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