HHsearch alignment for GI: 254780217 and conserved domain: cd03287

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes. 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 possess C-terminal domain with 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 c
Probab=93.95  E-value=0.18  Score=31.52  Aligned_cols=119  Identities=16%  Similarity=0.093  Sum_probs=58.8

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCHHHHHHHCCCCCCEEEECCCCHHHCCCCCCCCCHHH
Q ss_conf             16631179898889999999999817799886431210126788679999678987545300100010134212323788
Q gi|254780217|r   35 HALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAPVRMCNPDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVDE  114 (347)
Q Consensus        35 ha~Lf~Gp~GiGK~~~A~~~A~~llc~~~~~~~~~~~~~~~~~~~~~~~i~~~~hpd~~~i~~~~~~k~~~~~~~I~vd~  114 (347)
T Consensus        32 ~~~iiTGpN~~GKSt~lk~i~l~~ilaq~G~~vpa~~~~~~~~-------------d~i~~~i~~~d~~~~-~~StF~~e   97 (222)
T cd03287          32 YCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIF-------------DSVLTRMGASDSIQH-GMSTFMVE   97 (222)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHCEEECC-------------CEEEEECCCCCHHHC-CCCHHHHH
T ss_conf             4899978998872899999999999997267721456399635-------------759995067862344-52279999


Q ss_pred             HHHHHHHCCCCCCCCCCHHHHHHHHHHCCH-----HHHHHHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             755443102221111210353220554240-----001456777663034341676504433
Q gi|254780217|r  115 IRRIRYFLSLTANTGYWRVIMIDPVDGMNR-----NAANALLKSLEEPPQKVLFILISHASP  171 (347)
Q Consensus       115 IR~l~~~~~~~~~~~~~Ki~IId~ad~ln~-----~AaNALLK~LEEPp~~t~fiLit~~~~  171 (347)
T Consensus        98 ~~~~~~il~~~---~~~sLvliDEl~~GT~~~eg~ala~aile~l~~~-~~~~~i~tTH~~~  155 (222)
T cd03287          98 LSETSHILSNC---TSRSLVILDELGRGTSTHDGIAIAYATLHYLLEE-KKCLVLFVTHYPS  155 (222)
T ss_pred             HHHHHHHHHHC---CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHC-CCCEEEEECCCHH
T ss_conf             99999999867---8875442322468998357799999999999860-5889999476278