HHsearch alignment for GI: 254780947 and conserved domain: TIGR00580

>TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=100.00  E-value=0  Score=2826.43  Aligned_cols=934  Identities=40%  Similarity=0.673  Sum_probs=836.0

Q ss_pred             HHHCCCEECCCCCCCCEEEEECCEEEEECCCCCCC----EEEECCCCEEEEEEEEE-CCCCCCCCCCCEEEEECCCC--E
Q ss_conf             99828845545217831654574757306988872----68863487221015451-37485312221699943773--2
Q gi|254780947|r  150 LETNGFQRVNAVYKVGEYAVRGGILDVYEPTKKYP----VRLDFFGNTIDSLRLFD-SSTQRTIREISIFEINTLSE--V  222 (1187)
Q Consensus       150 Lv~~GY~Rv~~Ve~~GEFAvRGgIIDIFp~~~~~P----iRIEFFGDeIESIR~FD-p~TQRSi~~i~~i~I~Pa~E--~  222 (1187)
T Consensus         1 L~~~GY~r~~~V~~~GEFs~RG~I~DIfp~~~~~PntqavRi~ff~D~iesIr~FdP~~~q~~~~~l~~~~l~Pa~e~~i   80 (997)
T TIGR00580         1 LVELGYERVDLVEEEGEFSVRGDILDIFPPGSEAPNTQAVRIEFFGDEIESIREFDPVSDQRSLEELSEITLLPAKELEI   80 (997)
T ss_pred             CCCCCCCCCCCCCCCCCEEEECCCEEECCCCCCCCCCCEEEEEEECCEEEEEECCCCHHHHHHHHHHHHHCCCCHHHCCC
T ss_conf             97432112552010343355150002115778888743689972178576600248813343464234200253010003


Q ss_pred             ECCHHHHHHHHHHHHHHCCCCHHH------------CHHHHHHHCCCCCCCHHHHHHHHHCC-CCCCCCCCCCCCE----
Q ss_conf             179999999999999741737001------------57778997789878877767776148-7676733467613----
Q gi|254780947|r  223 MLTSQNISRFRENYLANFGTTTQE------------DPLYVAISQGRRYPGMEHWLPFFYQS-METIFPYLSEFCI----  285 (1187)
Q Consensus       223 il~~e~i~~fr~~~r~~f~~~~~~------------~~i~e~Is~g~~~~GiE~yLPlFye~-~~tLfDYLp~~~i----  285 (1187)
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~~e~l~~~~~g~~~~G~e~~lPl~~~~G~~~L~D~~~~~t~~~P~  160 (997)
T TIGR00580        81 LLEEETRARAKQNAARVEDAEKTETDKAKEILAVKILEELEALKEGKKKAGLEKFLPLFFEDGLSSLVDYLPDNTPEAPV  160 (997)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCHHHHHHHHCCCCCCHHHHCCCCEECCCCCCCCCCCCCCCCCCE
T ss_conf             65666666687788751003576641135454303523578887257744245552502007886411023354789888


Q ss_pred             ECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH-----HCCCCHHHHHHH-------HHCCCEEEECCCC
Q ss_conf             3465358999988999999989999986522202655678502-----116998999997-------5114608962675
Q gi|254780947|r  286 ITDPLVKETARKRSQLIQDYYEARLQYSSDKKQYSVYKPIAPE-----KLYLNYQQFDAL-------IQTTHKLVQMTAF  353 (1187)
Q Consensus       286 ii~~~~~e~~~~~~~~i~d~~e~~~~~~~~~~~~~~~~pl~Pe-----~Lyl~~~el~~l-------l~~~~~ii~l~~~  353 (1187)
T Consensus       161 i~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~----~~~~ehfl~~~~~~~~~l~~~~~veld~~k~~~~~~~l~~~  235 (997)
T TIGR00580       161 ILLDEPERFHEAA-EELQRELEEFYEALEEAKKLI----NPPSEHFLARLDLSFEELVLEVLVELDRLKTEHKAISLSEV  235 (997)
T ss_pred             EEECCHHHHHHHH-HHHHHHHHHHHHHHHHHHHCC----CCCHHHHCCCCCCCHHHHHHHHHHHHHHHHCCHHCCCHHHH
T ss_conf             9961755654899-999999999998777653067----87213110116773555555553223123111000331233


Q ss_pred             CCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCCHHCCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHHHHCCC
Q ss_conf             32222467337764146656682001001122220001858999999999986798299995894589999986776488
Q gi|254780947|r  354 NQQETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGGRFDKFLSHVAQQAQKGIKTIISASSQGALQHLIHLIESHGF  433 (1187)
Q Consensus       354 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~~~g~l~~L~~~I~~~~k~g~rViI~a~s~~~~eRL~elL~e~gI  433 (1187)
T Consensus       236 ~~~~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~ll~~~d~  303 (997)
T TIGR00580       236 QLESA------------ILSLKASEAIELAQKHSRLEFGEILAFKEELFRWLKAGFKVVLLAESESQAERLKSLLKEYDI  303 (997)
T ss_pred             HCCCC------------CCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHCCC
T ss_conf             20335------------557550344663046310245557899999999987498189996376326899999960588


