Mpetredi Week 5

Mitchell Petredis

Week 5

UniProt Exercise Journal

1. Navigated to http://www.uniprot.org instead of http://web.expasy.org/docs/swiss-prot_guideline.html as per week 5 instruction
2. Typed P00533 in search box on uniprot website.
   • Sent to http://www.uniprot.org/uniprot/P00533. Link describes Epidermal growth factor receptor (EGFR).
3. Clicked the 2.7.10.1 hyperlink.
   • Redirected to http://enzyme.expasy.org/EC/2.7.10.1. This link describes the receptor "protein-tyrosine kinase."
4. Located Quick Search Box (Under Query)
5. Noticed the quick links around the top of the page, under the Quick Search box. Each link directs you to a specific section of the entry
   • [Names]: States all the ways P00533 can be identified
   • [Attributes]: States the sequence length, sequence status, sequence processing, and protein existence of a subject.
   • [General annotation]: AKA Comments. Provides additional, brief information about the function, catalytic activity, enzyme regulation, subunit structure, sub cellular location, tissue specificity, post-translational modification, involvement in decease, and sequence similarities. Check this section first to get a basic idea of a subject before proceeding to the more fully detailed information.
   • [Ontologies]: Applies keywords relevant to the subject's properties.
   • [Interactions]: Vaguely describes the other subjects P00533 interacts with.
   • [Alt products]: States the isomers of the subject created by alternative splicing.
   • [Sequence annotation]
   • [Sequences]
   • [References]: Contains all materials used when compiling the report on P00533.
   • [Web links]
   • [Cross-refs]: This section provides other links pertaining to the same subject. Each link performs a different function from the others.
     • [EMBL]: Mostly contains raw data and results presented in an outline format.
     • [InterPro]: Information is presented in paragraph form with many descriptors.
     • [PDB]: Displays virtual models of the subject (P00533 in this case) and mentions what certain colors on the model indicates.
     • [Pfam]: Also displays a virtual model of the subject, but with less detail than PDB. It does provide other links to similar subjects and databases related to the searched subject
     • [RefSeq]: Directed to NCBI that contains similar or the information as uniprot, but not structured as easily as uniprot.
     • [GeneID]: Also directed to NCBI, but the presented information has less content and looks cleaner. Contains many links to other pages on and off NCBI.
   • [Entry info]
   • [Documents]
   • [Customize]: Use this to change the default ordering of sections.
6. Near the top right corner, information about the subject can be formatted for text, xml, ref/xml, gff, or fasta via designated orange buttons.

P00533, or Epidermal Growth Factor Receptor: A Brief Summary

I learned that P00533 is one of the many IDs for the epidermal growth factor receptor (EGFR), a human protein that can result in the formation of lung cancer. EGFR is completely sequenced with a length of 1210 AA that exists at the protein level. A very detailed report can be found at http://www.uniprot.org/uniprot/P00533, where anyone can find everything currently known about EGFR along with other links about EGFR from other freely available databases.

Individual Assignment Response to Questions

1. The purpose of this exercise was to become more familiar with the layout of information presented by UniProt for a particular sequence or protein.
2. I learned how to locate relevant information pertaining to this course.
3. I currently don't know how I will utilize the information for a certain sequence or protein in my project for this course.Mpetredi (talk) 14:28, 26 September 2013 (PDT)Mitchell Petredis