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