Vfr - UniProtKB: P55222 regulon and binding site collection of Pseudomonas aeruginosa PAO1


Sites are listed as curated.

AAATGTGATCTAGATCACATTT
ATTGTCACAACCGCACAG
AAGGCTGCGCGCTTGACAG
TCCTGAACGGTGCTGGCAT
TGGTCGAACGTTGTCATAG
AAATTGACTAATCGTTCACATTTG
ACCGTCTGAAGCAGTTCTCAT
AAATGTGATCTAGATCACATTT
CTCTGCAATCCAGTTCATAAAT
CATGCGGAACTGCATCACATTT
TTTTTTGCGGCAGATGGCATTT
TTATGGGCACCAGTTCACACTG
GGCAAATGGCTAGGTCACAGAA
AAATGTGATTTAAAACACATGA
AATTGTGATGAAGTTGGCATGA
GAAACAAGAGCTAGCTCACAC
AGTACGGGATCACAGTCCTGATAGCTGCGTCG

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

TTCGCATAAAATGTGATCTAGATCACATTTAA
TCATGGAATTGTCACAACCGCACAGTATCGCT
GGGTATGACGCTGTCAAGCGCGCAGCCTTGCC
TATCTGTTATGCCAGCACCGTTCAGGACGCAG
CCCCCTCCCTATGACAACGTTCGACCACCTGG
GTTAAGTCAAATGTGAACGATTAGTCAATTTT
CCGGCCGACCGTCTGAAGCAGTTCTCATTTAT
TTCGCATAAAATGTGATCTAGATCACATTTAA
ATTCACCACTCTGCAATCCAGTTCATAAATCC
GCGTGAAAAAATGTGATGCAGTTCCGCATGAC
AAGCACCGAAATGCCATCTGCCGCAAAAAACC
GTGGGGCGCAGTGTGAACTGGTGCCCATAATT
AGCAATTTTTCTGTGACCTAGCCATTTGCCTG
TCACTTGTTCATGTGTTTTAAATCACATTTTA
ACAACTATTCATGCCAACTTCATCACAATTTG
CCCGTGGCAGGTGTGAGCTAGCTCTTGTTTCG
CGACGCAGCTATCAGGACTGTGATCCCGTACT

