HHsearch alignment for GI: 254780814 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=94.88  E-value=0.064  Score=34.03  Aligned_cols=73  Identities=33%  Similarity=0.399  Sum_probs=48.6

Q ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCHHHCCHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             79998255754322334654430233005620334430587663236678888762578775332123567373899850
Q gi|254780814|r  426 ELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTD  505 (803)
Q Consensus       426 eL~ivEGDSAggsak~gRdr~~qai~PLrGKilNv~~a~~~~i~~n~Ei~~l~~~lG~~~g~~~~~~~~lrY~kiiimtD  505 (803)
T Consensus         2 ~viivEG~~d~~~l~~~~~~-~~~~~~~~G~~~~------------~~~~~~~~~~~------------~-~~~vii~~D   55 (83)
T cd00188           2 KLIIVEGPSDALALAQAGGY-GGAVVALGGHALN------------KTRELLKRLLG------------E-AKEVIIATD   55 (83)
T ss_pred             EEEEECCHHHHHHHHHHCCC-CEEEEEEEEEECC------------CHHHHHHHHHC------------C-CCEEEEECC
T ss_conf             79998888999999985699-9799997557384------------38999999876------------8-999999749


Q ss_pred             CCCCCCCHHHHHHHHHHHH
Q ss_conf             8888532899999999963
Q gi|254780814|r  506 ADVDGAHIRTLLLTFFFRQ  524 (803)
Q Consensus       506 aD~DG~HI~~Llltff~~~  524 (803)
T Consensus        56 ~D~~g~~~~~~~~~~~~~~   74 (83)
T cd00188          56 ADREGEAIALRLLELLKSL   74 (83)
T ss_pred             CCHHHHHHHHHHHHHHHHC
T ss_conf             8937999999999973234