HHsearch alignment for GI: 254780818 and conserved domain: cd05780
>cd05780 DNA_polB_Kod1_like_exo The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B D
Probab=98.14 E-value=5.8e-06 Score=57.21 Aligned_cols=122 Identities=17% Similarity=0.253 Sum_probs=71.0
Q ss_pred CCEEEEECCCC---CC-CCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHH
Q ss_conf 75899984678---88-888888999999999999880313798985888228865724202101232248521002344
Q gi|254780818|r 7 MRKIVFDIETT---GL-DSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSE 82 (245)
Q Consensus 7 mr~iv~D~ETT---Gl-~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~ 82 (245)
T Consensus 3 lkilsfDIE~~~~~g~P~p~~d~Ii~Is~~-~~~~----~~vi~~-~~----~~~----------~~v~~~~tE~eLL~~ 62 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFA-DEGG----NKVITW-KK----FDL----------PFVEVVKTEKEMIKR 62 (195)
T ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEE-ECCC----CEEEEE-CC----CCC----------CCEEEECCHHHHHHH
T ss_conf 429999999758999989888828999999-6899----789981-79----887----------745673899999999
Q ss_pred HHHHHHCCC-CEEEEECC-CCCCCEEEECHHCCCCCCC---------------------CCCHHCCCHHCCCCCCCCCCC
Q ss_conf 777530023-20231023-2243112100000112222---------------------100001100000001776422
Q gi|254780818|r 83 FWDFFNEQN-AEWIAHNA-KFDVGFINAELQRINKDPL---------------------DPSRIIDTLSIARRKHPSSRN 139 (245)
Q Consensus 83 f~~fi~~~~-~~lVaHNa-~FD~~fL~~el~r~~~~~~---------------------~~~~~iDTl~lar~~~p~~~~ 139 (245)
T Consensus 63 F~~~i~~~dPDii~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~~~l~sy 142 (195)
T cd05780 63 FIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRY 142 (195)
T ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHHCCCCCC
T ss_conf 99999872999999579878768999999999589864578886047997785079987686885549999752562401
Q ss_pred CHHHHHHHH
Q ss_conf 237899971
Q gi|254780818|r 140 DLNSLCKRY 148 (245)
Q Consensus 140 ~L~~l~~~~ 148 (245)
T Consensus 143 ~L~~Va~~~ 151 (195)
T cd05780 143 TLERVYEEL 151 (195)
T ss_pred CHHHHHHHH
T ss_conf 599999998