AlgR - UniProtKB: P26275 regulon and binding site collection of Pseudomonas aeruginosa PAO1


Sites are listed as curated.

TCGAGCCGTTCGTCGAGCGC
GCCTGCCGTTCATCCTCCTT
CCGTTTGGC
CCCTCGGGC
CCGTTCGTC
CCGTTGTTC
CCGTGCGTC
CCGTCGGTC
CCGTTGGCC
CCGTTTGGC
CCGTCGTTC
CCGTGGGCC
CCGGGCGTC
CCATGCTTC
GAACGACGG
CCGTTCGTCTGCAA
CCGTTCGTCCCTCC
TGGCGCTACCGTTCGTCCCTCCG
CTCAACCGTTCGTCTGCAAGT

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

TGATCGAGCCGTTCGTCGAGCGCC
GTTGCCTGCCGTTCATCCTCCTTT
TCCCAGGCCCGTTTGGCATGCTTT
TGTCCTGCCCCTCGGGCCGACCGT
GAGAACGACCGTTCGTCGTGCTCA
TGGTCATCCCGTTGTTCGTCGGTC
ACGCACCGCCGTGCGTCGGAACGC
TCCAGAGACCGTCGGTCATCAGGA
GGTCCATACCGTTGGCCTGTACTG
TCCCAGGCCCGTTTGGCATGCTTT
GCCACCACCCGTCGTTCCGTCATG
CCAGCGCGCCGTGGGCCGCGTGGC
TTGGGATGCCGGGCGTCCCCCCAT
CCCATTATCCATGCTTCCTCTCGC
GCCACCACCCGTCGTTCCGTCATG
CTACTCAACCGTTCGTCTGCAAGT
TGGCGCTACCGTTCGTCCCTCCGA
TGGCGCTACCGTTCGTCCCTCCGA
CTACTCAACCGTTCGTCTGCAAGT

