HHsearch alignment for GI: 254780351 and conserved domain: cd00186

>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=92.44  E-value=0.89  Score=24.89  Aligned_cols=54  Identities=17%  Similarity=0.249  Sum_probs=40.2

Q ss_pred             CCHHHHHHHH---CC-CCCHHHHHHHHHHHCCCEEEEECCCCCCEEEEEECHHHHHHHHHHHHHH
Q ss_conf             6889999985---47-7105679999999778878863610071056445788999999999999
Q gi|254780351|r   71 LTAGELRSRG---YY-LGSNVSYNLKKLIDLGFIKHQRSRIDKRSIRISLTQSGKEIAETISQLY  131 (171)
Q Consensus        71 ~t~~eLa~~l---~i-~~~tvs~~i~~Le~~G~i~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~  131 (171)
T Consensus       283 yTe~tLi~~Me~~GIGTpATra~IIe~L~~r~Yi~~~~-------~~l~~T~~G~~li~~l~~~~  340 (381)
T cd00186         283 YTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEK-------KKLIPTELGFAVIELLEKHF  340 (381)
T ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEEC-------CEEEECHHHHHHHHHHHHHH
T ss_conf             78999999765369987265989999998478099329-------99967378999999998754