>cd05781 DNA_polB_B3_exo The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain 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 also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarch

Probab=98.83 E-value=8.8e-08 Score=68.77 Aligned_cols=125 Identities=16% Similarity=0.121 Sum_probs=84.0 Q ss_pred CCEEEEECCCCC----CCCCCCEEEEEEEEEECCCCEECCEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCHHHH Q ss_conf 837999752788----9877260489999998389728040022662178887785789898579988996079997999 Q gi|254780661|r 3 NHFVIYDYETFG----RDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITPQKALRDGVVEAEF 78 (471) Q Consensus 3 ~~~v~~D~ETtG----~~~~~~~iiq~~~i~~d~~~~~~~~~~~~~~~~~~~~~p~p~a~~v~git~~~~~~~~~~~~e~ 78 (471) T Consensus 3 lk~lsfDIE~~~~~gfp~~~~d~Ii~Is~~~--~~g~~--~~--~~~-------------------------~~~~E~~l 51 (188) T cd05781 3 LKTLAFDIEVYSKYGTPNPRRDPIIVISLAT--SNGDV--EF--ILA-------------------------EGLDDRKI 51 (188) T ss_pred CEEEEEEEEECCCCCCCCCCCCCEEEEEEEE--CCCCE--EE--EEE-------------------------CCCCHHHH T ss_conf 4199999887689998998889789999996--89976--99--984-------------------------79998999 Q ss_pred HHHHHHHHHCCCC-EEEEEECHHHHHHHHHHHHHHHCCCCCC--------------CCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 9999999511796-5999505578999999999850785321--------------325688710015888865556532 Q gi|254780661|r 79 SRRIHQFFSVPNT-CIIGYNNIRFDDYYSRNIFYRNFYDSYR--------------WSWDNGNSRWDLLDVMRAIYAFSP 143 (471) Q Consensus 79 ~~~i~~~~~~~~~-~~ig~N~~~FD~~~lr~~~~r~~~~~y~--------------~~~~~~~~~~D~l~~~~~~~~~~p 143 (471) T Consensus 52 l~~f~~~i~~~~Pdii~gyN~~~FD~pyl~~Ra~~~~i~l~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~---- 127 (188) T cd05781 52 IREFVKYVKEYDPDIIVGYNSNAFDWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIP---- 127 (188) T ss_pred HHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHC---- T ss_conf 9999999987299999966986757899999999969985015567765122542069987899997789997624---- Q ss_pred HHCCCCCCCCCCCCCCHHHHHHHHCCCCC Q ss_conf 10024444454433108989987188764 Q gi|254780661|r 144 DGIQWPSRDDGATSFKLQDLALANGIEHV 172 (471) Q Consensus 144 ~~~~~~~~~~~~~~~kL~~la~~n~i~~~ 172 (471) T Consensus 128 ----------~l~sysL~~Va~~lg~~~k 146 (188) T cd05781 128 ----------EVKVKTLENVAEYLGVMKK 146 (188) T ss_pred ----------CCCCCCHHHHHHHHCCCCC T ss_conf ----------7564579999998541224

HHsearch alignment for GI: 254780661 and conserved domain: cd05781