HHsearch alignment for GI: 254780306 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=100.00 E-value=0 Score=824.30 Aligned_cols=375 Identities=51% Similarity=0.770 Sum_probs=339.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHCHHHHHHCC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEE
Q ss_conf 899999999999898740113789886414--676534226899999999999964137654400122331579965422
Q gi|254780306|r 132 LDLVNAYLARRALDYLVGFNLSPILWQKLP--GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTA 209 (837)
Q Consensus 132 ~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~--~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a 209 (837)
T Consensus 1 ~nL~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~lS~GRVQTPtL~lvv~Re~ei~~f~~~~y~~~-------------- 66 (381)
T cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI-------------- 66 (381)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEE--------------
T ss_conf 966899999999999973754399999848889975664488999999988999981898552885--------------
Q ss_pred EEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHC
Q ss_conf 33103583303310113566677764200156301000023322246852103799999887608889999999987621
Q gi|254780306|r 210 HLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYE 289 (837)
Q Consensus 210 ~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE 289 (837)
T Consensus 67 ------------------------------~~~~v~~~~~k~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE 116 (381)
T cd00186 67 ------------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYE 116 (381)
T ss_pred ------------------------------EEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf ------------------------------34899998751586479799468999999986069599999999999986
Q ss_pred CCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCEEEEECCCCCCHHC
Q ss_conf 35567212245531475544443056899997655200112376311---112556668877765247730234640000
Q gi|254780306|r 290 GIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKP---RIYSSKSKNAQEAHEAIRPNDFDFLPSKMK 366 (837)
Q Consensus 290 ~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~---r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~ 366 (837)
T Consensus 117 --------~g~ITYpRTDs~~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~~~-~~~ 187 (381)
T cd00186 117 --------AGLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRNPKRGKKEQGAHEAIRPTKVAPTP-ELE 187 (381)
T ss_pred --------CCEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCH-HHH
T ss_conf --------79265326765616999999999999976473344134431256778899977896896167888885-666
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCC
Q ss_conf 01999999999999999999852221100100136774079639999987488058856763267776321001014886
Q gi|254780306|r 367 QFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPY 446 (837)
Q Consensus 367 ~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~ 446 (837)
T Consensus 188 ~~l~~~e~~iY~LI~~rfla~~~~~~~~~~t~v~~~~~~----~~F~~~g~~i~~~Gw~~v~~~~~~-----~~~~~lp~ 258 (381)
T cd00186 188 ANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGG----EKFKASGKVLLEDGWLEVYPEEKD-----DEEEEPPP 258 (381)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECC----EEEEEEEEEEEECCHHHEECCCCC-----CCCCCCCC
T ss_conf 019999999999999999997464020368999999899----789999999976682004467787-----63235865
Q ss_pred CCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCC
Q ss_conf 45688211001101112346431017899874332102566551578999997322022147712220114200002233
Q gi|254780306|r 447 ISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLEN 526 (837)
Q Consensus 447 l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~ 526 (837)
T Consensus 259 l~~g~~~~~~~~~~~e~~TkPP~ryTe~tLi~~Me~~GIGTpATra~IIe~L~~r~Yi~~~~~~l~~T~~G~~li~~l~~ 338 (381)
T cd00186 259 LKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEK 338 (381)
T ss_pred CCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH
T ss_conf 35697787878788877438998778999999765369987265989999998478099329999673789999999987
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 665568988999999999998626013478999986767665
Q gi|254780306|r 527 FFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEK 568 (837)
Q Consensus 527 ~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~ 568 (837)
T Consensus 339 ~~~~i~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~ 380 (381)
T cd00186 339 HFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKI 380 (381)
T ss_pred HHHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf 545625978999999999999879998999999999999835