HHsearch alignment for GI: 255764515 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=99.84 E-value=9.1e-19 Score=131.94 Aligned_cols=299 Identities=19% Similarity=0.282 Sum_probs=172.7
Q ss_pred HHHHHHHHHHHH-C--CC---EEEEECCCCCHHHHHHHHHHHHHHCCC---CCEEEEECCHHHHHHHHHHH-HHHCCCCC
Q ss_conf 789999999996-7--98---099958899868999999999997599---94999916046569999999-98558888
Q gi|255764515|r 5 PHQTKIVDWILD-H--KR---CAIWASMGSGKTVSVLTALSYIHLWGE---KSVLVIAPLRVAQSVWTSEV-QRWSNFSH 74 (458)
Q Consensus 5 p~Q~~~v~~~~~-~--~~---~ll~~~~G~GKT~~al~~~~~l~~~~~---~~~LIv~P~~l~~~~W~~Ei-~kf~~~~~ 74 (458)
T Consensus 511 ~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~~gneylKQVavLVPTT~LA~QHf~tf~~RF~~f-P 589 (997)
T TIGR00580 511 PDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGNEYLKQVAVLVPTTILAQQHFETFKERFANF-P 589 (997)
T ss_pred HHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCEECEEEEECCHHHHHHHHHHHHHHHHCCC-C
T ss_conf 789999999999740689873465245488536888878887633878220116896270442777889999973789-8
Q ss_pred CEEEEEECCH--HHHHHH----HCCCCCEEEECCCCHHHHHHHCCCCCCCCEEECCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 1599985897--898887----3077986998064202334420001132204404531002465431156777766543
Q gi|255764515|r 75 MNISVITGTV--KQRTKV----LKTPAVLYVINFENLGWLVQELKGTWPFATIVVDESTKLKSFRLRQGSKTARALAKPA 148 (458)
Q Consensus 75 ~~~~~~~g~~--~~r~~~----~~~~~~i~i~s~e~~~~~~~~~~~~~~~~~iIiDEaH~lkn~~~~~~s~~~~~l~~~~ 148 (458)
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 HCCCEEEEECCCCHHHHCCCHHHHHHHCCCCCCCCCCHHHHHHHHCCHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 05980799658402310010134677517888775327788777369564033000024555545589999974245433
Q gi|255764515|r 149 WESERFIELTGTPSPNGLIDLWGQIWFLDKGKRLGRVFQSFVARWFNTTQIGSHIGAVRYTAKETAQKEIEAQLSDCCLS 228 (458)
Q Consensus 149 ~~~~~~l~LTgTPi~n~~~el~~ll~~l~~~~~l~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~ 228 (458)
T Consensus 659 -~~VDvLtlsATPIPRTL-----~MSl~----------------------------------------g~R----d-lS~ 687 (997)
T TIGR00580 659 -TSVDVLTLSATPIPRTL-----HMSLS----------------------------------------GIR----D-LSI 687 (997)
T ss_pred -CCCCEEEEECCCCHHHH-----HHHHH----------------------------------------HHH----H-HHH
T ss_conf -67656763378960558-----99987----------------------------------------553----3-221
Q ss_pred HHCCCCCCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCCCCC
Q ss_conf 20000100100110003452453689988899999985103345202234788887542035410002234300013433
Q gi|255764515|r 229 LDIADYQNIDKPILITKKVPLPQPVMKQYHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEK 308 (458)
Q Consensus 229 ~~~~~~~~l~~~~~~~~~v~l~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~~~~~~~~~~~~~~~~~~~k 308 (458)
T Consensus 688 I~TPP~~R~p---v~T~v~~~~~~~~~~--AI~rEL~R--gGQvFyv------------------------------~Nr 730 (997)
T TIGR00580 688 IATPPEDRLP---VRTFVMEYDDELVRE--AIRRELLR--GGQVFYV------------------------------HNR 730 (997)
T ss_pred CCCCCCCCCC---EEEEEECCCHHHHHH--HHHHHHCC--CCEEEEE------------------------------ECC
T ss_conf 0578887742---488774278689999--99975313--9818998------------------------------088
Q ss_pred CCCH---HHHHHCC-CCCEEEEHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCEEEEEHHHCCCCCCCCCCCCE
Q ss_conf 3325---6654124-88403422236788866410002653344589987642458855899844221116220017859
Q gi|255764515|r 309 IKAL---EVIIEKA-NAAPIIVAYHFNSDLARLQKAFPQGRTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNI 384 (458)
Q Consensus 309 ~~~l---~~il~~~-~~~kviif~~~~~~~~~i~~~~~~g~~~~~r~~~i~~f~~~~~~vli~s~~~~~~GlnL~~a~~~ 384 (458)
T Consensus 731 ie~i~~~~~~l~~LVP~arIai--------------aHGqM~e~eLE~~m~~F~~~~~~vLvcT-TIIE~GIDIPnA-NT 794 (997)
T TIGR00580 731 IESIEKLKTQLRELVPEARIAI--------------AHGQMTENELEEVMLEFYKGEFDVLVCT-TIIESGIDIPNA-NT 794 (997)
T ss_pred CCCHHHHHHHHHHCCCCEEEEE--------------EECCCCHHHHHHHHHHHHCCCCCEEEEH-HHHHCCCCHHHH-HH
T ss_conf 1357899999985084326788--------------8335684568999998626843301322-146505641001-26
Q ss_pred EE-EECCCCCHHHHHHHHHHHHCCCCHHCCCCCCEEEEEEEEC
Q ss_conf 99-9089989868644566662022020378775289999858
Q gi|255764515|r 385 LV-FFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQ 426 (458)
Q Consensus 385 iI-~~~~~wn~~~~~Q~~gRi~~~r~hR~Gq~~~v~v~~li~~ 426 (458)
T Consensus 795 iIi~~AD~FGLaQLYQLRGRVG--Rs~-----~~AYAYlL~~~ 830 (997)
T TIGR00580 795 IIIDRADKFGLAQLYQLRGRVG--RSK-----KKAYAYLLYPH 830 (997)
T ss_pred HHHHHHCCCCHHHHHHCCCEEC--CCC-----CEEEEEECCCC
T ss_conf 8687521147034745363120--587-----12689833477