HHsearch alignment for GI: 254780382 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=100.00 E-value=2.1e-39 Score=273.12 Aligned_cols=328 Identities=20% Similarity=0.286 Sum_probs=249.4
Q ss_pred CCCCHHHHHHHHH-CCCCCCCHHHHHHHHHHHC------CCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCC----CE
Q ss_conf 6988899999997-8798789899999999976------99799982798517899999999998606521478----27
Q gi|254780382|r 6 LGLSPKVVCAVLD-AGYVKPTPIQIKTIPLVLQ------RHDVCGIAQTGTGKTASFVLPMLTILEKGRARVRM----PR 74 (465)
Q Consensus 6 l~l~~~l~~~l~~-~~~~~pt~iQ~~~i~~~l~------g~dvi~~apTGsGKT~~~~lp~l~~l~~~~~~~~~----~~ 74 (465)
T Consensus 491 f~~D~e~~~~Fe~~FPfe-eT~DQ~~AI~eik~Dm~~~~~MDRL~CGDVGfGKTEVAmRAaFkAv~------~gneylKQ 563 (997)
T TIGR00580 491 FPPDDEWQAEFEDSFPFE-ETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVL------DGNEYLKQ 563 (997)
T ss_pred CCCCHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCHHHHHHHHHHHHHC------CCCCEECE
T ss_conf 988808999999838788-97789999999999740689873465245488536888878887633------87822011
Q ss_pred EEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC---CCH-HHHHHCCCCHHHHHHHCCCCCCCCCEEE
Q ss_conf 999828589999999998741023332210000122222222222---101-1221022102333320000001210010
Q gi|254780382|r 75 TLILEPTRELAAQVADNFEKYGKNYNLTVALLIGGIPFEAQNKKL---ERG-ADVLICTPGRILDHFNRGKLLMNNIEIL 150 (465)
Q Consensus 75 ~lil~PtreLa~Qi~~~~~~~~~~~~l~~~~~~gg~~~~~~~~~l---~~~-~~IiV~TP~rl~~~l~~~~~~l~~~~~l 150 (465)
T Consensus 564 VavLVPTT~LA~QHf~tf~~RF~~fPv~I~~LSRF~~~~E~~~iL~~la~G~iDI~IGT-----H~lL~k~v~FKdLGLl 638 (997)
T TIGR00580 564 VAVLVPTTILAQQHFETFKERFANFPVTIELLSRFRSAKEKKEILKELASGKIDILIGT-----HKLLQKDVKFKDLGLL 638 (997)
T ss_pred EEEECCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHCCCEEEEECC-----HHHHCCCEEEECCCCE
T ss_conf 68962704427778899999737898168752775673789999999755942266301-----0412785468638646
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf 25510000000100357887543102222233343211222211112222210013444321234642111112222110
Q gi|254780382|r 151 VIDEADRMLDMGFIPYIQNITSLVPFTRQTLLFSATMTDELQKVSENFLQNPKRIEVNTPSSTAETIEHCFVATYAQYSK 230 (465)
Q Consensus 151 ViDEah~l~~~gf~~~i~~i~~~~~~~~q~i~~SAT~~~~v~~l~~~~l~~~~~i~v~~~~~~~~~i~~~~~~~~~~~~~ 230 (465)
T Consensus 639 IiDEEQR-----FGV~~KE~lK~~~~~VDvLtlsATPIPRTL~MSl~g~RdlS~I~TPP~~R~p--v~-T~v~~~~~--- 707 (997)
T TIGR00580 639 IIDEEQR-----FGVKQKEKLKELKTSVDVLTLSATPIPRTLHMSLSGIRDLSIIATPPEDRLP--VR-TFVMEYDD--- 707 (997)
T ss_pred EEECCCC-----CCCCHHHHHCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCC--EE-EEEECCCH---
T ss_conf 9831434-----8831155530015676567633789605589998755332210578887742--48-87742786---
Q ss_pred HHHHHHH-CCCCCCCCCEEEEEECCCCCCCCCCCCCCC--CCCCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEHHHHHH
Q ss_conf 2444321-012234565067762134432222222222--3322222345420333234444201355238888466464
Q gi|254780382|r 231 KCALLQQ-LLQSQDTMKNGIIFCNQKKNVVNLCHSLEK--QGFSVCAIHGNIDQRSRMKILSNFKEGTIQLMVASDLAAR 307 (465)
Q Consensus 231 k~~~l~~-l~~~~~~~~k~iIF~~t~~~~~~l~~~L~~--~g~~v~~lhg~l~~~~R~~~~~~F~~g~~~vLV~Td~~~~ 307 (465)
T Consensus 708 --~~~~~AI~rEL~RgGQvFyv~Nrie~i~~~~~~l~~LVP~arIaiaHGqM~e~eLE~~m~~F~~~~~~vLvcTTIIE~ 785 (997)
T TIGR00580 708 --ELVREAIRRELLRGGQVFYVHNRIESIEKLKTQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFDVLVCTTIIES 785 (997)
T ss_pred --HHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEEHHHHHC
T ss_conf --899999997531398189980881357899999985084326788833568456899999862684330132214650
Q ss_pred HHCCCCCCEEEE-----ECCCCCHHHHHHHHHCCCCCCCCEEEEEEECHHHH------HHHHHHHH
Q ss_conf 407887650020-----02467789988752102458885399997788899------99999999
Q gi|254780382|r 308 GLDIPDVGHVFN-----FDVPNRAENYIHRIGRTGRAGRHGKAFTLVAKEDI------KHIDAIEK 362 (465)
Q Consensus 308 GiDip~v~~VI~-----~d~P~~~~~y~hR~GR~gR~g~~G~~i~~~~~~d~------~~~~~i~~ 362 (465)
T Consensus 786 GIDIPnANTiIi~~AD~FGL----aQLYQLRGRVGRs~~~AYAYlL~~~~~~Lt~~A~~RL~ai~~ 847 (997)
T TIGR00580 786 GIDIPNANTIIIDRADKFGL----AQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDALKRLEAIQE 847 (997)
T ss_pred CCCHHHHHHHHHHHHCCCCH----HHHHHCCCEECCCCCEEEEEECCCCCCCCCHHHHHHHHHHHH
T ss_conf 56410012686875211470----347453631205871268983347740014589999999973