Certainty levels

For those events with “speculation” attributes, Certainty levels can be determined according to the Speculation cues/Method cues. However, in some cases, it is difficult to determine the certainty levels, so that those events do not have any certainty levels.

Superposition suggests nucleophilic attack by the 4'-phosphopantetheine on the alpha-phosphate of ATP.
T1 MethodCue 0 13 Superposition
T2 SpeculationCue 14 22 suggests
T3 NucleophilicAttack 23 42 nucleophilic attack
T4 OtherCompound 50 71 4'-phosphopantetheine
T5 FunctionalGroup 78 94 alpha-phosphate
T6 OtherCompound 98 101 ATP
E1 NucleophilicAttack:T3 Agent:T4 Theme:T5 Cue:T2 Cue2:T1
R1 whole_part Arg1:T6 Arg2:T5
A1 Speculation E1
A2 Certainty E1 Probable

Asp40 is positioned appropriately to protonate the purine leaving group.
T1 AminoAcid 0 5 Asp40
T2 SpeculationCue 9 33 positioned appropriately
T3 Protonation 37 46 protonate
T4 OtherCompound 51 57 purine
T5 EntityProperty 58 71 leaving group
E1 Protonation:T3 Agent:T1 Theme:T4 Cue:T2
R1 corresponds_to Arg1:T5 Arg2:T4
A1 Speculation E1
A2 Certainty E1 Confirmed
A3 EntityAttribute T5 ReactivePart

Structural studies show that arcabose is modified upon binding.
T1 MethodCue 0 18 Structural studies
T2 SpeculationCue 19 23 show
T3 OtherCompound 29 37 arcabose
T4 BondFormation 41 49 modified
T5 Interaction 55 62 binding
E1 BondFormation:T4 Theme:T3 Cue:T1 Cue2:T2
E2 Interaction:T5 Theme:T3 Cue:T1 Cue2:T2
A1 Speculation E1
A2 Certainty E1 Confirmed
A3 Speculation E2
A4 Certainty E2 Confirmed

Molecular mechanics calculations show possible binding conformations.
T1 MethodCue 0 32 Molecular mechanics calculations
T2 SpeculationCue 33 37 show
T3 SpeculationCue 38 46 possible
T4 Interaction 47 54 binding
T5 EntityProperty 55 68 conformations
E1 Interaction:T4 Theme:T5 Cue:T1 Cue2:T2 Cue3:T3
A1 Speculation E1
A2 Certainty E1 Probable

The following table indicates Speculation cues/Method cues and corresponding certainty levels (Confirmed, Probable, Unlikely):