Lena Week 5

Electronic Journal for Uniprot exercise

• searched for primary accession number: P00533

• This is what the entry showed. It it the main page containing general information about EGFR.

• Clicked on EC 2.7.1.112 link, the link brought up this page. This page can help a person figure out a protein's enzymatic function.

• I navigated back to the original page, then clicked on the Comments heading to see what the comments where. I was directed to this page. The comments page hold useful information that just doesn't fit under any of the other headings.

• Again, I went back to the main page and scrolled down to the cross reference section. I found InterPro and clicked on a link for Graphical View. The page showed a visual for the domains and repeats of the protein.

• I also clicked on EMBL, this is the page that showed up. EMBL showed some basic information about the sequence I clicked on, and showed where repeats occured on the gene.

• I looked at PDB which gave an animation of the protein. I liked this page because it showed you the different domains on the protein.

• For the Pfam Link, I clicked on the graphical view and got this. The image shows the arrangement of Pfam domains on the P00533 sequence.

• I tried out RefSeq, which gave a list of papers where the sequence was referenced. This could be useful in finding out more for a research project.

• Lastly, under the Cross-refs, I tried out GeneID, which gave me this. It gave some general information and showed where the sequence was located genomically.

• Back on the main page, under the heading Ontologies, there were some keywords listed. I clicked on the keyword Tumor Supressor.

• On the main page, under Sequence Annotation, this is what shows up

• I clicked on FASTA on the top right corner to get protein sequence in plain text. Here is the result

>sp|P00533|EGFR_HUMAN Epidermal growth factor receptor OS=Homo sapiens GN=EGFR PE=1 SV=2

MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEV VLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALA VLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDF QNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGC TGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYV VTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFK NCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAF ENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKL FGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCN LLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVM GENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIPSIATGMVGALLLLLVV ALGIGLFMRRRHIVRKRTLRRLLQERELVEPLTPSGEAPNQALLRILKETEFKKIKVLGS GAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGI CLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAA RNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSY GVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPK FRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQ QGFFSSPSTSRTPLLSSLSATSNNSTVACIDRNGLQSCPIKEDSFLQRYSSDPTGALTED SIDDTFLPVPEYINQSVPKRPAGSVQNPVYHNQPLNPAPSRDPHYQDPHSTAVGNPEYLN TVQPTCVNSTFDSPAHWAQKGSHQISLDNPDYQQDFFPKEAKPNGIFKGSTAENAEYLRV APQSSEFIGA

About the EGFR-HUMAN Protein

The EGTR_HUMAN is a protein know as "epidermal growth factor receptor." The Epidermal growth factor and its receptor were found at Vanderbilt University by researcher Stanely Cohen. It is a member of the kinase protein superfamily and the subfamily of ErbB receptor. The protein in located on the plasma membrane and binds to ligands, including an epidermal growth factor and a transforming growth factor. Mutations affecting this protein could lead to cancer, particularly in the lungs.

Reflections

1. The purpose of the exercise was to get familiar with the layout and features of Uniprot, especially because we are going to be working with Uniprot a lot more this semester.
2. I learned a bit about which cross-ref links I liked, and how to go about accessing information about a specific protein.
3. I think I understood the exercise, but the information being present by some of the cross-ref pages seems really in depth and over my head. I feel like I don't yet know how to interpret all the information I am receiving.

Lena (talk) 17:25, 26 September 2013 (PDT)