HHsearch alignment for GI: 254780127 and conserved domain: cd05781

>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=99.07  E-value=1e-08  Score=75.87  Aligned_cols=155  Identities=17%  Similarity=0.234  Sum_probs=92.9

Q ss_pred             CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECCCEEEEEECCCCC--HHHHHHHHHHC--CCCCEEEEEEH-HH
Q ss_conf             978999804067887000460000268829999999838228999788842--21799999864--88981998630-77
Q gi|254780127|r    1 MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQS--AMPSDLLQYLR--DETVMCVAHNS-LF   75 (675)
Q Consensus         1 mk~l~lD~ET~s~~dl~~~Gl~~y~~~~~I~~i~~a~~~~~~~~~d~~~~~--~~~~~l~~~L~--~~~~~kv~HNa-~F   75 (675)
T Consensus         3 lk~lsfDIE~~~~~gfp~------~~~d~Ii~Is~~~~~g~~~~~~~~~~~E~~ll~~f~~~i~~~~Pdii-~gyN~~~F   75 (188)
T cd05781           3 LKTLAFDIEVYSKYGTPN------PRRDPIIVISLATSNGDVEFILAEGLDDRKIIREFVKYVKEYDPDII-VGYNSNAF   75 (188)
T ss_pred             CEEEEEEEEECCCCCCCC------CCCCCEEEEEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCEE-EECCCCCC
T ss_conf             419999988768999899------88897899999968997699984799989999999999987299999-96698675


Q ss_pred             HHHHHHH---HCCCCCC--------------------CCCEEEHHHHHH-HHC-CCCCHHHHHHHHCCCCCCHH-HHHCH
Q ss_conf             5999998---6299878--------------------650454588999-858-89997899998088986527-66376
Q gi|254780127|r   76 ERILFKK---TLGIDIP--------------------SKRWICTSVLAR-TNG-LPSSLKNACLALNFSEHLTK-MEEGK  129 (675)
Q Consensus        76 D~~vL~~---~lGi~i~--------------------~~~~~DTmi~A~-~l~-~p~sL~~la~~lgl~~~~~k-d~~gk  129 (675)
T Consensus        76 D~pyl~~Ra~~~~i~l~~gr~~~~~~~~~~~~~~~i~Gr~~iDl~~~~~~~~~l~sysL~~Va~~lg~~~k~e~~~~~~~  155 (188)
T cd05781          76 DWPYLVERARVLGVKLDVGRRGGSEPSTGVYGHYSITGRLNVDLYDFAEEIPEVKVKTLENVAEYLGVMKKSERVLIEWY  155 (188)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCCCCHH
T ss_conf             78999999999699850155677651225420699878999977899976247564579999998541224544657999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             576641002332013453112587689998988775399999999872
Q gi|254780127|r  130 ALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRL  177 (675)
Q Consensus       130 ~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~~~~L~~~L  177 (675)
T Consensus       156 ~I~~--------------~~-~~~~~r~~l~~YnlqDa~L~~~L~~KL  188 (188)
T cd05781         156 RIYE--------------YW-DDEKKRDILLKYNRDDARSTYGLAEKL  188 (188)
T ss_pred             HHHH--------------HH-HCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999--------------87-084121699999788799999998429