>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=97.93 E-value=2.9e-05 Score=57.03 Aligned_cols=158 Identities=11% Similarity=0.115 Sum_probs=90.0 Q ss_pred CCCCCCCCCCCC----CCCCCCCCCCCEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHC--CC Q ss_conf 685232332224----331100124420102577665443455023137443334565001788999974444202--22 Q gi|254780277|r 387 IGSASFKIITDT----MDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFE--NE 460 (976) Q Consensus 387 ~~~ia~DtETt~----ld~~~~~ivGisls~~~~~~~~~~~~~~~yip~~~~~~~d~~~~~~~~~evl~~L~~lle--~~ 460 (976) T Consensus 3 lkilsfDIE~~~~~g~P~p~~d~Ii~Is~~~~~~~~vi~~~~~----~~~------~v~~~~tE~eLL~~F~~~i~~~dP 72 (195) T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKF----DLP------FVEVVKTEKEMIKRFIEIVKEKDP 72 (195) T ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEEECCC----CCC------CEEEECCHHHHHHHHHHHHHHCCC T ss_conf 4299999997589999898888289999996899789981798----877------456738999999999999987299 Q ss_pred CCHHHHCCC-CHHHHHHHH----CCCCCC----------------------C--CCCHHHHHHHHCCCCCCCCHHHHHHH Q ss_conf 100110032-123788986----188666----------------------4--21002345543168766772466776 Q gi|254780277|r 461 HFLKIGHNI-KYDKLVLHR----YGISMR----------------------G--FEDIMLMSYVLDSGRSSHDIASIAQK 511 (976) Q Consensus 461 ~i~kIgHN~-KfD~~~L~~----~GI~l~----------------------~--i~DTmlaayLLdp~~~~~~L~~la~~ 511 (976) T Consensus 73 Dii-~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~-~~~~l~sy~L~~Va~~ 150 (195) T cd05780 73 DVI-YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVAR-RTLNLTRYTLERVYEE 150 (195) T ss_pred CEE-EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHH-HHCCCCCCCHHHHHHH T ss_conf 999-95798787689999999995898645788860479977850799876868855499997-5256240159999999 Q ss_pred HCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 224442233565432221000000123333222111112456776 Q gi|254780277|r 512 WLSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWLLL 556 (976) Q Consensus 512 yL~~~~~e~~~~~k~~~~~~~i~~e~~~~Yaa~Da~~t~~L~~~l 556 (976) T Consensus 151 ~Lg~~K~d~~~~~i~~~~~~~~~~~~l~~Yn~~D~~L~~~L~~K~ 195 (195) T cd05780 151 LFGIEKEDVPGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195) T ss_pred HHCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 839997889999999999759753888844599899999998529

HHsearch alignment for GI: 254780277 and conserved domain: cd05780