>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=98.32 E-value=1.5e-05 Score=54.43 Aligned_cols=127 Identities=20% Similarity=0.124 Sum_probs=81.6 Q ss_pred CEEEEECCCCC----CCCCCCEEEEEEEEEECCCCEECCEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCHHHHH Q ss_conf 37999752788----98772604899999983897280400226621788877857898985799889960799979999 Q gi|254780661|r 4 HFVIYDYETFG----RDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITPQKALRDGVVEAEFS 79 (471) Q Consensus 4 ~~v~~D~ETtG----~~~~~~~iiq~~~i~~d~~~~~~~~~~~~~~~~~~~~~p~p~a~~v~git~~~~~~~~~~~~e~~ 79 (471) T Consensus 4 kilsfDIE~~~~~g~P~p~~d~Ii~Is~~--~~~~~~---v--i~~~~~~----~~~---v~~---------~~tE~eLL 60 (195) T cd05780 4 KILSFDIEVLNHEGEPNPEKDPIIMISFA--DEGGNK---V--ITWKKFD----LPF---VEV---------VKTEKEMI 60 (195) T ss_pred CEEEEEEEECCCCCCCCCCCCCEEEEEEE--ECCCCE---E--EEECCCC----CCC---EEE---------ECCHHHHH T ss_conf 29999999758999989888828999999--689978---9--9817988----774---567---------38999999 Q ss_pred HHHHHHHHCCCC-EEEEEECHHHHHHHHHHHHHHHCCCCC----------------CCCCCCCCCCCCHHHHHHHHHHHH Q ss_conf 999999511796-599950557899999999985078532----------------132568871001588886555653 Q gi|254780661|r 80 RRIHQFFSVPNT-CIIGYNNIRFDDYYSRNIFYRNFYDSY----------------RWSWDNGNSRWDLLDVMRAIYAFS 142 (471) Q Consensus 80 ~~i~~~~~~~~~-~~ig~N~~~FD~~~lr~~~~r~~~~~y----------------~~~~~~~~~~~D~l~~~~~~~~~~ 142 (471) T Consensus 61 ~~F~~~i~~~dPDii~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~---- 136 (195) T cd05780 61 KRFIEIVKEKDPDVIYTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT---- 136 (195) T ss_pred HHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHH---- T ss_conf 9999999872999999579878768999999999589864578886047997785079987686885549999752---- Q ss_pred HHHCCCCCCCCCCCCCCHHHHHHHH Q ss_conf 2100244444544331089899871 Q gi|254780661|r 143 PDGIQWPSRDDGATSFKLQDLALAN 167 (471) Q Consensus 143 p~~~~~~~~~~~~~~~kL~~la~~n 167 (471) T Consensus 137 ----------~~l~sy~L~~Va~~~ 151 (195) T cd05780 137 ----------LNLTRYTLERVYEEL 151 (195) T ss_pred ----------CCCCCCCHHHHHHHH T ss_conf ----------562401599999998

HHsearch alignment for GI: 254780661 and conserved domain: cd05780