Q ss_pred             CCCCCCCCHH-----HHHCCCCCCEEEEEC-CCCCCCCCC--CEEEEECCCCCCCCCCCCCCCCCCCCCCC--CCCHHHH
Q ss_conf             7332345224-----552046684799981-044687466--56887120013731112212222222110--1224440
Q gi|254780947|r  434 KKIKKINTLT-----EINSLLKEEIAAVIL-PINQGFETK--HMILVTETDLLGKKIARRVVRKKNVHAQS--FFDSSNI  503 (1187)
Q Consensus       434 ~~~~~~~~~~-----~~~~~~~~~i~i~~~-~L~~GF~~~--kl~vITE~EIFG~k~~~r~~rkk~~~~~~--i~dl~eL  503 (1187)
T Consensus       304 ~~~~~~~p~~yP~~~~~~~~~~~~~~~~~g~~~~~gf~~~~~~la~i~~~elf~~r~~~~~~~~~~~~~~~~~i~~~~~L  383 (997)
T TIGR00580       304 AAKVIVEPLEYPALDSSQLLIPAVVYVLEGGELSSGFILPTAGLAVITESELFGSRVKRRPKKKRKKSKLTSKIEDLNEL  383 (997)
T ss_pred             CCCCCCCHHCCCCCCHHHHCCHHHHHHCCCCCCCCCEEECCCCEEEECCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             53110020002100235420124553102320135502225547898261467555420146666654333321001037


Q ss_pred             CCCCCEEECCCCCEEEECCCC-CCCCCCCCCEEEEEECCCCE-EEEEHHHHHHHHHH-CCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             323511203554233112310-14566666359999869987-99666752111100-3678885323434034899999
Q gi|254780947|r  504 EEGAIIVHAEHGIGRFVRLYS-IEVSGTFHDCLELHYADNAK-LFVPVENIDLISRY-STEITTVTLDKLGGSAWKTRKA  580 (1187)
Q Consensus       504 ~~GDyVVH~dHGIGrY~GLe~-l~v~G~~~DyL~IeYa~~Dk-LYVPv~~l~lIskY-g~~~~~p~L~kLGg~~W~k~K~  580 (1187)
T Consensus       384 ~~Gd~VVH~~hGIG~F~~l~~~~~~~g~~~DYL~l~Ya~~~k~LyvPve~~~li~rY~G~~~~~p~L~kLGg~~W~~~K~  463 (997)
T TIGR00580       384 KPGDYVVHKDHGIGKFLGLEKKLKVLGIERDYLVLEYAGEDKKLYVPVEQLDLISRYVGGEGKNPELDKLGGKSWEKTKA  463 (997)
T ss_pred             CCCCEEEECCCCCCEEHHHHHHHHHCCCCCCEEEEEECCCCCEEEECCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             99887775335850214223214424765241244402778668603312445533206788976410278388999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCHH
Q ss_conf             99999999999999999988740156778784678989984888887448999999987605988541443166543248
Q gi|254780947|r  581 NLKKRLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDLSSGRLMDRLICGDVGFGKT  660 (1187)
Q Consensus       581 Kakk~v~diA~eLl~lyA~R~~~~g~~f~~d~~~~~eFe~~FpyeET~DQ~~AI~eV~~Dmes~~PMDRLiCGDVGfGKT  660 (1187)
T Consensus       464 kv~~~v~~iA~~Li~lyA~R~~~~G~af~~D~e~~~~Fe~~FPfeeT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKT  543 (997)
T TIGR00580       464 KVKKSVKEIAAKLIELYAKRKASKGHAFPPDDEWQAEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKT  543 (997)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHH
T ss_conf             99999999999999999987515898898880899999983878897789999999999740689873465245488536


Q ss_pred             HHHHHHHHHHHCCC----CEEEEEECHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHCCCCCEEEEECH
Q ss_conf             99999998751127----54999824366555899999986067898335410666302567777531225760898520
Q gi|254780947|r  661 EIALRAAFIAVMNG----LQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHKKSITEGQVDIVIGTH  736 (1187)
Q Consensus       661 EVA~RAafkav~~g----kQvavlvPTTiLa~QH~~tf~~Rf~~~pv~i~~lsRf~~~~e~~~i~~~l~~G~idiviGTH  736 (1187)
T Consensus       544 EVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGTH  623 (997)
T TIGR00580       544 EVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIGTH  623 (997)
T ss_pred             HHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCH
T ss_conf             88887888763387822011689627044277788999997378981687527756737899999997559422663010


