HHsearch alignment for GI: 254780818 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=97.29  E-value=0.0009  Score=43.52  Aligned_cols=89  Identities=16%  Similarity=0.220  Sum_probs=51.9

Q ss_pred             CCCEEEEECCCCCCCCCCCEEEEEEEEEEECCEECCCEEEEEECCCCCCCCHHHEEECCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             77589998467888888888999999999999880313798985888228865724202101232248521002344777
Q gi|254780818|r    6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWD   85 (245)
Q Consensus         6 ~mr~iv~D~ETTGl~~~~d~Iieigav~i~~~~~~~~~f~~~i~P~~~~i~~~~~~ihGIt~~~l~~~p~f~ev~~~f~~   85 (245)
T Consensus         2 ~lki~s~DIE~~----~~~~i~~I~~~-~~~~---~~v~--~~~~~~-~~-------~~~---~v~~~~sE~eLL~~F~~   60 (193)
T cd05784           2 KLKVVSLDIETS----MDGELYSIGLY-GEGQ---ERVL--MVGDPE-DD-------APD---NIEWFADEKSLLLALIA   60 (193)
T ss_pred             CCEEEEEEECCC----CCCCEEEEEEE-CCCC---CEEE--EEECCC-CC-------CCC---EEEEECCHHHHHHHHHH
T ss_conf             830999996327----98888899998-6999---9899--997898-88-------997---79998999999999999


Q ss_pred             HHHCCCC-EEEEECC-CCCCCEEEECHHCCCC
Q ss_conf             5300232-0231023-2243112100000112
Q gi|254780818|r   86 FFNEQNA-EWIAHNA-KFDVGFINAELQRINK  115 (245)
Q Consensus        86 fi~~~~~-~lVaHNa-~FD~~fL~~el~r~~~  115 (245)
T Consensus        61 ~i~~~dPDiItG~N~~~FDiPYL~~R~~~~~i   92 (193)
T cd05784          61 WFAQYDPDIIIGWNVINFDLRLLQRRAEAHGL   92 (193)
T ss_pred             HHHHCCCCEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf             99862999999779877767899999998588