HHsearch alignment for GI: 254780619 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=95.41 E-value=0.1 Score=32.18 Aligned_cols=158 Identities=21% Similarity=0.255 Sum_probs=84.0
Q ss_pred HHHHHHHCCCCCHH--HHCCCCCCCCHHHHHHHHHHHCCCCCCEEEEEH-HHCCCCCCCCCCHHHHHHHHHHHHHHH---
Q ss_conf 88885204852000--102321135867899999862125765798704-430231134520123300034431024---
Q gi|254780619|r 498 IAEEVCEYFPLARI--SILSSDLEGGGGRLQLQLSAIAKGEIDIIIGTQ-LVAKGHNFPRMSLVGVVDGDLGLTNAD--- 571 (731)
Q Consensus 498 ~~e~l~~~fp~~~v--~~~d~d~~~~~~~~~~~~~~~~~~~~~ilvgTq-~i~kg~~fp~v~lv~il~aD~~l~~pd--- 571 (731)
T Consensus 577 Hf~tf~~RF~~fPv~I~~LSRF~--~~~E~~~iL~~la~G~iDI~IGTH~lL~k~v~FKdLGLlIi-DEEQRFGV~~KE~ 653 (997)
T TIGR00580 577 HFETFKERFANFPVTIELLSRFR--SAKEKKEILKELASGKIDILIGTHKLLQKDVKFKDLGLLII-DEEQRFGVKQKEK 653 (997)
T ss_pred HHHHHHHHHCCCCEEEEECCCCC--CCHHHHHHHHHHHCCCEEEEECCHHHHCCCEEEECCCCEEE-ECCCCCCCCHHHH
T ss_conf 88999997378981687527756--73789999999755942266301041278546863864698-3143488311555
Q ss_pred ---HHHH-----------HHHHHH-HHHHHHCCCCCCC-CCEEEEEECCCCC--HHHHHHHH-------------CCHHH
Q ss_conf ---5578-----------999998-7543110256678-8689999329864--88899995-------------89799
Q gi|254780619|r 572 ---LRSS-----------ERTFQL-LSQVTGRAGRFGL-KSLGLIQAYQPTH--PVMQALVS-------------GDADS 620 (731)
Q Consensus 572 ---~ra~-----------E~~~ql-l~qv~gRagr~~~-~g~v~iQt~~p~~--~~~~~~~~-------------~d~~~ 620 (731)
T Consensus 654 lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~pv~T~v~~~~~~~~~~AI~rEL~RgGQvFyv~Nrie~ 733 (997)
T TIGR00580 654 LKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLPVRTFVMEYDDELVREAIRRELLRGGQVFYVHNRIES 733 (997)
T ss_pred HCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf 30015676567633789605589998755332210578887742488774278689999999753139818998088135
Q ss_pred HHHHHHHHHHHCCCCCCHHEEEEEEECCCHHHHHHHHHHHHH
Q ss_conf 999999999981888801189998845998999999999998
Q gi|254780619|r 621 FYESEIRARESVNLPPFGRLAAVIISGTKYQEVENYAYNLKE 662 (731)
Q Consensus 621 f~~~el~~R~~~~~PPf~~~~~i~~~~~~~~~~~~~~~~~~~ 662 (731)
T Consensus 734 i~~~~~~l~---~LVP~arIaiaH-GqM~e~eLE~~m~~F~~ 771 (997)
T TIGR00580 734 IEKLKTQLR---ELVPEARIAIAH-GQMTENELEEVMLEFYK 771 (997)
T ss_pred HHHHHHHHH---HCCCCEEEEEEE-CCCCHHHHHHHHHHHHC
T ss_conf 789999998---508432678883-35684568999998626