predicted protein and sequence

Question

[mdfardin374]

Hello, I am interested in fetching all the predicted protein (proteins that do not have experimental evidence) of a particular organism or hypothetical proteins of an organism so that MS/MS analysis can be carried out to prove proteomic evidence. Can somebody please help me?

Answer 1

[fishgolden]

I use uniprot for such purpose.

It has PE line. https://www.uniprot.org/docs/userman.htm#PE_line

Check an example. https://www.uniprot.org/uniprot/Q8YW84.txt

Answer 2

[GenoMax]

Using EntrezDirect. This example uses Malus as an example.

$ esearch -db protein -query "MALUS DOMESTICA [ORGN]" | esummary | xtract -pattern DocumentSummary -element Caption | grep "^XP" | xargs -n 1 sh -c 'efetch -db protein -id "$0" -format fasta'