>cd06126 DEDDy DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. DEDDy exonucleases include the proofreading domains of DNA polymerases (families A and B), as well as RNases such as RNase D and Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, Bacillus-like DNA polymerases contain inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity.

Probab=99.04 E-value=5.7e-10 Score=91.29 Aligned_cols=156 Identities=21% Similarity=0.267 Sum_probs=105.4 Q ss_pred CCCCCCCCCCCCC--CCCCCCCCEEECCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHH Q ss_conf 5232332224331--10012442010257766544345502313744333456500178899997444420222100110 Q gi|254780277|r 389 SASFKIITDTMDA--FHSKPIAIAISTLDQKDDTSFKVETIFIDLSVHTSQDSTGKNTLTKEILSYLKKFFENEHFLKIG 466 (976) Q Consensus 389 ~ia~DtETt~ld~--~~~~ivGisls~~~~~~~~~~~~~~~yip~~~~~~~d~~~~~~~~~evl~~L~~lle~~~i~kIg 466 (976) T Consensus 1 vl~fDiE~~~~~~~~~~~pI~~i~~~~~~g~--------~~~~~~~~~~~~--~~~~~~E~~ll~~f~~~i~~~~dii~G 70 (181) T cd06126 1 VVAFDIETTPLVGGGGKGPIILIQLAVSAGE--------KFLLDVLTLTLD--AVDSADEKELLGELKAILEDYDDIKVG 70 (181) T ss_pred CEEEEEECCCCCCCCCCCCEEEEEEEECCCC--------EEEEEECCCCCC--CCCCCCHHHHHHHHHHHHHCCCCEEEE T ss_conf 9289862379899989998899999965997--------899986243467--556789999999999998308998999 Q ss_pred CCC-CHHHHHHHH----CCCCC----------------CC--CCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCCC Q ss_conf 032-123788986----18866----------------64--21002345543168766772466776224442233565 Q gi|254780277|r 467 HNI-KYDKLVLHR----YGISM----------------RG--FEDIMLMSYVLDSGRSSHDIASIAQKWLSYTRKEILKS 523 (976) Q Consensus 467 HN~-KfD~~~L~~----~GI~l----------------~~--i~DTmlaayLLdp~~~~~~L~~la~~yL~~~~~e~~~~ 523 (976) T Consensus 71 yN~~~FDlpyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~gr~~~D~~~~~~~~~~~~~~~~L~~va~~~lg~~K~~~~~~ 150 (181) T cd06126 71 YNIDSFDLPYLLNRAGELGIPLRRGRDRSSGSREEINIKGRILFDLLLAAKRLGVALPSYSLDALAEQLLGEGKEKVDQL 150 (181) T ss_pred ECCCCCCHHHHHHHHHHHCCCCHHCCCCCCCCCCEEEECCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHH T ss_conf 79977879999999999589701022666565504863485232199999984136465359999999749995669999 Q ss_pred CCCCCCCHHHCCHHHHHHHHHHHHHHHHHHH Q ss_conf 4322210000001233332221111124567 Q gi|254780277|r 524 RKSSIPIDKISDSQVQEHAIENSNVILQLWL 554 (976) Q Consensus 524 ~k~~~~~~~i~~e~~~~Yaa~Da~~t~~L~~ 554 (976) T Consensus 151 ~i~~~w~~~~~~~~~~~Y~~~Da~~tl~l~l 181 (181) T cd06126 151 AIKQAWRARPLLERLAEYAAADAYATLQIYL 181 (181) T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 9999886798669999999999999999769

HHsearch alignment for GI: 254780277 and conserved domain: cd06126