HHsearch alignment for GI: 254780991 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=99.67 E-value=1.8e-17 Score=149.39 Aligned_cols=431 Identities=18% Similarity=0.200 Sum_probs=247.3
Q ss_pred HHHCCCCCCHHHHHHHHHCCCCEEEECCCCCHHHHH----HHHCCCCCCHHHHHCCC-CCCCCHHHHCCCCCCHHHHH--
Q ss_conf 431176563387754533187247831788877888----73104442002221016-66400111000010000000--
Q gi|254780991|r 312 LVKQQYKRQDIGIIRGTFRVCGDSIEIFPSHLEDVA----WRVSMFGNDIEEISEFY-PLTGQKIRNVETIKIYANSH-- 384 (805)
Q Consensus 312 l~~~~Y~R~D~a~~RG~f~~rg~ILdsatps~Es~~----~Rie~f~deIe~I~~fD-plT~~~~~~~~~~~i~Pa~~-- 384 (805)
T Consensus 1 L~~~GY~r~~~V~~~GEFs~RG~I~DIfp~~~~~-PntqavRi~ff~D~iesIr~FdP~~~q~~~~~l~~~~l~Pa~e~~ 79 (997)
T TIGR00580 1 LVELGYERVDLVEEEGEFSVRGDILDIFPPGSEA-PNTQAVRIEFFGDEIESIREFDPVSDQRSLEELSEITLLPAKELE 79 (997)
T ss_pred CCCCCCCCCCCCCCCCCEEEECCCEEECCCCCCC-CCCCEEEEEEECCEEEEEECCCCHHHHHHHHHHHHHCCCCHHHCC
T ss_conf 9743211255201034335515000211577888-874368997217857660024881334346423420025301000
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCHHHHHC
Q ss_conf 02563678875455899899899887544332110012444477775332112014510113331144655562023302
Q gi|254780991|r 385 YVTPRPTLNTAMKYIKEELKMRLIELEKEGRLLEAQRLEQRITYDLEMLETTGSCQSIENYSRYLTGRNPGEPPPTLFEY 464 (805)
Q Consensus 385 ~v~~~e~l~~a~~~i~~el~~rl~~~~~~~~~~ea~rL~qR~~~dle~l~e~G~~~gienyS~~L~~r~~ge~P~tL~dY 464 (805)
T Consensus 80 i~~~~~~~~~~~~~~~~--~---~~~~~~~~~~~~~~L~~~~~e~l~~~~~g~~~~G~e~~lPl~~----~~G~~~L~D~ 150 (997)
T TIGR00580 80 ILLEEETRARAKQNAAR--V---EDAEKTETDKAKEILAVKILEELEALKEGKKKAGLEKFLPLFF----EDGLSSLVDY 150 (997)
T ss_pred CCCCHHHHHHHHHHHHH--H---CCCCCCCCCCHHHHHHCCCCHHHHHHHHCCCCCCHHHHCCCCE----ECCCCCCCCC
T ss_conf 36566666668778875--1---0035766411354543035235788872577442455525020----0788641102
Q ss_pred CCCCCE----EEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC--------CC
Q ss_conf 654421----321012344754454324565413332357665544432221110100121555454446--------86
Q gi|254780991|r 465 IPEDSL----LFVDESHVTIPQISGMYRGDFHRKATLAEYGFRLPSCMDNRPLRFEEWNCLRPTTIVVSA--------TP 532 (805)
Q Consensus 465 ~p~d~l----l~idesh~~~pqi~~~~~~d~~RK~~l~~~gfrlp~~~~n~pl~f~e~~~~~~~~~~~sa--------tP 532 (805)
T Consensus 151 ~~~~t~~~P~i~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~ehfl~~~~~~~~~l~~~~~veld~~k~~ 226 (997)
T TIGR00580 151 LPDNTPEAPVILLDEPERFHEAAEELQRELE----EFYEALEEAKKLINPPSEHFLARLDLSFEELVLEVLVELDRLKTE 226 (997)
T ss_pred CCCCCCCCCEEEECCHHHHHHHHHHHHHHHH----HHHHHHHHHHHCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 3354789888996175565489999999999----999877765306787213110116773555555553223123111
Q ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCCE---------ECCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 7542013220023432012446772000---------0133101688999999863023212466214789999999986
