>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=98.52 E-value=3.4e-06 Score=58.47 Aligned_cols=158 Identities=17% Similarity=0.192 Sum_probs=81.5 Q ss_pred CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEE--CCEE------------------EEEEECCCCHHHHHHHHHH Q ss_conf 9689998141789870004400112798199999998--4803------------------9999788810437999998 Q gi|254781193|r 1 MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGF--DDHP------------------VELWDCVHDPVMPQVLKEA 60 (675) Q Consensus 1 mk~i~lD~ET~~~~dl~~~Gl~~y~~~~~i~~i~~a~--~~~~------------------v~~~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 LRILSFDIECAGRK-----GVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDF 81 (230) T ss_pred CEEEEEEEEECCCC-----CCCCCCCCCCEEEEEEEEEECCCCCCEEEEEEEECCCCCCCCCEEEECCCHHHHHHHHHHH T ss_conf 04999999952699-----9998988883489999998279776047878982687888998799849999999999999 Q ss_pred HC--CCCCEEEEEEH-HHHHHHHHHH---CCCCC----------C-----------------------CCC-EEEHHHHH Q ss_conf 63--88981999730-7749999986---08998----------8-----------------------420-33168899 Q gi|254781193|r 61 LE--NTDVTIVAHNS-YFERTVLKAC---FNLDI----------P-----------------------IHR-WICTLVLA 100 (675) Q Consensus 61 L~--~~~~~kV~HNa-~FD~~~L~~~---~Gi~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-CCCCHHHHHHHCCCCCCHHH-HHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 98-67-89996898998299811004-37999986202112343323467858532899999989989999999963010 Q gi|254781193|r 101 RS-NG-LPSALKAVGEALKLSSQKME-EGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFKRLEP 177 (675) Q Consensus 101 ~~-l~-~~~sL~~la~~l~l~~~k~~-~~k~l~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~t~~L~~~l~~ 177 (675) T Consensus 161 r~~~~l~sY~L~~Va~~~-Lg~~K~d~~~~~i~~~~--------------~~~~~~~~~~~~Y~i~D~~L~~~L~~Kl~~ 225 (230) T cd05777 161 QRDYKLRSYSLNSVSAHF-LGEQKEDVHYSIITDLQ--------------NGNPETRRRLAVYCLKDAYLPLRLLDKLMC 225 (230) T ss_pred HHHCCHHHCCHHHHHHHH-HCCCCCCCCHHHHHHHH--------------HCCHHHHHHHHEECHHHHHHHHHHHHHHHH T ss_conf 975016336499999998-38998879999999999--------------479646456006426877999999999877 Q ss_pred CH Q ss_conf 40 Q gi|254781193|r 178 LS 179 (675) Q Consensus 178 ~~ 179 (675) T Consensus 226 ~~ 227 (230) T cd05777 226 LV 227 (230) T ss_pred HH T ss_conf 74

HHsearch alignment for GI: 254781193 and conserved domain: cd05777