Retrieve 'Enzymes By Compound' Filtered By Organism

Question

[Lo Sauer]

Dear all,

Kegg provides a function called enzymesbycompound yet I am unaware how to filter the results by the enzymes actually present within a given organism (in my case: Arapidopsis th.)

Aracyc provides exactly that, yet I haven't found any APIs for it?

The worst case scenario would be, to run another function that looks up the presence of each enzyme for the given organism.

The idea is to reconstruct or retrieve the metabolic network up to a certain number of edges, starting from one metabolite or enzyme

Any pointers, suggestions?

Update:

I think a fast way would be to retrieve all enzymes present in a given organism (Array1) and then just intersect it against the Array2 holding all enzymes for a given compound. Any pointers on getting an enzyme list for a given organism?

Links:

http://www.genome.jp/kegg/soap/doc/keggapi_javadoc_ja/keggapi/KEGGPortType.html

http://pmn.plantcyc.org/PLANT/substring-searchtype=NIL&object=acetylcoa&quickSearch=Quick+Search

Answer 1

[Damian Kao]

Here is the kegg page for Arapidopsis th.: http://www.genome.jp/dbget-bin/www_bget?gn:T00041

Links to the right of the page are all the kegg information they have for it. There is a link for enzymes.

[Lo Sauer]

thanks, very helpful; I usually avoid dbget and it didn't occur to me to look into it.

[Damian Kao]

Didn't they close down their public ftp few months ago? I think dbget might be the only way to access the data now.

[Lo Sauer]

regarding access: you are right. I wonder why only 69 enzymes/reactions are shown. The A.th TCA cycle alone has over 40 enzymes (http://en.wikipedia.org/wiki/File:A_thaliana_metabolic_network.png). Actual number should look something like this: See also: http://plantcyc.org/release_notes/content_statistics.faces

[Damian Kao]

Yeah you are right. Perhaps you should just download the AraCyc flat files and parse out the data with a script: http://www.plantcyc.org/downloads/data_downloads.faces

[Lo Sauer]

Right! The TAIR datasets. That's actually where I left off a month ago. Thanks.

[Lo Sauer]

I uploaded them up as sql-files a month ago. https://github.com/lsauer/Data-Hub/tree/master/databases/metabolic. (Should have consulted my work-journal first.) Any pointers regarding a webservice for retrieving the metabolic connectivity for a compound?