Assignment I: Primary sequence analysis of Prostaglandin H2 Synthase
In this assignment you will use BLASTp and Clustal Omega to create a protein sequence
alignment. Alignments are tools for analyzing the primary sequence of a protein and extracting
important information. Creating a protein sequence alignment is a common first step for
biochemists that study proteins, novel and known. The programs used in this assignment run
online, so you will not need to download them, just the appropriate output files.
Follow the instructions to analyze the primary sequence of a prostaglandin H2 synthase.
PART A: Finding the primary amino acid sequence of prostaglandin H2 synthase
1. Using the internet, go to the National Center for Biotechnology (NCBI) website
a. Search for Prostaglandin H2 Synthase by typing “Prostaglandin H2 Synthase 1PTH”
into the “protein” drop down menu. (Note: ‘1PTH’ is the PDB, or protein databank, ID.
More on this in assignment II.)
b. On the page that appears, click on the link for Chain A. You will open a file that
includes lots of information about this particular protein sequence. Use this page to
answer questions (1) and (2) below.
(1) State the organism genus-species and the common name accompanied with this protein
sequence
(2) List the primary literature article associated with this protein, include: date of publication,
journal, and authors.
(3) In your own words: What is PubMed? Give an example of something you
could learn about Prostaglandin H
2 Synthase from the PubMed database.
Copy and paste the FASTA sequence into a .txt or .docx file
The screenshot below will help you find the FASTA sequence. The text you
copy should include the carrot (>) and all of the information that follows.
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