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
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
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
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
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
cc_interaction |
Interacts with |
cc_subunit |
Subunit structure[CC] |
Expression
cc_developmental_stage |
Developmental stage |
cc_induction |
Induction |
cc_tissue_specificity |
Tissue specificity |
Gene Ontology (GO)
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
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
ft_intramem |
Intramembrane |
cc_subcellular_location |
Subcellular location[CC] |
ft_topo_dom |
Topological domain |
ft_transmem |
Transmembrane |
PTM / Processsing
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
structure_3d |
3D |
ft_strand |
Beta strand |
ft_helix |
Helix |
ft_turn |
Turn |
Date of
date_created |
Date of creation |
date_modified |
Date of last modification |
date_sequence_modified |
Date of last sequence modification |
version |
Entry version |
Family & Domains
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
xref_ccds |
CCDS |
xref_embl |
EMBL |
xref_pir |
PIR |
xref_refseq |
RefSeq |
3D Structure Databases
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
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
xref_bindingdb |
BindingDB |
xref_chembl |
ChEMBL |
xref_drugbank |
DrugBank |
xref_drugcentral |
DrugCentral |
xref_guidetopharmacology |
GuidetoPHARMACOLOGY |
xref_swisslipids |
SwissLipids |
Protein Family/Group Databases
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
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
xref_biomuta |
BioMuta |
xref_dmdm |
DMDM |
xref_dbsnp |
dbSNP |
2D Gel Databases
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
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
xref_abcd |
ABCD |
xref_antibodypedia |
Antibodypedia |
xref_cptc |
CPTC |
xref_dnasu |
DNASU |
Genome Annotation Databases
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
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
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
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
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
xref_bgee |
Bgee |
xref_cleanex |
CleanEx |
xref_collectf |
CollecTF |
xref_expressionatlas |
ExpressionAtlas |
xref_genevisible |
Genevisible |
Family And Domain Databases
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 |