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I am trying to get a protein sequence using this command:

curl https://www.uniprot.org/uniprot/A2Z669.fasta

But I don't get any output:

$ curl https://www.uniprot.org/uniprot/A2Z669.fasta
$ 

And no file is created.

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1 Answer 1

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The URL https://www.uniprot.org/uniprot/A2Z669.fasta redirects to https://rest.uniprot.org/uniprotkb/A2Z669.fasta. You can see this if you open it in your browser: clicking on the first link will take you to the address of the second.

Now, curl doesn't follow redirects by default, you need the -L option for that (see man curl):

-L, --location

(HTTP) If the server reports that the requested page has moved to a different location (indicated with a Location: header and a 3XX response code), this option makes curl redo the request on the new place. If used together with -i, --include or -I, --head, headers from all requested pages are shown.

So you need -L for curl to work here:

$ curl -L https://www.uniprot.org/uniprot/A2Z669.fasta
>sp|A2Z669|CSPLT_ORYSI CASP-like protein 5A2 OS=Oryza sativa subsp. indica OX=39946 GN=OsI_33147 PE=3 SV=1
MRASRPVVHPVEAPPPAALAVAAAAVAVEAGVGAGGGAAAHGGENAQPRGVRMKDPPGAP
GTPGGLGLRLVQAFFAAAALAVMASTDDFPSVSAFCYLVAAAILQCLWSLSLAVVDIYAL
LVKRSLRNPQAVCIFTIGDGITGTLTLGAACASAGITVLIGNDLNICANNHCASFETATA
MAFISWFALAPSCVLNFWSMASR

Or, alternatively, you can use wget which does follow redirects by default:

$ wget "https://www.uniprot.org/uniprot/A2Z669.fasta" 
--2023-12-10 16:21:46--  https://www.uniprot.org/uniprot/A2Z669.fasta
Loaded CA certificate '/etc/ssl/certs/ca-certificates.crt'
Resolving www.uniprot.org (www.uniprot.org)... 193.62.193.81
Connecting to www.uniprot.org (www.uniprot.org)|193.62.193.81|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://rest.uniprot.org/uniprot/A2Z669.fasta [following]
--2023-12-10 16:21:46--  https://rest.uniprot.org/uniprot/A2Z669.fasta
Resolving rest.uniprot.org (rest.uniprot.org)... 193.62.193.81
Connecting to rest.uniprot.org (rest.uniprot.org)|193.62.193.81|:443... connected.
HTTP request sent, awaiting response... 301 Moved Permanently
Location: https://rest.uniprot.org/uniprotkb/A2Z669.fasta [following]
--2023-12-10 16:21:46--  https://rest.uniprot.org/uniprotkb/A2Z669.fasta
Reusing existing connection to rest.uniprot.org:443.
HTTP request sent, awaiting response... 200 OK
Length: 314 [text/plain]
Saving to: ‘A2Z669.fasta.1’

A2Z669.fasta             100%[=======================================>]     314  --.-KB/s    in 0s      

2023-12-10 16:21:47 (8.57 MB/s) - ‘A2Z669.fasta.1’ saved [314/314]

That creates a A2Z669.fasta file in the current directory which will contain the sequence.

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