HHsearch alignment for GI: 254780306 and conserved domain: cd00188
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.86 E-value=0.0002 Score=52.24 Aligned_cols=72 Identities=33% Similarity=0.481 Sum_probs=59.7
Q ss_pred CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r 2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP 81 (837)
Q Consensus 2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~ 81 (837)
T Consensus 2 ~viivEG~~d~~~l~~~~~~~~~~~~~~G~~~~-------------------------~~~~~~~~~~~~~~~vii~~D~ 56 (83)
T cd00188 2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALN-------------------------KTRELLKRLLGEAKEVIIATDA 56 (83)
T ss_pred EEEEECCHHHHHHHHHHCCCCEEEEEEEEEECC-------------------------CHHHHHHHHHCCCCEEEEECCC
T ss_conf 799988889999999856999799997557384-------------------------3899999987689999997498
Q ss_pred CCHHHHHHHHHHHHHHH
Q ss_conf 70257999999999755
Q gi|254780306|r 82 DREGEAISWHVLDVLRQ 98 (837)
Q Consensus 82 DREGE~Iawhi~e~l~~ 98 (837)
T Consensus 57 D~~g~~~~~~~~~~~~~ 73 (83)
T cd00188 57 DREGEAIALRLLELLKS 73 (83)
T ss_pred CHHHHHHHHHHHHHHHH
T ss_conf 93799999999997323