Gene Index Page

Orthologous gene lists links:
Actinobacillus actinomycetemcomitans
Haemophilus influenzae
Pseudomonas aeruginosa
Shewanella putrefaciens
Salmonella typhi
Thiobacillus ferrooxidans
Vibrio cholerae
Yersinia pestis

Abstract link

McCue, L.A., Thompson, W., Carmack, C.S., Ryan, M.P., Liu, J.S.,
Derbyshire, V. and Lawrence, C.E.
Phylogenetic footprinting of transcription factor binding sites
in proteobacterial genomes NAR 2001 29:774-782. *

Study set gene list link

Known Ecoli TF-binding sites represented in the study set and predictions

* Reproduced with permission from NAR Online http://www.nar.oupjournals.org.

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aas abc abrB accB accD aceB aceE aceK ackA acnA acnB acpD acpP acrA acrD acrR acs ada add adhE adhP adiA adiY adk aefA aer agaR agaS agaZ agp ahpC ahpF aidB ais alaS aldA aldB aldH alkA alr amiA amn ampC ampD amyA ansA ansB ansP apbA aphA appA appC apt aqpZ araB araC araD araE araF araG araJ arcA arcB argA argC argD argE argG argH argI argR argS argT aroA aroB aroF aroG aroH aroK aroL aroM aroP arsR artJ artP ascG asd aslB asnA asnB asnC asnS aspA aspC aspS asr atoD atpF atpG atpI avtA b0011 b0235 b0379 b0380 b0502 b0539 b0753 b0805 b0817 b0822 b0836 b0845 b0846 b0847 b0866 b0868 b0878 b0919 b0947 b0955 b0959 b0964 b0967 b0968 b1012 b1045 b1057 b1085 b1168 b1180 b1191 b1200 b1284 b1327 b1329 b1330 b1342 b1377 b1408 b1423 b1428 b1431 b1432 b1433 b1436 b1439 b1446 b1448 b1450 b1451 b1452 b1463 b1472 b1481 b1491 b1498 b1501 b1513 b1519 b1520 b1525 b1541 b1543 b1582 b1583 b1587 b1588 b1592 b1593 b1598 b1600 b1601 b1604 b1605 b1624 b1625 b1626 b1627 b1640 b1643 b1647 b1648 b1649 b1657 b1667 b1675 b1688 b1706 b1707 b1722 b1724 b1725 b1726 b1728 b1729 b1731 b1741 b1758 b1759 b1760 b1770 b1776 b1781 b1808 b1809 b1811 b1815 b1820 b1821 b1825 b1827 b1832 b1833 b1836 b1841 b1843 b1904 b1953 b1955 b1956 b1957 b1966 b1970 b1971 b1973 b1976 b1983 b2016 b2070 b2073 b2074 b2080 b2086 b2097 b2146 b2248 b2249 b2250 b2253 b2258 b2290 b2291 b2294 b2295 b2299 b2322 b2324 b2331 b2339 b2340 b2342 b2343 b2350 b2373 b2374 b2375 b2377 b2379 b2380 b2389 b2390 b2392 b2431 b2432 b2434 b2462 b2463 b2466 b2475 b2494 b2496 b2503 b2504 b2505 b2511 b2531 b2532 b2534 b2595 b2603 b2619 b2659 b2666 b2667 b2670 b2680 b2682 b2710 b2736 b2740 b2748 b2789 b2792 b2809 