IHF - UniProtKB: P0A126 regulon and binding site collection of Pseudomonas putida


Sites are listed as curated.

AATCAATAATTTA
TTTTTTACAAAGAAAATCAATAATTTA

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

TTTTTTACAAAGAAAATCAATAATTTA
TTTTTTACAAAGAAAATCAATAATTTA

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_003350.1 P0A126 not specified AATCAATAATTTA -[75467:75479] Experimental technique details Beta-gal reporter assay - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details UV footprinting - Experimental technique details Visual sequence inspection (nan) xylA (pWWO_p094) , xylM (pWWO_p095) , xylC (pWWO_p096) , xylW (pWWO_p097) , xylU (pWWO_p098) , tnpA (pWWO_p099)
    ... ... xylA xylM xylC xylW xylU tnpA
    756 21958188
    NC_003350.1 P0A126 dimer TTTTTTACAAAGAAAATCAATAATTTA -[75467:75493] Experimental technique details Beta-gal reporter assay - Experimental technique details UV footprinting xylA (pWWO_p094) , xylM (pWWO_p095) , xylC (pWWO_p096) , xylW (pWWO_p097) , xylU (pWWO_p098) , tnpA (pWWO_p099)
    ... ... xylA xylM xylC xylW xylU tnpA
    757 11694511

    IHF - UniProtKB: P0A126 regulon and binding site collection of Pseudomonas putida KT2440


    Sites are listed as curated.

    TGTAAAATTATCG
    TACAGAGTTTTA
    TACAACTCGATG
    TACAAGATGATG
    ATCAATTTCATG
    ATCAGACATTTA
    TTCAAACGCATG
    TTCAAACGCATG
    ATCAGGAGATTA
    ATCAGCAGCTTG
    ATCAAGCAGTTG
    ATCAAGAACTTA
    AACAACAAGATG
    AACAGCAAGTTG
    ATCAAGGCTTTG
    ATCAAGGCTTTG
    TTCAAGGCCATG
    TTCAACGCCATG
    TACAGGGTCTTG
    AACAACACGATG
    TTCAGTTCCATG

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

    TGTAAAATTATCG
    TACAGAGTTTTAC
    TACAACTCGATGC
    TACAAGATGATGC
    ATCAATTTCATGG
    ATCAGACATTTAA
    TTCAAACGCATGA
    TTCAAACGCATGA
    ATCAGGAGATTAC
    ATCAGCAGCTTGT
    ATCAAGCAGTTGG
    ATCAAGAACTTAA
    AACAACAAGATGC
    AACAGCAAGTTGT
    ATCAAGGCTTTGA
    ATCAAGGCTTTGA
    TTCAAGGCCATGG
    TTCAACGCCATGC
    TACAGGGTCTTGA
    AACAACACGATGC
    TTCAGTTCCATGT

