HHsearch alignment for GI: 254780947 and conserved domain: PRK10689
>PRK10689 transcription-repair coupling factor; Provisional.
Probab=100.00 E-value=0 Score=3125.71 Aligned_cols=1125 Identities=34% Similarity=0.579 Sum_probs=1036.4
Q ss_pred HHCCCCEEEECCCCCCHHHHHHHHHHH-CCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCHHCCCCCHHHH
Q ss_conf 514886089803765227999999986-2998999929989999999999985799809985722467010048998999
Q gi|254780947|r 11 SEKYCKKITLSPVIDGTEGFILAEIAR-LGLSLVYICSDERILINLKKILTLVVPDIRVIIFPAWDCLPYDRVSPSPYVV 89 (1187)
Q Consensus 11 ~~k~~~~i~l~Gl~gs~~allla~l~~-~~rpilvI~~d~~~A~~l~~dL~~f~~~~~V~~FP~~E~LPYd~~sp~~di~ 89 (1187)
T Consensus 10 p~~aG~~~~l~gL~GSA~al~lA~l~~~~~~p~lvV~~d~~~A~~l~~dL~~f~~-~~V~~fP~wEtLPYd~~SP~~di~ 88 (1148)
T PRK10689 10 PVKAGDQRQLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTD-QMVMNLADWETLPYDSFSPHQDII 88 (1148)
T ss_pred CCCCCCEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHCCC-CCEEECCCHHCCCCCCCCCCHHHH
T ss_conf 8999971267788606999999999997099889991999999999999985489-725689721047766579986899
Q ss_pred HHHHHHHHHHHHCCCCCCCEEEEECHHHHHCCCCCHHHHHCCEEEEECCCCCCHHHHHHHHHHCCCEECCCCCCCCEEEE
Q ss_conf 99999999984124468876999566785236998668851548994097419999999999828845545217831654
Q gi|254780947|r 90 TRRLSCISNLVSFNSSKETIIVLTTVSAVMCRSVNIMSIKDYKLSIQSKDQIDMAKVIEKLETNGFQRVNAVYKVGEYAV 169 (1187)
Q Consensus 90 ~eRl~~L~~L~~~~~~~~~~IIVtt~~ALlqklpp~~~l~~~~l~L~vGd~id~~~L~~~Lv~~GY~Rv~~Ve~~GEFAv 169 (1187)
T Consensus 89 s~Rl~~L~~L~~----~~~~IvVttv~ALlqrlpP~~~l~~~~l~L~~G~~ld~d~L~~~L~~~GY~rv~~V~epGEFAv 164 (1148)
T PRK10689 89 SSRLSTLYQLPT----MQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRAQLDSAGYRHVDQVMEHGEYAT 164 (1148)
T ss_pred HHHHHHHHHHHC----CCCCEEEEEHHHHHCCCCCHHHHHHCCEEEECCCCCCHHHHHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf 999999998752----8999999768996222699899963738995878549999999999869915450588526987
Q ss_pred ECCEEEEECCCCCCCEEEECCCCEEEEEEEEECCCCCCCCCCCEEEEECCCCEECCHHHHHHHHHHHHHHCCCCHHHCHH
Q ss_conf 57475730698887268863487221015451374853122216999437732179999999999999741737001577
Q gi|254780947|r 170 RGGILDVYEPTKKYPVRLDFFGNTIDSLRLFDSSTQRTIREISIFEINTLSEVMLTSQNISRFRENYLANFGTTTQEDPL 249 (1187)
Q Consensus 170 RGgIIDIFp~~~~~PiRIEFFGDeIESIR~FDp~TQRSi~~i~~i~I~Pa~E~il~~e~i~~fr~~~r~~f~~~~~~~~i 249 (1187)
T Consensus 165 RGgIIDIFP~~~~~PvRIEFFgDEIESIR~FDp~TQRSi~~i~~i~I~Pa~E~~l~~~~i~~fr~~~re~f~~~~~~~~i 244 (1148)
T PRK10689 165 RGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHI 244 (1148)
T ss_pred ECCEEEECCCCCCCCEEEEECCCEEEEEEEECCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf 68989988899882669992497876367577010777467775999757256679899999999999873156226899
Q ss_pred HHHHHCCCCCCCHHHHHHHHHCC-CCCCCCCCCCCCEECCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 78997789878877767776148-76767334676133465-35899998899999998999998652220265567850
Q gi|254780947|r 250 YVAISQGRRYPGMEHWLPFFYQS-METIFPYLSEFCIITDP-LVKETARKRSQLIQDYYEARLQYSSDKKQYSVYKPIAP 327 (1187)
