BLAST Search Results

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Blast stands for Basic Local Alignment Search Tool.  Blast 2.0 is an algorithm which provides a method for rapid searching of nucleotide and protein databases. It detects local and global alignments, so regions of similarity in otherwise unrelated proteins can be found.  We used Blast 2.0 to determine a possible source organism, the function of the sequence, and the structure of the sequence (http://www.ncbi.nlm.nih.gov/Education).

Determining the structure and source of a Protein

We determined the nucleotide sequence of the GFP protein by using the pGLO plasmid and restriction enzyme map. 
See GFP in pGLO plasmid HERE.
See a mutant GFP HERE. 

pGLO plasmid from Bio-rad Laboratories

We then ran the Nucleotide Blast (blastn) program (http://www.ncbi.nlm.nih.gov) by inputting the sequence we determined (see above).  The best correlation was with the pBAD-GFPuv vector from Aequorea victoria.  It had a score of 1427 and an E-value of 0.0.

Score: 1427 bits (720)
Expect: 0.0
Identities: 720/720 (100%)
Strand: Plus/Plus

The next step was to use Blast Pairwise matching 
"BLAST 2 SEQUENCES VERSION BLASTN 2.2.4"
We used our determined GFP sequence (see above) and the sequence number of the Aequorea victoria (GI: 1490531).

Score: 1385 bits (720)
Expect: 0.0
Identities: 720/720 (100%)
Strand: Plus/Plus
There were no gaps present.