b2810 b2817 b2832 b2833 b2834 b2845 b2854 b2865 b2889 b2899 b2970 b2989 b2997 b2998 b3001 b3020 b3022 b3023 b3042 b3050 b3052 b3808 b4140 b4256 bacA barA bax betI betT bfr bglX bioA bioB bioH bisC blc bolA brnQ btuB btuC btuE cadA cadB cadC caiB caiC caiF caiT carA cbl cbpA cca cchB cdd cdh cdsA celA celB celC celF cfa chaA chaB cirA citA clpB clpP clpX cls cmk cmr cmtB coaA cobU codB cof corA cpdB cpsG cpxR crcA crcB creA creD crl crp csgB csgC csgD csiE cspA cspB cspD cspE cspG cspH cspI csrA cstA cstC cutA cutC cvpA cyaA cyaY cybB cybC cycA cydA cydD cynR cynT cyoA cysB cysD cysE cysH cysJ cysK cysM cysP cysQ cysS cysW cysZ cytR dacA dacB dacC dacD dadA dam damX dapA dapB dapF dbpA dcd dcm dcp dctA dcuA dcuB dcuC ddg ddlA deaD dedA def degQ degS deoA deoB deoC deoD deoR dfp dgkA dgt dinG dinI dinP div dksA dld dmsA dnaA dnaB dnaG dnaJ dnaK dnaQ dnaT dnaX dniR dppA dppB dps dsbB dsbG dsdC dsdX dsrB ebgA ebgR eco ecpD edd elaB elaD emrA emrD emrE emrK emrR endA eno entC entD entF envR epd erfK eutH evgA exuR fabA fabB fabF fabH fabI fabZ fadB fadD fadL fadR fba fbp fdhD fdhF fdnG fdoG fdrA feaB feaR fecA fecI feoA fepA fepB fepD fepE fes ffh fhiA fhlA fhuA fhuC fhuE fhuF fimA fimB fimZ fixA fixC fkpA fldA fldB flgA flgB flgG flgH flgK flgM flhB flhD fliA fliC fliD fliE fliF fliL fliO fliY fnr focA folA folC folD folE folX fpr frdA frr fruB fruR frwC fsr ftn ftsJ ftsK ftsN ftsY ftsZ fucA fucK fucP fucR fumA fumB fumC fur gabP galE galF galP galR galS galU gapA gapC_1 gatD gatR_1 gatR_2 gatY gcd gcl gcvA gcvP gcvR gcvT gdhA gef ggt gidA gidB glcC glcD glgB glgS glk glmS glmU glnA glnB glnD glnH glnK glnL glnP glnS gloA glpA glpD glpE glpF glpT glpX gltA gltJ gltP gltS gltX glyA glyQ gmhA gmk gnd gntK gntP gntR gntT gor gpmA gppA gpt greA greB grxA grxB grxC gshA gsk gsp gst guaA guaB guaC gutM gyrA hcaA1 hcaT hdeD helD hemA hemB hemC hemG hemH hemL hemM hemN hepA hflB hflK hflX hfq himD hisG hisJ hisQ hisS hlpA hlyE hmpA hnr hns holC holD holE hpt hrpA hsdM hsdR hslJ hslV htgA htpG htpX htrA htrB htrL hupA hupB hyaA hycA hycB hydH hydN hyfA hypA hypF iap ibpA ibpB icdA iciA iclR idnK idnR idnT ilvB ilvC ilvD ilvG_1 ilvI ilvY imp inaA infA ispB katE katG kbl kch kdgT kdpA kdtA kduI kgtP kup lacA lacI lacY lacZ lamB lasT ldcC ldhA lepA leuA leuO leuS lexA lgt lhr lig lipA lipB livH livJ livK lldP lolA lon