Alex J. George Week 8

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Week 8 Individual Journal

Retrieving Protein Sequences

  • After searching for dUTPase, I searched for "gp120 protein"
  • This search was not extensive enough, so I searched for "gp120 protein Human immunodeficiency virus type 1" which limited my results

Expasy gp120 search.png

  • I selected accession #O40505. however it is not reviewed, so it may not be the best selection
    • FASTA Sequence:

>tr|O40505|O40505_9HIV1 Gp120 protein (Fragment) OS=Human immunodeficiency virus 1 GN=gp120 PE=4 SV=1 ACSLAEEEVVIRSDNFTNNAKTIIVQLNESVVINCTRPNNNTRRSIPIGPGRAFYATGDI TGDIRQAHCTLNGTQWNNTLKQIVIKLREQFKNKTIVFSPSSGGDPEI

Reading a SWISS-PROT

  • Searched for ID "P00533"- an epidermal growth factor
  • General Info located at top:

EGFR General Info.png

  • Much more detailed info chronicled throughout page such as Function, references and comments

With gp120

  • Accession #O40505: Here is a screenshot of the information provided for this human gp120 protein
Gp120 seach general info.png

ORFing DNA Sequences

  • To ORF my DNA. I went to "http://www.ncbi.nlm.nih.gov/gorf/gorf.html" and copied the FASTA sequence of S2,V1, Clone 1 into the input field
  • Here is the resulting ORF of the DNA sequence from Subject 2, Visit 1, Clone 1 of the Markham et al. study
ORF for S2V1-1.png
  • Compared to P00533" from SWISS-PROT:
P00533 ORF.png

Single Protein Sequence- gp120

  • I obtained to amino acid sequence for gp 120 from SWISS-PROT by selecting a reviewed gp160 entry, P05883.
  • From P05883 main page, I scrolled to the "Molecule Processing" section and selected "surface protein gp120" which gave me its amino acid sequence
  • After entering this sequence into ProtParam, it gave me a bunch of results for the protein sequence. Here is a sample:
Gp120ProtParamAG.png

TMHMM- Transmembrane segments

  • The results from TMHMM tell me that gp120 definitely acts on the outside of the cell:
TMHMM result.png

ScanProsite

  • Here are the results after running the ScanProsite test:
Scanprosite.png


Individual Journals

  1. No Week 1 Journal
  2. Alex J. George Week 2
  3. Alex J. George Week 3
  4. Alex J. George Week 4
  5. Alex J. George Week 5
  6. Alex J. George Week 6
  7. Alex J. George Week 7
  8. Alex J. George Week 8
  9. Alex J. George Week 9
  10. Alex J. George Week 10
  11. Alex J. George Week 11
  12. Alex J. George Week 12
  13. Alex J. George Week 13

Shared Journals

  1. Week 2
  2. Week 3
  3. Week 4
  4. Week 5
  5. Week 6
  6. Week 7
  7. Week 8
  8. Week 9
  9. Week 11
  10. Week 12
  11. Week 13
  12. Week 14
  13. Week 15

Links

Course Home Page

Alex George

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