HHsearch alignment for GI: 254780327 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=92.14 E-value=0.72 Score=26.50 Aligned_cols=213 Identities=25% Similarity=0.272 Sum_probs=112.8
Q ss_pred HHHHCCCCEEEECCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHCCCCCC--H
Q ss_conf 98526973161089378975545851568621123489999997302484312566434889983032000013430--5
Q gi|254780327|r 308 TLFLRNRDYIVNRDEVVIIDEFTGRMMPGRRYSDGQHQALEAKERVKIQPENQTLSSITFQNYFLKYRKLSGMTGTA--S 385 (890)
Q Consensus 308 ~~~~~d~~Yiv~~~~v~ivDe~TGr~~~gr~~~~GlhQaieaKe~v~i~~e~~t~a~it~qn~Fr~y~kl~GmTGTa--~ 385 (890)
T Consensus 624 ~lL~k~v~FK--dLGLlIiDEE-------QRFG------V~~KE~lK~~~~~V--------------Dv-LtlsATPIPR 673 (997)
T TIGR00580 624 KLLQKDVKFK--DLGLLIIDEE-------QRFG------VKQKEKLKELKTSV--------------DV-LTLSATPIPR 673 (997)
T ss_pred HHHCCCEEEE--CCCCEEEECC-------CCCC------CCHHHHHCCCCCCC--------------CE-EEEECCCCHH
T ss_conf 4127854686--3864698314-------3488------31155530015676--------------56-7633789605
Q ss_pred HHHHHHHHHHCCCEEEECCCC--CEEEEECHHHHCCCHHHHHHHHHHHHHH--HHHCCCEEEEEEHHHHHHHHHHHHHHH
Q ss_conf 489999987199679807899--6224302034223778899999999999--974099079861116789999999986
Q gi|254780327|r 386 TEAEELANIYNLDVIEVPTNV--PVIRIDEHDEIYRTSEEKYAAIIAEIID--SHKKGQPVLVGTPSIEKSEYLASQLRK 461 (890)
Q Consensus 386 te~~Ef~~iY~l~v~~iPtnk--p~~r~d~~d~v~~t~~~k~~ai~~~i~~--~~~~grpvLvgt~sve~Se~ls~~L~~ 461 (890)
T Consensus 674 TL~MSl~g~RdlS~I~TPP~~R~pv~T-----~v----~~~~~~~~~~AI~rEL~RgGQ-vFyv~Nrie~i~~~~~~l~~ 743 (997)
T TIGR00580 674 TLHMSLSGIRDLSIIATPPEDRLPVRT-----FV----MEYDDELVREAIRRELLRGGQ-VFYVHNRIESIEKLKTQLRE 743 (997)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEE-----EE----ECCCHHHHHHHHHHHHCCCCE-EEEEECCCCCHHHHHHHHHH
T ss_conf 589998755332210578887742488-----77----427868999999975313981-89980881357899999985
Q ss_pred CCCCHH---HHHHHHHHHHHHHHHHH--CCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHH
Q ss_conf 077102---23102247788888753--0558704887502446655402767557888651135755300899999999
Q gi|254780327|r 462 HKFTKF---QILNALYHEKEAYIISQ--AGIPGAVTIATNMAGRGTDIQLGGNVAMRIEHELANISDEEIRNKRIKMIQE 536 (890)
Q Consensus 462 ~~~~~h---~vLNAk~~~~Ea~Iia~--AG~~g~vTiATNMAGRGTDI~Lgg~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 536 (890)
T Consensus 744 --LVP~arIaiaHGqM~e~eLE~~m~~F~~~~~~vLvcTTIIE~GIDI---PnANTiIi~-------------------- 798 (997)
T TIGR00580 744 --LVPEARIAIAHGQMTENELEEVMLEFYKGEFDVLVCTTIIESGIDI---PNANTIIID-------------------- 798 (997)
T ss_pred --CCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHCCCCH---HHHHHHHHH--------------------
T ss_conf --0843267888335684568999998626843301322146505641---001268687--------------------
Q ss_pred HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHCCCCCCCCCCCCEEEEEECCCHHHHHHCCHHHHHHHH
Q ss_conf 877643334540762799826775323355420543456686723899842301454202101344542
Q gi|254780327|r 537 EVQSLKEKAIVAGGLYVISTERHESRRIDNQLRGRSGRQGDPGRSKFYLSLQDDLMRIFGSPRMESFLR 605 (890)
Q Consensus 537 ~~~~~~~~v~~~GGL~VigterhesrRid~QlrGRagRQGdpG~s~f~~SleD~l~r~Fgsdri~~lm~ 605 (890)
T Consensus 799 -----~A---D~FGLaQL-----------YQLRGRVGRs~~~AYAYlL~~~~~~Lt-~~A~~RL~ai~~ 847 (997)
T TIGR00580 799 -----RA---DKFGLAQL-----------YQLRGRVGRSKKKAYAYLLYPHQKALT-EDALKRLEAIQE 847 (997)
T ss_pred -----HH---CCCCHHHH-----------HHCCCEECCCCCEEEEEECCCCCCCCC-HHHHHHHHHHHH
T ss_conf -----52---11470347-----------453631205871268983347740014-589999999973