LexA , LexA , LexA regulon and binding site collection in Mycobacterium leprae TN , Mycobacterium smegmatis str. MC2 155 , Mycobacterium tuberculosis H37Rv

LexA - UniProtKB: A0QVY5 regulon and binding site collection of Mycobacterium leprae TN

Sites are listed as curated.

GAACACATGTTT

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

GAACACATGTTT

Motif structure	Inverted repeat
GC-content	33.33%
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	1	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_002677.1	A0QVY5	dimer	GAACACATGTTT	-[1175762:1175773]	Experimental technique details EMSA (ECO:0001807) EMSA - ECO:0001807 Electro-mobility shift-assays (or gel retardation assays) are a standard way of assessing TF-binding. A fragment of DNA of interest is amplified and labeled with a fluorophore. The fragment is left to incubate in a solution containing abundant TF and non-specific DNA (e.g. randomly cleaved DNA from salmon sperm, of all things) and then a gel is run with the incubated sample and a control (sample that has not been in contact with the TF). If the TF has bound the sample, the complex will migrate more slowly than unbound DNA through the gel, and this retarded band can be used as evidence of binding. The unspecific DNA ensures that the binding is specific to the fragment of interest and that any non-specific DNA-binding proteins left-over in the TF purification will bind there, instead of on the fragment of interest. EMSAs are typically carried out in a bunch of fragments, shown as multiple double (control+experiment) lanes in a wide picture. Certain additional controls are run in at least one of the fragments to ascertain specificity. In the most basic of these, specific competitor (the fragment of interest or a known positive control, unlabelled) is added to the reaction. This should sequester the TF and hence make the retardation band disappear, proving that the binding is indeed specific - Experimental technique details Site directed mutagenesis (ECO:0005667) Site directed mutagenesis - ECO:0005667 Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge	ML1004 , ML1001 , ML1002 , lexA (ML1003)	386	9427395

LexA - UniProtKB: A0QVY5 regulon and binding site collection of Mycobacterium smegmatis str. MC2 155

Sites are listed as curated.

GAACAGGTGTTC

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

GAACAGGTGTTC

Motif structure	Inverted repeat
GC-content	50.00%
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	1	0	0

Genome	TF	TF conformation	Site sequence	Site location	Experimental techniques	Gene regulation	Curations	PMIDs
NC_008596.1	A0QVY5	dimer	GAACAGGTGTTC	+[2792243:2792254]	Experimental technique details EMSA (ECO:0001807) EMSA - ECO:0001807 Electro-mobility shift-assays (or gel retardation assays) are a standard way of assessing TF-binding. A fragment of DNA of interest is amplified and labeled with a fluorophore. The fragment is left to incubate in a solution containing abundant TF and non-specific DNA (e.g. randomly cleaved DNA from salmon sperm, of all things) and then a gel is run with the incubated sample and a control (sample that has not been in contact with the TF). If the TF has bound the sample, the complex will migrate more slowly than unbound DNA through the gel, and this retarded band can be used as evidence of binding. The unspecific DNA ensures that the binding is specific to the fragment of interest and that any non-specific DNA-binding proteins left-over in the TF purification will bind there, instead of on the fragment of interest. EMSAs are typically carried out in a bunch of fragments, shown as multiple double (control+experiment) lanes in a wide picture. Certain additional controls are run in at least one of the fragments to ascertain specificity. In the most basic of these, specific competitor (the fragment of interest or a known positive control, unlabelled) is added to the reaction. This should sequester the TF and hence make the retardation band disappear, proving that the binding is indeed specific - Experimental technique details Site directed mutagenesis (ECO:0005667) Site directed mutagenesis - ECO:0005667 Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge - Experimental technique details xylE reporter assay xylE reporter assay A reporter assay based on the fusion of a promoter of interest with the xylE gene, which produces catechol dioxygenase, capable of converting the colorless substrate catechol to yellow hydroxymuconic semialdehyde.	recA (MSMEG_2723) , MSMEG_2737 , MSMEG_2736 , dapF (MSMEG_2735) , miaA (MSMEG_2734) , MSMEG_2733 , MSMEG_2732 , MSMEG_2731 , MSMEG_2730 , miaB (MSMEG_2729) , MSMEG_2728 , MSMEG_2727 , MSMEG_2726 , MSMEG_2725 , recX (MSMEG_2724) , MSMEG_2704 , hypE (MSMEG_2705) , gmhA (MSMEG_2706) , MSMEG_2707 , MSMEG_2709 , MSMEG_2708 , MSMEG_2710 , hypF (MSMEG_2711) , hypC (MSMEG_2712) , MSMEG_2713 , MSMEG_2714 , MSMEG_2715 , MSMEG_2716 , MSMEG_2717 , MSMEG_2718 , MSMEG_2719 , MSMEG_2720 , hypB (MSMEG_2721) , hypA (MSMEG_2722) , MSMEG_2738	385	9427395

LexA - UniProtKB: A0QVY5 regulon and binding site collection of Mycobacterium tuberculosis H37Rv

Sites are listed as curated.

TCGAACAGGTGTTCGG

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

TCGAACAGGTGTTCGG

Motif structure	Inverted repeat
GC-content	56.25%
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	1	0	0

Genome	TF	TF conformation	Site sequence	Site location	Experimental techniques	Gene regulation	Curations	PMIDs
NC_000962.3	A0QVY5	dimer	TCGAACAGGTGTTCGG	-[3051531:3051546]	Experimental technique details Beta-gal reporter assay Beta-gal reporter assay Reporter assay using the beta-galactosidase (lacZ) gene. The lacZ gene is typically fused to the promoter of interest. Differential regulation of the promoter mediated by the TF is assessed by induction of the system and evaluation of lacZ expression. Bacteria expressing lacZ appear blue when grown on a X-gal medium. The assay is often performed using a plasmid borne construction on a lacZ(def) strain. - Experimental technique details Site directed mutagenesis (ECO:0005667) Site directed mutagenesis - ECO:0005667 Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site.	recA (Rv2737c) , ephG (Rv2740) , Rv2739c , Rv2738c , Rv2737A , Rv2734 , Rv2735c , recX (Rv2736c)	388	12029045

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.

GAACAGGTGTTC
GAACACATGTTT
TCGAACAGGTGTTCGG

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

TCGAACAGGTGTTCGT
TCAAACATGTGTTCGA
TCGAACAGGTGTTCGG

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.