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