    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_002947.3 P0A126 dimer TGTAAAATTATCG +[5101743:5101755] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) phhA (PP_4490) , phhR (PP_4489) , phhB (PP_4491)
      ... ... phhA phhR phhB
      426 17217960
      NC_002947.3 P0A126 , P0A128 dimer TACAGAGTTTTA +[9237:9248] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) rpmH (PP_0009) , rnpA (PP_0008) , PP_0007 , yidC (PP_0006) , trmE (PP_0005) , dnaA (PP_0010) , dnaN (PP_0011) , recF (PP_0012) , gyrB (PP_0013)
      ... ... rpmH rnpA PP_0007 yidC trmE dnaA dnaN recF gyrB
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TACAACTCGATG +[458942:458953] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) pqqC (PP_0378) , pqqD (PP_0377) , pqqB (PP_0379) , pqqE (PP_0376) , PP_0375
      ... ... pqqC pqqD pqqB pqqE PP_0375
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TACAAGATGATG +[947605:947616] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) hmpA (PP_0808) , PP_0807 , dsbB (PP_0809) , cyoups1 (PP_0810) , cyoups2 (PP_0811) , cyoA (PP_0812) , cyoB (PP_0813) , cyoC (PP_0814) , cyoD (PP_0815) , cyoE-2 (PP_0816)
      ... ... hmpA PP_0807 dsbB cyoups1 cyoups2 cyoA cyoB cyoC cyoD cyoE-2
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAATTTCATG +[973588:973599] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_0837 , secF (PP_0836)
      ... ... PP_0837 secF
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAGACATTTA +[1142417:1142428] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) arcD (PP_1002) , arcA (PP_1001) , argI (PP_1000) , PP_1003
      ... ... arcD arcA argI PP_1003
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TTCAAACGCATG +[1142825:1142836] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) arcD (PP_1002) , arcA (PP_1001) , argI (PP_1000) , PP_1003
      ... ... arcD arcA argI PP_1003
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TTCAAACGCATG +[1142825:1142836] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) arcD (PP_1002) , arcA (PP_1001) , argI (PP_1000) , PP_1003
      ... ... arcD arcA argI PP_1003
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAGGAGATTA +[1243092:1243103] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_1083 , PP_1084
      ... ... PP_1083 PP_1084
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAGCAGCTTG +[1627287:1627298] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) mucA (PP_1428) , algN (PP_1429) , algU (PP_1427) , nadB (PP_1426) , algY (PP_1430)
      ... ... mucA algN algU nadB algY
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAAGCAGTTG +[1667426:1667437] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) rpsP (PP_1462) , rimM (PP_1463) , ffh (PP_1461) , PP_1460 , PP_1459 , trmD (PP_1464) , rplS (PP_1465) , PP_1466
      ... ... rpsP rimM ffh PP_1460 PP_1459 trmD rplS PP_1466
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAAGAACTTA +[2572994:2573005] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_2256 , aer-1 (PP_2257) , PP_2258
      ... ... PP_2256 aer-1 PP_2258
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer AACAACAAGATG +[3070084:3070095] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_2680 , PP_2681 , PP_2682 , PP_2683
      ... ... PP_2680 PP_2681 PP_2682 PP_2683
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer AACAGCAAGTTG +[3974508:3974519] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_3503 , PP_3504
      ... ... PP_3503 PP_3504
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAAGGCTTTG +[5013527:5013538] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_4418 , PP_4417
      ... ... PP_4418 PP_4417
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer ATCAAGGCTTTG +[5013527:5013538] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_4418 , PP_4417
      ... ... PP_4418 PP_4417
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TTCAAGGCCATG +[5017864:5017875] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_4421 , PP_4422
      ... ... PP_4421 PP_4422
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TTCAACGCCATG +[5225787:5225798] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_4605 , PP_4604
      ... ... PP_4605 PP_4604
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TACAGGGTCTTG +[1358606:1358617] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_1183
      ... ... PP_1183
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer AACAACACGATG +[1471715:1471726] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) algJ (PP_1279) , algF (PP_1278) , algA (PP_1277) , PP_1287 , PP_1286 , algK (PP_1285) , algE (PP_1284) , PP_1283 , algX (PP_1282) , algL (PP_1281) , algI (PP_1280)
      ... ... algJ algF algA PP_1287 PP_1286 algK algE PP_1283 algX algL algI
      790 22510163
      NC_002947.3 P0A126 , P0A128 dimer TTCAGTTCCATG +[5017406:5017417] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) PP_4421 , PP_4422
      ... ... PP_4421 PP_4422
      790 22510163

      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.

      TGTAAAATTATCG
      AATCAATAATTTA
      TTTTTTACAAAGAAAATCAATAATTTA
      TACAGAGTTTTA
      TACAACTCGATG
      TACAAGATGATG
      ATCAATTTCATG
      ATCAGACATTTA
      TTCAAACGCATG
      TTCAAACGCATG
      ATCAGGAGATTA
      ATCAGCAGCTTG
      ATCAAGCAGTTG
      ATCAAGAACTTA
      AACAACAAGATG
      AACAGCAAGTTG
      ATCAAGGCTTTG
      ATCAAGGCTTTG
      TTCAAGGCCATG
      TTCAACGCCATG
      TACAGGGTCTTG
      AACAACACGATG
      TTCAGTTCCATG

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

      ACACTTGCCGAGTTTTGTAAAATTATCG
      TTTTTTACAAAGAAAATCAATAATTTAG
      TTTTTTACAAAGAAAATCAATAATTTAG
      ATGAATTACGGGGTGTACAGAGTTTTAC
      CTCACAGACTGTATTTACAACTCGATGC
      CTGACCACCCACTTCTACAAGATGATGC
      GCTGCGATGAAAACCATCAATTTCATGG
      TAGTTTTCCGGATGAATCAGACATTTAA
      AGCCCGCAAGGCTGTTTCAAACGCATGA
      AGCCCGCAAGGCTGTTTCAAACGCATGA
      CGGTTTTTCACCCTCATCAGGAGATTAC
      TAACCCAGGAAGAGGATCAGCAGCTTGT
      TATCGTCCGGCGGCGATCAAGCAGTTGG
      TAATTCCCATTTAGAATCAAGAACTTAA
      ACCCTGCTCAAGGGCAACAACAAGATGC
      GGTTTTTTGAAGTAAAACAGCAAGTTGT
      ATCCTTACCAGGTACATCAAGGCTTTGA
      ATCCTTACCAGGTACATCAAGGCTTTGA
      GATATCGACGCCCTCTTCAAGGCCATGG
      ACCCAGTTGCAAGTGTTCAACGCCATGC
      TGGCGAGTCAGTGGGTACAGGGTCTTGA
      GACACGCGCTGGTCGAACAACACGATGC
      CCGATGCAGACGTATTTCAGTTCCATGT
      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.