Curation Information

Publication
Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica.;Zwir I, Shin D, Kato A, Nishino K, Latifi T, Solomon F, Hare JM, Huang H, Groisman EA;Proceedings of the National Academy of Sciences of the United States of America 2005 Feb 22; 102(8):2862-7 [15703297]
TF
PhoP [P23836, view regulon]
Reported TF sp.
Escherichia coli str. K-12 substr. MG1655
Reported site sp.
Escherichia coli str. K-12 substr. MG1655
Created by
Erill Lab
Curation notes
-

Experimental Process

Activated genes identified with DNA-array on low Mg2+ induction. Binding sites predicted with machine learning method based on submotif PSSM.

Transcription Factor Binding Sites


TTCTGTATATGTCATGTTGATGG
TTCTGTATATGTCATGTTGATGG
TTCTGTATATGTCATGTTGATGG
TTTTGTTTATAATTGGTTGATCC
ACTTGTTTAGAAACGATTGATAG
ACTTGTTTAGAAACGATTGATAG
GCTGGTTGAGCATTTGTTGAAAA
TTTTGTTGATATTTCGTTGAAGT
TTTTGTTGATATTTCGTTGAAGT
ATTTGTTGTTTCATTGTTAAAAA
ATTTGTTGTTTCATTGTTAAAAA
TTCTGTATATGTCATGTTGATGG
TTCTGTATATGTCATGTTGATGG
TTCTGTATATGTCATGTTGATGG
TTTTGTTTATAATTGGTTGATCC
ACTTGTTTAGAAACGATTGATAG
ACTTGTTTAGAAACGATTGATAG
GCTGGTTGAGCATTTGTTGAAAA
TTTTGTTGATATTTCGTTGAAGT
TTTTGTTGATATTTCGTTGAAGT
ATTTGTTGTTTCATTGTTAAAAA
ATTTGTTGTTTCATTGTTAAAAA

Gene Regulation

Regulated genes for each binding site 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. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
TTCTGTATATGTCATGTTGATGG hdeD,
... ... hdeD dctR yhiD hdeB hdeA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TTCTGTATATGTCATGTTGATGG hdeA,
... ... hdeA hdeD dctR yhiD hdeB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TTCTGTATATGTCATGTTGATGG hdeD,
... ... hdeD dctR yhiD hdeB hdeA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TTTTGTTTATAATTGGTTGATCC slyB,
... ... slyB slyA dtpA gstA pdxY tyrS pdxH mliC anmK
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ACTTGTTTAGAAACGATTGATAG rstA,
... ... rstA fumA fumC tus rstB ydgI folM ydgC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ACTTGTTTAGAAACGATTGATAG rstA,
... ... rstA fumA fumC tus rstB ydgI folM ydgC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
GCTGGTTGAGCATTTGTTGAAAA ompX,
... ... ompX mntS yliL ybiP rhtA ybiS ybiR mntR rybA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TTTTGTTGATATTTCGTTGAAGT ybjX,
... ... ybjX cspD macB macA ybjD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TTTTGTTGATATTTCGTTGAAGT ybjX,
... ... ybjX cspD macB macA ybjD
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ATTTGTTGTTTCATTGTTAAAAA yiaG,
... ... yiaG yiaD ghrB yiaF
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ATTTGTTGTTTCATTGTTAAAAA yiaG,
... ... yiaG yiaD ghrB yiaF
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Machine learning prediction (ECO:0005649) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer