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