HHsearch alignment for GI: 254780636 and conserved domain: cd05784

>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=97.08  E-value=0.0019  Score=39.28  Aligned_cols=139  Identities=17%  Similarity=0.096  Sum_probs=72.2

Q ss_pred             CCCEEEECCCCCCCCCCCEEEEEEEEECC-CCEEEEC------------CCCCCCCCHHHHHHHH--CCCCCEEECCC-C
Q ss_conf             98279971777898544507999984189-4289974------------6577857067767773--23640230100-0
Q gi|254780636|r   20 VDAIAVDTETLGLMPRRDRLCIVQLSPGD-GTVDIIR------------IAAGQKNAPNLVGMLV--DEKREKIFHYG-R   83 (207)
Q Consensus        20 ~~~iaiDtEt~~l~~~~~~l~LiQl~~~~-~~~~l~~------------~~~~~~~~~~L~~ll~--d~~i~KV~Hn~-~   83 (207)
T Consensus         3 lki~s~DIE~~~~~----~i~~I~~~~~~~~~v~~~~~~~~~~~~~v~~~~sE~eLL~~F~~~i~~~dPDiI-tG~N~~~   77 (193)
T cd05784           3 LKVVSLDIETSMDG----ELYSIGLYGEGQERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDII-IGWNVIN   77 (193)
T ss_pred             CEEEEEEECCCCCC----CEEEEEEECCCCCEEEEEECCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEE-EECCCCC
T ss_conf             30999996327988----888999986999989999789888997799989999999999999986299999-9779877


Q ss_pred             HHHHHHHHHHH---CC------------------------CCC--HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC-C
Q ss_conf             01688865420---00------------------------000--045789886521100000088777654200246-7
Q gi|254780636|r   84 FDIAVLFYTFG---VR------------------------VRP--VFCTKIASRLTRTYTNQHGLKDNLKELLGINIS-K  133 (207)
Q Consensus        84 ~D~~~L~~~~g---i~------------------------~~~--i~DT~ias~l~~~~~~~~~L~~L~~~~lg~~ld-K  133 (207)
T Consensus        78 FDiPYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~~~l~sy~Ld~Va~~~LGe~K~~~  157 (193)
T cd05784          78 FDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELLGEGKLIH  157 (193)
T ss_pred             CCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             76789999999858864336578850598768562699997887841729999760735114348889999838775445


Q ss_pred             CC--EEC----CCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             52--003----656544323689999864599999999
Q gi|254780636|r  134 AQ--QSS----DWSADDLSDEQLQYAASDVVHLHALRL  165 (207)
Q Consensus       134 ~~--q~S----dW~~rpLs~~Qi~YAA~Dv~~l~~L~~  165 (207)
T Consensus       158 ~~~~~~~~i~~l~~~d~--~k~~~Yni~D~~Lv~rLf~  193 (193)
T cd05784         158 DVDDRGAEIERLFREDK--LALARYNLQDCELVWRIFE  193 (193)
T ss_pred             CCCCCHHHHHHHHHCCC--HHHEEEHHHHHHHHHHHHC
T ss_conf             65555888999886590--3610320277999999749