How can I get all proteins coded by mitochondrial genome or plastid genome from UniProt. I see UniProt has multiple filtering and search parameters but I could not distinguish between proteins/genes coded by nuclear DNA and mitochondrial or plastid genomes.
I specifically want UniProt (rather than e.g. Organelle Genome Resources) because usually annotation of proteins uses UniProt ids.
Any suggestions?
You can use the UniProt Advanced search for this.
If you look at this help page https://www.uniprot.org/help/advanced_search, in particular the first example screenshot, you can type "encoded" where the screenshot has "structure". Then you can choose your organelle. For Plastid, for example, this will translate into the query syntax organelle:plastid :
https://www.uniprot.org/uniprot/?query=organelle%3APlastid&sort=score
Several other organelles are available, of course, e.g. Mitochondrion :
https://www.uniprot.org/uniprot/?query=organelle%3AMitochondrion&sort=score
Please don't hesitate to contact the UniProt helpdesk. We can unfortunately not guarantee to monitor all available forums as closely as we would like to, and can answer much more promptly when contacted directly.
