Is There Any File That Links The Enzyme Comission Number To Gi Numbers?

Question

[Tawny]

I am wondering if anyone has come across a file that would allow me to find gi numbers associated with an enzyme comission (ec) number. What I want to do is get a list of sequences associated with a list of enzyme numbers.

Answer 1

[Chris]

The SwissProt flat file contains those data. The EC number could be found in the DE field, the GI (gene identifier) in one of the DR lines. An example could be found e.g. in the entry 3HAO_RALME.

[Tawny]

Chris, Thank you for pointing me to the SwissProt site. Can you be a little more specific? I am searching through the SwissProt FTP page and am not finding a file that would contain the data I am looking for.

[Chris]

Here you go: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.dat.gz

Answer 2

[Tawny]

I have taken the time to search through the uniprot_sprot.dat file. It is somewhat useful for my purposes. For example; the file contains numerous entries for the ec number 1.13.11 but the enzyme I am interested in is 1.13.11.38 and is not in the file.

Does anyone know of another resource that would allow me to retrieve a list of gi numbers based on a list of ec numbers?

[Chris]

This one is contained in TrEMBL, the other (bigger) part of Uniprot. You'll find its flatfile at the same URL as the uniprot_sprot file.

Answer 3

[Chris Evelo]

That might actually be because there are no proteins known for 1.13.11.38 which is supposed to be a bacterial enzyme function. See: and search for your enzyme. While there are links to other enzyme databases the UniProt link only goes to 1.13.11 (all of them, so you could browse to check). Interestingly the trEMBL (translated EMBL) proteins should be in UniProt as well though, so they should show up here,

Are you looking for a specific species?

Answer 4

[Mary]

I just happened to be looking at KEGG for something else and noticed that they have gi and EC on records: http://www.kegg.jp/dbget-bin/www_bget?hsa:100507855 . You might look there.

EDIT to add, here's one with your EC of interest: http://www.kegg.jp/dbget-bin/www_bget?mva:Mvan_0468 but there are multiple genes associated with that if you look at the ENZYME page: http://www.kegg.jp/dbget-bin/www_bget?ec:1.13.11.38