>cd05160 DNA_polB_exo The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. 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. This 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 contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and

Probab=98.40 E-value=6.6e-06 Score=57.27 Aligned_cols=147 Identities=16% Similarity=0.115 Sum_probs=78.1 Q ss_pred EEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECC-CEEE----------------------EEECCCCCHHHHHHHH Q ss_conf 8999804067887000460000268829999999838-2289----------------------9978884221799999 Q gi|254780127|r 3 KLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDD-EPVK----------------------LWDRTEQSAMPSDLLQ 59 (675) Q Consensus 3 ~l~lD~ET~s~~dl~~~Gl~~y~~~~~I~~i~~a~~~-~~~~----------------------~~d~~~~~~~~~~l~~ 59 (675) T Consensus 1 vlsfDIE~~~~~gf----P~p--~~d~Ii~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~eLL~~F~~ 74 (200) T cd05160 1 VLSFDIETLPNVGG----PEP--SRDPIICISYADSFQGHKVVFLLKVSTHGDDIEAGFIDGIEVEYFDDEKELLKRFFD 74 (200) T ss_pred CEEEEEEECCCCCC----CCC--CCCEEEEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHH T ss_conf 97999832799997----899--988089999999359999998864355676765467799699996999999999999 Q ss_pred HHC--CCCCEEEEEEH-HHHHHHHHH---HCCCCCC---------------------CCCEEEHHHHHHHH-C-CCCCHH Q ss_conf 864--88981998630-775999998---6299878---------------------65045458899985-8-899978 Q gi|254780127|r 60 YLR--DETVMCVAHNS-LFERILFKK---TLGIDIP---------------------SKRWICTSVLARTN-G-LPSSLK 110 (675) Q Consensus 60 ~L~--~~~~~kv~HNa-~FD~~vL~~---~lGi~i~---------------------~~~~~DTmi~A~~l-~-~p~sL~ 110 (675) T Consensus 75 ~i~~~dPDii-~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~~~l~sy~Ld 153 (200) T cd05160 75 IIREYDPDIL-TGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVKRDFKLKSYTLD 153 (200) T ss_pred HHHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHHHHHCCCCCCHH T ss_conf 9997099999-972677784889999999969885554673454543575059973677860289999975324665399 Q ss_pred HHHHH-HCCCCCCHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99998-088986527663765766410023320134531125876899989887753999999998 Q gi|254780127|r 111 NACLA-LNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFK 175 (675) Q Consensus 111 ~la~~-lgl~~~~~kd~~gk~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~~~~L~~ 175 (675) T Consensus 154 ~Va~~~Lg~~K~d---~~~~~~~~~~-------------~---~~d~~k~~~Y~~~D~~L~~~L~e 200 (200) T cd05160 154 AVAEELLGEGKEK---VDGEIIEDLE-------------W---EEDLERLLEYNLKDAELTLQILE 200 (200) T ss_pred HHHHHHHCCCCCC---CCHHHHHHHH-------------H---CCCCHHHHHEEHHHHHHHHHHHC T ss_conf 9999984999787---8989999998-------------7---38914866025999998999759

HHsearch alignment for GI: 254780127 and conserved domain: cd05160