HHsearch alignment for GI: 254780277 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=97.39  E-value=0.00029  Score=49.69  Aligned_cols=156  Identities=15%  Similarity=0.149  Sum_probs=79.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHC--CCCCHH
Q ss_conf             685232332224331100124420102577665443455023137443334565001788999974444202--221001
Q gi|254780277|r  387 IGSASFKIITDTMDAFHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFE--NEHFLK  464 (976)
Q Consensus       387 ~~~ia~DtETt~ld~~~~~ivGisls~~~~~~~~~~~~~~~yip~~~~~~~d~~~~~~~~~evl~~L~~lle--~~~i~k  464 (976)
T Consensus         3 lki~s~DIE~~~~----~~i~~I~~~~~~~~~v~~~~~~------~-~~~~~~v~~~~sE~eLL~~F~~~i~~~dPDiI-   70 (193)
T cd05784           3 LKVVSLDIETSMD----GELYSIGLYGEGQERVLMVGDP------E-DDAPDNIEWFADEKSLLLALIAWFAQYDPDII-   70 (193)
T ss_pred             CEEEEEEECCCCC----CCEEEEEEECCCCCEEEEEECC------C-CCCCCEEEEECCHHHHHHHHHHHHHHCCCCEE-
T ss_conf             3099999632798----8888999986999989999789------8-88997799989999999999999986299999-


Q ss_pred             HHCCC-CHHHHHHHH----CCCCC------------------------CC--CCCHHHHHHHHCCCCCCCCHHHHHHHHC
Q ss_conf             10032-123788986----18866------------------------64--2100234554316876677246677622
Q gi|254780277|r  465 IGHNI-KYDKLVLHR----YGISM------------------------RG--FEDIMLMSYVLDSGRSSHDIASIAQKWL  513 (976)
Q Consensus       465 IgHN~-KfD~~~L~~----~GI~l------------------------~~--i~DTmlaayLLdp~~~~~~L~~la~~yL  513 (976)
T Consensus        71 tG~N~~~FDiPYL~~R~~~~~i~~~~~r~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~~~~~~~l~sy~Ld~Va~~~L  150 (193)
T cd05784          71 IGWNVINFDLRLLQRRAEAHGLPLRLGRGGSPLNWRQSGKPGQGFLSLPGRVVLDGIDALKTATYHFESFSLENVAQELL  150 (193)
T ss_pred             EECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEECCEEEECHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             97798777678999999985886433657885059876856269999788784172999976073511434888999983


Q ss_pred             CCCCCCCCCCC--CCCCCCHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             44422335654--322210000001233332221111124567
Q gi|254780277|r  514 SYTRKEILKSR--KSSIPIDKISDSQVQEHAIENSNVILQLWL  554 (976)
Q Consensus       514 ~~~~~e~~~~~--k~~~~~~~i~~e~~~~Yaa~Da~~t~~L~~  554 (976)
T Consensus       151 Ge~K~~~~~~~~~~~i~~l~~~d~~k~~~Yni~D~~Lv~rLf~  193 (193)
T cd05784         151 GEGKLIHDVDDRGAEIERLFREDKLALARYNLQDCELVWRIFE  193 (193)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCHHHEEEHHHHHHHHHHHHC
T ss_conf             8775445655558889998865903610320277999999749