HHsearch alignment for GI: 254780306 and conserved domain: cd03363

>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. 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=100.00  E-value=2.3e-37  Score=299.55  Aligned_cols=122  Identities=50%  Similarity=0.798  Sum_probs=115.8

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCC-CCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
Q ss_conf             91899779047877887508998999942511007865578676667-44068877654899999999987099899946
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKE-FEMIWNIDPSSQKHLQNIIHAVKSSTILILAT   79 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~-f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAt   79 (837)
T Consensus         1 K~LvIvEsPskak~I~~~LG~~y~V~as~GHl~~L~~~~~~~~~~~~~~~p~~~~~~~k~k~i~~ik~l~~~ad~viiAt   80 (123)
T cd03363           1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVIPGKKKVVKELKKLAKKADEIYLAT   80 (123)
T ss_pred             CEEEEEECHHHHHHHHHHHCCCCEEEEECCCHHHCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
T ss_conf             91999958788999999819996999711502315776467775457853377966417889999999985099899848


Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             997025799999999975512578871699998037989999998622
Q gi|254780306|r   80 DPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        80 D~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
T Consensus        81 D~DrEGE~I~~~i~~~~~~-----~~~~~Ri~f~~iT~~aI~~A~~nP  123 (123)
T cd03363          81 DPDREGEAIAWHLAEVLKL-----KKNVKRVVFNEITKEAIKEALKNP  123 (123)
T ss_pred             CCCCCHHHHHHHHHHHHCC-----CCCCEEEEEECCCHHHHHHHHHCC
T ss_conf             9982479999999999589-----999728999256999999999682