Method 3: Search the Entrez Gene database for a gene of interest, view its protein translation in the Entrez Protein database, then follow the link from the protein sequence record to Related Structures

• Use the Entrez Gene search page to retrieve gene record(s) of interest.
  For example, try a search for:
  
  

  prostaglandin AND synthase AND human[organism]
  OR
  PTGS1[Gene] AND human[Organism]



• Open the Entrez Gene record of interest (for example, Gene ID 5742 for PTGS1) and select the Table of Contents link for Reference Sequences to see a list of the genomic, mRNA, and protein reference sequences for that gene.



• Click on the NP_xxxxxx accession number for the protein of interest to view its sequence record.
  For example, open NP_000953 to view the protein sequence for prostaglandin G/H synthase 1



• Scroll to the "Related Information" menu in the right margin of the record and select the option for "Related Structures (Summary)."



• On the Related Structures page, click on the pink bar that represents the alignment footprint in the graphic display of hits, or on the "[+]" in the first column of the table display to see an alignment between your query sequence and the structure-based protein sequences.



• On the sequence alignment display, press the View Structure and Alignment in Cn3D button to open an interactive view of the sequence alignment and corresponding 3D structure. The Cn3D program must be present on your computer in order for the button to work; the program is free and takes only a minutes to install.

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See also: How to align a query protein to a similar sequence from a 3D structure and interactively view sequence/structure relationships.