rbioapi (version 0.8.2)

rba_uniprot_features_search: Search UniProt protein sequence features

Description

UniProt maintains sequence annotations (features) that describe regions in the protein sequence. Using this function, you can search and retrieve UniProt proteins' sequence annotations (features). you may also refine your search query with variety of modifiers.

Usage

rba_uniprot_features_search(
  accession = NULL,
  gene = NULL,
  exact_gene = NULL,
  protein = NULL,
  reviewed = NULL,
  organism = NULL,
  taxid = NULL,
  categories = NULL,
  types = NULL,
  ...
)

Value

List where each element corresponds to one UniProt entity returned by your search query. The element itself is a sub-list containing all information that UniProt has about that entity.

Arguments

accession

UniProtKB primary or secondary accession(s). You can supply up to 100 accession numbers.

gene

UniProt gene name(s). You can supply up to 20 gene names. e.g. if you supply "CD40", "CD40 ligand" will also be included.

exact_gene

UniProt exact gene name(s). You can supply up to 20 exact gene names. e.g. if you supply "CD40", "CD40 ligand" will not be included in the results.

protein

UniProt protein name

reviewed

Logical: If TRUE, only return "UniProtKB/Swiss-Prot" (reviewed) entries; If FALSE, only return TrEMBL (un-reviewed) entries.

organism

Organism name.

taxid

NIH-NCBI Taxon ID. You can supply up to 20 taxon IDs.

categories

Sequence annotation (Features) categories (subsection). accepted values are: "MOLECULE_PROCESSING", "TOPOLOGY", "SEQUENCE_INFORMATION", "STRUCTURAL", "DOMAINS_AND_SITES", "PTM", "VARIANTS" and/or "MUTAGENESIS". You can supply up to 8 categories.

types

Sequence annotation (Features) types. accepted values are: "INIT_MET", "SIGNAL", "PROPEP", "TRANSIT", "CHAIN", "PEPTIDE", "TOPO_DOM", "TRANSMEM", "DOMAIN", "REPEAT", "CA_BIND", "ZN_FING", "DNA_BIND", "NP_BIND", "REGION", "COILED", "MOTIF", "COMPBIAS", "ACT_SITE", "METAL", "BINDING", "SITE", "NON_STD", "MOD_RES", "LIPID", "CARBOHYD", "DISULFID", "CROSSLNK", "VAR_SEQ", "VARIANT", "MUTAGEN", "UNSURE", "CONFLICT", "NON_CONS", "NON_TER", "HELIX", "TURN", "STRAND" and/or "INTRAMEM". You can supply up to 20 types.

...

rbioapi option(s). See rba_options's arguments manual for more information on available options.

Corresponding API Resources

"GET https://www.ebi.ac.uk/proteins/api/features"

Details

Note that this is a search function. Thus, you are not required to fill every argument; You may use whatever combinations of arguments you see fit for your query.
UniProt Entries are grouped in two sections:

1. Reviewed(Swiss-Prot): Manually annotated records with information extracted from literature and curator-evaluated computational analysis.

2. Unreviewed (TrEMBL): Computationally analyzed records that await full manual annotation.

References

• The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research, 2024;, gkae1010, https://doi.org/10.1093/nar/gkae1010

• Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin, The Proteins API: accessing key integrated protein and genome information, Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W539–W544, https://doi.org/10.1093/nar/gkx237

• Proteins API Documentation

• Citations note on UniProt website

See Also

Other "UniProt - Features": rba_uniprot_features()

Examples

# \donttest{
rba_uniprot_features_search(accession = "Q99616")
# }
# \donttest{
rba_uniprot_features_search(gene = "cd40")
# }
# \donttest{
rba_uniprot_features_search(gene = "cd40 ligand")
# }
# \donttest{
rba_uniprot_features_search(gene = "cd40",  reviewed = TRUE)
# }
# \donttest{
rba_uniprot_features_search(accession = "Q99616",
    categories = c("MOLECULE_PROCESSING", "TOPOLOGY"))
# }
# \donttest{
rba_uniprot_features_search(accession = "Q99616", types = "DISULFID")
# }