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_002516.2 P55222 not specified AAATGTGATCTAGATCACATTT +[1557881:1557902] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) lasR (PA1430) , rsaL (PA1431) , PA1429
    ... ... lasR rsaL PA1429
    246 9190808
    NC_002516.2 P55222 not specified ATTGTCACAACCGCACAG -[3890856:3890873] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) rhlR (PA3477) , rhlB (PA3478) , rhlA (PA3479)
    ... ... rhlR rhlB rhlA
    244 21719541
    NC_002516.2 P55222 not specified AAGGCTGCGCGCTTGACAG -[3890707:3890725] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) rhlR (PA3477) , rhlB (PA3478)
    ... ... rhlR rhlB
    245 21719541
    NC_002516.2 P55222 not specified TCCTGAACGGTGCTGGCAT -[3890761:3890779] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) rhlR (PA3477) , rhlB (PA3478) , rhlA (PA3479)
    ... ... rhlR rhlB rhlA
    245 21719541
    NC_002516.2 P55222 not specified TGGTCGAACGTTGTCATAG -[3890811:3890829] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) rhlR (PA3477) , rhlB (PA3478) , rhlA (PA3479)
    ... ... rhlR rhlB rhlA
    245 21719541
    NC_002516.2 P55222 not specified AAATTGACTAATCGTTCACATTTG +[1187458:1187481] 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) fleQ (PA1097) , fleS (PA1098) , fleR (PA1099)
    ... ... fleQ fleS fleR
    572 12218009
    NC_002516.2 P55222 not specified ACCGTCTGAAGCAGTTCTCAT -[2487482:2487502] 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) ptxR (PA2258) , ptxS (PA2259) , PA2260 , PA2261 , PA2262 , PA2263
    ... ... ptxR ptxS PA2260 PA2261 PA2262 PA2263
    575 18227247
    NC_002516.2 P55222 dimer AAATGTGATCTAGATCACATTT +[1557881:1557902] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) lasR (PA1430)
    ... ... lasR
    593 17159200
    NC_002516.2 P55222 dimer CTCTGCAATCCAGTTCATAAAT -[1242643:1242664] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) toxA (PA1148)
    ... ... toxA
    593 17159200
    NC_002516.2 P55222 dimer CATGCGGAACTGCATCACATTT +[3962079:3962100] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) algD (PA3540) , alg8 (PA3541) , alg44 (PA3542) , algK (PA3543) , algE (PA3544) , algG (PA3545) , algX (PA3546) , algL (PA3547)
    ... ... algD alg8 alg44 algK algE algG algX algL
    594 17159200
    NC_002516.2 P55222 dimer TTTTTTGCGGCAGATGGCATTT -[5924441:5924462] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) algZ (PA5262) , algR (PA5261) , hemC (PA5260) , hemD (PA5259) , PA5258 , PA5257 , argH (PA5263)
    ... ... algZ algR hemC hemD PA5258 PA5257 argH
    594 17159200
    NC_002516.2 P55222 dimer TTATGGGCACCAGTTCACACTG -[950690:950711] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) pbpG (PA0869)
    ... ... pbpG
    594 17159200
    NC_002516.2 P55222 dimer GGCAAATGGCTAGGTCACAGAA +[5680789:5680810] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) pilM (PA5044) , pilN (PA5043) , pilO (PA5042) , pilP (PA5041) , pilQ (PA5040) , aroK (PA5039) , aroB (PA5038) , PA5037 , ponA (PA5045)
    ... ... pilM pilN pilO pilP pilQ aroK aroB PA5037 ponA
    594 17159200
    NC_002516.2 P55222 dimer AAATGTGATTTAAAACACATGA -[921705:921726] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) plcH (PA0844) , plcR (PA0843) , PA0842
    ... ... plcH plcR PA0842
    594 17159200
    NC_002516.2 P55222 dimer AATTGTGATGAAGTTGGCATGA -[3722908:3722929] Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) plcN (PA3319)
    ... ... plcN
    594 17159200
    NC_002516.2 P55222 not specified GAAACAAGAGCTAGCTCACAC +[5282990:5283010] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) cbpA (PA4704) , PA4703 , prrF1 (PA4704.1) , prrF2 (PA4704.2)
    ... ... cbpA PA4703 prrF1 prrF2
    666 19801409
    NC_002516.2 P55222 not specified AGTACGGGATCACAGTCCTGATAGCTGCGTCG -[706859:706890] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details In-vitro transcription (ECO:0001204) vfr (PA0652) , PA0653
    ... ... vfr PA0653
    784 20494996

    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.

    AAATGTGATCTAGATCACATTT
    ATTGTCACAACCGCACAG
    AAGGCTGCGCGCTTGACAG
    TCCTGAACGGTGCTGGCAT
    TGGTCGAACGTTGTCATAG
    AAATTGACTAATCGTTCACATTTG
    ACCGTCTGAAGCAGTTCTCAT
    AAATGTGATCTAGATCACATTT
    CTCTGCAATCCAGTTCATAAAT
    CATGCGGAACTGCATCACATTT
    TTTTTTGCGGCAGATGGCATTT
    TTATGGGCACCAGTTCACACTG
    GGCAAATGGCTAGGTCACAGAA
    AAATGTGATTTAAAACACATGA
    AATTGTGATGAAGTTGGCATGA
    GAAACAAGAGCTAGCTCACAC
    AGTACGGGATCACAGTCCTGATAGCTGCGTCG

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

    TTCGCATAAAATGTGATCTAGATCACATTTAA
    TCATGGAATTGTCACAACCGCACAGTATCGCT
    GGGTATGACGCTGTCAAGCGCGCAGCCTTGCC
    TATCTGTTATGCCAGCACCGTTCAGGACGCAG
    CCCCCTCCCTATGACAACGTTCGACCACCTGG
    GTTAAGTCAAATGTGAACGATTAGTCAATTTT
    CCGGCCGACCGTCTGAAGCAGTTCTCATTTAT
    TTCGCATAAAATGTGATCTAGATCACATTTAA
    ATTCACCACTCTGCAATCCAGTTCATAAATCC
    GCGTGAAAAAATGTGATGCAGTTCCGCATGAC
    AAGCACCGAAATGCCATCTGCCGCAAAAAACC
    GTGGGGCGCAGTGTGAACTGGTGCCCATAATT
    AGCAATTTTTCTGTGACCTAGCCATTTGCCTG
    TCACTTGTTCATGTGTTTTAAATCACATTTTA
    ACAACTATTCATGCCAACTTCATCACAATTTG
    CCCGTGGCAGGTGTGAGCTAGCTCTTGTTTCG
    CGACGCAGCTATCAGGACTGTGATCCCGTACT
    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.