HHsearch alignment for GI: 254780306 and conserved domain: cd03362

>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=99.97  E-value=1.6e-30  Score=248.23  Aligned_cols=124  Identities=28%  Similarity=0.431  Sum_probs=106.7

Q ss_pred             CCEEEECCHHHHHHHHHHHCC------------------CCEEEEEECCCEECCCCC---------CCCCCCCCCCEEEE
Q ss_conf             918997790478778875089------------------989999425110078655---------78676667440688
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGS------------------NYKVLSSFGHIRDLPAKK---------GSVLPEKEFEMIWN   53 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~------------------~y~V~as~GHirdLp~~~---------~~v~~~~~f~p~y~   53 (837)
T Consensus         1 m~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~~~~~~~~~~~~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~~~~~~~~~~~   80 (151)
T cd03362           1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLK   80 (151)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHCCCCCHHHCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             99999889899999999848996114765433211368988999750232144530223544357855576788771589


Q ss_pred             ECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             77654899999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   54 IDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        54 v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
T Consensus        81 ~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~ei~~~~~~---~~~~~v~R~~fs~lT~~~I~~A~~nL  151 (151)
T cd03362          81 VDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKC---VKRKPVKRAWFSSLTPKAIRRAFKNL  151 (151)
T ss_pred             ECCCHHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEEECCCHHHHHHHHHCC
T ss_conf             885489999999999853998998778872045999999998488---88985689998048999999999758