lpdA lpp lpxC lrhA lrp lysA lysC lysP lysR lysU malE malF malI malK malM malP malS malT malX malZ manA manX manY maoC map marR mazG mbhA mdaB mdh mdoB mdoG melA melB melR menA menD menF menG mesJ metA metB metC metE metF metG metH metJ metK metR mfd mglA mglB mgsA mgtA mhpA mhpT minC mioC mlc mltA mltB mltC moaA mobA modA modE modF moeA mog mopB motA mrcA mrcB mreB mreC mrp mrr msbB mscL msrA msyB mtlA mtlD mtr murA murB murC mutH mutM mutS mutT mutY mviN nac nadA nadB nadC nadE nagA nagB nagD nagE nanA nanT napF narG narK narP narQ narU narX narZ ndh ndk nfnB nfo nhaA nhaB nhaR nirB nirC nlp nlpC nlpD nrdA nrdB nrdD nrdG nrdH nrfA nrfE ntpA nuoA nuoC nuoM nuoN nupC nupG ompA ompC ompR ompT ompX oppA oppB oraA osmB osmC osmE osmY otsB oxyR pabB pabC panB panD parC pbpG pckA pcnB pdhR pdxB pdxH pdxK pdxY pepA pepB pepD pepE pepN pepQ pepT perM perR pfkA pfkB pflA pflB pflD pfs pgi pgk pgpB pgsA pheA pheP pheS phnA phnB phnC phnE phnL phoB phoE phoP phoR pitA pitB pldA pldB plsB plsC plsX pmbA pmrD pncB pnp pntA polA polB potA potF poxB ppa ppc ppdA ppdD pphA pphB ppiA ppiB ppiC ppk ppsA pqiA prfB prfC priA priC prkB prlC proB proC proP proS proV proX proY prpB prpR prsA psd psiF pspA pspB pspE pspF pssA pssR pstB pstC pstS pta pth ptr ptrB ptsG ptsH ptsN purA purC purE purH purL purM purR purT purU putA putP pykA pykF pyrC pyrD pyrE pyrF pyrG pyrH qor queA radC rbfA rbsD rbsK rcsA rcsC rcsF recA recN recQ relA rep rfaD rfaH rfaQ rfaZ rfbA rfbB rfe rhaB rhaD rhaS rhaT rhlB rhlE rho ribA ribB ribE ribH rimJ rimK rimL rmf rna rnb rnc rnd rne rnhA rnk rnt rob rph rpiA rpiB rpiR rplJ rplK rplL rplM rplN rplT rplU rplY rpmB rpmE rpmF rpmI rpoB rpoC rpoD rpoE rpoH rpoN rpoS rpoZ rpsA rpsB rpsF rpsG rpsJ rpsL rpsM rpsO rpsP rpsT rpsU rspA rstA rsuA rtcB rtcR rtn ruvA sanA sapA sbcB sbcD sbmA sbmC sbp sdaA sdaB sdaC sdhC sdiA secA secB secE secG selA selD seqA serA serB serC serS sfcA sfhB sfmA sfmC sgaT sgcA sgcC sgcX shiA slpA slt slyA slyB slyD slyX smf_1 smf_2 smp smpA smpB sms smtA sodA sodB sodC sohB solA soxR soxS speB speC speE speF sppA spr sprT spy srlA srlR ssb sseB sspA stpA sucC sufI sugE suhB sulA surA syd tag talA talB tar tbpA tdcA tdcB tdk tehA tesA tesB tgt thdF thiC thiG thiL thiM thrA thrS tig tktA tldD tnaA tnaB tolA tolB tolC tonB topA torC torR torS torT tpiA tpx treA treB treC treF treR trg