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=92.44 E-value=0.43 Score=27.26 Aligned_cols=52 Identities=17% Similarity=0.424 Sum_probs=27.9
Q ss_pred CCCEEEECCCCCCCCCCCCCHHHHHHHHH-HCCCCCCCCHHHHHHHHHHCCEEE
Q ss_conf 11001101112346431017899874332-102566551578999997322022
Q gi|254780306|r 453 LIATETNASQHFTEPPPRYSESSLIKKME-EIGIGRPSTYATILETLYKRKYVI 505 (837)
Q Consensus 453 ~~~~~~~~~~~~TkPP~rytEasLik~mE-~~GIGrPSTyA~II~~L~~R~YV~ 505 (837)
T Consensus 69 ~~v~~~~~k~~~~~pP~pf~l~~Lq~~a~~~~g~s~~-~tl~iaQ~LYE~g~IT 121 (381)
T cd00186 69 AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAK-KTMQIAQKLYEAGLIT 121 (381)
T ss_pred EEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCHH-HHHHHHHHHHHCCEEE
T ss_conf 8999987515864797994689999999860695999-9999999998679265