HHsearch alignment for GI: 254780222 and conserved domain: cd01030

>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=100.00  E-value=0  Score=380.91  Aligned_cols=114  Identities=54%  Similarity=0.816  Sum_probs=112.5

Q ss_pred             EEEEEECCCCCCCCHHHCCCCCCEEEEEECCEECCHHHHHHHHHHCCHHHHHHHHHHCCCCCCCC-CCCCCCCCCEEEEE
Q ss_conf             37997327676421001011222012211231314454108776322889999988256654333-33465525189997
Q gi|254780222|r  464 TELFIVEGDSAGGSAKQARNRSNQAVLPLRGKILNVASAGSEKIRNNQQIMDLVQALGCRTRSQY-REEDLRYEKVIIMT  542 (686)
Q Consensus       464 ~eL~lvEGDSA~gsAk~grdr~~qgi~PLRGKiLNv~~as~~ki~~N~Ei~~l~~~lGl~~g~~~-~~~~LRYgkIiImT  542 (686)
T Consensus         1 c~L~l~EGdSA~g~~~~~rd~~~~gv~pLrGK~lNv~~~~~~ki~~N~Ei~~l~~~LGl~~~~~~~~~~~LRYgkIii~t   80 (115)
T cd01030           1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT   80 (115)
T ss_pred             CEEEEECCCCCHHHHHHHCCCCCEEEEECCCCCCCHHHCCHHHHHCCHHHHHHHHHHCCCCCCCCCCHHHCCCCCEEEEE
T ss_conf             97999647453455542048675899852781466666889898709789999999677989653536348627448987


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
Q ss_conf             79877146889999999987088863393899309
Q gi|254780222|r  543 DADVDGAHIASLLLTFFYQEMYDLIEQKHLFLISP  577 (686)
Q Consensus       543 DaD~DGsHI~~Lll~ff~~~~p~Li~~g~v~~~~t  577 (686)
T Consensus        81 DaD~DG~HI~~Lll~ff~~~~P~L~~~G~vyi~~T  115 (115)
T cd01030          81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT  115 (115)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEC
T ss_conf             89997579999999999998199998791799859