>cd05784 DNA_polB_II_exo The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (PolII) and similar bacterial proteins. PolII 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. 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 has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. PolII is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in a

Probab=98.61 E-value=1.1e-07 Score=68.98 Aligned_cols=156 Identities=17% Similarity=0.244 Sum_probs=82.2 Q ss_pred CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECCCEEEEEECCCCCHHHHHHHHHHC--CCCCEEEEEEH-HHHH Q ss_conf 97899980406788700046000026882999999983822899978884221799999864--88981998630-7759 Q gi|254780127|r 1 MSKLFIDIETRSPQPLPKVGVWAYAEQAVITLCAYAWDDEPVKLWDRTEQSAMPSDLLQYLR--DETVMCVAHNS-LFER 77 (675) Q Consensus 1 mk~l~lD~ET~s~~dl~~~Gl~~y~~~~~I~~i~~a~~~~~~~~~d~~~~~~~~~~l~~~L~--~~~~~kv~HNa-~FD~ 77 (675) T Consensus 3 lki~s~DIE~~~~~~i~~I~~~~~~-~~~v~~~~~~~~~~~~~v~~~~sE~eLL~~F~~~i~~~dPDiI-tG~N~~~FDi 80 (193) T cd05784 3 LKVVSLDIETSMDGELYSIGLYGEG-QERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDII-IGWNVINFDL 80 (193) T ss_pred CEEEEEEECCCCCCCEEEEEEECCC-CCEEEEEECCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEE-EECCCCCCCH T ss_conf 3099999632798888899998699-9989999789888997799989999999999999986299999-9779877767 Q ss_pred HHHHHH---CCCCC------------------------CCCCEEEHHHHHHH--HC-CCCCHHHHHHH-HCCCCCCHH-H Q ss_conf 999986---29987------------------------86504545889998--58-89997899998-088986527-6 Q gi|254780127|r 78 ILFKKT---LGIDI------------------------PSKRWICTSVLART--NG-LPSSLKNACLA-LNFSEHLTK-M 125 (675) Q Consensus 78 ~vL~~~---lGi~i------------------------~~~~~~DTmi~A~~--l~-~p~sL~~la~~-lgl~~~~~k-d 125 (675) T Consensus 81 PYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~~~l~sy~Ld~Va~~~LGe~K~~~~~~ 160 (193) T cd05784 81 RLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLIHDVD 160 (193) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 89999999858864336578850598768562699997887841729999760735114348889999838775445655 Q ss_pred HHCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 63765766410023320134531125876899989887753999999998 Q gi|254780127|r 126 EEGKALIARFCKGSIDSPPYDCTRANHVQAWQLFGEYCKRDVEATRELFK 175 (675) Q Consensus 126 ~~gk~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~~~~L~~ 175 (675) T Consensus 161 ~~~~~i~~l--------------~---~~d~~k~~~Yni~D~~Lv~rLf~ 193 (193) T cd05784 161 DRGAEIERL--------------F---REDKLALARYNLQDCELVWRIFE 193 (193) T ss_pred CCHHHHHHH--------------H---HCCCHHHEEEHHHHHHHHHHHHC T ss_conf 558889998--------------8---65903610320277999999749

HHsearch alignment for GI: 254780127 and conserved domain: cd05784