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