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 P26275 not specified TCGAGCCGTTCGTCGAGCGC -[3893923:3893942] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) rhlA (PA3479) , PA3480 , PA3481
    ... ... rhlA PA3480 PA3481
    268 17766417
    NC_002516.2 P26275 not specified GCCTGCCGTTCATCCTCCTT -[3889858:3889877] Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) rhlI (PA3476) , rhlR (PA3477)
    ... ... rhlI rhlR
    271 17766417
    NC_002516.2 P26275 not specified CCGTTTGGC +[5098167:5098175] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) fimU (PA4550) , pilV (PA4551) , pilW (PA4552) , pilX (PA4553) , pilY1 (PA4554) , pilY2 (PA4555) , pilE (PA4556) , fimT (PA4549) , lytB (PA4557)
    ... ... fimU pilV pilW pilX pilY1 pilY2 pilE fimT lytB
    325 18178737
    NC_002516.2 P26275 not specified CCCTCGGGC +[5098126:5098134] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) fimU (PA4550) , pilV (PA4551) , pilW (PA4552) , pilX (PA4553) , pilY1 (PA4554) , pilY2 (PA4555) , pilE (PA4556) , fimT (PA4549) , lytB (PA4557)
    ... ... fimU pilV pilW pilX pilY1 pilY2 pilE fimT lytB
    325 18178737
    NC_002516.2 P26275 dimer CCGTTCGTC +[3509275:3509283] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) ibpA (PA3126) , PA3125 , PA3124 , PA3123 , PA3122 , PA3127 , PA3128 , PA3129 , PA3130 , PA3131 , PA3132 , PA3133
    ... ... ibpA PA3125 PA3124 PA3123 PA3122 PA3127 PA3128 PA3129 PA3130 PA3131 PA3132 PA3133
    458 15317771
    NC_002516.2 P26275 dimer CCGTTGTTC +[1956295:1956303] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) lon (PA1803) , clpX (PA1802) , clpP (PA1801) , tig (PA1800) , hupB (PA1804) , PA1804.1 , ppiD (PA1805) , fabI (PA1806) , PA1807 , PA1808 , PA1809 , PA1810 , PA1811
    ... ... lon clpX clpP tig hupB PA1804.1 ppiD fabI PA1807 PA1808 PA1809 PA1810 PA1811
    458 15317771
    NC_002516.2 P26275 dimer CCGTGCGTC -[5692480:5692488] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) hslV (PA5053) , PA5052 , argS (PA5051) , hslU (PA5054) , PA5055
    ... ... hslV PA5052 argS hslU PA5055
    458 15317771
    NC_002516.2 P26275 dimer CCGTCGGTC -[5101629:5101637] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) pilY1 (PA4554) , pilX (PA4553) , pilW (PA4552) , pilV (PA4551) , fimU (PA4550) , fimT (PA4549) , pilY2 (PA4555) , PA4548 , pilR (PA4547) , pilS (PA4546) , pilE (PA4556) , lytB (PA4557) , PA4558 , lspA (PA4559) , ileS (PA4560) , ribF (PA4561) , PA4562
    ... ... pilY1 pilX pilW pilV fimU fimT pilY2 PA4548 pilR pilS pilE lytB PA4558 lspA ileS ribF PA4562
    459 15317771
    NC_002516.2 P26275 dimer CCGTTGGCC -[5097185:5097193] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) fimT (PA4549) , fimU (PA4550) , pilV (PA4551) , pilW (PA4552) , pilX (PA4553) , pilY1 (PA4554) , pilY2 (PA4555) , PA4548 , pilR (PA4547) , pilS (PA4546) , pilE (PA4556) , lytB (PA4557) , PA4558 , lspA (PA4559) , ileS (PA4560) , ribF (PA4561) , PA4562
    ... ... fimT fimU pilV pilW pilX pilY1 pilY2 PA4548 pilR pilS pilE lytB PA4558 lspA ileS ribF PA4562
    459 15317771
    NC_002516.2 P26275 dimer CCGTTTGGC +[5098167:5098175] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) fimT (PA4549) , fimU (PA4550) , pilV (PA4551) , pilW (PA4552) , pilX (PA4553) , pilY1 (PA4554) , pilY2 (PA4555) , PA4548 , pilR (PA4547) , pilS (PA4546) , pilE (PA4556) , lytB (PA4557) , PA4558 , lspA (PA4559) , ileS (PA4560) , ribF (PA4561) , PA4562
    ... ... fimT fimU pilV pilW pilX pilY1 pilY2 PA4548 pilR pilS pilE lytB PA4558 lspA ileS ribF PA4562
    459 15317771
    NC_002516.2 P26275 dimer CCGTCGTTC -[2412135:2412143] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details S1 nuclease protection (ECO:0005666) hcnA (PA2193) , hcnB (PA2194) , hcnC (PA2195) , PA2192
    ... ... hcnA hcnB hcnC PA2192
    460 15317771
    NC_002516.2 P26275 dimer CCGTGGGCC -[2414774:2414782] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details S1 nuclease protection (ECO:0005666) hcnC (PA2195) , hcnB (PA2194) , hcnA (PA2193) , PA2196 , PA2197 , PA2198 , PA2199 , PA2200 , PA2201 , PA2202 , PA2203 , PA2204
    ... ... hcnC hcnB hcnA PA2196 PA2197 PA2198 PA2199 PA2200 PA2201 PA2202 PA2203 PA2204
    460 15317771
    NC_002516.2 P26275 dimer CCGGGCGTC +[1696334:1696342] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) ccoN2 (PA1557) , ccoO2 (PA1556) , ccoQ2 (PA1555.1) , ccoP2 (PA1555) , PA1558 , PA1559 , PA1560 , aer (PA1561)
    ... ... ccoN2 ccoO2 ccoQ2 ccoP2 PA1558 PA1559 PA1560 aer
    461 15317771
    NC_002516.2 P26275 dimer CCATGCTTC -[1696383:1696391] Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) ccoN2 (PA1557) , ccoO2 (PA1556) , ccoQ2 (PA1555.1) , ccoP2 (PA1555) , PA1558 , PA1559 , PA1560 , aer (PA1561)
    ... ... ccoN2 ccoO2 ccoQ2 ccoP2 PA1558 PA1559 PA1560 aer
    461 15317771
    NC_002516.2 P26275 other GAACGACGG +[2412135:2412143] Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) hcnA (PA2193) , hcnB (PA2194) , hcnC (PA2195)
    ... ... hcnA hcnB hcnC
    752 15466037
    NC_002516.2 P26275 monomer CCGTTCGTCTGCAA +[3962063:3962076] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) algD (PA3540) , alg8 (PA3541) , alg44 (PA3542) , algK (PA3543) , algE (PA3544) , algG (PA3545) , algX (PA3546) , algL (PA3547)
    ... ... algD alg8 alg44 algK algE algG algX algL
    755 1900366
    NC_002516.2 P26275 monomer CCGTTCGTCCCTCC +[3961987:3962000] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) algD (PA3540) , alg8 (PA3541) , alg44 (PA3542) , algK (PA3543) , algE (PA3544) , algG (PA3545) , algX (PA3546) , algL (PA3547)
    ... ... algD alg8 alg44 algK algE algG algX algL
    755 1900366
    NC_002516.2 P26275 not specified TGGCGCTACCGTTCGTCCCTCCG +[3961979:3962001] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) algD (PA3540) , alg8 (PA3541) , alg44 (PA3542) , algK (PA3543) , algE (PA3544) , algG (PA3545) , algX (PA3546) , algL (PA3547)
    ... ... algD alg8 alg44 algK algE algG algX algL
    763 1907266
    NC_002516.2 P26275 not specified CTCAACCGTTCGTCTGCAAGT +[3962058:3962078] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Visual sequence inspection (nan) algD (PA3540) , alg8 (PA3541) , alg44 (PA3542) , algK (PA3543) , algE (PA3544) , algG (PA3545) , algX (PA3546) , algL (PA3547)
    ... ... algD alg8 alg44 algK algE algG algX algL
    763 1907266

