1. Bioinformatics Research Group
Metabolite Tracing
Markus Krummenacker
Bioinformatics Research Group
SRI, International
May 19, 2010 1

2. Metabolite Tracing
The Pathway Tools Navigator has a mode for stepwise tracing a path in the reaction network.
Enter with Overviews->Metabolite Tracing
Given a start compound and direction (forward or backward), reactions are followed until a branch point is reached.
The user can make a choice of which branch(es) to follow. 2

3. Tracing Display 3

4. Limiting Branching
The following common compounds are not followed in a trace (stored in *default-ignore-cpds*):
(WATER PROTON E- AMMONIA OH CARBON-DIOXIDE |Pi| PPI OXYGEN-MOLECULE HYDROGEN-MOLECULE HCO3 AMMONIUM HSO3 H2CO3 HS SULFATE HYDROGEN- PEROXIDE CL- HCL ADP ATP NAD NADH NADP NADPH FAD FADH2 |NAD(P)| |NAD(P)H|) 4

5. Show Trace as Pathway
The trace can be displayed as a temporary pathway, with View->Show Selected Path in New Window 5