Q ss_pred             HHHCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHCCCCCCEEECCCCCCCCEEEEEE
Q ss_conf             65427852023656997222330088899886316788489995353408899997122254122015788775379998
Q gi|254780947|r  737 ALLNPKITFANLGLIIIDEEQHFGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLISMPPINRIACRTSIS  816 (1187)
Q Consensus       737 ~ll~~~v~f~~LgLliiDEEqrFGV~~Ke~lk~~~~~vdvLtlsATPIPRTL~msl~g~rd~S~i~tpP~~R~~v~T~v~  816 (1187)
T Consensus       624 ~lL~k~v~FKdLGLlIiDEEQRFGV~~KE~lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~pv~T~v~  703 (997)
T TIGR00580       624 KLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLPVRTFVM  703 (997)
T ss_pred             HHHCCCEEEECCCCEEEECCCCCCCCHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEE
T ss_conf             41278546863864698314348831155530015676567633789605589998755332210578887742488774


Q ss_pred             ECCHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCE
Q ss_conf             57978989999989871885999826446928899999861654648886134674789999999963887579761020
Q gi|254780947|r  817 IFDPLVVRETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNAFYEGQYDVLLSTSIV  896 (1187)
Q Consensus       817 ~~~~~~i~~ai~rEl~RgGQvf~v~nrv~~i~~~~~~l~~l~p~~~i~vaHGqm~~~~le~~m~~F~~~~~dvLv~TtIi  896 (1187)
T Consensus       704 ~~~~~~~~~AI~rEL~RgGQvFyv~Nrie~i~~~~~~l~~LVP~arIaiaHGqM~e~eLE~~m~~F~~~~~~vLvcTTII  783 (997)
T TIGR00580       704 EYDDELVREAIRRELLRGGQVFYVHNRIESIEKLKTQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFDVLVCTTII  783 (997)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHH
T ss_conf             27868999999975313981899808813578999999850843267888335684568999998626843301322146


Q ss_pred             ECCCCCCCCCEEEEECHHHCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             03633223326676250235886045532210356767369999668888898899999999972556524899999985
Q gi|254780947|r  897 ESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRILQSLNTLGAGFQLASYDLD  976 (1187)
Q Consensus       897 EsGlDip~aNTiii~~ad~~GLaqlyQlrGRVGRs~~~ayayl~~~~~~~l~~~a~kRL~ai~~~~~lGsGf~iA~~Dle  976 (1187)
T Consensus       784 E~GIDIPnANTiIi~~AD~FGLaQLYQLRGRVGRs~~~AYAYlL~~~~~~Lt~~A~~RL~ai~~f~eLGaGf~iA~hDlE  863 (997)
T TIGR00580       784 ESGIDIPNANTIIIDRADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDALKRLEAIQEFSELGAGFKIALHDLE  863 (997)
T ss_pred             HCCCCHHHHHHHHHHHHCCCCHHHHHHCCCEECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCC
T ss_conf             50564100126868752114703474536312058712689833477400145899999999730113521678863110


Q ss_pred             HCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH--------CCCCCCCCCC--CCEEECCCCCCCCHHHCCCHHHHH
Q ss_conf             116300046111553898338999999999999982--------8887676666--525654885116734389988899
Q gi|254780947|r  977 IRGTGNLLGEEQSGHIREIGFELYQKMLEETVASIK--------GQKDLVESDW--SPQVLIEASVMIPESYVSDINLRL 1046 (1187)
Q Consensus       977 iRGaG~llG~~QsG~i~~vG~~ly~~ml~~av~~~k--------g~~~~~~~~~--~~~i~~~~~~~ip~~yi~d~~~rl 1046 (1187)
T Consensus       864 IRGaGNLLG~eQSG~I~~vGfdLY~~lL~eAi~~~~~~yraaa~~~~-~~~~e~~~~~~I~L~~~afIP~dYI~~~~~rl  942 (997)
T TIGR00580       864 IRGAGNLLGEEQSGHIESVGFDLYVELLEEAIEELKDDYRAAADGQK-PPKLEEAKEVDIELPYSAFIPDDYIADDELRL  942 (997)
T ss_pred             CCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCEEECCCCCCCCCHHHHHHHHHH
T ss_conf             03550012601264065677899999999999998755555421688-41003665634614741148821113189999


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCEEEE
Q ss_conf             9999875089989999999997762488988999999999999999986975999
Q gi|254780947|r 1047 SLYRRLGNITDHADISHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDKMD 1101 (1187)
Q Consensus      1047 ~~Y~ri~~~~~~~~~~~~~~el~drfG~~P~~~~~l~~~~~lk~~~~~~~i~~i~ 1101 (1187)
T Consensus       943 ~~YkRi~~~~~~~E~~~i~~El~DRFG~~P~e~~~L~~~a~lK~~a~~l~i~~l~  997 (997)
T TIGR00580       943 ELYKRIASAETEEEVEKIRDELIDRFGPLPEEVEELLAVARLKLLARKLGIEKLK  997 (997)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             9978776226975899999975114678707899999999999999771666689