Question: MSMS data: going from GI to Protein ID
0
gravatar for anne
2.4 years 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 • 415 views
ADD COMMENTlink modified 2.4 years ago by genomax89k • written 2.4 years ago by anne0
0
gravatar for natasha.sernova
2.4 years 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 2.4 years ago • written 2.4 years ago by natasha.sernova3.7k
0
gravatar for genomax
2.4 years ago by
genomax89k
United States
genomax89k 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 2.4 years ago by genomax89k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 809 users visited in the last hour