HHsearch alignment for GI: 254780545 and conserved domain: cd03283

>cd03283 ABC_MutS-like MutS-like 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 slid
Probab=95.24  E-value=0.036  Score=34.66  Aligned_cols=107  Identities=26%  Similarity=0.438  Sum_probs=65.3

Q ss_pred             CCCCEEECCCCCHHHHHHHHHHHCC-----CC---------CCEECC----CHHHH----HHHHHHCCHHHHHHHHHHHH
Q ss_conf             3331100378742588899997424-----69---------970205----85788----64442033245999999998
Q gi|254780545|r  180 IPHGVLLVGPPGTGKTLLARAVAGE-----AN---------VPFFTI----SGSDF----VELFVGVGASRVRDMFEQAK  237 (647)
Q Consensus       180 ~p~g~ll~GppGtGKTlla~a~a~e-----~~---------~~f~~~----~~s~~----~~~~~g~g~~~vr~lf~~a~  237 (647)
T Consensus        24 ~~~~~iiTGpN~~GKSt~Lk~i~l~~ilaq~G~~vpa~~~~~~~~~i~t~i~~~d~~~~~~S~F~-~E~~~~~~il~~~~  102 (199)
T cd03283          24 KKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFY-AELRRLKEIVEKAK  102 (199)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCEEEHHHEEECCCEEEEEEECCCHHHCCCCHHH-HHHHHHHHHHHHHC
T ss_conf             98589998999986599999999999999968938624478233089999834751224535799-99999999999724


Q ss_pred             HHCCHHEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC
Q ss_conf             737801206323564144557898862688988998998530323577829999629810088
Q gi|254780545|r  238 NNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLD  300 (647)
Q Consensus       238 ~~~p~iifiDeida~~~~r~~~~~~~~~e~~~~ln~ll~~mdg~~~~~~v~vi~aTn~~~~lD  300 (647)
T Consensus       103 ~~~~sLvliDEl~-----~GT~----~~eg~a~a~a~le~l~---~-~~~~~iitTH~~~l~~  152 (199)
T cd03283         103 KGEPVLFLLDEIF-----KGTN----SRERQAASAAVLKFLK---N-KNTIGIISTHDLELAD  152 (199)
T ss_pred             CCCCEEEEECCCC-----CCCC----HHHHHHHHHHHHHHHH---H-CCCEEEEECCCHHHHH
T ss_conf             8985799614324-----7998----6789999999999998---6-7987999887289886