HHsearch alignment for GI: 254780762 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=97.16  E-value=0.005  Score=41.79  Aligned_cols=81  Identities=28%  Similarity=0.412  Sum_probs=60.8

Q ss_pred             CEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             36999835889999975174013421012100200026811128899999851578554999946997868999999998
Q gi|254780762|r   83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDK  162 (201)
Q Consensus        83 ~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~  162 (201)
T Consensus         1 ~~viivEG~~d~~~l~~~~~~~~~~~~~~G~~~~---------~~~~~~~~~~~~-~~~vii~~D~D~~g~~~~~~~~~~   70 (83)
T cd00188           1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALN---------KTRELLKRLLGE-AKEVIIATDADREGEAIALRLLEL   70 (83)
T ss_pred             CEEEEECCHHHHHHHHHHCCCCEEEEEEEEEECC---------CHHHHHHHHHCC-CCEEEEECCCCHHHHHHHHHHHHH
T ss_conf             9799988889999999856999799997557384---------389999998768-999999749893799999999997


Q ss_pred             HCCCCCEEEEE
Q ss_conf             20179808874
Q gi|254780762|r  163 LKGIDVKITRL  173 (201)
Q Consensus       163 lk~~~ikitrl  173 (201)
T Consensus        71 ~~~~~~~~~~~   81 (83)
T cd00188          71 LKSLGKKVRRL   81 (83)
T ss_pred             HHHCCCCEEEE
T ss_conf             32349847998