MalI regulon and binding site collection in Escherichia coli str. K-12 substr. MG1655

MalI - UniProtKB: P18811 regulon and binding site collection of Escherichia coli str. K-12 substr. MG1655

Sites are listed as curated.

GGTAAAACGTTTTATC
GATAAAACGTTTTATC

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

GGTAAAACGTTTTATC
GATAAAACGTTTTATC

Motif structure	Inverted repeat
GC-content	28.13%
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	2	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_000913.2	P18811	dimer	GGTAAAACGTTTTATC	-[1697234:1697249]	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 Multiple sequence alignment (MSA) (ECO:0005556) Multiple sequence alignment (MSA) - ECO:0005556 MSA can be used to align promoter regions and highlight regions of conservation that may be indicative of transcription factor binding sites. - Experimental technique details Random mutagenesis (ECO:0005530) Random mutagenesis - ECO:0005530 Non-targeted mutagenesis. Typically accomplished in vivo by means of radiation or a DNA-damaging agent, or in vitro using degenerate PCR. Not frequently used in TF-binding site determination. It is sometimes used to investigate the effect of mutations in transcription factor binding domains, in conjunction with expression assays. - 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	malI (b1620) , ydgJ (b1624) , add (b1623) , malY (b1622) , malX (b1621) , hdhA (b1619)	551	20141531
NC_000913.2	P18811	dimer	GATAAAACGTTTTATC	+[1697312:1697327]	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 Multiple sequence alignment (MSA) (ECO:0005556) Multiple sequence alignment (MSA) - ECO:0005556 MSA can be used to align promoter regions and highlight regions of conservation that may be indicative of transcription factor binding sites. - Experimental technique details Random mutagenesis (ECO:0005530) Random mutagenesis - ECO:0005530 Non-targeted mutagenesis. Typically accomplished in vivo by means of radiation or a DNA-damaging agent, or in vitro using degenerate PCR. Not frequently used in TF-binding site determination. It is sometimes used to investigate the effect of mutations in transcription factor binding domains, in conjunction with expression assays. - 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	malY (b1622) , malX (b1621) , ydgJ (b1624) , add (b1623) , hdhA (b1619) , malI (b1620)	551	20141531

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.

GGTAAAACGTTTTATC
GATAAAACGTTTTATC

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

GGTAAAACGTTTTATC
GATAAAACGTTTTATC

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.