FIS regulon and binding site collection in Pasteurella multocida subsp. multocida str. Pm70

FIS - UniProtKB: P57902 regulon and binding site collection of Pasteurella multocida subsp. multocida str. Pm70

Sites are listed as curated.

GACCAAAAATAAATC
GATTATATTTTAAAT

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

GACCAAAAATAAATC
ATTTAAAATATAATC

Motif structure	Direct repeat
GC-content	16.67%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	100%	0%	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_002663.1	P57902	dimer	GACCAAAAATAAATC	+[914442:914456]	Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) Ad-hoc qualitative phenotype observation - ECO:0005674 A non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter. The observed phenotype should be described in the experimental notes. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	phyA (PM0773) , hyaE (PM0774) , hexD (PM0778) , hexC (PM0779) , hexB (PM0780) , phyB (PM0772) , PM0771 , PM0770 , hrpA (PM0769) , PM0775 , PM0776 , PM0777 , hexA (PM0781) , PM0782 , PM0783 , PM0784 , PM0785 , PM0786	486	20140235
NC_002663.1	P57902	dimer	GATTATATTTTAAAT	+[914566:914580]	Experimental technique details Ad-hoc qualitative phenotype observation (ECO:0005674) Ad-hoc qualitative phenotype observation - ECO:0005674 A non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter. The observed phenotype should be described in the experimental notes. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	phyA (PM0773) , hyaE (PM0774) , hexD (PM0778) , hexC (PM0779) , hexB (PM0780) , phyB (PM0772) , PM0771 , PM0770 , hrpA (PM0769) , PM0775 , PM0776 , PM0777 , hexA (PM0781) , PM0782 , PM0783 , PM0784 , PM0785 , PM0786	486	20140235

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.

GACCAAAAATAAATC
GATTATATTTTAAAT

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

GACCAAAAATAAATC
ATTTAAAATATAATC

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.