Question: MSMS data: going from GI to Protein ID
0
gravatar for anne
19 months ago by
anne0
anne0 wrote:

Hi

I have MSMS data which include a GI for the idenitfede protein. How can I get from that to a protein ID? For exampel it is a Bifidobacterium, Carbamoylphosphate synthase large subunit, GI241190667 so I would like a BIF_XXX.

sequence genome • 327 views
ADD COMMENTlink modified 19 months ago by genomax75k • written 19 months ago by anne0
0
gravatar for natasha.sernova
19 months ago by
natasha.sernova3.7k
natasha.sernova3.7k wrote:

Go to NCBI-site: www.ncbi.nlm.nih.gov

find 'protein' in the left menu, insert your GI-number (only number)

it will give you its identifier.

Your protein new identifier is can be found here

https://www.ncbi.nlm.nih.gov/protein/WP_004218885.1?

ADD COMMENTlink modified 19 months ago • written 19 months ago by natasha.sernova3.7k
0
gravatar for genomax
19 months ago by
genomax75k
United States
genomax75k wrote:

I am not sure what BIF_XXX is but you can get an idea of what the GI is for by using NCBI unix utils like this.

$ efetch -db protein -id "241190667" -format fasta | grep ">"
>YP_002968061.1 carbamoylphosphate synthase large subunit [Bifidobacterium animalis subsp. lactis Bl-04]
ADD COMMENTlink written 19 months ago by genomax75k
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