HHsearch alignment for GI: 254780277 and conserved domain: cd05160

>cd05160 DNA_polB_exo The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. 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 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 contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and
Probab=97.60  E-value=0.00014  Score=51.93  Aligned_cols=162  Identities=18%  Similarity=0.138  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCC----CCCCCCCCCEEECCCCCCCCCCCCCCEECCCCC-CCCCCC-CC-CCCCHHHHHHHHHHHHC--CC
Q ss_conf             23233222433----110012442010257766544345502313744-333456-50-01788999974444202--22
Q gi|254780277|r  390 ASFKIITDTMD----AFHSKPIAIAISTLDQKDDTSFKVETIFIDLSV-HTSQDS-TG-KNTLTKEILSYLKKFFE--NE  460 (976)
Q Consensus       390 ia~DtETt~ld----~~~~~ivGisls~~~~~~~~~~~~~~~yip~~~-~~~~d~-~~-~~~~~~evl~~L~~lle--~~  460 (976)
T Consensus         2 lsfDIE~~~~~gfP~p~~d~Ii~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~eLL~~F~~~i~~~dP   81 (200)
T cd05160           2 LSFDIETLPNVGGPEPSRDPIICISYADSFQGHKVVFLLKVSTHGDDIEAGFIDGIEVEYFDDEKELLKRFFDIIREYDP   81 (200)
T ss_pred             EEEEEEECCCCCCCCCCCCEEEEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCCC
T ss_conf             79998327999978999880899999993599999988643556767654677996999969999999999999997099


Q ss_pred             CCHHHHCCC-CHHHHHHH----HCCCCCC---------------------C--CCCHHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf             100110032-12378898----6188666---------------------4--210023455431687667724667762
Q gi|254780277|r  461 HFLKIGHNI-KYDKLVLH----RYGISMR---------------------G--FEDIMLMSYVLDSGRSSHDIASIAQKW  512 (976)
Q Consensus       461 ~i~kIgHN~-KfD~~~L~----~~GI~l~---------------------~--i~DTmlaayLLdp~~~~~~L~~la~~y  512 (976)
T Consensus        82 Dii-~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k-~~~~l~sy~Ld~Va~~~  159 (200)
T cd05160          82 DIL-TGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVK-RDFKLKSYTLDAVAEEL  159 (200)
T ss_pred             CEE-EECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHH-HHHCCCCCCHHHHHHHH
T ss_conf             999-9726777848899999999698855546734545435750599736778602899999-75324665399999998


Q ss_pred             CCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             244422335654322210000001233332221111124567
Q gi|254780277|r  513 LSYTRKEILKSRKSSIPIDKISDSQVQEHAIENSNVILQLWL  554 (976)
Q Consensus       513 L~~~~~e~~~~~k~~~~~~~i~~e~~~~Yaa~Da~~t~~L~~  554 (976)
T Consensus       160 Lg~~K~d~~~~~~~~~-~~~~d~~k~~~Y~~~D~~L~~~L~e  200 (200)
T cd05160         160 LGEGKEKVDGEIIEDL-EWEEDLERLLEYNLKDAELTLQILE  200 (200)
T ss_pred             HCCCCCCCCHHHHHHH-HHCCCCHHHHHEEHHHHHHHHHHHC
T ss_conf             4999787898999999-8738914866025999998999759