HHsearch alignment for GI: 254780814 and conserved domain: cd03365

>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: 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). This glutamate and two aspartates, cluster together to form a highly acid surface patch. 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 cofact
Probab=100.00  E-value=2.9e-43  Score=355.03  Aligned_cols=112  Identities=40%  Similarity=0.661  Sum_probs=106.8

Q ss_pred             EEEEEEECCCCCCCCCCCC---CCCCEEEEECCCCCCCHHHCCHHHHHCCHHHHHHHHHHCCCCCCCC-CCCCCCCCCCE
Q ss_conf             1799982557543223346---5443023300562033443058766323667888876257877533-21235673738
Q gi|254780814|r  425 SELFLVEGDSAGGSAKQGR---SRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDS-FDINKLRYHKI  500 (803)
Q Consensus       425 ~eL~ivEGDSAggsak~gR---dr~~qai~PLrGKilNv~~a~~~~i~~n~Ei~~l~~~lG~~~g~~~-~~~~~lrY~ki  500 (803)
T Consensus         1 CtL~l~EGDSA~g~a~~g~~~~~r~~~gv~PLrGK~lNv~~~~~~ki~~N~Ei~~l~~~LGl~~g~~~~~d~~~LRYgkI   80 (120)
T cd03365           1 CTLILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYESTKSLRYGRL   80 (120)
T ss_pred             CEEEEECCCCCHHHHHHCCCCCCCCEEEEEECCCEECCHHHCCHHHHHCCHHHHHHHHHHCCCCCCCCCCCHHHCCCCEE
T ss_conf             97999768474778872246558751789741887611522768777528889999999856767665565212788858


Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHHHHHH-CCEEEE
Q ss_conf             998508888532899999999963077874-895999
Q gi|254780814|r  501 IIMTDADVDGAHIRTLLLTFFFRQMPSLIH-NGFLYI  536 (803)
Q Consensus       501 iimtDaD~DG~HI~~Llltff~~~~~~li~-~g~~yi  536 (803)
T Consensus        81 iI~tDaDvDG~HI~~LlltfF~~~~P~Li~~~gFi~~  117 (120)
T cd03365          81 MIMTDQDHDGSHIKGLLINFIHSFWPSLLKIPGFLVE  117 (120)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf             9987898865789999999999981998655685665