[2409491:2409506] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_2056
    ... ... CDR20291_2056
    645 24713082
    NC_013316.1 A0A0H3NC35 dimer AAGAACTAAAGTTCCT +[976785:976800] Experimental technique details Comparative genomics search (ECO:0005622) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Surface plasmon resonance CDR20291_0804 , CDR20291_0803 , CDR20291_0802
    ... ... CDR20291_0804 CDR20291_0803 CDR20291_0802
    645 24713082

    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.

    AGGAACAAATGTTTGC
    GAGAACAAATGTTTGT
    TAGAACATAAGTTTTT
    AGGAACTAATGTTCGA
    CAGAACAGTAGTTCCA
    TAGAACATAAAAATTT
    TTGAACTTTAGTTTCT
    AAGAACATCTGAAAAG
    CAGAACTATTATTTTA
    ATGAACTTAGGTTTCT
    ATGAACTATTGTTTTA
    TGGAACTTTGGTTCAG
    GTGAACCAATGTTTGA
    TGGAACTTTAGTTCTA
    AAAAACACCCGTTCTG
    AAGAACTAAAGTTCCT

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

    AGGAACAAATGTTTGC
    GAGAACAAATGTTTGT
    AAAAACTTATGTTCTA
    AGGAACTAATGTTCGA
    TGGAACTACTGTTCTG
    AAATTTTTATGTTCTA
    AGAAACTAAAGTTCAA
    AAGAACATCTGAAAAG
    CAGAACTATTATTTTA
    AGAAACCTAAGTTCAT
    ATGAACTATTGTTTTA
    TGGAACTTTGGTTCAG
    GTGAACCAATGTTTGA
    TGGAACTTTAGTTCTA
    AAAAACACCCGTTCTG
    AGGAACTTTAGTTCTT
    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.