Metabolite Tracing
Markus Krummenacker
Bioinformatics Research Group
SRI, International
May 19, 2010
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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.
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Tracing Display
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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 HYDROGENPEROXIDE CL- HCL ADP ATP NAD NADH NADP NADPH FAD
FADH2 |NAD(P)| |NAD(P)H|)
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Show Trace as Pathway
 The
trace can be displayed as a temporary pathway,
with View->Show Selected Path in New Window
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