HHsearch alignment for GI: 254780270 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=94.12 E-value=0.17 Score=30.06 Aligned_cols=109 Identities=19% Similarity=0.292 Sum_probs=63.2
Q ss_pred CCEEEEECCCCCCHHHHHHHHHHHH-----CC----CEEEEEC-----CCCCCHHHHCCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf 7359986056565027999999770-----88----2499861-----88888888356320014567128999998327
Q gi|254780270|r 366 GLILCFVGPPGVGKTSLAQSIAKAT-----GR----QYVRMSL-----GGVYDEADIRGHRRTYIGSMPGRIIQSLKRAK 431 (820)
Q Consensus 366 g~il~l~gppgvGKts~~~sia~al-----~r----~f~~isl-----gg~~d~~~i~gh~~ty~ga~pg~ii~~l~~~~ 431 (820)
T Consensus 29 ~~~~iiTGpN~gGKSt~lkti~l~~ilaq~G~~vpa~~~~~~~~~~i~~~i~~~d~~~~~~StF~~E~~-~~~~il~~~- 106 (213)
T cd03281 29 PSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLY-QVSKALRLA- 106 (213)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCEEECCEEEECCCCEEEEECCHHHHHCCCCHHHHHHH-HHHHHHHHC-
T ss_conf 259999899987659999999999999985885767403997212237676764344413258999999-999999858-
Q ss_pred CCCEEEEEECHHHHHHHCCC-CHHHHHHHHCCCCCCC----CEEEEECCC
Q ss_conf 88739999331554231177-1155665540600168----133201035
Q gi|254780270|r 432 RSNPLLLLDEIDKMGSDLRG-DPSAALLEVLDPAQNS----SFVDHYLEV 476 (820)
Q Consensus 432 ~~npv~~ldeidk~~~~~~g-dp~~allevldp~qn~----~f~d~y~~~ 476 (820)
T Consensus 107 ~~~sLvliDEl~~GT~~~eg~ala~a~le~l~~~~~~~~~~~~tTH~~~L 156 (213)
T cd03281 107 TRRSLVLIDEFGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHEL 156 (213)
T ss_pred CCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHH
T ss_conf 88865877313478883567999999999999658876649998972787