HHsearch alignment for GI: 254780750 and conserved domain: pfam00488

>pfam00488 MutS_V MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.
Probab=100.00  E-value=0  Score=587.45  Aligned_cols=233  Identities=56%  Similarity=0.920  Sum_probs=223.7

Q ss_pred             CCCEECCCCCCEEECCCCCHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             85121047871400004680588763102877044434563587777664399996778440789999999999999719
Q gi|254780750|r  601 YCRPIIDNSTNFIVKDGRHPIVEKTLKQQSSKPFIANDCDLSCPNDKNSGKLWLLTGPNMGGKSTFLRQNALIVIMAQMG  680 (920)
Q Consensus       601 y~rP~i~~~~~l~i~~gRHPviE~~l~~~~~~~fVpNdi~l~~~~~~~~~~~~iiTGpNmgGKSt~lRqval~vilAQiG  680 (920)
T Consensus         1 y~~P~~~~~~~l~i~~~rHPll~~~~----~~~~VpNdi~l~~----~~~~~~iiTGpN~sGKSt~Lk~igl~~~lAq~G   72 (234)
T pfam00488         1 YVRPEFTESDALHIEGGRHPVVEAVL----AENFVPNDVSLGK----ERSRILLITGPNMGGKSTYLRQVALIVIMAQIG   72 (234)
T ss_pred             CCCCEECCCCCEEEEECCCCEEECCC----CCCEECCEEEECC----CCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             97887858996899976687697257----9976876589779----961699997887776199999999999999836


Q ss_pred             CCCCHHHCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             85303532068221056765237661138532899999999999958998569993258898805679999999999997
Q gi|254780750|r  681 SYVPASYAHIGIVDKLFSRVGSADNLASGRSTFMVEMIETASILNQATNQSFVILDEIGRGTATLDGLSIAWATIEYLHE  760 (920)
Q Consensus       681 ~fVPA~~a~i~~~D~IftRiGa~D~l~~g~STF~vEm~e~~~IL~~at~~SLVllDElGrGTst~DG~aiA~aile~l~~  760 (920)
T Consensus        73 ~~VPA~~a~~~~~d~I~~~i~~~dsl~~~~StF~~e~~~~~~il~~~~~~sLvliDEl~~GT~~~eg~al~~aile~L~~  152 (234)
T pfam00488        73 SFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLETANILHNATDKSLVILDELGRGTSTYDGLAIAWAVAEHLAE  152 (234)
T ss_pred             CCEEECCEEEECCCEEEEEECCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             87422205996365599985675334466117999999999999738877322014245899834679999999999997


Q ss_pred             HCCCEEEEECCCHHHHHHHHHCCCEEEEEEEEEEECCEEEEEEEEEECCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             26984999748757976643068858999999960992778777744789887789999982999899999999999998
Q gi|254780750|r  761 TNRCRGLLATHFHELTDLSKSLKRFHNATLQVSDSNEGIIFLHKVIPGIADHSYGIQVGKLAGLPNTVISRAYDILKTFE  840 (920)
Q Consensus       761 ~~~~~~lfaTHy~eL~~l~~~~~~v~n~~~~~~~~~~~i~flykl~~G~~~~Sygi~vA~laG~p~~vi~~A~~~~~~le  840 (920)
T Consensus       153 ~~~~~~i~tTH~~~L~~l~~~~~~v~~~~m~~~~~~~~~~f~Ykl~~G~~~~s~ai~ia~~~G~p~~ii~rA~~i~~~le  232 (234)
T pfam00488       153 KIRARTLFATHYHELTKLAEKLPAVKNVHMAAVETNGDIVFLYKVKPGAADKSYGIHVAELAGLPESVVERAREVLAELE  232 (234)
T ss_pred             HCCCEEEEEECHHHHHHHHHHCCCCCCEEEEEEEECCEEEEEEEECCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             35977999713577999987476444148999998997869999775899983999999991969999999999999986


Q ss_pred             H
Q ss_conf             7
Q gi|254780750|r  841 K  841 (920)
Q Consensus       841 ~  841 (920)
T Consensus       233 ~  233 (234)
T pfam00488       233 D  233 (234)
T ss_pred             C
T ss_conf             6