Known Ecoli TF-binding Sites Represented in the Study Set and Predictions


For each of these transcription factors, links are provided to those E.coli genes for which our most probable motif prediction corresponded with a documented site for that transcription factor. Links are also provided to those E.coli genes for which the most probable motif prediction was detected by Scan as being a probable site for that transcription factor. The clustered models used in the Scans for each transciption factor are also provided.

Transcription Factor Sites Detected in Study Set Predictions Additional Probable Sites in Predictions Clustered Models
ada ada aidB alkA nuoN yieG yieH ada.16.palindrome.sn
araC araB araE araJ araB araE araJ araC.17.palindrome.sn
arcA glcC gltA lpdA sodA b1450 b2290 gltA ndk sdhC yjiT yjjP arcA.16.palindrome.sn
argP (iciA) dnaA dnaA argP.16.palindrome.sn
argR argA argC argD argG argI argR carA argA argE argR artJ mdh yjgD argR.16.palindrome.sn
carP N/A N/A N/A
cpxR cpxR htrA ppiA htrA nfnB ybhP ybhQ cpxR.16.palindrome.sn
crp ansB araB cdd cyaA cytR deoC flhD glpA glpD glpF lacZ malE malS melA mtlA nupG proP srlA tdcA tsx udp uxuA aspA b1541 b4140 gcd malS mglB mltB mtlA nanA srlA uxuA yaeG yahN ycdZ yhcS yjcB yjcC yjiY yjjI ylaD yqeF ysgA crp.16.palindrome.sn
cspA gyrA N/A N/A
cynR cynR tehA cynR.16.palindrome.sn
cysB cysB cysK N/A cysB.16.palindrome.sn
cytR cytR nupG tsx deaD yceL cytR.16.palindrome.sn
deoR N/A N/A N/A
dnaA N/A N/A N/A
dgsA (mlc) malT manX mlc ptsH mlc ptsG dgsA.16.palindrome.sn
fadR fadB fadD iclR deoB fadR kdpA metH ygjL fadR.17.palindrome.sn
fhlA fdhF hycB N/A fhlA.16.palindrome.sn
fis aldB hns ndh proP oppA fis.16.palindrome.sn
flhCD N/A N/A N/A
fnr cydA fdnG narK nirB b2504 cydA hmpA narX ung yciC yciD yfiD yjhB ykgA fnr.16.palindrome.sn
fruR epd fruB pfkA ppsA adhE b2389 glk ychE yeeX yeiO fruR.16.palindrome.sn
fur cirA fepA fepB fur sodA tonB adhE b0805 b1451 b1452 b1688 entC fecI fepA fur gpmA priC tonB ychE yfiF yhhX yhhY yojI fur.17.palindrome.sn
galR galE galP galS gntK galR.16.palindrome.sn
gcvA gcvA gcvT N/A gcvA.16.palindrome.sn
glpR glpA glpD glpF gcd nanA yddG yhaG yiiU yjjI glpR.16.palindrome.sn
iclR aceB aceB iclR.16.palindrome.sn
ihf focA himD ilvG_1 ndh ompR ybaL ihf.16.palindrome.sn
ilvY ilvC ilvY yafB ilvY.16.palindrome.sn
lacI N/A N/A N/A
lexA b1741 dinI lexA polB recA recN ruvA sulA umuD uvrA uvrD yjiW b0959 b1808 b1809 dinP sbmC yebG lexA.16.palindrome.sn
lrp dadA gcvT lrp lysU ompC ilvB lysU lrp.17.palindrome.sn
malT malP N/A N/A
marR marR guaB ptsN xseA ydeB marR.16.palindrome.sn
melR melA melR melR.17.palindrome.sn
metJ metA metC metE metF metJ abc bioA bioB metB metR yaeD ybdH ybdL yjaB metJ.16.palindrome.sn
metR glyA ycaN metR.17.palindrome.sn
modE dmsA modA b0817 b2998 dmsA ybhK modE.16.palindrome.sn
nagC glmU manX nagB fimA glmU nagE ybfM yjiT nagC.17.palindrome.sn
narL frdA narK frdA gltP yedE yjeA narL.17.palindrome.sn
narP N/A N/A N/A
ntrC glnA glnH glnL glnH glnK yihK ntrC.17.palindrome.sn
ompR fadL b2666 b2667 glpE yadN yegH ompR.17.palindrome.sn
oxyR dps katG oxyR b2505 kdgT mdoG ygjG oxyR.17.palindrome.sn
pdhR pdhR exuR glcC glcD lldP yadQ ybaW pdhR.17.palindrome.sn
phoB phoB phoE pstS ugpB phoE ribA sbcD phoB.16.palindrome.sn
purR cvpA purA purE purH purL purM purT pyrC pyrD purH ycdO yfhD yicE purR.16.palindrome.sn
rhaR rhaS clpB ybdF rhaR.17.palindrome.sn
rhaS N/A N/A N/A
soxR soxS soxR soxR.16.palindrome.sn
soxS sodA maoC ycdS ydbH soxS.17.palindrome.sn
torR torC hpt leuO napF yhfL yiiG torR.16.palindrome.sn
trpR mtr trpE trpR yciV trpR.16.palindrome.sn
tyrR aroF aroG aroL aroP tyrP tyrR adiY b1841 yadG tyrR.16.palindrome.sn



Click here to download the raw data file for all the clustered models used in the scans.

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Bayesian Bioinformatics Program at the Biometrics Laboratory of Wadsworth Center.