Alex J. George Week 8

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

>tr|O40505|O40505_9HIV1 Gp120 protein (Fragment) OS=Human immunodeficiency virus 1 GN=gp120 PE=4 SV=1 ACSLAEEEVVIRSDNFTNNAKTIIVQLNESVVINCTRPNNNTRRSIPIGPGRAFYATGDI TGDIRQAHCTLNGTQWNNTLKQIVIKLREQFKNKTIVFSPSSGGDPEI
 * I selected accession #O40505. however it is not reviewed, so it may not be the best selection
 * FASTA Sequence:

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: