Which Kegg Rpair Kinds Are Relevant?

Question

[mgalactus]

Hi all,

the KEGG Rpair database is used to understand which compounds in a reaction_id are used in the pathway maps.

In fact, according to the kegg website:

In general, a reaction consists of multiple reactant pairs, and the one that appears on the KEGG metabolic pathway map is called the main pair

The problem is, there are some other cases which are not so clear to me; when looking at all the possible kind of rpairs we get:

• main
• trans
• leave
• ligase leave
• main ligase
• main leave
• main trans
• main cofac
• main cofac leave
• cofac leave
• ligase
• cofac

My question therefore is: should I include also the other "main" types in a metabolic network reconstruction?

Answer 1

[mgalactus]

I got a reply from the KEGG support:

"Thank you for your interest in the KEGG/GenomeNet service. RPAIR entries with several different types mean that they are used in different ways and all the related types are listed. Therefore you can use all the RPAIR entries with a main type."

So basically all the rpair entries containing the keyword main should be used in metabolic network reconstruction.