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This vignette describes all the columns of data (aka return fields) you can request from UniProt’s UniProtKB database. This is relevant for uniprot_map() when mapping to UniProtKB and for uniprot_search() when database = "uniprotkb". These tables have been scraped from this page on the UniProt website.

  • field = string to use in the fields argument
  • label = name of column that will be returned

Names & Taxonomy

field label
accession Entry
id Entry Name
gene_names Gene Names
gene_primary Gene Names (primary)
gene_synonym Gene Names (synonym)
gene_oln Gene Names (ordered locus)
gene_orf Gene Names (ORF)
organism_name Organism
organism_id Organism ID
protein_name Protein names
xref_proteomes Proteomes
lineage Taxonomic lineage
lineage_ids Taxonomic lineage (IDs)
virus_hosts Virus hosts

Sequences

field label
cc_alternative_products Alternative products
ft_var_seq Alternative sequence
error_gmodel_pred Erroneous gene model prediction
fragment Fragment
organelle Gene encoded by
length Length
mass Mass
cc_mass_spectrometry Mass spectrometry
ft_variant Natural variant
ft_non_cons Non-adjacent residues
ft_non_std Non-standard residue
ft_non_ter Non-terminal residue
cc_polymorphism Polymorphism
cc_rna_editing RNA editing
sequence Sequence
cc_sequence_caution Sequence caution
ft_conflict Sequence conflict
ft_unsure Sequence uncertainty
sequence_version Sequence version

Function

field label
absorption Absorption
ft_act_site Active site
cc_activity_regulation Activity regulation
ft_binding Binding site
cc_catalytic_activity Catalytic activity
cc_cofactor Cofactor
ft_dna_bind DNA binding
ec EC number
cc_function Function [CC]
kinetics Kinetics
cc_pathway Pathway
ph_dependence pH dependence
redox_potential Redox potential
rhea Rhea ID
ft_site Site
temp_dependence Temperature dependence

Miscellaneous

field label
annotation_score Annotation
cc_caution Caution
comment_count Comment Count
feature_count Features
keywordid Keyword ID
keyword Keywords
cc_miscellaneous Miscellaneous [CC]
protein_existence Protein existence
reviewed Reviewed
tools Tools
uniparc_id UniParc

Interaction

field label
cc_interaction Interacts with
cc_subunit Subunit structure[CC]

Expression

field label
cc_developmental_stage Developmental stage
cc_induction Induction
cc_tissue_specificity Tissue specificity

Gene Ontology (GO)

field label
go_p Gene ontology (biological process)
go_c Gene ontology (cellular component)
go Gene ontology (GO)
go_f Gene ontology (molecular function)
go_id Gene ontology IDs

Pathology & Biotech

field label
cc_allergen Allergenic properties
cc_biotechnology Biotechnological use
cc_disruption_phenotype Disruption phenotype
cc_disease Involvement in disease
ft_mutagen Mutagenesis
cc_pharmaceutical Pharmaceutical use
cc_toxic_dose Toxic dose

Subcellular location

field label
ft_intramem Intramembrane
cc_subcellular_location Subcellular location[CC]
ft_topo_dom Topological domain
ft_transmem Transmembrane

PTM / Processsing

field label
ft_chain Chain
ft_crosslnk Cross-link
ft_disulfid Disulfide bond
ft_carbohyd Glycosylation
ft_init_met Initiator methionine
ft_lipid Lipidation
ft_mod_res Modified residue
ft_peptide Peptide
cc_ptm Post-translational modification
ft_propep Propeptide
ft_signal Signal peptide
ft_transit Transit peptide

Structure

field label
structure_3d 3D
ft_strand Beta strand
ft_helix Helix
ft_turn Turn

Publications

field label
lit_pubmed_id PubMed ID

Date of

field label
date_created Date of creation
date_modified Date of last modification
date_sequence_modified Date of last sequence modification
version Entry version

Family & Domains

field label
ft_coiled Coiled coil
ft_compbias Compositional bias
cc_domain Domain[CC]
ft_domain Domain[FT]
ft_motif Motif
protein_families Protein families
ft_region Region
ft_repeat Repeat
ft_zn_fing Zinc finger

Sequence Databases

field label
xref_ccds CCDS
xref_embl EMBL
xref_pir PIR
xref_refseq RefSeq

3D Structure Databases

field label
xref_alphafolddb AlphaFoldDB
xref_bmrb BMRB
xref_pcddb PCDDB
xref_pdb PDB
xref_pdbsum PDBsum
xref_sasbdb SASBDB
xref_smr SMR

Protein-Protein Interaction Databases

field label
xref_biogrid BioGRID
xref_corum CORUM
xref_complexportal ComplexPortal
xref_dip DIP
xref_elm ELM
xref_intact IntAct
xref_mint MINT
xref_string STRING

Chemistry Databases

field label
xref_bindingdb BindingDB
xref_chembl ChEMBL
xref_drugbank DrugBank
xref_drugcentral DrugCentral
xref_guidetopharmacology GuidetoPHARMACOLOGY
xref_swisslipids SwissLipids

