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