HHsearch alignment for GI: 254780382 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=95.29  E-value=0.012  Score=35.89  Aligned_cols=98  Identities=10%  Similarity=0.205  Sum_probs=76.9

Q ss_pred             CCCCCCCCCHHHHHHHHCCCCCCCC----CEEEEEECCCCCCCCCCCCCC----CCCCCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf             1112222110244432101223456----506776213443222222222----23322222345420333234444201
Q gi|254780382|r  221 FVATYAQYSKKCALLQQLLQSQDTM----KNGIIFCNQKKNVVNLCHSLE----KQGFSVCAIHGNIDQRSRMKILSNFK  292 (465)
Q Consensus       221 ~~~~~~~~~~k~~~l~~l~~~~~~~----~k~iIF~~t~~~~~~l~~~L~----~~g~~v~~lhg~l~~~~R~~~~~~F~  292 (465)
T Consensus       533 L~CGDVGfGKTEVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la  612 (997)
T TIGR00580       533 LVCGDVGFGKTEVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELA  612 (997)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHH
T ss_conf             65245488536888878887633878220116896270442777889999973789816875277567378999999975


Q ss_pred             CCCCEEEEEH-HHHHHHHCCCCCCEEE
Q ss_conf             3552388884-6646440788765002
Q gi|254780382|r  293 EGTIQLMVAS-DLAARGLDIPDVGHVF  318 (465)
Q Consensus       293 ~g~~~vLV~T-d~~~~GiDip~v~~VI  318 (465)
T Consensus       613 ~G~iDI~IGTH~lL~k~v~FKdLGLlI  639 (997)
T TIGR00580       613 SGKIDILIGTHKLLQKDVKFKDLGLLI  639 (997)
T ss_pred             CCCEEEEECCHHHHCCCEEEECCCCEE
T ss_conf             594226630104127854686386469