NtrC - UniProtKB: Q88CY1 regulon and binding site collection of Pseudomonas putida KT2440


Sites are listed as curated.

CGCCCTATTCCGGTGCG
CGCAGCTTTAATGTGCA
CGCCCCTGCTTTGTGCG
TGCACATTTTTCGCGCA
CGCACCGAAATTGTGCA

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

CGCCCTATTCCGGTGCG
TGCACATTAAAGCTGCG
CGCACAAAGCAGGGGCG
TGCACATTTTTCGCGCA
TGCACAATTTCGGTGCG

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.

Site sequence Experimental techniques Gene regulation Curations PMIDs
CGCCCTATTCCGGTGCG Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details In-vitro transcription (ECO:0001204) - Experimental technique details Site directed mutagenesis (ECO:0005667) gdhA (PP_0675)
... ... gdhA
588 20735780
CGCAGCTTTAATGTGCA Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) codB (PP_3187) , PP_3188 , codA (PP_3189)
... ... codB PP_3188 codA
589 19648236
CGCCCCTGCTTTGTGCG Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) ureD (PP_2842) , ureA (PP_2843) , ureB (PP_2844) , ureC (PP_2845) , ureE (PP_2846) , ureJ (PP_2847) , ureF (PP_2848) , ureG (PP_2849) , PP_2850
... ... ureD ureA ureB ureC ureE ureJ ureF ureG PP_2850
589 19648236
TGCACATTTTTCGCGCA Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) PP_5234 , amtB (PP_5233) , PP_5235
... ... PP_5234 amtB PP_5235
589 19648236
CGCACCGAAATTGTGCA Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Visual sequence inspection (nan) PP_5234 , amtB (PP_5233) , PP_5235
... ... PP_5234 amtB PP_5235
589 19648236

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.

CGCCCTATTCCGGTGCG
CGCAGCTTTAATGTGCA
CGCCCCTGCTTTGTGCG
TGCACATTTTTCGCGCA
CGCACCGAAATTGTGCA

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

CGCCCTATTCCGGTGCG
TGCACATTAAAGCTGCG
CGCACAAAGCAGGGGCG
TGCACATTTTTCGCGCA
TGCACAATTTCGGTGCG
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.