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