HHsearch alignment for GI: 254780601 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=93.95 E-value=0.33 Score=27.34 Aligned_cols=169 Identities=19% Similarity=0.270 Sum_probs=98.3
Q ss_pred HHHHHHHCC--CCCCC----CEEEEECCCHHHHHHHHHHHHH----CCCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEEE
Q ss_conf 245542001--02356----4167751302334565555542----2666301048999999999986654488149985
Q gi|254780601|r 231 RDNAIVNIL--RYHGA----KNAIVFCSTRASVSRFTKVLAE----HLFQVVALSGELSQQERSNALQMMRDGRARVCIA 300 (573)
Q Consensus 231 k~~~l~~ll--~~~~~----~~~ivF~~t~~~~~~l~~~L~~----~g~~~~~lhg~~~q~~R~~~~~~fr~g~~~vLV~ 300 (573)
T Consensus 542 KTEVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IG 621 (997)
T TIGR00580 542 KTEVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIG 621 (997)
T ss_pred HHHHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEEC
T ss_conf 36888878887633878220116896270442777889999973789816875277567378999999975594226630
Q ss_pred CC-CCCCCCCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCEEEEEECHHHHHHHHHHHHHH-HCCCCCCCCCCHHHH
Q ss_conf 38-6500145788733897058874789998603010378886025640599999999999985-066410568999998
Q gi|254780601|r 301 TD-VAARGIDLPDLELVIHAELSSNPENLLHRSGRTGRAGRKGMSVFVIPQNMQRRAERLFREA-NVSVVWEPAPSVEAI 378 (573)
Q Consensus 301 TD-vaaRGiDi~~v~~Vin~d~P~~~~~yvHR~GRtgRag~~G~ai~l~~~~e~~~~~~i~~~~-~~~~~~~~~Ps~eeI 378 (573)
T Consensus 622 TH~lL~k~v~FKdLGLlIi-----DEE---Q------RFGV~----------~KE~lK~~~~~VDvLtlsATPIPRTL~M 677 (997)
T TIGR00580 622 THKLLQKDVKFKDLGLLII-----DEE---Q------RFGVK----------QKEKLKELKTSVDVLTLSATPIPRTLHM 677 (997)
T ss_pred CHHHHCCCEEEECCCCEEE-----ECC---C------CCCCC----------HHHHHCCCCCCCCEEEEECCCCHHHHHH
T ss_conf 1041278546863864698-----314---3------48831----------1555300156765676337896055899
Q ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-HHHCCC
Q ss_conf 88899865544310122204557766666542004789999999-862011
Q gi|254780601|r 379 RERDAQRILQDPLFLDSIQGDEKKMVDVLLAKHDPEKIAAGFLR-IHRAGL 428 (573)
Q Consensus 379 ~~~~~~~l~~~~~~~~~~~~~~~~~~e~Ll~~~dpe~IAaALlk-l~~~~~ 428 (573)
T Consensus 678 S---l~g~R-d-lS~I~TPP~~R~pv~T~v~~~~~~~~~~AI~rEL~RgGQ 723 (997)
T TIGR00580 678 S---LSGIR-D-LSIIATPPEDRLPVRTFVMEYDDELVREAIRRELLRGGQ 723 (997)
T ss_pred H---HHHHH-H-HHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHCCCCE
T ss_conf 9---87553-3-221057888774248877427868999999975313981