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