PilR regulon and binding site collection in Geobacter sulfurreducens PCA

PilR - UniProtKB: Q74D24 regulon and binding site collection of Geobacter sulfurreducens PCA

Sites are listed as curated.

GGCAAAATTTGGCATG

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

GGCAAAATTTGGCATG

Motif structure	Direct repeat
GC-content	43.75%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	100%	0%	0%	0%
TF conformation	Monomer	Dimer	Tetramer	Other	Not specified
TF conformation	0%	0%	0%	0%	100%
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_002939.5	Q74D24	not specified	GGCAAAATTTGGCATG	+[1642063:1642078]	Experimental technique details Luciferase reporter assay (ECO:0005648) Luciferase reporter assay - ECO:0005648 A type of reporter assay . The idea is identical to a betagalactosidase assay, but here fluorescence of luciferase gene product is used as the reporter. - Experimental technique details Regular expression search (ECO:0005662) Regular expression search - ECO:0005662 Similar to a PSSM search, a regular expression search looks for patterns in DNA, by making use of "degenerate" symbols and parenthetic constructs. For instance, [ATA (N:4–6) STGTC] indicates a pattern of ATA followed by 4 to 6 variable characters (N) and a suffix starting with a "strong" (S=G or C) base and the sequence TGTC.	pilA-N (GSU1496) , pilR (GSU1495) , pilS (GSU1494) , pilC (GSU1493) , pilT-4 (GSU1492) , pilB (GSU1491) , aroE (GSU1490) , GSU1489 , GSU1488 , ribF (GSU1487) , tatC (GSU1486) , rnr (GSU1485) , pilA-C (GSU1497) , xapA (GSU1498) , xapB (GSU1499) , GSU1500 , xapD (GSU1501) , xapE (GSU1502) , xapF (GSU1503) , xapG (GSU1504) , xapH (GSU1505) , xapI (GSU1506) , xapJ (GSU1507) , GSU1508 , GSU1509 , GSU1510 , GSU1510.1 , GSU1511 , GSU1512 , GSU1513 , GSU1514 , GSUR026 , thrS (GSU1515) , infC (GSU1516) , rpmI (GSU1517) , rplT (GSU1518) , pheS (GSU1519) , pheT (GSU1520) , ihfA-1 (GSU1521) , GSU1522 , GSUR027 , surE (GSU1523) , pcm (GSU1524) , rpoS (GSU1525) , apt (GSU1526) , GSUR028	449	20708667

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.

GGCAAAATTTGGCATG

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

GGCAAAATTTGGCATG

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.