trmA trpE trpR trxA trxB trxC tsf tsr tsx ttdA ttk tufA tufB tus tyrB tyrP tyrR tyrS ubiC ubiE ubiG ubiX ucpA udhA udk udp ugd ugpA ugpB uhpA uhpT umuD ung upp uraA usg ushA uspA uvrA uvrB uvrC uvrD uvrY uxaB uxaC uxuA uxuB uxuR vacJ wcaA wcaJ wcaK wecD wrbA wza wzzB xapA xapB xapR xasA xerD xseA xseB xthA xylA xylB xylE xylF xylG xylR yaaA yaaF yaaH yaaI yaaJ yaaU yabB yabF yabH yabI yabM yabN yacE yacH yacL yadC yadD yadE yadF yadG yadI yadN yadQ yadR yaeD yaeG yaeH yaeM yaeO yaeQ yaeS yafA yafB yafC yafD yafH yafJ yafK yafM yafV yagU yahD yahK yahN yahO yaiA yaiB yaiC yaiD yaiE yaiH yaiM yaiT yaiU yajB yajD yajF yajG yajI yajK yajO yajQ yajR ybaB ybaC ybaD ybaE ybaJ ybaK ybaL ybaN ybaO ybaP ybaR ybaS ybaU ybaV ybaW ybaX ybaY ybaZ ybbA ybbB ybbI ybbK ybbL ybbQ ybbS ybbT ybbU ybbX ybbY ybcI ybcL ybcQ ybcY ybdA ybdF ybdG ybdH ybdJ ybdK ybdL ybdN ybdO ybdQ ybdR ybdS ybeB ybeC ybeD ybeF ybeJ ybeK ybeL ybeQ ybeW ybeX ybeZ ybfA ybfE ybfF ybfM ybfN ybgA ybgC ybgE ybgH ybgI ybgR ybhA ybhB ybhC ybhE ybhH ybhI ybhK ybhL ybhP ybhQ ybiF ybiH ybiI ybiJ ybiK ybiN ybiP ybiS ybiT ybiU ybjC ybjD ybjE ybjG ybjM ybjN ybjO ybjP ybjW ybjX ycaC ycaD ycaL ycaN ycaO ycaP ycaQ ycaR ycbB ycbC ycbG ycbK ycbP ycbQ ycbR ycbW ycbY yccA yccF ycdC ycdO ycdS ycdW ycdX ycdZ yceA yceB yceC yceD yceE yceF yceK yceL yceP ycfD ycfF ycfJ ycfQ ycfR ycfS ycfU ycgB ycgL ycgN ycgR ycgW ychE ychF ychH ychJ ychK ychM ychN ychP yciA yciC yciD yciF yciG yciI yciK yciL yciN yciR yciS yciV yciW ycjD ycjG ycjI ycjJ ycjL ycjW ycjX ycjZ ydaA ydaD ydaJ ydaL ydaO ydbA_1 ydbA_2 ydbC ydbH ydbK ydcF ydcG ydcN yddA yddE yddG ydeA ydeB ydeD ydeF ydeI ydeJ ydeK ydeV ydeW ydfA ydfG ydfH ydfI ydgA ydgC ydgR ydhA ydhB ydhC ydhD ydhE ydhO ydiA ydiC ydiJ ydiS ydjA yeaA yeaD yeaF yeaG yeaH yeaL yeaM yeaN yeaQ yeaR yeaS yeaT yeaU yeaV yeaX yeaZ yebA yebE yebF yebG yebH yebK yebU yecA yecD yecF yecG yecH yecI yecK yecM yedA yedD yedE yedI yedL yedU yedW yeeA yeeF yeeX yegD yegE yegH yegQ yegT yegW yehR yehU yehV yehZ yeiE yeiG yeiH yeiK yeiO yeiP yeiQ yeiR yejA yejG yejH yejK yejL yfaD yfaH yfaO yfbK yfbS yfcB yfcC yfcE yfcF yfcG yfcI yfcU yfdC yfeC yfeH yfeK yfeN yfeR yfeT yfeU yffB yffG yffH yfgA yfgB yfhB yfhD yfhE yfhG yfhH yfhK yfhL yfhO yfiD yfiE yfiF yfiK yfiM yfjB yfjI ygaA ygaC ygaD ygaG ygaM ygaU ygbA ygbE ygbI ygbL ygcA ygcB ygcF ygcM ygdH ygdL ygdP ygeA ygeG