HHsearch alignment for GI: 254780636 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=97.76 E-value=0.00014 Score=45.91 Aligned_cols=145 Identities=16% Similarity=0.246 Sum_probs=81.2
Q ss_pred CCCEEEECCCCCC----CCCCCEEEEEEEEECCCCEEEECCCCC-----------CCCCHHHHHHH--HCCCCCEEECCC
Q ss_conf 9827997177789----854450799998418942899746577-----------85706776777--323640230100
Q gi|254780636|r 20 VDAIAVDTETLGL----MPRRDRLCIVQLSPGDGTVDIIRIAAG-----------QKNAPNLVGML--VDEKREKIFHYG 82 (207)
Q Consensus 20 ~~~iaiDtEt~~l----~~~~~~l~LiQl~~~~~~~~l~~~~~~-----------~~~~~~L~~ll--~d~~i~KV~Hn~ 82 (207)
T Consensus 3 lkilsfDIE~~~~~g~P~p~~d~Ii~Is~~~~~~~~vi~-~~~~~~~~v~~~~tE~eLL~~F~~~i~~~dPDii-~GyN~ 80 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVIT-WKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVI-YTYNG 80 (195)
T ss_pred CCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCEEEE-ECCCCCCCEEEECCHHHHHHHHHHHHHHCCCCEE-EECCC
T ss_conf 429999999758999989888828999999689978998-1798877456738999999999999987299999-95798
Q ss_pred -CHHHHHHHHHHH---CCC----------------------C--CHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCC-
Q ss_conf -001688865420---000----------------------0--00457898865211000000887776542002467-
Q gi|254780636|r 83 -RFDIAVLFYTFG---VRV----------------------R--PVFCTKIASRLTRTYTNQHGLKDNLKELLGINISK- 133 (207)
Q Consensus 83 -~~D~~~L~~~~g---i~~----------------------~--~i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ldK- 133 (207)
T Consensus 81 ~~FD~pYl~~R~~~~~~~~~~gr~~~~~~~~~~g~~~~~~i~Gr~~lD~~~~~~~~-~~l~sy~L~~Va~~~Lg~~K~d~ 159 (195)
T cd05780 81 DNFDFPYLKKRAEKLGIELDLGRDGSEIKIQRGGFNNASEIKGRIHVDLYPVARRT-LNLTRYTLERVYEELFGIEKEDV 159 (195)
T ss_pred CCCCHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCEEEEECCEEEEEHHHHHHHH-CCCCCCCHHHHHHHHHCCCCCCC
T ss_conf 78768999999999589864578886047997785079987686885549999752-56240159999999839997889
Q ss_pred C-CEECC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5-20036-5654432368999986459999999999
Q gi|254780636|r 134 A-QQSSD-WSADDLSDEQLQYAASDVVHLHALRLQF 167 (207)
Q Consensus 134 ~-~q~Sd-W~~rpLs~~Qi~YAA~Dv~~l~~L~~~l 167 (207)
T Consensus 160 ~~~~i~~~~~~~~~~~~l~~Yn~~D~~L~~~L~~K~ 195 (195)
T cd05780 160 PGEEIAEAWDSGENLERLFRYSMEDAKYTYEIGKEF 195 (195)
T ss_pred CHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 999999999759753888844599899999998529