Q Consensus 250 ~e~Is~g~~~~GiE~yLPlFye~-~~tLfDYLp~~~iii~~-~~~e~~~~~~~~i~d~~e~~~~~~~~~~~~~~~~pl~P 327 (1187)
T Consensus 245 y~~is~g~~~~GiE~ylPLff~e~l~tLfDYLp~~~liv~~~~l~~~~e~~~~~i~~~~e~~-------~~d~~rp~l~p 317 (1148)
T PRK10689 245 YQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENR-------GVDPMRPLLPP 317 (1148)
T ss_pred HHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHCCCCEEEEECHHHHHHHHHHHHHHHHHHHHC-------CCCCCCCCCCH
T ss_conf 99986689745177860320265423688737777399964189999999999999999864-------67745678997
Q ss_pred HHCCCCHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCCHHCCCHHHHHHHHHHHHHC
Q ss_conf 21169989999975114608962675322224673377641466566820010011222200018589999999999867
Q gi|254780947|r 328 EKLYLNYQQFDALIQTTHKLVQMTAFNQQETAHNRVVHLNAFPGKSWVPSAVQKIESQDNWESGGRFDKFLSHVAQQAQK 407 (1187)
Q Consensus 328 e~Lyl~~~el~~ll~~~~~ii~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~~~~~~~~~g~l~~L~~~I~~~~k~ 407 (1187)
T Consensus 318 ~~L~l~~~el~~~L~~~~~i~-l~~~~~~~~~~~~~~~~~~~p----------------~~~~~~~~~~~l~~L~~~i~~ 380 (1148)
T PRK10689 318 ESLWLRVDELFSELKNWPRVQ-LKTEHLPEKAANTNLGFQKLP----------------DLAVQAQQKAPLDALRKFLES 380 (1148)
T ss_pred HHHCCCHHHHHHHHHHCCEEE-EECCCCCCCCCCCCCCCCCCC----------------CCCCCCCCHHHHHHHHHHHHH
T ss_conf 884489999999997477377-521346543456675643276----------------634200002369999999995
Q ss_pred -CCEEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCHHHHHCCCCCCEEEEECCCCCCCCC--CCEEEEECCCCCCCCCCC
Q ss_conf -98299995894589999986776488733234522455204668479998104468746--656887120013731112
Q gi|254780947|r 408 -GIKTIISASSQGALQHLIHLIESHGFKKIKKINTLTEINSLLKEEIAAVILPINQGFET--KHMILVTETDLLGKKIAR 484 (1187)
Q Consensus 408 -g~rViI~a~s~~~~eRL~elL~e~gI~~~~~~~~~~~~~~~~~~~i~i~~~~L~~GF~~--~kl~vITE~EIFG~k~~~ 484 (1187)
T Consensus 381 ~~~~vi~~~~s~g~re~L~elL~~~~i~~~~i~~-~~~---~~~~~~~l~i~~l~~GF~~~~~~lavITE~eIfG~r~~r 456 (1148)
T PRK10689 381 FDGPVVFSVESEGRREALGELLARIKIAPKRIMR-LDE---ASDRGRYLMIGAAEHGFIDTVRNLALICESDLLGERVAR 456 (1148)
T ss_pred CCCEEEEEECCHHHHHHHHHHHHHCCCCCEECCC-HHH---CCCCCEEEEECCCCCCCCCCCCCEEEEEHHHHHCHHHHC
T ss_conf 6982999968878999999999876998634166-656---256864999833445641466757998658851304321
Q ss_pred CCCCCCC-C-CCCCCCCHHHHCCCCCEEECCCCCEEEECCCCCCCCCCCCCEEEEEECCCCEEEEEHHHHHHHHHH-CCC
Q ss_conf 2122222-2-211012244403235112035542331123101456666635999986998799666752111100-367
Q gi|254780947|r 485 RVVRKKN-V-HAQSFFDSSNIEEGAIIVHAEHGIGRFVRLYSIEVSGTFHDCLELHYADNAKLFVPVENIDLISRY-STE 561 (1187)
Q Consensus 485 r~~rkk~-~-~~~~i~dl~eL~~GDyVVH~dHGIGrY~GLe~l~v~G~~~DyL~IeYa~~DkLYVPv~~l~lIskY-g~~ 561 (1187)
T Consensus 457 rr~~~rk~~~~~~~i~~l~eL~~GDyVVH~dHGIGrY~GL~~iev~G~~~DyL~LeYa~~DkLYVPVeqL~lIsKY~G~~ 536 (1148)
T PRK10689 457 RRQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYANDAKLYVPVSSLHLISRYAGGA 536 (1148)
T ss_pred CCHHHCCCCCHHHHHHHHHHCCCCCEECCCCCCEEEEECCEEEEECCCCCCEEEEEECCCCEEEEEHHHHCCEEECCCCC
T ss_conf 32010023571543213876788986221125756760418984088222259999769986985679822142114899
