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=99.90 E-value=4.6e-22 Score=183.76 Aligned_cols=323 Identities=21% Similarity=0.282 Sum_probs=218.3
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCCE-EEEEEECCCCHHHHHHHHHHHC---
Q ss_conf 205740266678887421588775477518888884389999999988739733-7998633764699999999971---
Q gi|254780991|r 117 LKNGKIWTPHRSWSINNHSKDITFFQMQTDYHPSGDQPAAIAQLLKGIHSREKV-QLLLGVTGSGKTFTMAKVIEAM--- 192 (805)
Q Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~f~l~~~~~P~gdQ~~Ai~~L~~~l~~g~~~-qlL~GVTGSGKTevya~lI~~~--- 192 (805)
T Consensus 485 ~~~G~af~~D---~e~~~-----~Fe~~FPfeeT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~~ 556 (997)
T TIGR00580 485 ASKGHAFPPD---DEWQA-----EFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLD 556 (997)
T ss_pred HCCCCCCCCC---HHHHH-----HHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf 1589889888---08999-----999838788977899999999997406898734652454885368888788876338
Q ss_pred C----CCEEEEECCHHHHHHHHHHHHHHCCCC--EEEEEEECCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf 9----978999316346899999999867898--3899862134444210155543210221035889999999999998
Q gi|254780991|r 193 Q----RPAIVMAPNKILAAQLYSEFKNFFPHN--AVEYFVSYYDYYQPEAYVPRTDTYIEKESSINEQIDRMRHSATRSL 266 (805)
Q Consensus 193 g----r~aLvLvPei~La~QL~~rfk~~Fp~n--~V~~f~S~~~~yqpEay~p~~d~~i~k~~s~n~~i~~~R~~a~~~l 266 (805)
T Consensus 557 gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~-------------------------~~E~~~iL~~l 611 (997)
T TIGR00580 557 GNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRS-------------------------AKEKKEILKEL 611 (997)
T ss_pred CCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC-------------------------CHHHHHHHHHH
T ss_conf 78220116896270442777889999973789816875277567-------------------------37899999997
Q ss_pred HCCCCEEEECCHHHHCCCCCHHHHHCCEEEEECCC-CCCHHHHHHHHHHCCCCCCHHHHHHHHHCCCCEEE-ECCCCCHH
Q ss_conf 54998499827789616898347722579994198-11178753234311765633877545331872478-31788877
Q gi|254780991|r 267 LERNDCIVVSSVSCIYGIGSVESYSQMIVQLKIGD-SVEQKELLSSLVKQQYKRQDIGIIRGTFRVCGDSI-EIFPSHLE 344 (805)
Q Consensus 267 ~~~~~~IVVgsrSAIfgl~~P~~~lglIIvdEehd-~~~~~~~~~~l~~~~Y~R~D~a~~RG~f~~rg~IL-dsatps~E 344 (805)
T Consensus 612 a~G~iDI~IGTH~lL-~k~v~FKdLGLlIiDEEQRFGV~~KE~lK~-----------------~~~~VDvLtlsATP--- 670 (997)
T TIGR00580 612 ASGKIDILIGTHKLL-QKDVKFKDLGLLIIDEEQRFGVKQKEKLKE-----------------LKTSVDVLTLSATP--- 670 (997)
T ss_pred HCCCEEEEECCHHHH-CCCEEEECCCCEEEECCCCCCCCHHHHHCC-----------------CCCCCCEEEEECCC---
T ss_conf 559422663010412-785468638646983143488311555300-----------------15676567633789---
Q ss_pred HHHHHHCCCCCCHHHHHCCCCCCCCHHHHCCCCCCHHHH-----HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888731044420022210166640011100001000000-----002563678875455899899899887544332110
Q gi|254780991|r 345 DVAWRVSMFGNDIEEISEFYPLTGQKIRNVETIKIYANS-----HYVTPRPTLNTAMKYIKEELKMRLIELEKEGRLLEA 419 (805)
Q Consensus 345 s~~~Rie~f~deIe~I~~fDplT~~~~~~~~~~~i~Pa~-----~~v~~~e~l~~a~~~i~~el~~rl~~~~~~~~~~ea 419 (805)
