HHsearch alignment for GI: 254780945 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=100.00 E-value=0 Score=1068.19 Aligned_cols=412 Identities=37% Similarity=0.561 Sum_probs=389.1
Q ss_pred HHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf 77655554320357678775789999863024679889999999998410013430788621442236999999733444
Q gi|254780945|r 240 LLLMRKQFKKEIGIPINVEGKIAQKILRNIPFSPTKSQESAIKDILQDMSQKNRMLRILQGDVGSGKTLVALIAMAAAVE 319 (700)
Q Consensus 240 l~~~r~~~~~~~~~~~~~~~~~~~~f~~~LPF~LT~~Q~~ai~eI~~Dl~~~~pM~RLLQGDVGSGKTiVA~~A~l~~~~ 319 (700)
T Consensus 476 Li~lyA~R~~~~G~af~~D~e~~~~Fe~~FPfeeT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~ 555 (997)
T TIGR00580 476 LIELYAKRKASKGHAFPPDDEWQAEFEDSFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL 555 (997)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHC
T ss_conf 99999987515898898880899999983878897789999999999740689873465245488536888878887633
Q ss_pred HH----CCEEEEEHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCC
Q ss_conf 30----54588612799999999862110145786589962464225667687762134754864111201334554444
Q gi|254780945|r 320 AG----GQAVIMAPIGILAQQHYEFIKKYTQNTQIIVEIITGNMPQAHRRKALERIAHGQAHIIIGTHALFQDSIQYYKL 395 (700)
Q Consensus 320 ~G----~Q~alMaPTEILA~QH~~~~~~~~~~~~i~v~lLtg~~~~~er~~i~~~i~~G~~~iiIGTHAL~q~~v~F~~L 395 (700)
T Consensus 556 ~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGTH~lL~k~v~FKdL 635 (997)
T TIGR00580 556 DGNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIGTHKLLQKDVKFKDL 635 (997)
T ss_pred CCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCHHHHCCCEEEECC
T ss_conf 87822011689627044277788999997378981687527756737899999997559422663010412785468638
Q ss_pred CEEEECCCCCCCHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCHHHHCCCCCCCCCCEEEEEECCCHHHHHHHH
Q ss_conf 17885210133568899874025677610101013227899997520101111023557666207999702002689999
Q gi|254780945|r 396 ILVIVDEQHRFGVQQRLKLTQKATAPHVLLMTATPIPRTLVLTSLGDIDISKITEKPAGRKPIKTVIIPINRIDEVIERL 475 (700)
Q Consensus 396 gLvViDEQHRFGV~QR~~L~~Kg~~ph~L~MtATPIPRTLal~~ygdldvS~i~e~P~gR~~I~T~~~~~~~~~~~~~~i 475 (700)
T Consensus 636 GLlIiDEEQRFGV~~KE~lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~pv~T~v~~~~~-~~~~~AI 714 (997)
T TIGR00580 636 GLLIIDEEQRFGVKQKEKLKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLPVRTFVMEYDD-ELVREAI 714 (997)
T ss_pred CCEEEECCCCCCCCHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCH-HHHHHHH
T ss_conf 646983143488311555300156765676337896055899987553322105788877424887742786-8999999
Q ss_pred HHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC-CEECCCCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCC
Q ss_conf 76310387389997120122111210146666666866371-03120146998999999999755986999980034104
Q gi|254780945|r 476 KVVLSEGKKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS-SIAIIHGRMSDIDKESVMDSFKNGTCKLLIATTVIEVG 554 (700)
Q Consensus 476 ~~~l~~g~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~-~v~~lHGkm~~~ek~~~m~~F~~g~~~iLvaTtviEVG 554 (700)
T Consensus 715 ~rEL~RgGQvFyv~Nrie--------~i~~~~~~l~~LVP~arIaiaHGqM~e~eLE~~m~~F~~~~~~vLvcTTIIE~G 786 (997)
T TIGR00580 715 RRELLRGGQVFYVHNRIE--------SIEKLKTQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFDVLVCTTIIESG 786 (997)
T ss_pred HHHHCCCCEEEEEECCCC--------CHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCC
T ss_conf 975313981899808813--------578999999850843267888335684568999998626843301322146505
Q ss_pred CCCCCCCEEEEECHHHCCHHHHHHHHHCCCCCCCCEEEEEEECC--CCCHHHHHHHHHHHHHCH---HHHHHHHHHHHCC
Q ss_conf 68887658998585254746887730116678983599997088--899879999999984142---5899999985206
Q gi|254780945|r 555 IDVVDASIIIIENAEHFGLAQLHQLRGRVGRGEEISSCILLYHP--PLSKNSYTRLSVLKNTED---GFLIAEEDLKQRK 629 (700)
Q Consensus 555 vdvpna~~mvI~~aerfGLsqLHQLRGRVGRg~~~s~c~l~~~~--~~~~~~~~Rl~~l~~~~d---Gf~iAe~Dl~lRG 629 (700)
T Consensus 787 IDIPnANTiIi~~AD~FGLaQLYQLRGRVGRs~~~AYAYlL~~~~~~Lt~~A~~RL~ai~~f~eLGaGf~iA~hDlEIRG 866 (997)
T TIGR00580 787 IDIPNANTIIIDRADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDALKRLEAIQEFSELGAGFKIALHDLEIRG 866 (997)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHCCCEECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf 64100126868752114703474536312058712689833477400145899999999730113521678863110035
Q ss_pred CCCCCCCHHCCCCCCCCCCHHHHH--HHHHHHHHHHH
Q ss_conf 300026000698744000388759--99999999999
Q gi|254780945|r 630 EGEILGIKQSGMPKFLIAQPELHD--SLLEIARKDAK 664 (700)
Q Consensus 630 ~G~~~G~~QsG~~~~~~~d~~~d~--~ll~~a~~~a~ 664 (700)
T Consensus 867 aGNLLG~eQSG----~I~~vGfdLY~~lL~eAi~~~~ 899 (997)
T TIGR00580 867 AGNLLGEEQSG----HIESVGFDLYVELLEEAIEELK 899 (997)
T ss_pred CHHHCCCCCCC----HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 50012601264----0656778999999999999987