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

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

Tracing Display 3

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

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