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UniProtKB query fields

Supported query fields for searching specific data in UniProtKB (see also query syntax).

Field Example Description
accession accession:P62988 Lists all entries with the primary or secondary accession number P62988.
active active:no Lists all obsolete entries.
annotation annotation:(type:non-positional)
annotation:(type:mod_res "Pyrrolidone carboxylic acid" evidence:experimental)
Lists all entries with:
author author:ashburner Lists all entries with at least one reference co-authored by Michael Ashburner.
cdantigen cdantigen:CD233 Lists all entries whose cluster of differentiation number is CD233 (see cdlist.txt).
citation citation:("intracellular structural proteins")
citation:(author:ashburner journal:nature) citation:9169874
Lists all entries with a literature citation:
  • containing the phrase "intracellular structural proteins" in either title or abstract
  • co-authored by Michael Ashburner and published in Nature
  • with the PubMed identifier 9169874
cluster cluster:UniRef90_A5YMT3 Lists all entries in the UniRef 90% identity cluster whose representative sequence is UniProtKB entry A5YMT3 (about UniRef).
count annotation:(type:transmem count:5)
annotation:(type:transmem count:[5 TO *])
annotation:(type:cofactor count:[3 TO *])
Lists all entries with:
  • exactly 5 transmembrane regions
  • 5 or more transmembrane regions
  • 3 or more Cofactor comments
created created:[20121001 TO *]
reviewed:yes AND created:[current TO *]
Lists all entries created since October 1st 2012.
Lists all new UniProtKB/Swiss-Prot entries in the last release.
database database:(type:pfam)
database:(type:pdb 1aut)
Lists all entries with:
  • a cross-reference to the Pfam database
  • a cross-reference to the PDB database entry 1aut
(see Databases cross-referenced in UniProtKB and Database mapping)
ec ec: Lists all beta-galactosidases (Enzyme nomenclature database).
evidence annotation:(type:signal evidence:ECO_0000269)
(type:mod_res phosphoserine evidence:ECO_0000269)
annotation:(type:function AND evidence:ECO_0000255)
Lists all entries with:
  • a signal sequence whose positions have been experimentally proven
  • experimentally proven phosphoserine sites
  • a function manually asserted according to rules
(see Evidence attribution)
existence existence:"inferred from homology" See Protein existence criteria.
family family:serpin Lists all entries belonging to the Serpin family of proteins (Index of protein domains and families).
fragment fragment:yes Lists all entries with an incomplete sequence.
gene gene:HPSE Lists all entries for proteins encoded by gene HPSE, but also by HPSE2.
gene_exact gene_exact:HPSE Lists all entries for proteins encoded by gene HPSE, but excluding variations like HPSE2 or HPSE_0.
goa goa:(cytoskeleton)
Lists all entries associated with:
  • a GO term containing the word "cytoskeleton"
  • the GO term Actin cytoskeleton and any subclasses
host host:mouse
Lists all entries for viruses infecting:
  • organisms with a name containing the word "mouse" (including Arabidopsis thaliana (Mouse-ear cress)!)
  • Mus musculus (Mouse)
  • all mammals (all taxa classified under the taxonomy node for Mammalia)
id id:P00750 Returns the entry with the primary accession number P00750.
inn inn:Anakinra Lists all entries whose "International Nonproprietary Name" is Anakinra.
interactor interactor:P00520 Lists all entries describing interactions with the protein described by entry P00520.
keyword keyword:toxin Lists all entries associated with the keyword Toxin (UniProtKB Keywords).
length length:[500 TO 700] Lists all entries describing sequences of length between 500 and 700 residues.
lineage This field is a synonym for the field taxonomy.
mass mass:[500000 TO *] Lists all entries describing sequences with a mass of at least 500,000 Da.
method method:maldi
Lists all entries for proteins identified by: matrix-assisted laser desorption/ionization (MALDI), crystallography (X-Ray). The method field searches names of physico-chemical identification methods in the 'Biophysicochemical properties' subsection of the 'Function' section, the 'Publications' and 'Cross-references' sections.
mnemonic mnemonic:ATP6_HUMAN Lists all entries with entry name (ID) ATP6_HUMAN. Searches also obsolete entry names (What is the difference between an accession number (AC) and the entry name?).
modified modified:[20120101 TO 20120301]
reviewed:yes AND modified:[current TO *]
Lists all entries that were last modified between January and March 2012.
Lists all UniProtKB/Swiss-Prot entries modified in the last release.
name name:"prion protein" Lists all entries for prion proteins.
organelle organelle:Mitochondrion Lists all entries for proteins encoded by a gene of the mitochondrial chromosome.
organism organism:"Ovis aries"
Lists all entries for proteins expressed in sheep (first 2 examples) and organisms whose name contains the term "sheep" (UniProt taxonomy).
plasmid plasmid:ColE1 Lists all entries for proteins encoded by a gene of plasmid ColE1 (Controlled vocabulary of plasmids).
proteome proteome:UP000005640 Lists all entries from the human proteome.
proteomecomponent proteomecomponent:"chromosome 1" and organism:9606 Lists all entries from the human chromosome 1.
replaces replaces:P02023 Lists all entries that were created from a merge with entry P02023 (see FAQ).
reviewed reviewed:yes Lists all UniProtKB/Swiss-Prot entries (about UniProtKB).
scope scope:mutagenesis Lists all entries containing a reference that was used to gather information about mutagenesis (Entry view: "Cited for", See 'Publications' section of the user manual).
sequence sequence:P05067-9 Lists all entries containing a link to isoform 9 of the sequence described in entry P05067. Allows searching by specific sequence identifier.
sequence_modified sequence_modified:[20120101 TO 20120301]
reviewed:yes AND sequence_modified:[current TO *]
Lists all entries whose sequences were last modified between January and March 2012.
Lists all UniProtKB/Swiss-Prot entries whose sequences were modified in the last release.
source source:intact Lists all entries containing a GO term whose annotation source is the IntAct database.
strain strain:wistar Lists all entries containing a reference relevant to strain wistar (Lists of strains in reference comments and Taxonomy help: organism strains).
taxonomy taxonomy:40674 Lists all entries for proteins expressed in Mammals. This field is used to retrieve entries for all organisms classified below a given taxonomic node (taxonomy classification).
tissue tissue:liver Lists all entries containing a reference describing the protein sequence obtained from a clone isolated from liver (Controlled vocabulary of tissues).
web web:wikipedia Lists all entries for proteins that are described in Wikipedia.
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