HHsearch alignment for GI: 254780945 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=97.56 E-value=0.00051 Score=51.09 Aligned_cols=117 Identities=21% Similarity=0.437 Sum_probs=98.9
Q ss_pred HHHHHHHHHHHCCC----CEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCC---CEECCCCCCCHHHHHHHHHHHHCCC
Q ss_conf 26899997631038----7389997120122111210146666666866371---0312014699899999999975598
Q gi|254780945|r 469 DEVIERLKVVLSEG----KKAYWICPQIEEKKESNFRSVVERFNSLHEHFTS---SIAIIHGRMSDIDKESVMDSFKNGT 541 (700)
Q Consensus 469 ~~~~~~i~~~l~~g----~q~y~VcPlIeese~~~~~~~~~~~~~l~~~~~~---~v~~lHGkm~~~ek~~~m~~F~~g~ 541 (700)
T Consensus 544 EVAmRAaFkAv~~gneylKQVavLVPT--------T~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~ 615 (997)
T TIGR00580 544 EVAMRAAFKAVLDGNEYLKQVAVLVPT--------TILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGK 615 (997)
T ss_pred HHHHHHHHHHHCCCCCEECEEEEECCH--------HHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 888878887633878220116896270--------442777889999973789816875277567378999999975594
Q ss_pred EEEEEECH-HHHCCCCCCCCCEEEEECHHHCCHHH---HHHHHHCCCCCCCCEEEEEEECCCC
Q ss_conf 69999800-34104688876589985852547468---8773011667898359999708889
Q gi|254780945|r 542 CKLLIATT-VIEVGIDVVDASIIIIENAEHFGLAQ---LHQLRGRVGRGEEISSCILLYHPPL 600 (700)
Q Consensus 542 ~~iLvaTt-viEVGvdvpna~~mvI~~aerfGLsq---LHQLRGRVGRg~~~s~c~l~~~~~~ 600 (700)
T Consensus 616 iDI~IGTH~lL~k~v~FKdLGLlIiDEEQRFGV~~KE~lK~~~~~V-------DvLtlsATPI 671 (997)
T TIGR00580 616 IDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELKTSV-------DVLTLSATPI 671 (997)
T ss_pred EEEEECCHHHHCCCEEEECCCCEEEECCCCCCCCHHHHHCCCCCCC-------CEEEEECCCC
T ss_conf 2266301041278546863864698314348831155530015676-------5676337896