KEGG pathways

Question

[mrashad]

Dear all,

How can I identify the genes responsible for producing specific products in KEGG pathways?

For instance, in the Tryptophan metabolism pathway, tryptophan [C00078] is converted to indole [C00463] by the enzyme 4.1.99.1, encoded by the gene tnaA (K01667).

My question is: Is it possible to determine, across all KEGG pathways, the products generated by the action of specific genes, as seen in the case of the tnaA gene in Tryptophan metabolism? If so, how can this be achieved using R or python?

[GenoMax]

Not R or Python but using the KEGG REST API you can do something like this. You question also goes back and forth about gene names and EC numbers etc.

Note: KEGG requires a license for extensive use so this may not work for a large number of queries. Please respect KEGG's acceptable use policy.

Get the reactions associated with the EC number

$ curl "https://rest.kegg.jp/link/reaction/ec:4.1.99.1"
ec:4.1.99.1     rn:R00673
ec:4.1.99.1     rn:R12758
ec:4.1.99.1     rn:R11100
ec:4.1.99.1     rn:R11099

Then use the reaction number to identify the products (output truncated for display here)

$ curl "https://rest.kegg.jp/get/R00673"
ENTRY       R00673                      Reaction
NAME        L-tryptophan indole-lyase (deaminating; pyruvate-forming)
DEFINITION  L-Tryptophan + H2O <=> Indole + Pyruvate + Ammonia
EQUATION    C00078 + C00001 <=> C00463 + C00022 + C00014

[mrashad]

yeah it is a part of the answer. I finally found relation between genes and compounds through KO and reactions using KeggLink function in KeggRest library

Answer 1

[alserg]

You can use KEGG api as suggest by GenoMax. In R there is a KEGGREST package.

Bassically you need to get all of the tryptophan reactions with https://rest.kegg.jp/link/rn/cpd:C00078 and you can connect reactions with orthologies using https://rest.kegg.jp/link/rn/ko

[mrashad]

yeah thanks a lot. I found indirect relation between genes and compound through reactions and KO.

Answer 2

[lieven.sterck]

not sure if there are any of the shelf tools that will do this but those numbers correspond (or are) EC-numbers. Those you can look up in the EC database which will give you a name (or rather catalytic function of an enzyme). That specific reaction type enzyme you can then look for in your species of interest.

With a bit of programming you likely can whip something together to achieve this automatically.

note: it will not be as easy as stated above for all genes/reactions as there are still many blanks for a lot of species.