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Calculation of minimal synthesis pathways starting from the seed and producing a specified target metabolite. [read more...]

A scope includes those metabolites which can be synthesized form a specified set of seed compounds. An important biochemical question is how a particular product (the target) can be synthesized with a minimal number of reactions from a given set of substrates. The algorithm presented here is able to calculate a pathway performing the synthesis in a minimal number of consecutive steps. The algorithm works as follows: Starting from the seed, an expansion process is preformed as described above. The number of consecutive synthesis steps necessary to produce the target is already determined by the iteration step in which the target was incorporated. During the process, it is recorded which metabolites enable which reactions and which reactions produce which metabolites. With this information, the synthesis pathway is now assembled in a reverse order starting from the target. The obtained pathways in general are not simply unbranched chains but contain reactions which operate in parallel. There may exist other pathways with a smaller total number of reactions which can perform the same conversion, however none with a smaller number of consecutive steps.

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Reaction Set:
User defined reaction set (Rxxxxx,Ryyyyy,...):

Irreversibility
Cofactor functionality:
ATP/ADPNAD/NADH
NADP/NADPHCoA
Select the reaction set on which the scope calculation will be performed. "Irreversibility" defines whether irreversible reactions can only be traversed in forward direction.
When selecting "cofactor functionalities", reactions depending on certain cofactors can operate also without them. The algorithms ensure that no compounds are synthesized from the cofactors itself.
 
Seed: Enter the initial substrates which will be used for synthesizing all the other compounds of the scope. Enter metabolite names separated by ";".
 
Target: Enter the target compound which is synthesized from the seed. At the moment only one target is allowed.
 
Output: Link to KEGG database Compound and Reaction IDs will be linked to the corresponding entries in KEGG.
compound redraw limit: Compounds taking part in more reactions than the specified limit will be drawn separately for each reaction to disentangle the layout. Hence, a value of 1 will draw only separate reactions.

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