Analyzing a protein based on the multiple sequence alignment

[KaylaElaine21]

Based on the project "Computational Exploration of Protein Function."
I have been doing this project on Peptidoglycan Recognition Protein 1 (PGLYRP1). The part i am currently stuck on is how to determine which part of the protein is important based on the multiple sequence alignment. I ran the alignment with 5 species.. Also from determining the important parts, how do i formulate and test a hypothesis about the protein's function(s) and the protein's 3D structure?
*Attached is the MSA results. (protein)

[Limeybean]

Hi KaylaElaine21,

Before I get to your question I just wanted to let you know that UniProt (http://www.uniprot.org/uniprot/O75594#ref6) is also a great web resource.

So the premise of "Computational Exploration of Protein Function" is that if some protein is really important (i.e. required for basic cellular function) it probably is not changing much over evolutionary time. A non protein example would be 16S ribosomal RNA. It is very important for translation and has many conserved regions within gene sequence and can be used to identify microbes across the two domains of prokaryotes (http://en.wikipedia.org/wiki/16S_ribosomal_RNA).

I know that this example seems tangental but if you looking at the clustal alignment of PGLYRP1 are there regions that are different across species or that remain the same. Also remember that there are different groups of amino acids and that they form very different 3-D structures (http://en.wikipedia.org/wiki/Secondary_ ... _structure). A change from an hydrophobic amino acid to another hydrophobic amino acid with change protein structure less than a change from an hydrophilic amino acid to an hydrophobic amino acid.

Good Luck!
Emily

[hhemken]

KaylaElaine21,

This topic should be discussed in the Life, Earth, and Social Sciences forum. You will get more genomics- and biology-savvy eyes on it there.

Good luck!

Heinz Hemken