HHsearch alignment for GI: 254780606 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=97.10 E-value=0.0081 Score=38.30 Aligned_cols=132 Identities=16% Similarity=0.169 Sum_probs=74.4
Q ss_pred CCEEECCHHHC---CC-EEEEECCCCCHHHHHHHHHHHHHHHCCHHHEEEEEECCCCCEECCCCCCCCEEEEEEECHHHH
Q ss_conf 87321120114---84-699707875344799999999998568011079997234210001257752000044441787
Q gi|254780606|r 402 GESVIADLANM---PH-ILVAGTTGSGKSVAINTMIMSLLYRLRPDECRMIMVDPKMLELSVYDGIPHLLTPVVTNPKKA 477 (744)
Q Consensus 402 g~~~~~dl~~~---PH-~lvaG~TgsGKS~~l~~~i~sl~~~~~p~~~~~~liD~k~~~~~~~~~~ph~~~~v~~~~~~~ 477 (744)
T Consensus 28 ~~~VpNdi~l~~~~~~~~iiTGpN~sGKSt~Lk~igl~~~lAq~G-----~~VPA~~a~~~~~d~I---~~-~i~~~dsl 98 (234)
T pfam00488 28 ENFVPNDVSLGKERSRILLITGPNMGGKSTYLRQVALIVIMAQIG-----SFVPAESARIGIVDRI---FT-RIGASDDL 98 (234)
T ss_pred CCEECCEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHC-----CCEEECCEEEECCCEE---EE-EECCCCHH
T ss_conf 976876589779961699997887776199999999999999836-----8742220599636559---99-85675334
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEHHHHHHHHHHCCHHHH----HHH
Q ss_conf 6899999986676999999807786799999886420267766654323386799984456876753103589----999
Q gi|254780606|r 478 VMALKWAVREMEERYRKMSHLSVRNIKSYNERISTMYGEKPQGCGDDMRPMPYIVIIVDEMADLMMVAGKEIE----GAI 553 (744)
Q Consensus 478 ~~~l~~~~~em~~r~~~~~~~~~~~i~~~n~~~~~~~~~~~~~~~~~~~~~p~ivvviDE~a~l~~~~~~~~e----~~~ 553 (744)
T Consensus 99 ~~~~StF~~e~~~~~~il~~~~~-----------------------------~sLvliDEl~~--GT~~~eg~al~~ail 147 (234)
T pfam00488 99 ASGRSTFMVEMLETANILHNATD-----------------------------KSLVILDELGR--GTSTYDGLAIAWAVA 147 (234)
T ss_pred HCCCCHHHHHHHHHHHHHHHCCC-----------------------------CCEECCCCCCC--CCCHHHHHHHHHHHH
T ss_conf 46611799999999999973887-----------------------------73220142458--998346799999999
Q ss_pred HHHHHHHHCCEEEEEEEECCCCC
Q ss_conf 99999642013589998516544
Q gi|254780606|r 554 QRLAQMARAAGIHLIMATQRPSV 576 (744)
Q Consensus 554 ~~la~~~ra~GihlilatQrp~~ 576 (744)
T Consensus 148 e~L~~~---~~~~~i~tTH~~~L 167 (234)
T pfam00488 148 EHLAEK---IRARTLFATHYHEL 167 (234)
T ss_pred HHHHHH---CCCEEEEEECHHHH
T ss_conf 999973---59779997135779