HHsearch alignment for GI: 254780661 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=97.95  E-value=0.00015  Score=47.93  Aligned_cols=128  Identities=18%  Similarity=0.061  Sum_probs=75.4

Q ss_pred             CCEEEEECCCCCCCCCCCEEEEEEEEEECCCCEECCEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCHHHHHHHH
Q ss_conf             83799975278898772604899999983897280400226621788877857898985799889960799979999999
Q gi|254780661|r    3 NHFVIYDYETFGRDVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITPQKALRDGVVEAEFSRRI   82 (471)
Q Consensus         3 ~~~v~~D~ETtG~~~~~~~iiq~~~i~~d~~~~~~~~~~~~~~~~~~~~~p~p~a~~v~git~~~~~~~~~~~~e~~~~i   82 (471)
T Consensus         3 lki~s~DIE~~~----~~~i~~I~~~--~~~~~---~v--~~~~~~~~---~------~~~~---v~~~~-sE~eLL~~F   58 (193)
T cd05784           3 LKVVSLDIETSM----DGELYSIGLY--GEGQE---RV--LMVGDPED---D------APDN---IEWFA-DEKSLLLAL   58 (193)
T ss_pred             CEEEEEEECCCC----CCCEEEEEEE--CCCCC---EE--EEEECCCC---C------CCCE---EEEEC-CHHHHHHHH
T ss_conf             309999963279----8888899998--69999---89--99978988---8------9977---99989-999999999


Q ss_pred             HHHHHCCCC-EEEEEECHHHHHHHHHHHHHHHCCCCCCC------------------CCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             999511796-59995055789999999998507853213------------------25688710015888865556532
Q gi|254780661|r   83 HQFFSVPNT-CIIGYNNIRFDDYYSRNIFYRNFYDSYRW------------------SWDNGNSRWDLLDVMRAIYAFSP  143 (471)
Q Consensus        83 ~~~~~~~~~-~~ig~N~~~FD~~~lr~~~~r~~~~~y~~------------------~~~~~~~~~D~l~~~~~~~~~~p  143 (471)
T Consensus        59 ~~~i~~~dPDiItG~N~~~FDiPYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~----  134 (193)
T cd05784          59 IAWFAQYDPDIIIGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTAT----  134 (193)
T ss_pred             HHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCC----
T ss_conf             9999862999999779877767899999998588643365788505987685626999978878417299997607----


Q ss_pred             HHCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             100244444544331089899871
Q gi|254780661|r  144 DGIQWPSRDDGATSFKLQDLALAN  167 (471)
Q Consensus       144 ~~~~~~~~~~~~~~~kL~~la~~n  167 (471)
T Consensus       135 --~-------~l~sy~Ld~Va~~~  149 (193)
T cd05784         135 --Y-------HFESFSLENVAQEL  149 (193)
T ss_pred             --C-------CHHHHHHHHHHHHH
T ss_conf             --3-------51143488899998