HHsearch alignment for GI: 254781193 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=98.74  E-value=7.9e-08  Score=69.07  Aligned_cols=153  Identities=20%  Similarity=0.241  Sum_probs=83.7

Q ss_pred             CCEEEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEECCEEEEEEECCCCHHHHHHHHHHHC--CCCCEEEEEEH-HHHH
Q ss_conf             96899981417898700044001127981999999984803999978881043799999863--88981999730-7749
Q gi|254781193|r    1 MATLFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFDDHPVELWDCVHDPVMPQVLKEALE--NTDVTIVAHNS-YFER   77 (675)
Q Consensus         1 mk~i~lD~ET~~~~dl~~~Gl~~y~~~~~i~~i~~a~~~~~v~~~d~~~~~~~~~~l~~~L~--~~~~~kV~HNa-~FD~   77 (675)
T Consensus         3 lki~s~DIE~~~~~~i~~I~~~~~~-~~~v~~~~~~~~~~~~~v~~~~sE~eLL~~F~~~i~~~dPDi-ItG~N~~~FDi   80 (193)
T cd05784           3 LKVVSLDIETSMDGELYSIGLYGEG-QERVLMVGDPEDDAPDNIEWFADEKSLLLALIAWFAQYDPDI-IIGWNVINFDL   80 (193)
T ss_pred             CEEEEEEECCCCCCCEEEEEEECCC-CCEEEEEECCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCE-EEECCCCCCCH
T ss_conf             3099999632798888899998699-998999978988899779998999999999999998629999-99779877767


Q ss_pred             HHHHHH---CCCCCC-----------------------CCC-EEEHHHHHHH--HC-CCCCHHHHHHHCCCCCCHHHH--
Q ss_conf             999986---089988-----------------------420-3316889998--67-899968989982998110043--
Q gi|254781193|r   78 TVLKAC---FNLDIP-----------------------IHR-WICTLVLARS--NG-LPSALKAVGEALKLSSQKMEE--  125 (675)
Q Consensus        78 ~~L~~~---~Gi~i~-----------------------~~~-~~DTmi~A~~--l~-~~~sL~~la~~l~l~~~k~~~--  125 (675)
T Consensus        81 PYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~~~l~sy~Ld~Va~~~-LGe~K~~~~~  159 (193)
T cd05784          81 RLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQEL-LGEGKLIHDV  159 (193)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCCCCHHHHHHHHHHHHH-HCCCCCCCCC
T ss_conf             899999998588643365788505987685626999978878417299997607351143488899998-3877544565


Q ss_pred             ---HHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---799998620211234332346785853289999998998999999996
Q gi|254781193|r  126 ---GKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFK  173 (675)
Q Consensus       126 ---~k~l~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~t~~L~~  173 (675)
T Consensus       160 ~~~~~~i~~l~-----------------~~d~~k~~~Yni~D~~Lv~rLf~  193 (193)
T cd05784         160 DDRGAEIERLF-----------------REDKLALARYNLQDCELVWRIFE  193 (193)
T ss_pred             CCCHHHHHHHH-----------------HCCCHHHEEEHHHHHHHHHHHHC
T ss_conf             55588899988-----------------65903610320277999999749