HHsearch alignment for GI: 254780217 and conserved domain: cd03282
>cd03282 ABC_MSH4_euk MutS4 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=94.41 E-value=0.1 Score=33.46 Aligned_cols=134 Identities=14% Similarity=0.117 Sum_probs=66.5
Q ss_pred CEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCCHHHHHHHCCCCCCEEEECCCCHHHCCCCCCCCCHH
Q ss_conf 81663117989888999999999981779988643121012678867999967898754530010001013421232378
Q gi|254780217|r 34 HHALLFEGEQGIGKATLGFRYAGHVLQNPDFSKAPVRMCNPDPCSPFVKQMASHALHDFLYLSYSLNPKTGKWRTVITVD 113 (347)
Q Consensus 34 ~ha~Lf~Gp~GiGK~~~A~~~A~~llc~~~~~~~~~~~~~~~~~~~~~~~i~~~~hpd~~~i~~~~~~k~~~~~~~I~vd 113 (347)
T Consensus 29 ~~~~iITGpN~gGKSt~Lktigl~~ilAq~G~~vpA~~a~~-------------~~~d~I~t~i~~~d~i~-~~~StF~~ 94 (204)
T cd03282 29 SRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATL-------------PIFNRLLSRLSNDDSME-RNLSTFAS 94 (204)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCEEEHHHCCC-------------CCCCEEEEEECCCCCCC-CCCCHHHH
T ss_conf 25999989998871999999999999999689167132103-------------36677899987666100-66458999
Q ss_pred HHHHHHHHCCCCCCCCCCHHHHHHHHHHCCH-----HHHHHHHHHHHHCCCCCCEEEEECCCCCCCH--HHHCEEEEEEC
Q ss_conf 8755443102221111210353220554240-----0014567776630343416765044335730--25203698864
Q gi|254780217|r 114 EIRRIRYFLSLTANTGYWRVIMIDPVDGMNR-----NAANALLKSLEEPPQKVLFILISHASPTILS--TIRSRCLSIKF 186 (347)
Q Consensus 114 ~IR~l~~~~~~~~~~~~~Ki~IId~ad~ln~-----~AaNALLK~LEEPp~~t~fiLit~~~~~il~--TI~SRc~~i~f 186 (347)
T Consensus 95 E~~~~~~il~~~---~~~sLvliDEl~~GT~~~eg~a~a~aile~l~~~--~~~~i~tTH~~-~L~~l~~~~~~v~n~~m 168 (204)
T cd03282 95 EMSETAYILDYA---DGDSLVLIDELGRGTSSADGFAISLAILECLIKK--ESTVFFATHFR-DIAAILGNKSCVVHLHM 168 (204)
T ss_pred HHHHHHHHHHHC---CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHC--CCEEEEECCHH-HHHHHHHHCCCEEEEEE
T ss_conf 999999999858---8898798543348998678999999999999967--98799989768-99998863888499999
Q ss_pred C
Q ss_conf 7
Q gi|254780217|r 187 N 187 (347)
Q Consensus 187 ~ 187 (347)
T Consensus 169 ~ 169 (204)
T cd03282 169 K 169 (204)
T ss_pred E
T ss_conf 9