HHsearch alignment for GI: 254780762 and conserved domain: cd03363
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. 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 base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=96.79 E-value=0.014 Score=38.75 Aligned_cols=60 Identities=23% Similarity=0.365 Sum_probs=43.2
Q ss_pred HHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 89999985157855499994699786899999999820179808874146748820666347999999830
Q gi|254780762|r 127 IQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRS 197 (201)
Q Consensus 127 i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~~ikitrla~GiP~G~~ley~D~~TL~~Al~~ 197 (201)
T Consensus 63 i~~ik~l~--~~ad~viiAtD~DrEGE~I~~~i~~~~~~-~~~~~Ri~f--------~~iT~~aI~~A~~n 122 (123)
T cd03363 63 VKELKKLA--KKADEIYLATDPDREGEAIAWHLAEVLKL-KKNVKRVVF--------NEITKEAIKEALKN 122 (123)
T ss_pred HHHHHHHH--HHCCEEEECCCCCCCHHHHHHHHHHHHCC-CCCCEEEEE--------ECCCHHHHHHHHHC
T ss_conf 99999998--50998998489982479999999999589-999728999--------25699999999968