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