Where can I find the wild type sequences?

Question

[ganuongphap]

I am advised that the FASTA sequences in Uniprot is the wild type. However when I check the sequence of HIV-1 protease in Uniprot, I see it isn't the same as in 1MUI, the wild type as this side stated.

The FASTA in Uniprot:

PQVTLWQRPIVTIKIGGQLKEALLDTGADDTVLEEMSLPGKWKPKMIGGIGGFIKVRQYDQVSIEICGHKAIGTVLIGPTPVNIIGRNLLTQLGCTLNF

The one in 1MUI:

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Which is the true wild type?

[karl.stamm]

Those two are pretty close. Probably different strains from around the world?

[ganuongphap]

I don't know. What do you think?

[karl.stamm]

I think whoever is researching HIV (you, not me) should dig deeper to find where the sequences came from; read the publications and methods. While it seems possible they are unique strains, it is well outside my research area. These databases are a starting point and you're going to have to understand what they mean.

Answer 1

[Bert Overduin]

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?".