Taur.vil Week 5

Week 5 Individual Journal

• Traveled to the uniprot website
• Queried P00533, page for the epidermal growth factor receptor(EGFR) appeared
• Found the general information for the entry at the bottom of the page
• Found the name and origin near the top of the page
• Found references near the middle of the page (also observed a bar at the top of the page with each section title, a very helpful tool). Currently 84+ references instead of the 19 mentioned in the book.
• Found the comments section under the general annotations field
• Found the cross-references section which was quite difficult to comprehend.
  • EMBL: I visited the European Nucleotide Archive EMBL-EBI. This database contained the mRNA transcript and protein sequence for EGFR along with general information, taxonomy, and main features of the gene.
  • InterPro: The example of an InterPro site I found for EGFR was also hosted by EMBL-EBI. This database contained a general description of the gene and it's close relatives and identified it as a Cellular Component, directing me to the GO:0016020 membrane page. If it had found any, this database would have also provided information about the domain relationships.
  • PDB: PDB databases provided information for the 3D structure of the protein. Several of these were theoretical structures which were no longer available due to a change in curation procedure (ex 1DNQ. Still available were experimentally determined structures like 1IVO. This database contained a PDB structure file, a 3D viewer for the protein, a summary of structure origin, the quaternary structure of the protein, and a summary of similar structures.
  • Pfam
  • RefSeq
  • GeneID
• Found the keywords under the ontology title (a system that makes little sense). Some of the keywords were ATP-binding, Tumor Suppressor, and Alternative Splicing.
• In the sequence annotation area (or features), I found information about the regions, natural variations, mutagenesis experiments, natural AA modifications, and secondary structure of the protein.

By Tauras Vilgalys

As part of Biological Databases

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