ygeH ygeX ygfA ygfB ygfE ygfF ygfO ygfT ygfU ygfY ygfZ yggA yggB yggE yggG yggH yggJ yggM yggN yggR yggS yghA yghB yghK ygiD ygiE ygiF ygiG ygiH ygiM ygiP ygiR ygiW ygiX ygjD ygjF ygjG ygjH ygjI ygjL ygjN ygjQ ygjR ygjT ygjU ygjV yhaG yhaH yhaJ yhaK yhaM yhaO yhaP yhaQ yhbC yhbE yhbL yhbM yhbP yhbQ yhbT yhbU yhbW yhbX yhbY yhcB yhcC yhcG yhcJ yhcK yhcL yhcM yhcN yhcO yhcR yhcS yhdA yhdG yhdH yhdJ yhdN yhdR yhdT yhdU yhdV yhdW yhdY yheA yheO yheR yheS yhfA yhfC yhfK yhfL yhfM yhfZ yhgE yhgF yhgH yhgI yhgN yhhA yhhF yhhK yhhM yhhN yhhP yhhQ yhhU yhhW yhhX yhhY yhhZ yhiD yhiI yhiN yhiO yhiP yhiR yhiU yhjA yhjB yhjC yhjD yhjE yhjG yhjJ yhjK yhjR yhjS yhjV yhjW yhjX yhjY yiaD yiaE yiaF yiaG yiaH yiaI yiaJ yiaK yiaM yiaT yiaU yiaY yibD yibF yibK yibL yibN yibO yibQ yicC yicE yicF yicG yicH yicJ yicL yidA yidC yidE yidH yidK yidQ yidX yidY yieE yieG yieH yieJ yieM yieN yieP yifB yifE yifK yifM_2 yigC yigE yigG yigI yigJ yigK yigL yigM yigN yihA yihD yihE yihG yihI yihK yihL yihN yihQ yihU yihV yihX yiiF yiiG yiiM yiiP yiiQ yiiR yiiU yijC yijO yijP yjaB yjaD yjaE yjaI yjbA yjbB yjbC yjbD yjbE yjbF yjbJ yjbK yjbN yjbQ yjcB yjcC yjcD yjcE yjcH yjcO yjcQ yjcR yjcS yjcW yjcX yjdB yjdE yjdF yjdH yjdL yjeA yjeB yjeF yjeH yjeI yjeJ yjeM yjeN yjeQ yjeR yjeS yjeT yjfA yjfG yjfH yjfI yjfK yjfN yjfP yjfQ yjfR yjfY yjgA yjgB yjgD yjgH yjgI yjgK yjgN yjgP yjgR yjhB yjhF yjhI yjhP yjhU yjiA yjiE yjiH yjiJ yjiO yjiP yjiQ yjiR yjiT yjiU yjiW yjiX yjiY yjjB yjjI yjjK yjjN yjjP yjjQ yjjT yjjU yjjV ykfC ykfD ykgA ykgB ykgC ykgD ykgE ykgJ ykgM ylaB ylaC ylaD ylbC ylbE ylcA ylcB yleA yleB yliG yliI yliJ yljA ymcC ymdD ymfC ymgE ynaF ynaJ yneH yneJ ynfL ynfM ynhG yniC yoaE yoaF yodB yohC yohD yohF yohI yohJ yohL yohM yojH yojI yojL yojN yqaB yqcD yqcE yqeF yqeI yqgA yqgC yqhA yqhC yqhD yqhE yqiE yqjA yqjC yqjF yqjG yqjH yqjI yraI yraL yraM yrbA yrbF yrbG yrbL yrdA yrdD yrfD yrfE yrfF yrhB ysgA ytfE ytfF ytfG ytfH ytfJ ytfK ytfL ytfM ytfQ ytfR zipA zntA zwf



If you like an electronic copy of our entire data set, please send an email request to mccue@wadsworth.org

Bayesian Bioinformatics Program at the Biometrics Laboratory of Wadsworth Center.            

Click here to access predictions described in: L.A. McCue, W. Thompson, C.S. Carmack, and C.E. Lawrence. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Research, in press.