uniprot
Fetches UniProt entries based on their accession numbers.

The uniprot command expects UniProt accession numbers as input. The source of this input can be command line arguments or standard input. If input is supplied using multiple sources at the same time, the order of priority as described above is used.

Command line arguments

If input is supplied using command line arguments, the accession numbers must be separated by spaces.

Example

$ uniprot C6JD41 Q06JG4
MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAVGDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK
MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN

Standard input

If the command is run without arguments, uniprot will read its input from standard input. When standard input is used, a single UniProt accession number per line is expected.

Example

$ cat input.txt
C6JD41
Q06JG4
$ cat input | uniprot
MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAVGDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK
MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN

The uniprot command outputs the UniProt entry for each of the input accession numbers. By default, only the protein sequences are returned. By using the --format parameter, this can be changed to fasta, txt, xml, rdf or gff. All output is written to standard output.

--format / -f Specify the output format

By default, the uniprot command only returns the protein sequence of the UniProt entry. The --format option allows you to select another format. Supported formats are sequence, fasta, txt, xml, rdf, and gff.

Example

$ uniprot --format fasta C6JD41 Q06JG4
>tr|C6JD41|C6JD41_9FIRM 10 kDa chaperonin OS=Ruminococcus sp. 5_1_39BFAA GN=groS PE=3 SV=1
MTLVPLGDRVVLKQVEAEETTKSGIVLPGQAQEKPQQAEVVAVGPGGVVDGKEVKMEVAV
GDKVIYSKYSGTEVKMDGTEYIIVKQNDILAIVK
>sp|Q06JG4|16D10_MELHA CLAVATA3/ESR (CLE)-related protein 16D10 OS=Meloidogyne hapla GN=16D10 PE=2 SV=1
MFTNSIKNLIIYLMPLMVTLMLLSVSFVDAGKKPSGPNPGGNN

--help / -h Display help

This flag displays the help.