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


CATTAATTATGCAAAATTTATGG
CATTGTTTAGGGTTTGTTTAATT
CACTGTTTATATTTTGTTTAGTA
CATTGTTTAGGTTTTGTTTAAGT
CAGTTTTTAAAAACTGTTTAAAG
ATTTGTTTAAGGAATGATTAATT
GCTGGTTTATTTAATGTTTACCC
TCTGGTTTATCGTTGGTTTAGTT
CAGCGTATAGCTTATGTTTATAA
CAGCGTATAGCTTATGTTTATAA
TGCCGTTGATAAAGAGTTTATCT
TGCTATTTACAAGCTGATAACAA
TGATATTTCGTTGAAGTTAATGA
CACTATTGATGTTTGGTTAAGAT
TGTTATTTTTAGCCGGTTTAAAT
AGATATATAACGTCGGTTTATAA
ACATATTGCTCCACTGTTTATAT
ACATAGTTAGGCGCTGTTTAACT
ACATAGTTAGGCGCTGTTTAACT
TGGTATTCACGAAAAGTTTATGT
ACCTGATGAAAACTTGTTTAGAA
CATTAATTATGCAAAATTTATGG
CATTGTTTAGGGTTTGTTTAATT
CACTGTTTATATTTTGTTTAGTA
CATTGTTTAGGTTTTGTTTAAGT
CAGTTTTTAAAAACTGTTTAAAG
ATTTGTTTAAGGAATGATTAATT
GCTGGTTTATTTAATGTTTACCC
TCTGGTTTATCGTTGGTTTAGTT
CAGCGTATAGCTTATGTTTATAA
CAGCGTATAGCTTATGTTTATAA
TGCCGTTGATAAAGAGTTTATCT
TGCTATTTACAAGCTGATAACAA
TGATATTTCGTTGAAGTTAATGA
CACTATTGATGTTTGGTTAAGAT
TGTTATTTTTAGCCGGTTTAAAT
AGATATATAACGTCGGTTTATAA
ACATATTGCTCCACTGTTTATAT
ACATAGTTAGGCGCTGTTTAACT
ACATAGTTAGGCGCTGTTTAACT
TGGTATTCACGAAAAGTTTATGT
ACCTGATGAAAACTTGTTTAGAA

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
CATTAATTATGCAAAATTTATGG mipA,
... ... mipA yeaI yeaH yeaG gapA yeaD yeaE
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) - activator dimer
CATTGTTTAGGGTTTGTTTAATT
... ... ybcV essD rrrD rzpD rzoD borD
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) - activator dimer
CACTGTTTATATTTTGTTTAGTA ompT,
... ... ompT envY pauD
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) - activator dimer
CATTGTTTAGGTTTTGTTTAAGT yrbL,
... ... yrbL yhcC arcB arcZ elbB mtgA yrbG kdsD kdsC lptC lptA lptB rpoN hpf ptsN yhbJ npr
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) - activator dimer
CAGTTTTTAAAAACTGTTTAAAG insH,
... ... insH yejM proL yejO narP yejL
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) - activator dimer
ATTTGTTTAAGGAATGATTAATT mipA,
... ... mipA yeaI yeaH yeaG gapA yeaD yeaE
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) - activator dimer
GCTGGTTTATTTAATGTTTACCC phoP,
... ... phoP rluE nudJ mnmA hflD purB pepT ycfD phoQ
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) - activator dimer
TCTGGTTTATCGTTGGTTTAGTT mgtA,
... ... mgtA mgtL treC treB treR
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) - activator dimer
CAGCGTATAGCTTATGTTTATAA gadY,
... ... gadY gadX gadW
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) - activator dimer
CAGCGTATAGCTTATGTTTATAA gadY,
... ... gadY gadX gadW
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) - activator dimer
TGCCGTTGATAAAGAGTTTATCT pmrD,
... ... pmrD rbn elaA elaB menF menD menH menB menC menE arnB arnC arnA arnD arnT arnE arnF
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) - activator dimer
TGCTATTTACAAGCTGATAACAA gadE,
... ... gadE arrS
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) - activator dimer
TGATATTTCGTTGAAGTTAATGA 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) - activator dimer
CACTATTGATGTTTGGTTAAGAT 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) - activator dimer
TGTTATTTTTAGCCGGTTTAAAT nmpC,
... ... nmpC borD rzoD rzpD rrrD essD insH
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) - activator dimer
AGATATATAACGTCGGTTTATAA ygdR,
... ... ygdR omrB omrA aas lplT tas mutH ygdQ
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) - activator dimer
ACATATTGCTCCACTGTTTATAT ompT,
... ... ompT envY pauD
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) - activator dimer
ACATAGTTAGGCGCTGTTTAACT mgrB,
... ... mgrB kdgR yobH yebO
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) - activator dimer
ACATAGTTAGGCGCTGTTTAACT yebO,
... ... yebO mgrB kdgR yobH
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) - activator dimer
TGGTATTCACGAAAAGTTTATGT 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) - activator dimer
ACCTGATGAAAACTTGTTTAGAA 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) - activator dimer