HHsearch alignment for GI: 254780750 and conserved domain: TIGR01070
>TIGR01070 mutS1 DNA mismatch repair protein MutS; InterPro: IPR005748 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure , and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts . This entry represents a family of MutS proteins.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair.
Probab=100.00 E-value=0 Score=2046.16 Aligned_cols=850 Identities=37% Similarity=0.642 Sum_probs=794.4
Q ss_pred CCHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCE
Q ss_conf 89168999999987799299998088222007999999986181891078899888762656176699999999988985
Q gi|254780750|r 25 STPMMRQYIEIKSINPDSLVFYRMGDFYELFFDDALLASRCLGITLTKRGKHLGKDIPMCGVPVHTANHYIQKLIKIGHR 104 (920)
Q Consensus 25 ~TP~~~Qy~~iK~~~~D~il~fr~G~FYE~f~~DA~~aa~~L~i~lt~r~~~~~~~~pmaGvP~~~l~~yl~~Lv~~Gyk 104 (920)
T Consensus 1 ~tPmmQQY~~lK~~~PD~lLffRmGDFYElFyeDAk~Aa~~L~I~LT~R~~sA~~~IPMAGiPyHs~~~Y~~~L~~~G~~ 80 (863)
T TIGR01070 1 LTPMMQQYLKLKAEHPDALLFFRMGDFYELFYEDAKKAAQLLDISLTSRGQSADEPIPMAGIPYHSVEAYLEKLVKQGYK 80 (863)
T ss_pred CCCCHHHHHHHHHHCCCHHHHHHCCCEEECCHHHHHHHHHHHCCHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf 98702578999864751577641363001107899999985032002457888888884787588899999999863986
Q ss_pred EEEEEECCCHHHHHHCCCCCCEEEEEEEEECCCCEECCHHCCCCCCCEEEEEEECCCEEEEEEEECCCCEEEEEECC-HH
Q ss_conf 99995028978874128998455458999775303020103878773699999529849999999786559996058-78
Q gi|254780750|r 105 IAICEQIESPLEAKKRGNKSLVRRNVVRLVTPGTLTEDQLLSPTDSNYLMAVARIRTEWAIAWIDISTGIFKISTSN-HD 183 (920)
Q Consensus 105 VaiveQ~E~p~~~~~~~~~~~v~R~Vt~IiTpGT~~d~~~l~~~~~nyL~aI~~~~~~~Gia~iDisTG~~~~~~~~-~d 183 (920)
T Consensus 81 VAIcEQ~eDP~~a-----kG~V~ReVVq~iTPGTv~Deall~er~~N~lAai~~~~~~fGLA~lD~~tG~F~~~~~~~~e 155 (863)
T TIGR01070 81 VAICEQIEDPKTA-----KGVVKREVVQIITPGTVSDEALLPERQDNLLAAIAQESNGFGLATLDLTTGEFKVTELADKE 155 (863)
T ss_pred EEEECCCCCHHHC-----CCCEEEEEEEEECCCEECCCCCCHHHHHHHHEEEEECCCCCCEEEEEEEECCEEEECCCCHH
T ss_conf 8985368886465-----78625689898528711135664033411212100068852147852243510022000178
Q ss_pred HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCEECCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHH-HHHHHHHHH
Q ss_conf 9999985229857997077689678998874238815718521147134478899870878642102444-346888777
Q gi|254780750|r 184 RLISDIMRIDPREIIFSEKELSHAEYKSLFETLGNVAVAQPNVFFDHSISESRIADYYNITTVDTFGSFS-QVEKTAAAA 262 (920)
Q Consensus 184 ~l~~~L~~l~P~EIii~~~~~~~~~~~~l~~~~~~~~~~~~~~~f~~~~~~~~l~~~~~~~~l~~~~~~~-~~~~~a~~a 262 (920)
T Consensus 156 ~l~~El~r~~p~E~l~~~~l~e~~~~---~~--rrG~~RR~~Wef~~~~a~~~~e~~f~~~dl~~~~~~~~~~~~~A~g~ 230 (863)
T TIGR01070 156 TLLAELQRLNPAEVLLAEDLSEEEAI---EL--RRGLRRRPLWEFRLDTAVLSLEKQFETEDLKGLGLRNAPLGLKAAGC 230 (863)
T ss_pred HHHHHHHCCCCEEEEECCCCCHHHHH---HH--CCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 99999860797388616572012799---96--37875788542331136887625766346410000234036678889
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCEEEECCHHHCCEEEEECCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHCCCHH
Q ss_conf 76436874112222221134457454014251332015454127877641278763012343378999986310023456
