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Print Article: KA-03245

How do I locate a RefSeq or UniProtKB (Swiss-Prot) sequence that is identical to my protein of interest at NCBI?

To find out if there is a curated protein record representing an identical sequence for your protein of interest, try one of these two approaches:

1. Compare your sequence to RefSeq or UniProtKB sequences using Protein BLAST:

  • Go to the BLAST® home page and click on the Protein BLAST box.
  • Paste the sequence in the Enter Query Sequence box.
  • In the Choose Search Set section select one of the following as your Database:
    • Reference proteins (refseq_protein)
    • UniProtKB/Swiss-Prot (swissprot)
  • Conduct the search (no other parameter adjustments are needed) by clicking the BLAST button.
  • Check the Alignments section of the BLAST results page. You have located an identical protein if your sequence (query) aligns to a sequence in the database (subject) in its entire length with 100% identity (no mismatches).
  • Click on the Sequence ID link of the subject sequence (the curated record) that is located above the alignment to access its record in the Protein database.

2. If you have a protein record identifier, search the Protein database:

  • Enter the identifier in the search box of the Protein database. As in this example search, you can retrieve more than one record if the identifier is something other than a Protein database accession number.
  • Select the record that you want (for example, ABI93900.1, from the previous search example).
  • Click on the Identical Proteins link under the record's title at the top of the page.
  • In the Identical Protein Report, look for entries that are designated as RefSeq or Swiss-Prot in the Source column (the first column of the table).
  • Access the RefSeq/Swiss-Prot record of interest by clicking on the accession link in the Protein column.
  • For RefSeq entries you will be able to access the coding region (CDS) for the protein by selecting the links in the CDS Region in Nucleotide column.