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