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