HHsearch alignment for GI: 254780762 and conserved domain: cd03362
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. 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=91.63 E-value=0.49 Score=28.39 Aligned_cols=53 Identities=23% Similarity=0.326 Sum_probs=39.2
Q ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHHCCC-CCEEEEEECCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 785549999469978689999999982017-9808874146748820666347999999830
Q gi|254780762|r 137 KKIRELIFAISATIEGQTTAHYIMDKLKGI-DVKITRLAYGIPMGSELDYLDDGTIFEAIRS 197 (201)
Q Consensus 137 ~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~~-~ikitrla~GiP~G~~ley~D~~TL~~Al~~ 197 (201)
T Consensus 97 ~~ad~ii~atD~DrEGE~I~~ei~~~~~~~~~~~v~R~~fs--------~lT~~~I~~A~~n 150 (151)
T cd03362 97 KRADEIVIATDADREGELIGREILEYAKCVKRKPVKRAWFS--------SLTPKAIRRAFKN 150 (151)
T ss_pred HHCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEE--------CCCHHHHHHHHHC
T ss_conf 53998998778872045999999998488889856899980--------4899999999975