>cd05777 DNA_polB_delta_exo The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The 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 contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polyme

Probab=98.40 E-value=8.1e-06 Score=56.67 Aligned_cols=157 Identities=13% Similarity=0.167 Sum_probs=77.9 Q ss_pred CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEE--CCCE--E----------------EEEECCCCCHHHHHHHHH Q ss_conf 9789998040678870004600002688299999998--3822--8----------------999788842217999998 Q gi|254780127|r 1 MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAW--DDEP--V----------------KLWDRTEQSAMPSDLLQY 60 (675) Q Consensus 1 mk~l~lD~ET~s~~dl~~~Gl~~y~~~~~I~~i~~a~--~~~~--~----------------~~~d~~~~~~~~~~l~~~ 60 (675) T Consensus 7 lki~sfDIE~~s~~g-----~fP~p~~D~Ii~I~~~~~~~~~~~~~~~~v~~l~~~~~i~~~~V~~~~tE~eLL~~F~~~ 81 (230) T cd05777 7 LRILSFDIECAGRKG-----VFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDF 81 (230) T ss_pred CEEEEEEEEECCCCC-----CCCCCCCCCEEEEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCHHHHHHHHHHH T ss_conf 049999999526999-----998988883489999998279776047878982687888998799849999999999999 Q ss_pred HC--CCCCEEEEEEH-HHHHHHHHHH---CCCCC----------------------------------CCCCEEEHHHHH Q ss_conf 64--88981998630-7759999986---29987----------------------------------865045458899 Q gi|254780127|r 61 LR--DETVMCVAHNS-LFERILFKKT---LGIDI----------------------------------PSKRWICTSVLA 100 (675) Q Consensus 61 L~--~~~~~kv~HNa-~FD~~vL~~~---lGi~i----------------------------------~~~~~~DTmi~A 100 (675) T Consensus 82 i~~~dPDii-tGyN~~~FD~pYL~~Ra~~l~~~~~~~lgr~~~~~~~~~~~~~~s~~~g~~~~~~~~i~Gr~~lD~~~~~ 160 (230) T cd05777 82 VQEVDPDII-TGYNICNFDLPYLLERAKALKLNTFPFLGRIKNIKSTIKDTTFSSKQMGTRETKEINIEGRIQFDLLQVI 160 (230) T ss_pred HHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCCHHHHCCCCCCCCEEECCCCCCCCCCCCEEEEEEECCEEHHHHHHHH T ss_conf 998099999-9636667887899999999688614541766787635741652223126400269987587599999999 Q ss_pred HH-HC-CCCCHHHHHHH-HCCCCCCHHHHHCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98-58-89997899998-08898652766376576641002332013453112587689998988775399999999872 Q gi|254780127|r 101 RT-NG-LPSSLKNACLA-LNFSEHLTKMEEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFKRL 177 (675) Q Consensus 101 ~~-l~-~p~sL~~la~~-lgl~~~~~kd~~gk~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~~~~L~~~L 177 (675) T Consensus 161 r~~~~l~sY~L~~Va~~~Lg~~K~d~---~~~~i~~--------------~~~~~~~~~~~~~~Y~i~D~~L~~~L~~Kl 223 (230) T cd05777 161 QRDYKLRSYSLNSVSAHFLGEQKEDV---HYSIITD--------------LQNGNPETRRRLAVYCLKDAYLPLRLLDKL 223 (230) T ss_pred HHHCCHHHCCHHHHHHHHHCCCCCCC---CHHHHHH--------------HHHCCHHHHHHHHEECHHHHHHHHHHHHHH T ss_conf 97501633649999999838998879---9999999--------------994796464560064268779999999998 Q ss_pred CCC Q ss_conf 002 Q gi|254780127|r 178 IPL 180 (675) Q Consensus 178 ~~~ 180 (675) T Consensus 224 ~~~ 226 (230) T cd05777 224 MCL 226 (230) T ss_pred HHH T ss_conf 777

HHsearch alignment for GI: 254780127 and conserved domain: cd05777