HHsearch alignment for GI: 254780129 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=99.65  E-value=1.4e-15  Score=108.63  Aligned_cols=167  Identities=19%  Similarity=0.240  Sum_probs=109.6

Q ss_pred             CHHHHHHHHHHHH---C---CCCEEEECCCCCHHHHHHHHHHHHHHCCC---CCEEEEECCCCCHHHHHHHHHHHCCCCC
Q ss_conf             4899999999996---7---98199968999889999999999974089---9489972331013788999985155346
Q gi|254780129|r    6 KPHQIVMVNWLLS---H---DRCALWASMGSGKTVSVLFALSTIKILDP---RPVLIIAPLRVAQYVWKDEVERWSAFSD   76 (220)
Q Consensus         6 rp~Q~~a~~~~~~---~---~~~~l~~~~G~GKT~~ai~~~~~~~~~~~---~~~LIi~P~s~~~~~W~~e~~~~~~~~~   76 (220)
T Consensus       510 T~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~RF~~fP  589 (997)
T TIGR00580       510 TPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKERFANFP  589 (997)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHHHHCCCC
T ss_conf             77899999999997406898734652454885368888788876338782201168962704427778899999737898


Q ss_pred             CEEEEEECCCCC--C---CCC-CCCCCCEEEECHHHHHCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             069986112101--1---223-4567662786566731000000002472000025122013654332036999999985
Q gi|254780129|r   77 MTVSSLIGSERQ--R---IKA-LNTPAHLYIINFENIPWLVKMKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVA  150 (220)
Q Consensus        77 ~~~~~~~~~~~~--~---~~~-~~~~~~~~i~~~~~l~~~~~~~~~~~~~~~iIiDEaH~~kn~~~~~~~k~~k~l~~~~  150 (220)
T Consensus       590 v~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGTH~lL~k~v----~FKdLGLlIiDEEQRF-------GV~~KE~lK~~~  658 (997)
T TIGR00580       590 VTIELLSRFRSAKEKKEILKELASGKIDILIGTHKLLQKDV----KFKDLGLLIIDEEQRF-------GVKQKEKLKELK  658 (997)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCHHHHCCCE----EEECCCCEEEECCCCC-------CCCHHHHHCCCC
T ss_conf             16875277567378999999975594226630104127854----6863864698314348-------831155530015


Q ss_pred             HCCCCEEEEECCCCCCCCH-HHHHHH--HHHH--CCCCCC
Q ss_conf             1379879983165324888-999999--9982--888534
Q gi|254780129|r  151 FSKVKRFIELTGTPSPNGL-IDLWGQ--IWFL--DKGKRL  185 (220)
Q Consensus       151 ~~~~~~~l~LTgTPi~n~~-~el~~l--l~~l--~p~~~~  185 (220)
T Consensus       659 --~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~  696 (997)
T TIGR00580       659 --TSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRL  696 (997)
T ss_pred             --CCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             --67656763378960558999875533221057888774