>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=98.71 E-value=4.6e-07 Score=64.88 Aligned_cols=152 Identities=20% Similarity=0.288 Sum_probs=84.8 Q ss_pred CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECCCE-EEEEEC---------CCCCHHHHHHHHHHC--CCCCEE Q ss_conf 97899980406788700046000026882999999983822-899978---------884221799999864--889819 Q gi|254780127|r 1 MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEP-VKLWDR---------TEQSAMPSDLLQYLR--DETVMC 68 (675) Q Consensus 1 mk~l~lD~ET~s~~dl~~~Gl~~y~~~~~I~~i~~a~~~~~-~~~~d~---------~~~~~~~~~l~~~L~--~~~~~k 68 (675) T Consensus 3 lkilsfDIE~~~~~g~P~------p~~d~Ii~Is~~~~~~~~vi~~~~~~~~~v~~~~tE~eLL~~F~~~i~~~dPDii- 75 (195) T cd05780 3 LKILSFDIEVLNHEGEPN------PEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVI- 75 (195) T ss_pred CCEEEEEEEECCCCCCCC------CCCCCEEEEEEEECCCCEEEEECCCCCCCEEEECCHHHHHHHHHHHHHHCCCCEE- T ss_conf 429999999758999989------8888289999996899789981798877456738999999999999987299999- Q ss_pred EEEEH-HHHHHHHHH---HCCCCCC----------------------CCCEEEHHHHHH-HHC-CCCCHHHHHHH-HCCC Q ss_conf 98630-775999998---6299878----------------------650454588999-858-89997899998-0889 Q gi|254780127|r 69 VAHNS-LFERILFKK---TLGIDIP----------------------SKRWICTSVLAR-TNG-LPSSLKNACLA-LNFS 119 (675) Q Consensus 69 v~HNa-~FD~~vL~~---~lGi~i~----------------------~~~~~DTmi~A~-~l~-~p~sL~~la~~-lgl~ 119 (675) T Consensus 76 ~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~~~l~sy~L~~Va~~~Lg~~ 155 (195) T cd05780 76 YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEELFGIE 155 (195) T ss_pred EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHHCCCCCCCHHHHHHHHHCCC T ss_conf 95798787689999999995898645788860479977850799876868855499997525624015999999983999 Q ss_pred CCCHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8652766376576641002332013453112587689998988775399999999872 Q gi|254780127|r 120 EHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRL 177 (675) Q Consensus 120 ~~~~kd~~gk~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~~~~L~~~L 177 (675) T Consensus 156 K~d---~~~~~i~~~~--------------~~-~~~~~~l~~Yn~~D~~L~~~L~~K~ 195 (195) T cd05780 156 KED---VPGEEIAEAW--------------DS-GENLERLFRYSMEDAKYTYEIGKEF 195 (195) T ss_pred CCC---CCHHHHHHHH--------------HC-CCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 788---9999999999--------------75-9753888844599899999998529

HHsearch alignment for GI: 254780127 and conserved domain: cd05780