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