HHsearch alignment for GI: 254780306 and conserved domain: cd01028

>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. 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 b
Probab=99.97  E-value=1.1e-30  Score=249.36  Aligned_cols=123  Identities=38%  Similarity=0.592  Sum_probs=107.8

Q ss_pred             CCEEEECCHHHHHHHHHHHCC------------CCEEEEEECCCEECCCCCCCCCC-------CCCCCEEEEECCCHHHH
Q ss_conf             918997790478778875089------------98999942511007865578676-------66744068877654899
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGS------------NYKVLSSFGHIRDLPAKKGSVLP-------EKEFEMIWNIDPSSQKH   61 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~------------~y~V~as~GHirdLp~~~~~v~~-------~~~f~p~y~v~~~~kk~   61 (837)
T Consensus         1 ~~LiIaEKPs~ak~Ia~~Lg~~~~~~~~~~~~~~~~v~~~~GHl~~l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (142)
T cd01028           1 KVLIIAEKPSKAKTIAKILGKGSKKKGFYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQ   80 (142)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCHHHH
T ss_conf             98999889999999999968996556753468988999964400046881025750005865457888069989656999


Q ss_pred             HHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   62 LQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        62 ~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
T Consensus        81 ~~~i~~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~----~~~~v~R~~fsslT~~~I~~A~~nl  142 (142)
T cd01028          81 LKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC----DNKPVKRAWFSEITPKAIREAFKNL  142 (142)
T ss_pred             HHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC----CCCCCEEEEEECCCHHHHHHHHHCC
T ss_conf             9999999861999998889982279999999999578----8999278998357999999999758