HHsearch alignment for GI: 254780606 and conserved domain: cd03281

>cd03281 ABC_MSH5_euk MutS5 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=97.04  E-value=0.0055  Score=39.47  Aligned_cols=121  Identities=13%  Similarity=0.222  Sum_probs=68.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCHHHEEEEEECCCCCEECCCCCCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69970787534479999999999856801107999723421000125775200004444178768999999866769999
Q gi|254780606|r  415 ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVTNPKKAVMALKWAVREMEERYRK  494 (744)
Q Consensus       415 ~lvaG~TgsGKS~~l~~~i~sl~~~~~p~~~~~~liD~k~~~~~~~~~~ph~~~~v~~~~~~~~~~l~~~~~em~~r~~~  494 (744)
T Consensus        32 ~iiTGpN~gGKSt~lkti~l~~ilaq~G~---~v--pa~~~~~~~~~~i---~~-~i~~~d~~~~~~StF~~E~~~~~~i  102 (213)
T cd03281          32 MVITGPNSSGKSVYLKQVALIVFLAHIGS---FV--PADSATIGLVDKI---FT-RMSSRESVSSGQSAFMIDLYQVSKA  102 (213)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHCC---CE--EECCEEEECCCCE---EE-EECCHHHHHCCCCHHHHHHHHHHHH
T ss_conf             99989998765999999999999998588---57--6740399721223---76-7676434441325899999999999


Q ss_pred             HHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHCCHHHHHH----HHHHHHHHHCCEEEEEEE
Q ss_conf             9980778679999988642026776665432338679998445687675310358999----999999642013589998
Q gi|254780606|r  495 MSHLSVRNIKSYNERISTMYGEKPQGCGDDMRPMPYIVIIVDEMADLMMVAGKEIEGA----IQRLAQMARAAGIHLIMA  570 (744)
Q Consensus       495 ~~~~~~~~i~~~n~~~~~~~~~~~~~~~~~~~~~p~ivvviDE~a~l~~~~~~~~e~~----~~~la~~~ra~Gihlila  570 (744)
T Consensus       103 l~~~~-----------------------------~~sLvliDEl~~--GT~~~eg~ala~a~le~l~~~~~-~~~~~~~t  150 (213)
T cd03281         103 LRLAT-----------------------------RRSLVLIDEFGK--GTDTEDGAGLLIATIEHLLKRGP-ECPRVIVS  150 (213)
T ss_pred             HHHCC-----------------------------CCCEEEEEECCC--CCCHHHHHHHHHHHHHHHHHCCC-CCCEEEEE
T ss_conf             98588-----------------------------886587731347--88835679999999999996588-76649998


Q ss_pred             ECCCCC
Q ss_conf             516544
Q gi|254780606|r  571 TQRPSV  576 (744)
Q Consensus       571 tQrp~~  576 (744)
T Consensus       151 TH~~~L  156 (213)
T cd03281         151 THFHEL  156 (213)
T ss_pred             CCHHHH
T ss_conf             972787