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