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