Q gi|254780750|r 263 AISYIKKTQMVNKPTIGYPEREDIQSTLFIDSAARSNLEILRTLSGSREQSLLKTIDYSITGAGGRLFAERIASPLTDST 342 (920)
Q Consensus 263 ll~Yl~~~~~~~~~~i~~~~~~~~~~~m~LD~~Tl~nLEI~~~~~g~~~gSL~~~Ln~t~T~~G~RlLr~wL~~PL~d~~ 342 (920)
T Consensus 231 LL~Ya~~TQ~~~L~Hl~p~~~~~~~d~~~ld~At~rnLEl~~nlrgG~~~tL~svLD~t~TAMG~RLL~~Wl~~PL~d~~ 310 (863)
T TIGR01070 231 LLQYAKRTQRTALPHLRPVRLYELQDFVQLDAATRRNLELTENLRGGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDRE 310 (863)
T ss_pred HHHHHHHHHCCCCCCCCCEEEECHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHH
T ss_conf 99999986102443036302455487773578876531000344678877630000446799861589986116632137
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 78989999997402212588999997520483444456775210000212068999998655675430258457787676
Q gi|254780750|r 343 KINTRLDSINFFIQNPILINPIQKILKSSPDVPRSLSRLKIGRGEPKDIAVIRDGIRSGINILNLFLKNDLPEELRGAVE 422 (920)
Q Consensus 343 ~I~~R~daVe~l~~~~~~~~~l~~~L~~i~DleRll~ri~~~~~~p~dl~~L~~sl~~~~~i~~~l~~~~~~~~l~~~~~ 422 (920)
T Consensus 311 ~l~~Rq~~V~~l~~~f~~~~~L~~~L~~v~DlERla~Rv~l~~a~PrDL~~Lr~~L~~lP~lra~l~~~~-~~~l~~l~~ 389 (863)
T TIGR01070 311 VLEARQDTVETLLRHFFLREDLRPLLKEVGDLERLAARVALGNARPRDLARLRTALEQLPELRALLEELE-QPKLQALAK 389 (863)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHH
T ss_conf 7999999999998521012115898888877999999987327898899999999998699999862115-568999998
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEE
Q ss_conf 57767899999999985431012210460101685411455799886389999977687788738875110255862237
Q gi|254780750|r 423 KLKKLPQSLEKTLSSMLSDDLPTFKRDGGFLRDGADASLDETRSLRDQSKRIIASLQLKYAEETKIKNLKIKHNNNLGYF 502 (920)
Q Consensus 423 ~l~~l~~~l~~~l~~~i~~~~~~~~~~~~~ik~g~d~eLD~lr~~~~~~~~~l~~l~~~~~~~~~i~sLki~~n~~~gy~ 502 (920)
T Consensus 390 ~~~~~~e-l~eLL~~Al~e~PP~~v~dGG~I~~GYd~~LDe~R~~~~~g~~yl~~LE~rErE~TGi~tLKvGyN~v~GYY 468 (863)
T TIGR01070 390 QLDDLSE-LLELLERALIENPPLVVRDGGVIREGYDEELDEYRALSREGTDYLAELEARERERTGIPTLKVGYNAVFGYY 468 (863)
T ss_pred HHHCCCC-HHHHHHHHCCCCCCCEEECCCEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEE
T ss_conf 5001674-699999704688692650486123578863799999987578999999988776358864551454211026
Q ss_pred EEECCHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf 62041143334411168765279852120001113456664334643777776433447888765430112579888899
Q gi|254780750|r 503 IEVTSSSASVLKKDLESKDRFIHRQTMSNLTRFTTLELIDLENRITNATNSALLIELESFEILSNAIIEQSESLDNASQV 582 (920)
Q Consensus 503 iEV~~~~~~~i~~~~~~~~~~i~~qt~~~~~Rf~t~eL~~l~~~i~~~~~~~~~~e~~~~~~l~~~i~~~~~~l~~~~~~ 582 (920)
T Consensus 469 i~vt~~q~~~~Pe-----~~Y~R~qTLKnaERyi~PELKe~E~~~L~a~~~~~~lE~elf~elre~~~~~~~~Lq~~A~~ 543 (863)
T TIGR01070 469 IEVTRGQLHKVPE-----AHYIRRQTLKNAERYITPELKEKEDKVLEAKGKALALEKELFEELRELLKKYLEALQEAAKA 543 (863)
T ss_pred EECCCHHHCCCCC-----CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5226133304875-----56446667788755675789999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHCCCCCEECCCCCCEEECCCCCHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEECCCCCC
Q ss_conf 98677887788877525885121047871400004680588763102877044434563587777664399996778440
