Lets see an example. The reaction R00344 is mentioned as irrversible in KEGG
http://www.genome.jp/dbget-bin/www_bget?rn:R00344
Although, in TCA this reaction should be in reverse direction. I mean it should produce ATP by ADP not should consume ATP as KEGG said.
How can we refine such kind of inconsistency?
The type attribute specifies the distinction of reversible and irreversible reactions, which are indicated by bi-directional and uni-directional arrows in the KEGG pathways. Note that the terms "reversible" and "irreversible" do not necessarily reflect biochemical properties of each reaction. They rather indicate the direction of the reaction drawn on the pathway map that is extracted from text books and literature.
Brenda is a better resource to find out the reversibility of reaction.
Ashmit,
Reaction directionalities are not "usually" correct in KEGG. You can check the correct reaction directionality in BiGG knowledge base, since the metabolic reconstructions provided in BiGG are manually curated and their directionalities can be "trusted" much more than those provided in KEGG.
Nevertheless, in case of your KEGG reaction, you can check the manually curated equivalent reaction abbreviation in BiGG database (refer to attached image). As you may see, the irreversible reaction of PC produces one phosphate by converting ATP into ADP. You may find other corresponding reactions in MetaNetX repository (here).
You may find the same result here on MetaCyc: http://metacyc.org/META/NEW-IMAGE?type=REACTION&object=PYRUVATE-CARBOXYLASE-RXN
Good luck.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology