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