Q gi|254780991|r 533 GSWELEQCQGIIVEQIIRPTGLVDPPVE---------IRSARTQVEDVYDEINLAAQQGLRILLTVLTKRMAEDLTEYLY 603 (805)
Q Consensus 533 g~~e~e~~~~~~~eqi~rptg~idp~ie---------ir~~~~qvddl~~ei~~~~~~~~R~l~~~~tkr~~e~l~~~~~ 603 (805)
T Consensus 227 ~-------~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~r~~~ll~ 299 (997)
T TIGR00580 227 H-------KAISLSEVQLESAILSLKASEAIELAQKHSRLEFGEILAFKEELFRWLKAGFKVVLLAESESQAERLKSLLK 299 (997)
T ss_pred H-------HCCCHHHHHCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHH
T ss_conf 0-------003312332033555755034466304631024555789999999998749818999637632689999996
Q ss_pred HCCCEEEECCCCCC--HHHHHHHHHHHHCCCCCEEEEHHHHHCCCCCCCCCEEEEECCCCCCCC----CCHHHHHHHHH-
Q ss_conf 35966873257645--789999999973189869998458753578777117999628856744----46013776654-
Q gi|254780991|r 604 ERNIRVRYMHSEVK--TLERIEIIRDLRLGKFDVLVGINLLREGLDIPECGLVAILDADKEGFL----RSKTSLIQTIG- 676 (805)
Q Consensus 604 ~~~i~~~~~h~~~~--~~~r~~il~~~~~g~~diLvgt~~~akGlD~p~v~lV~i~dAD~~~f~----~~~~~~~q~~G- 676 (805)
T Consensus 300 ~~d~~~~~~~~p~~yP~~~~---~~~~~~~~~~~~-~g~~~~~gf~~~~~~la~i~~~elf~~r~~~~~~~~~~~~~~~~ 375 (997)
T TIGR00580 300 EYDIAAKVIVEPLEYPALDS---SQLLIPAVVYVL-EGGELSSGFILPTAGLAVITESELFGSRVKRRPKKKRKKSKLTS 375 (997)
T ss_pred HCCCCCCCCCCHHCCCCCCH---HHHCCHHHHHHC-CCCCCCCCEEECCCCEEEECCHHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 05885311002000210023---542012455310-23201355022255478982614675554201466666543333
Q ss_pred --HHCCC-CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC------CHHHHHH-HHHHHHHHHHHHHHHHHH
Q ss_conf --31279-9866999824898899999998788888888768871885------3023466-777665666555555554
Q gi|254780991|r 677 --RAARN-VNSKVILYADTITKSIQLAIDETTRRREKQLEHNKKHNIN------PQSVKEK-IMEVIDPILLEDAATTNI 746 (805)
Q Consensus 677 --RagR~-~~G~~il~ad~~t~~~~~ai~e~~rrr~~q~~~n~~~~i~------p~~i~k~-i~~~~~~~~~~~~~~~~~ 746 (805)
T Consensus 376 ~i~~~~~L~~Gd~VVH~----------~hGIG~F~~l~~~-~~~~g~~~DYL~l~Ya~~~k~LyvPve~~~li~rY~G~~ 444 (997)
T TIGR00580 376 KIEDLNELKPGDYVVHK----------DHGIGKFLGLEKK-LKVLGIERDYLVLEYAGEDKKLYVPVEQLDLISRYVGGE 444 (997)
T ss_pred HHHHHHCCCCCCEEEEC----------CCCCCEEHHHHHH-HHHCCCCCCEEEEEECCCCCEEEECCCHHHHHHHHCCCC
T ss_conf 21001037998877753----------3585021422321-442476524124440277866860331244553320678
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 33334312797889999999999999999741
Q gi|254780991|r 747 SIDAQQLSLSKKKGKAHLKSLRKQMHLAADNL 778 (805)
Q Consensus 747 ~~~~~~~~~~~~~~~~~i~~l~~~m~~aa~~l 778 (805)
T Consensus 445 ~~~p~L~kLGg~~W~~~K~kv~~~v~~iA~~L 476 (997)
T TIGR00580 445 GKNPELDKLGGKSWEKTKAKVKKSVKEIAAKL 476 (997)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89764102783889999999999999999999