<p>I am advised that the FASTA sequences in Uniprot is the wild type. However when I check the sequence of HIV-1 protease in <a href="http://www.uniprot.org/uniprot/O90777">Uniprot</a>, I see it isn&#39;t the same as in 1MUI, the wild type as <a href="http://hivdb.stanford.edu/pages/3DStructures/pr.html">this side</a> stated.</p>

<p>The FASTA in Uniprot:</p>

<pre>
PQVTLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMSLPGKWKPKMIGGIGGFIKVRQYDQVSIEICGHKAIGTVLIGPTPVNIIGRNLLTQLGCTLNF</pre>

<p>The one in 1MUI:</p>

<pre>
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF</pre>

<p>Which is the true wild type?</p>

I am not a HIV expert, but as far as I know there is so much variability in the HIV-1 protease, that there is no such thing as a wildtype or consensus sequence for this protein.

Also, it is good to realise that UniProtKB consists of two parts: UniProtKB/Swiss-Prot, which is manually annotated and reviewed and therefore of very high quality, and UniProtKB/TrEMBL, which is automatically annotated and not reviewed and therefore of much lower quality. See also this FAQ: ["Why is UniProtKB composed of 2 sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL?"][1].

 [1]: http://www.uniprot.org/faq/7