HHsearch alignment for GI: 254780545 and conserved domain: cd03280
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and 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 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, a
Probab=94.08 E-value=0.17 Score=29.85 Aligned_cols=104 Identities=20% Similarity=0.386 Sum_probs=56.8
Q ss_pred CCCEEECCCCCHHHHHHHHHHHC-----CCC----------CCEE-----CCCHHH-H---HHHHHHCCHHHHHHHHHHH
Q ss_conf 33110037874258889999742-----469----------9702-----058578-8---6444203324599999999
Q gi|254780545|r 181 PHGVLLVGPPGTGKTLLARAVAG-----EAN----------VPFF-----TISGSD-F---VELFVGVGASRVRDMFEQA 236 (647)
Q Consensus 181 p~g~ll~GppGtGKTlla~a~a~-----e~~----------~~f~-----~~~~s~-~---~~~~~g~g~~~vr~lf~~a 236 (647)
T Consensus 28 ~~~~iiTGpN~sGKSt~lk~i~l~~iLAq~G~~vpa~~~~~~~~~d~i~~~i~~~d~~~~~~S~F~-~E~~~~~~il~~~ 106 (200)
T cd03280 28 KRVLVITGPNAGGKTVTLKTLGLLTLMAQSGLPIPAAEGSSLPVFENIFADIGDEQSIEQSLSTFS-SHMKNIARILQHA 106 (200)
T ss_pred CEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCEEECCCEECCCCCEEEEEECCCCCHHHHHHHHH-HHHHHHHHHHHHC
T ss_conf 339999889877509999999999999997778001100472665678888467336667787999-9999999999858
Q ss_pred HHHCCHHEEHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCC
Q ss_conf 8737801206323564144557898862688988998998530323577829999629810088
Q gi|254780545|r 237 KNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLD 300 (647)
Q Consensus 237 ~~~~p~iifiDeida~~~~r~~~~~~~~~e~~~~ln~ll~~mdg~~~~~~v~vi~aTn~~~~lD 300 (647)
T Consensus 107 ~--~~sLvliDE~~-----~gTn----~~eg~~~a~a~l~~l~---~-~~~~~i~tTH~~eL~~ 155 (200)
T cd03280 107 D--PDSLVLLDELG-----SGTD----PVEGAALAIAILEELL---E-RGALVIATTHYGELKA 155 (200)
T ss_pred C--CCCEEEECCCC-----CCCC----HHHHHHHHHHHHHHHH---H-CCCEEEEECCCHHHHH
T ss_conf 8--88879755666-----8988----7899999999999998---5-7997999897178998