HHsearch alignment for GI: 254781193 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=98.88 E-value=7.2e-08 Score=69.33 Aligned_cols=152 Identities=22% Similarity=0.241 Sum_probs=89.6
Q ss_pred CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECCEE-EEEEEC---------CCCHHHHHHHHHHHC--CCCCEE
Q ss_conf 96899981417898700044001127981999999984803-999978---------881043799999863--889819
Q gi|254781193|r 1 MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHP-VELWDC---------VHDPVMPQVLKEALE--NTDVTI 68 (675)
Q Consensus 1 mk~i~lD~ET~~~~dl~~~Gl~~y~~~~~i~~i~~a~~~~~-v~~~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 LKILSFDIEVLNHEGE------PNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVI- 75 (195)
T ss_pred CCEEEEEEEECCCCCC------CCCCCCCEEEEEEEECCCCEEEEECCCCCCCEEEECCHHHHHHHHHHHHHHCCCCEE-
T ss_conf 4299999997589999------898888289999996899789981798877456738999999999999987299999-
Q ss_pred EEEEH-HHHHHHHHHH---CCCCCC---------------------CCC-EEEHHHHHHH-HC-CCCCHHHHHHHCCCCC
Q ss_conf 99730-7749999986---089988---------------------420-3316889998-67-8999689899829981
Q gi|254781193|r 69 VAHNS-YFERTVLKAC---FNLDIP---------------------IHR-WICTLVLARS-NG-LPSALKAVGEALKLSS 120 (675)
Q Consensus 69 V~HNa-~FD~~~L~~~---~Gi~i~---------------------~~~-~~DTmi~A~~-l~-~~~sL~~la~~l~l~~ 120 (675)
T Consensus 76 ~GyN~~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~~~l~sy~L~~Va~~~-Lg~ 154 (195)
T cd05780 76 YTYNGDNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRTLNLTRYTLERVYEEL-FGI 154 (195)
T ss_pred EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHHCCCCCCCHHHHHHHH-HCC
T ss_conf 9579878768999999999589864578886047997785079987686885549999752562401599999998-399
Q ss_pred CHHH-HHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 1004-379999862021123433234678585328999999899899999999630
Q gi|254781193|r 121 QKME-EGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRL 175 (675)
Q Consensus 121 ~k~~-~~k~l~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~t~~L~~~l 175 (675)
T Consensus 155 ~K~d~~~~~i~~~~~---------------~~~~~~~l~~Yn~~D~~L~~~L~~K~ 195 (195)
T cd05780 155 EKEDVPGEEIAEAWD---------------SGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CCCCCCHHHHHHHHH---------------CCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 978899999999997---------------59753888844599899999998529