HHsearch alignment for GI: 254780661 and conserved domain: cd06126
>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=98.46 E-value=7.1e-06 Score=56.52 Aligned_cols=130 Identities=19% Similarity=0.017 Sum_probs=83.4
Q ss_pred EEEECCCCCCCC--CCCEEEEEEEEEECCCCEECCEEEEEEECCCCCCCCCHHHHHHHCCCHHHHHHCCCCHHHHHHHHH
Q ss_conf 999752788987--726048999999838972804002266217888778578989857998899607999799999999
Q gi|254780661|r 6 VIYDYETFGRDV--ALDRPAQFAGVRVDRQWEKIESTEVFFCKPADDYLPDPEAVFITGITPQKALRDGVVEAEFSRRIH 83 (471)
Q Consensus 6 v~~D~ETtG~~~--~~~~iiq~~~i~~d~~~~~~~~~~~~~~~~~~~~~p~p~a~~v~git~~~~~~~~~~~~e~~~~i~ 83 (471)
T Consensus 2 l~fDiE~~~~~~~~~~~pI~~i~~~-~~~g~~~~-----~~~--~~~~~~~~~--------------~-~~E~~ll~~f~ 58 (181)
T cd06126 2 VAFDIETTPLVGGGGKGPIILIQLA-VSAGEKFL-----LDV--LTLTLDAVD--------------S-ADEKELLGELK 58 (181)
T ss_pred EEEEEECCCCCCCCCCCCEEEEEEE-ECCCCEEE-----EEE--CCCCCCCCC--------------C-CCHHHHHHHHH
T ss_conf 2898623798999899988999999-65997899-----986--243467556--------------7-89999999999
Q ss_pred HHHHCCCCEEEEEECHHHHHHHHHHHHHHHCCCCCCC----------CCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 9951179659995055789999999998507853213----------256887100158888655565321002444445
Q gi|254780661|r 84 QFFSVPNTCIIGYNNIRFDDYYSRNIFYRNFYDSYRW----------SWDNGNSRWDLLDVMRAIYAFSPDGIQWPSRDD 153 (471)
Q Consensus 84 ~~~~~~~~~~ig~N~~~FD~~~lr~~~~r~~~~~y~~----------~~~~~~~~~D~l~~~~~~~~~~p~~~~~~~~~~ 153 (471)
T Consensus 59 ~~i~~~~dii~GyN~~~FDlpyL~~R~~~l~~~~~~~~~~~~~~~~~~~~~gr~~~D~~~~~~~~~-------------~ 125 (181)
T cd06126 59 AILEDYDDIKVGYNIDSFDLPYLLNRAGELGIPLRRGRDRSSGSREEINIKGRILFDLLLAAKRLG-------------V 125 (181)
T ss_pred HHHHCCCCEEEEECCCCCCHHHHHHHHHHHCCCCHHCCCCCCCCCCEEEECCCCCCCHHHHHHHHC-------------C
T ss_conf 998308998999799778799999999995897010226665655048634852321999999841-------------3
Q ss_pred CCCCCCHHHHHHHHCCCC
Q ss_conf 443310898998718876
Q gi|254780661|r 154 GATSFKLQDLALANGIEH 171 (471)
Q Consensus 154 ~~~~~kL~~la~~n~i~~ 171 (471)
T Consensus 126 ~~~~~~L~~va~~~lg~~ 143 (181)
T cd06126 126 ALPSYSLDALAEQLLGEG 143 (181)
T ss_pred CCCCCCHHHHHHHHCCCC
T ss_conf 646535999999974999