HHsearch alignment for GI: 254780222 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=96.27  E-value=0.011  Score=37.80  Aligned_cols=74  Identities=39%  Similarity=0.416  Sum_probs=52.7

Q ss_pred             EEEEEECCCCCCCCHHHCCCCCCEEEEEECCEECCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEC
Q ss_conf             37997327676421001011222012211231314454108776322889999988256654333334655251899977
Q gi|254780222|r  464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQYREEDLRYEKVIIMTD  543 (686)
Q Consensus       464 ~eL~lvEGDSA~gsAk~grdr~~qgi~PLRGKiLNv~~as~~ki~~N~Ei~~l~~~lGl~~g~~~~~~~LRYgkIiImTD  543 (686)
T Consensus         1 ~~viivEG~~d~~~l~~~~~~-~~~~~~~~G~~~~------------~~~~~~~~~~~~------------~~~vii~~D   55 (83)
T cd00188           1 KKLIIVEGPSDALALAQAGGY-GGAVVALGGHALN------------KTRELLKRLLGE------------AKEVIIATD   55 (83)
T ss_pred             CEEEEECCHHHHHHHHHHCCC-CEEEEEEEEEECC------------CHHHHHHHHHCC------------CCEEEEECC
T ss_conf             979998888999999985699-9799997557384------------389999998768------------999999749


Q ss_pred             CCCCCHHHHHHHHHHHHHH
Q ss_conf             9877146889999999987
Q gi|254780222|r  544 ADVDGAHIASLLLTFFYQE  562 (686)
Q Consensus       544 aD~DGsHI~~Lll~ff~~~  562 (686)
T Consensus        56 ~D~~g~~~~~~~~~~~~~~   74 (83)
T cd00188          56 ADREGEAIALRLLELLKSL   74 (83)
T ss_pred             CCHHHHHHHHHHHHHHHHC
T ss_conf             8937999999999973234