HHsearch alignment for GI: 254781193 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=98.59  E-value=2e-06  Score=60.02  Aligned_cols=146  Identities=19%  Similarity=0.203  Sum_probs=83.1

Q ss_pred             EEEEECCCCCCCCCCCCCHHHCCCCEEEEEEEEEC--CEE---------------------EEEEECCCCHHHHHHHHHH
Q ss_conf             99981417898700044001127981999999984--803---------------------9999788810437999998
Q gi|254781193|r    4 LFIDFETRSPIDLTKCGICKYAEDVCVILFAFGFD--DHP---------------------VELWDCVHDPVMPQVLKEA   60 (675)
Q Consensus         4 i~lD~ET~~~~dl~~~Gl~~y~~~~~i~~i~~a~~--~~~---------------------v~~~d~~~~~~~~~~l~~~   60 (675)
T Consensus         2 lsfDIE~~~~~g----fP~p--~~d~Ii~Is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~E~eLL~~F~~~   75 (200)
T cd05160           2 LSFDIETLPNVG----GPEP--SRDPIICISYADSFQGHKVVFLLKVSTHGDDIEAGFIDGIEVEYFDDEKELLKRFFDI   75 (200)
T ss_pred             EEEEEEECCCCC----CCCC--CCCEEEEEEEEEECCCEEEEEEEECCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHH
T ss_conf             799983279999----7899--9880899999993599999988643556767654677996999969999999999999


Q ss_pred             HC--CCCCEEEEEEH-HHHHHHHHH---HCCCCCC--------------------CCC-EEEHHHHHHHH--CCCCCHHH
Q ss_conf             63--88981999730-774999998---6089988--------------------420-33168899986--78999689
Q gi|254781193|r   61 LE--NTDVTIVAHNS-YFERTVLKA---CFNLDIP--------------------IHR-WICTLVLARSN--GLPSALKA  111 (675)
Q Consensus        61 L~--~~~~~kV~HNa-~FD~~~L~~---~~Gi~i~--------------------~~~-~~DTmi~A~~l--~~~~sL~~  111 (675)
T Consensus        76 i~~~dPDii-~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~~~l~sy~Ld~  154 (200)
T cd05160          76 IREYDPDIL-TGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVKRDFKLKSYTLDA  154 (200)
T ss_pred             HHHCCCCEE-EECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHHHHHCCCCCCHHH
T ss_conf             997099999-9726777848899999999698855546734545435750599736778602899999753246653999


Q ss_pred             HHHHCCCCCCHHH-HHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8998299811004-3799998620211234332346785853289999998998999999996
Q gi|254781193|r  112 VGEALKLSSQKME-EGKELIARFCKGETHECLYDRNKPNHREAWRLFGEYCKGDVTVTREIFK  173 (675)
Q Consensus       112 la~~l~l~~~k~~-~~k~l~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~Ya~~Dv~~t~~L~~  173 (675)
T Consensus       155 Va~~~-Lg~~K~d~~~~~~~~~~----------------~~~d~~k~~~Y~~~D~~L~~~L~e  200 (200)
T cd05160         155 VAEEL-LGEGKEKVDGEIIEDLE----------------WEEDLERLLEYNLKDAELTLQILE  200 (200)
T ss_pred             HHHHH-HCCCCCCCCHHHHHHHH----------------HCCCCHHHHHEEHHHHHHHHHHHC
T ss_conf             99998-49997878989999998----------------738914866025999998999759