Q: Is there a metabolite localization database for a model organism?
How: literature mining, MALDI imaging, Raman-spectroscopy based methods such as Coherent Anti-Stokes Raman Scattering,..
Links, input and feedback of the biostar commmunity is as always dearly appreciated.
One example: the Human Metabolome Database, contains localization data. An example record page for propane-1,3-diamine - scroll down and look for the "Cellular Location" field. First time I've looked at it, so unsure how the information is derived.
Worth noting too that there are several good protein subcellular localization databases; you'd expect to find the metabolite(s) for a pathway in the same location as the enzymes that catalyse the reactions, so might be an alternative way into the problem.
The BiGG database also has compartment information, and a very liberal, Open license. It has a 'compartments' field with values including cytosol, nucleus, ER, extra-organism, lysosome, mitoncondria, peroxisome, and golgi. You can search for any metabolite (some 1500 when I just checked) and export this list as a text file.
You can find more info in their paper: Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. Ø., "BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions", BMC Bioinformatics, 11:213, (2010).
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
I think you could indeed assume that proteins will generally be near the site of the metabolites they interact with, but if the metabolite is formed by an enzyme reaction it might move away fast. Biotransformation (drug metabolizing) enzymes are a classic example. They catch lipophilic metabolites which are getting more hydrophilic and move away.
It seems the cellular location information is missing from the HMDB 3.5 XML export :(