HHsearch alignment for GI: 254780217 and conserved domain: cd03243
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=95.49 E-value=0.048 Score=36.15 Aligned_cols=132 Identities=17% Similarity=0.146 Sum_probs=68.4
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCHHHHHHHCCCCCCEEEECCCCHH--HCCCCCCCCCH
Q ss_conf 1663117989888999999999981779988643121012678867999967898754530010001--01342123237
Q gi|254780217|r 35 HALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAPVRMCNPDPCSPFVKQMASHALHDFLYLSYSLNP--KTGKWRTVITV 112 (347)
Q Consensus 35 ha~Lf~Gp~GiGK~~~A~~~A~~llc~~~~~~~~~~~~~~~~~~~~~~~i~~~~hpd~~~i~~~~~~--k~~~~~~~I~v 112 (347)
T Consensus 30 ~~~iiTGpN~sGKSt~lkti~l~~~laq~G~~vpa~~~~~-------------~~~~~i~~~~~~~d~~~~~~S~F~~e~ 96 (202)
T cd03243 30 RLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASI-------------PLVDRIFTRIGAEDSISDGRSTFMAEL 96 (202)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCEEEECCCEE-------------ECCCEEEEEECCCHHHHCCCCHHHHHH
T ss_conf 2899989988753999999999999998387372044689-------------446669998466024443535499999
Q ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCH-----HHHHHHHHHHHHCCCCCCEEEEECCCC-CCCHHHHCEEEEEEC
Q ss_conf 88755443102221111210353220554240-----001456777663034341676504433-573025203698864
Q gi|254780217|r 113 DEIRRIRYFLSLTANTGYWRVIMIDPVDGMNR-----NAANALLKSLEEPPQKVLFILISHASP-TILSTIRSRCLSIKF 186 (347)
Q Consensus 113 d~IR~l~~~~~~~~~~~~~Ki~IId~ad~ln~-----~AaNALLK~LEEPp~~t~fiLit~~~~-~il~TI~SRc~~i~f 186 (347)
T Consensus 97 ~~~~~i~~~~~------~~slvliDE~~~gT~~~eg~~la~a~l~~l~~--~~~~~i~tTH~~~L~~~~~~~~~~~~~~~ 168 (202)
T cd03243 97 LELKEILSLAT------PRSLVLIDELGRGTSTAEGLAIAYAVLEHLLE--KGCRTLFATHFHELADLPEQVPGVKNLHM 168 (202)
T ss_pred HHHHHHHHHCC------CCCEEEECCCCCCCCHHHHHHHHHHHHHHHHH--CCCEEEEEECCHHHHHHHHCCCCEEEEEE
T ss_conf 99999998677------77724205234799867879999999999985--36849998253888875313897499999
Q ss_pred C
Q ss_conf 7
Q gi|254780217|r 187 N 187 (347)
Q Consensus 187 ~ 187 (347)
T Consensus 169 ~ 169 (202)
T cd03243 169 E 169 (202)
T ss_pred E
T ss_conf 9