LexA regulon and binding site collection in Burkholderia thailandensis E264

LexA - UniProtKB: Q2SVP7 regulon and binding site collection of Burkholderia thailandensis E264

Sites are listed as curated.

CTGTATTTTTATACAG
CTGTGTTTTTGTACAG
CTGTTTTTTTATACAG
CTGGTTCGACGGCCAG

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

CTGTATTTTTATACAG
CTGTGTTTTTGTACAG
CTGTTTTTTTATACAG
CTGGTTCGACGGCCAG

Motif structure	Inverted repeat
GC-content	39.06%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	0%	100%	0%	0%
TF conformation	Monomer	Dimer	Tetramer	Other	Not specified
TF conformation	0%	100%	0%	0%	0%
Binding site type	Motif-associated	Variable-motif-associated	Non-motif-associated
Binding site type	4	0	0

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_007651.1	Q2SVP7	dimer	CTGTATTTTTATACAG	-[2839879:2839894]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time.	lexA (BTH_I2481) , BTH_I2480 , cysT (BTH_I2479) , BTH_I2478 , BTH_I2477 , BTH_I2476 , BTH_I2482	403	23872555
NC_007651.1	Q2SVP7	dimer	CTGTGTTTTTGTACAG	+[2097788:2097803]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time.	BTH_I1859 , BTH_I1858	403	23872555
NC_007651.1	Q2SVP7	dimer	CTGTTTTTTTATACAG	+[740770:740785]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time.	recA (BTH_I0643) , recX (BTH_I0644) , BTH_I0642 , BTH_I0641	403	23872555
NC_007651.1	Q2SVP7	dimer	CTGGTTCGACGGCCAG	+[488947:488962]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details RNA-Seq (ECO:0005664) RNA-Seq - ECO:0005664 In RNA-seq, RNA is extracted from the cell at a given time and reverse transcribed to obtain cDNA. This cDNA is then sequenced. This provides a snapshot of the "transcriptome" of an organism at a given time.	dnaE2 (BTH_I0445) , BTH_I0444 , BTH_I0443 , BTH_I0442 , BTH_I0441 , BTH_I0440	403	23872555

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.

CTGTATTTTTATACAG
CTGTGTTTTTGTACAG
CTGTTTTTTTATACAG
CTGGTTCGACGGCCAG

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

CTGTATTTTTATACAG
CTGTGTTTTTGTACAG
CTGTTTTTTTATACAG
CTGGTTCGACGGCCAG

To generate the weblogo, aligned binding sites are used.

	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.