    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.

    TCGAGCCGTTCGTCGAGCGC
    GCCTGCCGTTCATCCTCCTT
    CCGTTTGGC
    CCCTCGGGC
    CCGTTCGTC
    CCGTTGTTC
    CCGTGCGTC
    CCGTCGGTC
    CCGTTGGCC
    CCGTTTGGC
    CCGTCGTTC
    CCGTGGGCC
    CCGGGCGTC
    CCATGCTTC
    GAACGACGG
    CCGTTCGTCTGCAA
    CCGTTCGTCCCTCC
    TGGCGCTACCGTTCGTCCCTCCG
    CTCAACCGTTCGTCTGCAAGT

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

    TGATCGAGCCGTTCGTCGAGCGCC
    GTTGCCTGCCGTTCATCCTCCTTT
    TCCCAGGCCCGTTTGGCATGCTTT
    TGTCCTGCCCCTCGGGCCGACCGT
    GAGAACGACCGTTCGTCGTGCTCA
    TGGTCATCCCGTTGTTCGTCGGTC
    ACGCACCGCCGTGCGTCGGAACGC
    TCCAGAGACCGTCGGTCATCAGGA
    GGTCCATACCGTTGGCCTGTACTG
    TCCCAGGCCCGTTTGGCATGCTTT
    GCCACCACCCGTCGTTCCGTCATG
    CCAGCGCGCCGTGGGCCGCGTGGC
    TTGGGATGCCGGGCGTCCCCCCAT
    CCCATTATCCATGCTTCCTCTCGC
    GCCACCACCCGTCGTTCCGTCATG
    CTACTCAACCGTTCGTCTGCAAGT
    TGGCGCTACCGTTCGTCCCTCCGA
    TGGCGCTACCGTTCGTCCCTCCGA
    CTACTCAACCGTTCGTCTGCAAGT
    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.