T Consensus 671 -IPRTL~MS--------------l~g~RdlS~I~TPP~~R~pv~T~v~~~~~~~-------------------------- 709 (997)
T TIGR00580 671 -IPRTLHMS--------------LSGIRDLSIIATPPEDRLPVRTFVMEYDDEL-------------------------- 709 (997)
T ss_pred -CHHHHHHH--------------HHHHHHHHHCCCCCCCCCCEEEEEECCCHHH--------------------------
T ss_conf -60558999--------------8755332210578887742488774278689--------------------------
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCCCCHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 01244447777533211201451011333114465556202330265442132101234475445432456541333235
Q gi|254780991|r 420 QRLEQRITYDLEMLETTGSCQSIENYSRYLTGRNPGEPPPTLFEYIPEDSLLFVDESHVTIPQISGMYRGDFHRKATLAE 499 (805)
Q Consensus 420 ~rL~qR~~~dle~l~e~G~~~gienyS~~L~~r~~ge~P~tL~dY~p~d~ll~idesh~~~pqi~~~~~~d~~RK~~l~~ 499 (805)
T Consensus 710 -------------------------------------------------------------------------------- 709 (997)
T TIGR00580 710 -------------------------------------------------------------------------------- 709 (997)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEECCCCCHHHHHHHHHHHHH
Q ss_conf 76655444322211101001215554544468675420132200234320124467720000133101688999999863
Q gi|254780991|r 500 YGFRLPSCMDNRPLRFEEWNCLRPTTIVVSATPGSWELEQCQGIIVEQIIRPTGLVDPPVEIRSARTQVEDVYDEINLAA 579 (805)
Q Consensus 500 ~gfrlp~~~~n~pl~f~e~~~~~~~~~~~satPg~~e~e~~~~~~~eqi~rptg~idp~ieir~~~~qvddl~~ei~~~~ 579 (805)
T Consensus 710 -----------------------------------------------------------------------~~~AI~rEL 718 (997)
T TIGR00580 710 -----------------------------------------------------------------------VREAIRREL 718 (997)
T ss_pred -----------------------------------------------------------------------HHHHHHHHH
T ss_conf -----------------------------------------------------------------------999999753
Q ss_pred HCCCCCCCC----CHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCCCCCCCCCEEE
Q ss_conf 023212466----2147899999999863596687325764578999999997318986999845875357877711799
Q gi|254780991|r 580 QQGLRILLT----VLTKRMAEDLTEYLYERNIRVRYMHSEVKTLERIEIIRDLRLGKFDVLVGINLLREGLDIPECGLVA 655 (805)
Q Consensus 580 ~~~~R~l~~----~~tkr~~e~l~~~~~~~~i~~~~~h~~~~~~~r~~il~~~~~g~~diLvgt~~~akGlD~p~v~lV~ 655 (805)
T Consensus 719 ~RgGQvFyv~Nrie~i~~~~~~l~~LVP~arIa--iaHGqM~e~eLE~~m~~F~~~~~~vLvcTTIIE~GIDIPnANTiI 796 (997)
T TIGR00580 719 LRGGQVFYVHNRIESIEKLKTQLRELVPEARIA--IAHGQMTENELEEVMLEFYKGEFDVLVCTTIIESGIDIPNANTII 796 (997)
T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEE--EEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCCCCHHHHHHHH
T ss_conf 139818998088135789999998508432678--883356845689999986268433013221465056410012686
Q ss_pred EECCCCCCCCCCHHHHHHHHHHHCC-CCCCEEEEEEC
Q ss_conf 9628856744460137766543127-99866999824
Q gi|254780991|r 656 ILDADKEGFLRSKTSLIQTIGRAAR-NVNSKVILYAD 691 (805)
Q Consensus 656 i~dAD~~~f~~~~~~~~q~~GRagR-~~~G~~il~ad 691 (805)
T Consensus 797 i~~AD~FGL----aQLYQLRGRVGRs~~~AYAYlL~~ 829 (997)
T TIGR00580 797 IDRADKFGL----AQLYQLRGRVGRSKKKAYAYLLYP 829 (997)
T ss_pred HHHHCCCCH----HHHHHCCCEECCCCCEEEEEECCC
T ss_conf 875211470----347453631205871268983347