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
- 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:
- 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

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

- Compared to P00533" from SWISS-PROT:

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:

TMHMM- Transmembrane segments
- The results from TMHMM tell me that gp120 definitely acts on the outside of the cell:

ScanProsite
- Here are the results after running the ScanProsite test:

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