Protein Family/Group Databases

field label
xref_allergome Allergome
xref_cazy CAZy
xref_clae CLAE
xref_esther ESTHER
xref_imgt_gene-db IMGT_GENE-DB
xref_merops MEROPS
xref_moondb MoonDB
xref_moonprot MoonProt
xref_peroxibase PeroxiBase
xref_rebase REBASE
xref_tcdb TCDB
xref_unilectin UniLectin

PTM Databases

field label
xref_carbonyldb CarbonylDB
xref_depod DEPOD
xref_glycosmos GlyCosmos
xref_glyconnect GlyConnect
xref_glygen GlyGen
xref_metosite MetOSite
xref_phosphositeplus PhosphoSitePlus
xref_swisspalm SwissPalm
xref_iptmnet iPTMnet

Genetic Variation Databases

field label
xref_biomuta BioMuta
xref_dmdm DMDM
xref_dbsnp dbSNP

2D Gel Databases

field label
xref_compluyeast-2dpage COMPLUYEAST-2DPAGE
xref_dosac-cobs-2dpage DOSAC-COBS-2DPAGE
xref_ogp OGP
xref_reproduction-2dpage REPRODUCTION-2DPAGE
xref_swiss-2dpage SWISS-2DPAGE
xref_ucd-2dpage UCD-2DPAGE
xref_world-2dpage World-2DPAGE

Proteomic Databases

field label
xref_cptac CPTAC
xref_epd EPD
xref_massive MassIVE
xref_maxqb MaxQB
xref_pride PRIDE
xref_paxdb PaxDb
xref_peptideatlas PeptideAtlas
xref_promex ProMEX
xref_proteomicsdb ProteomicsDB
xref_topdownproteomics TopDownProteomics
xref_jpost jPOST

Protocols And Materials Databases

field label
xref_abcd ABCD
xref_antibodypedia Antibodypedia
xref_cptc CPTC
xref_dnasu DNASU

Genome Annotation Databases

field label
xref_ensembl Ensembl
xref_ensemblbacteria EnsemblBacteria
xref_ensemblfungi EnsemblFungi
xref_ensemblmetazoa EnsemblMetazoa
xref_ensemblplants EnsemblPlants
xref_ensemblprotists EnsemblProtists
xref_geneid GeneID
xref_gramene Gramene
xref_kegg KEGG
xref_mane-select MANE-Select
xref_patric PATRIC
xref_ucsc UCSC
xref_vectorbase VectorBase
xref_wbparasite WBParaSite
xref_wbparasitetranscriptprotein WBParaSiteTranscriptProtein

Organism-Specific Databases

field label
xref_agr AGR
xref_arachnoserver ArachnoServer
xref_araport Araport
xref_cgd CGD
xref_ctd CTD
xref_conoserver ConoServer
xref_disgenet DisGeNET
xref_echobase EchoBASE
xref_flybase FlyBase
xref_genecards GeneCards
xref_genereviews GeneReviews
xref_hgnc HGNC
xref_hpa HPA
xref_legiolist LegioList
xref_leproma Leproma
xref_mgi MGI
xref_mim MIM
xref_maizegdb MaizeGDB
xref_malacards MalaCards
xref_niagads NIAGADS
xref_opentargets OpenTargets
xref_orphanet Orphanet
xref_pharmgkb PharmGKB
xref_pombase PomBase
xref_pseudocap PseudoCAP
xref_rgd RGD
xref_sgd SGD
xref_tair TAIR
xref_tuberculist TubercuList
xref_veupathdb VEuPathDB
xref_vgnc VGNC
xref_wormbase WormBase
xref_xenbase Xenbase
xref_zfin ZFIN
xref_dictybase dictyBase
xref_euhcvdb euHCVdb
xref_nextprot neXtProt

Phylogenomic Databases

field label
xref_genetree GeneTree
xref_hogenom HOGENOM
xref_inparanoid InParanoid
xref_ko KO
xref_oma OMA
xref_orthodb OrthoDB
xref_phylomedb PhylomeDB
xref_treefam TreeFam
xref_eggnog eggNOG

Enzyme And Pathway Databases

field label
xref_brenda BRENDA
xref_biocyc BioCyc
xref_pathwaycommons PathwayCommons
xref_plantreactome PlantReactome
xref_reactome Reactome
xref_sabio-rk SABIO-RK
xref_signor SIGNOR
xref_signalink SignaLink
xref_unipathway UniPathway

Miscellaneous Databases

field label
xref_biogrid-orcs BioGRID-ORCS
xref_chitars ChiTaRS
xref_evolutionarytrace EvolutionaryTrace
xref_genewiki GeneWiki
xref_genomernai GenomeRNAi
xref_phi-base PHI-base
xref_pro PRO
xref_pharos Pharos
xref_rnact RNAct

Gene Expression Databases

field label
xref_bgee Bgee
xref_cleanex CleanEx
xref_collectf CollecTF
xref_expressionatlas ExpressionAtlas
xref_genevisible Genevisible

Family And Domain Databases

field label
xref_cdd CDD
xref_disprot DisProt
xref_gene3d Gene3D
xref_hamap HAMAP
xref_ideal IDEAL
xref_interpro InterPro
xref_panther PANTHER
xref_pirsf PIRSF
xref_prints PRINTS
xref_prosite PROSITE
xref_pfam Pfam
xref_prodom ProDom
xref_sfld SFLD
xref_smart SMART
xref_supfam SUPFAM
xref_tigrfams TIGRFAMs