>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=98.52 E-value=1.6e-06 Score=60.65 Aligned_cols=141 Identities=23% Similarity=0.145 Sum_probs=87.8 Q ss_pred EEEECCCCCC----CCCCCEEEEEEEEEECCCCEECCEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCHHHHHHH Q ss_conf 9997527889----877260489999998389728040022662178887785789898579988996079997999999 Q gi|254780661|r 6 VIYDYETFGR----DVALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITPQKALRDGVVEAEFSRR 81 (471) Q Consensus 6 v~~D~ETtG~----~~~~~~iiq~~~i~~d~~~~~~~~~~~~~~~~~~~~~p~p~a~~v~git~~~~~~~~~~~~e~~~~ 81 (471) T Consensus 2 lsfDIE~~~~~gfP~p~~d~Ii~Is~~~~-~~~----~~~~~~~~-~~~~~~~~~~~~~~~~---~v~~~-~~E~eLL~~ 71 (200) T cd05160 2 LSFDIETLPNVGGPEPSRDPIICISYADS-FQG----HKVVFLLK-VSTHGDDIEAGFIDGI---EVEYF-DDEKELLKR 71 (200) T ss_pred EEEEEEECCCCCCCCCCCCEEEEEEEEEE-CCC----EEEEEEEE-CCCCCCCCCCCCCCCE---EEEEE-CCHHHHHHH T ss_conf 79998327999978999880899999993-599----99998864-3556767654677996---99996-999999999 Q ss_pred HHHHHHCCCC-EEEEEECHHHHHHHHHHHHHHHCCCCCCCC---------------CCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 9999511796-599950557899999999985078532132---------------568871001588886555653210 Q gi|254780661|r 82 IHQFFSVPNT-CIIGYNNIRFDDYYSRNIFYRNFYDSYRWS---------------WDNGNSRWDLLDVMRAIYAFSPDG 145 (471) Q Consensus 82 i~~~~~~~~~-~~ig~N~~~FD~~~lr~~~~r~~~~~y~~~---------------~~~~~~~~D~l~~~~~~~~~~p~~ 145 (471) T Consensus 72 F~~~i~~~dPDii~GyN~~~FD~pyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~Gr~~lD~~~~~k~~~------ 145 (200) T cd05160 72 FFDIIREYDPDILTGYNIDDFDLPYLLERAKALGIKLDDIGRRSGQEKSSGETERAAVKGRVVFDLLRAVKRDF------ 145 (200) T ss_pred HHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCEEEEEECCEEEEHHHHHHHHHH------ T ss_conf 99999970999999726777848899999999698855546734545435750599736778602899999753------ Q ss_pred CCCCCCCCCCCCCCHHHHHHHHCCC Q ss_conf 0244444544331089899871887 Q gi|254780661|r 146 IQWPSRDDGATSFKLQDLALANGIE 170 (471) Q Consensus 146 ~~~~~~~~~~~~~kL~~la~~n~i~ 170 (471) T Consensus 146 --------~l~sy~Ld~Va~~~Lg~ 162 (200) T cd05160 146 --------KLKSYTLDAVAEELLGE 162 (200) T ss_pred --------CCCCCCHHHHHHHHHCC T ss_conf --------24665399999998499

HHsearch alignment for GI: 254780661 and conserved domain: cd05160