Curation Information

Publication
Discovery of Fur binding site clusters in Escherichia coli by information theory models.;Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD;Nucleic acids research 2007; 35(20):6762-77 [17921503]
TF
Fur [P0A9A9, view regulon]
Reported TF sp.
Escherichia coli str. K-12 substr. MG1655
Reported site sp.
Escherichia coli str. K-12 substr. MG1655
Created by
Urooq Aqeel
Curation notes
-

Experimental Process

PSSM used to locate the site. EMSA used to verify the binding site.

Transcription Factor Binding Sites


TATCTTTATAATAATCATTCTCGTTTACGTT
TATATTAATGATAATCACTATCACCATATCG
CATGATAATGAAATTAATTATCGTTATCGAT
TCTTTTAATGATAATAATTCTCATTATATTG
ATTGGTAATGAGAATAATTAACAATTAAAGA
CCGTAAAGTGATAATGATTATCATCTACATA
TACCACTATGATAATCAATATCATATGGGTT
AACATAAATGAAAATAATTATCATTACAGTA
CGTCGAATTGATAGTCGTTCTCATTACTATT
AACAATAAAAATAATCAGTAATATTAAATAG
ATTTTTAATGTGAATTATTTCCATACAACTA
CGAGACAATAATAATCATTCTCATTCGCACT
TATCTTTATAATAATCATTCTCGTTTACGTT
TATATTAATGATAATCACTATCACCATATCG
CATGATAATGAAATTAATTATCGTTATCGAT
TCTTTTAATGATAATAATTCTCATTATATTG
ATTGGTAATGAGAATAATTAACAATTAAAGA
CCGTAAAGTGATAATGATTATCATCTACATA
TACCACTATGATAATCAATATCATATGGGTT
AACATAAATGAAAATAATTATCATTACAGTA
CGTCGAATTGATAGTCGTTCTCATTACTATT
AACAATAAAAATAATCAGTAATATTAAATAG
ATTTTTAATGTGAATTATTTCCATACAACTA
CGAGACAATAATAATCATTCTCATTCGCACT

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
TATCTTTATAATAATCATTCTCGTTTACGTT
... ... mrcB fhuA fhuC fhuB fhuD
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TATATTAATGATAATCACTATCACCATATCG
... ... yahA betT betI yahC yahB betA betB
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
CATGATAATGAAATTAATTATCGTTATCGAT
... ... fepC fepG fepD fepB entS fepE
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TCTTTTAATGATAATAATTCTCATTATATTG
... ... galE galT galK galM gpmA
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ATTGGTAATGAGAATAATTAACAATTAAAGA
... ... kch yciY cls yciU oppF oppD oppC oppB oppA ychE
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
CCGTAAAGTGATAATGATTATCATCTACATA
... ... ydfO ynfO pinQ tfaQ stfQ nohQ
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
TACCACTATGATAATCAATATCATATGGGTT
... ... yoaB yoaA yeaZ yeaY yeaV yeaW yeaX rnd fadD
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
AACATAAATGAAAATAATTATCATTACAGTA
... ... insC insD yoeA yoeH
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
CGTCGAATTGATAGTCGTTCTCATTACTATT
... ... dkgA yqhD yqhC yghB metC exbD exbB
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
AACAATAAAAATAATCAGTAATATTAAATAG
... ... agaR yhaV prlF garD rnpB garK garR garL garP
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
ATTTTTAATGTGAATTATTTCCATACAACTA
... ... bfd bfr gspO gspM gspL gspK gspJ gspI gspH gspG gspF gspE gspD gspB gspA gspC
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer
CGAGACAATAATAATCATTCTCATTCGCACT
... ... yhhY yhhW yhhX ryhB
Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - repressor dimer