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