Q gi|254780750|r 583 IAIIDISIALAILAKEQNYCRPIIDNSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGG 662 (920)
Q Consensus 583 ia~lD~l~SlA~~a~~~~y~rP~i~~~~~l~i~~gRHPviE~~l~~~~~~~fVpNdi~l~~~~~~~~~~~~iiTGpNmgG 662 (920)
T Consensus 544 laELDVL~~LAe~A~~~~y~~P~F~d~~~~~I~~GRHPVVE~Vl~---~~~fvpN~~~m~-----~nr~~lliTGPNM~G 615 (863)
T TIGR01070 544 LAELDVLANLAEVAETLHYTRPRFGDDPELRIREGRHPVVEKVLD---RQPFVPNDLEMA-----DNRRLLLITGPNMGG 615 (863)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEECC---CCCCCCCCCCCC-----CCCEEEEEECCCCCC
T ss_conf 889999999999997448968701367614675088770434465---778677756558-----885688886687975
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC
Q ss_conf 78999999999999971985303532068221056765237661138532899999999999958998569993258898
Q gi|254780750|r 663 KSTFLRQNALIVIMAQMGSYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFVILDEIGRGT 742 (920)
Q Consensus 663 KSt~lRqval~vilAQiG~fVPA~~a~i~~~D~IftRiGa~D~l~~g~STF~vEm~e~~~IL~~at~~SLVllDElGrGT 742 (920)
T Consensus 616 KSTYmRQtALIallAqiGSfVPA~~a~Lp~~D~IFTRIGAsDDLasG~STFMVEM~E~aNil~~AT~~SLvL~DE~GRGT 695 (863)
T TIGR01070 616 KSTYMRQTALIALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLLDEIGRGT 695 (863)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 31799999999999982785350423028846320111513324799643006789999999986651022331034530
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHC
Q ss_conf 80567999999999999726984999748757976643068858999999960992778777744789887789999982
Q gi|254780750|r 743 ATLDGLSIAWATIEYLHETNRCRGLLATHFHELTDLSKSLKRFHNATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGKLA 822 (920)
Q Consensus 743 st~DG~aiA~aile~l~~~~~~~~lfaTHy~eL~~l~~~~~~v~n~~~~~~~~~~~i~flykl~~G~~~~Sygi~vA~la 822 (920)
T Consensus 696 STyDGlaLA~A~aE~lh~~irA~TLFATHYfELT~L~~~L~~l~NvHv~A~E~~g~~vFlH~v~~GpAsKSYG~~VA~lA 775 (863)
T TIGR01070 696 STYDGLALAWAIAEYLHEHIRAKTLFATHYFELTALEEKLPRLANVHVAALEHNGTIVFLHQVLPGPASKSYGLAVAALA 775 (863)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHCCCEEEEEEEEEECCCCEEEEEEECCCCCCCCHHHHHHHHC
T ss_conf 01678999999999986232121200145567513753486415435433661881589863157988643369999871
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----------HHHCCCHHHHHCCCCCHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf 9998999999999999987630001111211-----------11100001120035473899999860782227989999
Q gi|254780750|r 823 GLPNTVISRAYDILKTFEKLYHHNQKDMRLY-----------YPEIQTKESKNNLSKNDKLFVEKIKCLNLDEMSPLTAL 891 (920)
Q Consensus 823 G~p~~vi~~A~~~~~~le~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~al 891 (920)
T Consensus 776 GlP~~vi~RA~~~L~~LE~~s~~~~~p~~~~~~~~~~~q~~lf~~~e~~~~~e~L~~kekqvidafksLdpd~ltP~qAl 855 (863)
T TIGR01070 776 GLPKDVIARARQILTELEARSTESEAPLRKAQKKAEPEQLSLFDEAETHPLLEELAKKEKQVIDAFKSLDPDDLTPLQAL 855 (863)
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
T ss_conf 89888999999999999852888741333465412104667634303627899998621368877652787787979999
Q ss_pred HHHHHHHH
Q ss_conf 99999999
Q gi|254780750|r 892 KTLYAVKA 899 (920)
Q Consensus 892 ~~l~~lk~ 899 (920)
T Consensus 856 ~~Ly~LK~ 863 (863)
T TIGR01070 856 NLLYELKK 863 (863)
T ss_pred HHHHHHCC
T ss_conf 99997239