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHC
Q ss_conf 88853234340348999999999999999999999998874015677878467898998488888744899999998760
Q gi|254780947|r 562 ITTVTLDKLGGSAWKTRKANLKKRLEDLAQKLVDIAAKRAIHSVPPLMVSQDLYSQFIKRFPHVETEDQEKAIDAVIQDL 641 (1187)
Q Consensus 562 ~~~p~L~kLGg~~W~k~K~Kakk~v~diA~eLl~lyA~R~~~~g~~f~~d~~~~~eFe~~FpyeET~DQ~~AI~eV~~Dm 641 (1187)
T Consensus 537 ~~~p~LdKLGg~~W~k~K~Kakk~i~diA~eLl~lYA~R~~~~G~af~~d~~~~~eFe~~FpyeET~DQl~AI~eV~~DM 616 (1148)
T PRK10689 537 EENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDM 616 (1148)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 98876110256258999999999999999999999998720568867898499999996099978768999999998776
Q ss_pred CCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHHH
Q ss_conf 59885414431665432489999999875112754999824366555899999986067898335410666302567777
Q gi|254780947|r 642 SSGRLMDRLICGDVGFGKTEIALRAAFIAVMNGLQVAVIAPTTLLVRQHFRLFSERFQGFSVRIASISRFVQTKEAALHK 721 (1187)
Q Consensus 642 es~~PMDRLiCGDVGfGKTEVA~RAafkav~~gkQvavlvPTTiLa~QH~~tf~~Rf~~~pv~i~~lsRf~~~~e~~~i~ 721 (1187)
T Consensus 617 es~~PMDRLiCGDVGfGKTEVA~RAAFkav~~gkQVavlvPTTiLA~QH~~tF~~Rf~~~pv~i~~LsRf~s~ke~~~i~ 696 (1148)
T PRK10689 617 CQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMLSRFRSAKEQTQIL 696 (1148)
T ss_pred HCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH
T ss_conf 38867741567688887799999999999963980899836622379999999987641573377503888899999999
Q ss_pred HHHCCCCCEEEEECHHHHCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHCCCCCCEE
Q ss_conf 53122576089852065427852023656997222330088899886316788489995353408899997122254122
Q gi|254780947|r 722 KSITEGQVDIVIGTHALLNPKITFANLGLIIIDEEQHFGVKHKEALKETHTGVHVLTLSATPIPRTLQLAITGVRELSLI 801 (1187)
Q Consensus 722 ~~l~~G~idiviGTH~ll~~~v~f~~LgLliiDEEqrFGV~~Ke~lk~~~~~vdvLtlsATPIPRTL~msl~g~rd~S~i 801 (1187)
T Consensus 697 ~~l~~G~idIvIGTH~ll~~dv~f~~LGLlIiDEEqrFGV~~KE~lk~l~~~vdvLtltATPIPRTL~msl~G~rdlS~i 776 (1148)
T PRK10689 697 AEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSII 776 (1148)
T ss_pred HHHHCCCCCEEEHHHHHHCCCCCCCCCCEEEECCCHHCCHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHCCCCCEEEE
T ss_conf 99866998776204888669865466643786010213799999997228998789762556446999988077330221
Q ss_pred ECCCCCCCCEEEEEEECCHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
Q ss_conf 01578877537999857978989999989871885999826446928899999861654648886134674789999999
Q gi|254780947|r 802 SMPPINRIACRTSISIFDPLVVRETLMREYYRGGQSFYVCPRLSDLEKCYTFLQSEVPELKIAMAHGQMSPKNLEDKMNA 881 (1187)
Q Consensus 802 ~tpP~~R~~v~T~v~~~~~~~i~~ai~rEl~RgGQvf~v~nrv~~i~~~~~~l~~l~p~~~i~vaHGqm~~~~le~~m~~ 881 (1187)
T Consensus 777 ~tpP~~R~~v~T~v~~~~~~~i~eai~re~~rggq~~~~~~~~~~i~~~~~~~~~~~p~~~~~~~hg~m~~~~~e~~m~~ 856 (1148)
T PRK10689 777 ATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMND 856 (1148)
T ss_pred CCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHH
T ss_conf 36999898708998358729999999999981880899953254199999999974877718999899998999999999
Q ss_pred HHCCCCCEEEECCCEECCCCCCCCCEEEEECHHHCCCCHHHHHHHHCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHH
Q ss_conf 96388757976102003633223326676250235886045532210356767369999668888898899999999972
Q gi|254780947|r 882 FYEGQYDVLLSTSIVESGLDLPKANTMIVQRADMFGLAQLYQLRGRVGRSKIASFALFLLPENRPLTAAAQKRLRILQSL 961 (1187)
Q Consensus 882 F~~~~~dvLv~TtIiEsGlDip~aNTiii~~ad~~GLaqlyQlrGRVGRs~~~ayayl~~~~~~~l~~~a~kRL~ai~~~ 961 (1187)
T Consensus 857 f~~~~~~~l~~ttiie~g~dip~ant~ii~~a~~~gl~ql~qlrgrvgr~~~~ayaYll~~~~~~lt~~A~kRL~ai~~~ 936 (1148)
T PRK10689 857 FHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASL 936 (1148)
T ss_pred HHCCCCCEEEECCEEECCCCCCCCCEEEEECHHHCCHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf 97599889998978765866778847999753214557777543655778870799998678777898999999999970
Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCC---CCCCEEECCCCCCCCHHH
Q ss_conf 55652489999998511630004611155389833899999999999998288876766---665256548851167343
Q gi|254780947|r 962 NTLGAGFQLASYDLDIRGTGNLLGEEQSGHIREIGFELYQKMLEETVASIKGQKDLVES---DWSPQVLIEASVMIPESY 1038 (1187)
Q Consensus 962 ~~lGsGf~iA~~DleiRGaG~llG~~QsG~i~~vG~~ly~~ml~~av~~~kg~~~~~~~---~~~~~i~~~~~~~ip~~y 1038 (1187)
T Consensus 937 ~~lGsGf~iA~~DLeIRGaG~lLG~~QsG~i~~vG~~lY~~mL~~av~~lk~~~~~~~~~~~~~~~~i~l~~~a~iP~~Y 1016 (1148)
T PRK10689 937 EDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDF 1016 (1148)
T ss_pred CCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCCCCCCCHHH
T ss_conf 67764399999877227785678864563155506999999999999998667877643345667059548776389465
Q ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEEECCCCCCC
Q ss_conf 89988899999987508998999999999776248898899999999999999998697599960985999963888889
Q gi|254780947|r 1039 VSDINLRLSLYRRLGNITDHADISHFKEEMVDRFGPLPIEVIHLLKVVFLKLLCRIANIDKMDIGLKGIIIQFRHKTFSN 1118 (1187)
Q Consensus 1039 i~d~~~rl~~Y~ri~~~~~~~~~~~~~~el~drfG~~P~~~~~l~~~~~lk~~~~~~~i~~i~~~~~~~~~~f~~~~~~~ 1118 (1187)
T Consensus 1017 i~d~~~rl~~Ykri~~~~~~~~~~~~~~El~DRfG~lP~~~~~L~~~~~lk~~~~~~gi~~i~~~~~~~~~~f~~~~~~~ 1096 (1148)
T PRK10689 1017 IPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLGIRKLEGNEKGGFIEFAEKNHVD 1096 (1148)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECCCEEEEEECCCCCCC
T ss_conf 69978999999998609999999999999997669997899999999999999997597189606970799966899999
Q ss_pred HHHHHHHHHHCCCEEEECCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999837880999189816999718998899999999999999863
Q gi|254780947|r 1119 PEALLQYIAQQKGKIIIRPDQNLVFDCLLPTINQRFFEAKRIITHLINMT 1168 (1187)
Q Consensus 1119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~ 1168 (1187)
T Consensus 1097 ~~~l~~~i~~~~~~~~~~~~~~l~~~~~~~~~~~r~~~~~~~~~~l~~~~ 1146 (1148)
T PRK10689 1097 PAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENA 1146 (1148)
T ss_pred HHHHHHHHHHCCCCEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999848884898899637998279998999999999999999864