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Peptide Search in UniProt

BioCodeKb - Bioinformatics Knowledgebase

Peptides are short chains of between two and fifty amino acids, linked by peptide bonds. Examples of peptides are the hormone oxytocin, glutathione (stimulates tissue growth), melittin (honey bee venom), the pancreatic hormone insulin, and glucagon (a hyperglycemic factor). They do not have well defined structure.

Peptide Search

This peptide search tool allows us to submit peptide sequences of at least 3 residues as an input and to find all UniProtKB sequences which have an exact match to the query sequence. To access the tool, click on the 'Peptide search' link in the header which is at the top of every page on the UniProt website.

The Peptide search results display proteins that have exact match to the query sequence in a table with filters on the left hand side. An active peptide is defined as a small polypeptide (<= 40 to 50 amino acid long) that is processed (e.g. by proteolytic cleavage) from a larger precursor protein and has a well defined biological activity on its own. There can be more than one 'Peptide' subsection per protein entry. Each peptide has a stable identifier.

Subsections of Peptide Search

There are subsectionsof the 'PTM / Processing' section, describes the position and length of an active peptide in the mature protein. The processing events that may contribute to the formation of a mature peptide are described in the 'Initiator methionine', 'Propeptide', 'Signal' and 'Transit peptide' subsections.

The 'Description' field of each 'Peptide' corresponds to the peptide name listed in the 'Protein name' subsection, under the heading "Cleaved into the following x chains:", where 'x' represents the number of chains described in the 'PTM/Processing' section.

A user can input a query peptide and specify whether to search the entire UniProtKB or limit the search to sequences from one or more selected organisms. For the latter, a user can either enter an organism name/taxonomic ID of a UniProt complete proteome or select a set of organisms from the UniProt reference proteomes. Additional options are provided to;

  1. Restrict the matches in UniRef100 representative sequences to reduce redundancy

  2. Equate isobaric leucine and isoleucine to support MS-based proteomics.

The match results are summarized by organism and taxonomic group as pie charts and listed as tables, along with annotations, matched region(s) in the protein sequence and hypertext links to corresponding databases. The match results can be

sorted by different fields and browsed by organisms, taxonomic group or taxonomy tree.

Locating occurrences of a specific peptide in a protein sequence database of Peptide search in Uniprot is important for protein identification in proteomics studies as well as for sequence-based protein retrieval

Although exact peptide matching is algorithmically simple, quickly locating a peptide in a large protein sequence database has become challenging, as the number of protein sequences exponentially increases. So far, to our knowledge, no other peptide match services provide all of the key characteristics in our new service, including search speed, support for any query peptide of ≥3 amino acids long covered in UniProt.


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