How can I find fasta sequences for gp120 and gp41?

Question

[mark.pekarsky]

Hello everyone,

I’m looking for DNA .fasta sequences for the Env gp120 and gp41 proteins. Here’s what I’ve been doing: I start by searching for "gp120 hiv-1" on UniProt, but I keep getting results for gp160 instead. When I click on the specific subtype I’m interested in, the descriptions mention gp120 and gp41, but when I go to the sequence tab, it leads me to whole genome sequences, which don’t specify where gp120 or gp41 are located.

Can someone guide me on how to find the precise sequences for gp120 and gp41? Thanks!

Answer 1

[GenoMax]

I’m looking for DNA .fasta sequences for the Env gp120 and gp41 proteins

gp120: https://www.ncbi.nlm.nih.gov/nuccore/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp120 (nucleotide)

gp120: https://www.ncbi.nlm.nih.gov/protein/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp120 (protein)

gp41: https://www.ncbi.nlm.nih.gov/nuccore/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp41 (nucleotide)

gp41 : https://www.ncbi.nlm.nih.gov/protein/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp41 (protein)

For all searches:

Click on Summary menu --> Select fasta.

Use Send to drop down on right side --> Save file to local desktop

[mark.pekarsky]

Thank you! However I need to find gp120 and 41 for the following HIV-1 strains: A, B, C, D, N, and O. That is why I was using UniProt, and these ones that you have suggested seem to be just different patients.

Thanks again.

[GenoMax]

https://www.ncbi.nlm.nih.gov/nuccore/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp120+AND+strain+A

https://www.ncbi.nlm.nih.gov/nuccore/?term=txid11676%5BOrganism%3Aexp%5D+AND+gp120+AND+strain+B

etc.

That is why I was using UniProt

UniProt is protein sequence database.

[mark.pekarsky]

That's correct, you can start from the protein section and scroll down to find the nucleotide sequence. Again, thanks for your help!