Question: How accurate is UniProt?
0
gravatar for alexille5640
12 months ago by
alexille564010
alexille564010 wrote:

I am curious about the reliability of Uniprot amino acid sequences?

Say I want to do the following:

  1. Reverse translate a reviewed Uniprot amino acid sequence into a nucleotide sequence (using Sequence Manipulation Suite Reverse Translate)
  2. Synthesize that nucleotide sequence in vitro into an expression vector plasmid
  3. Transfect cells with that plasmid for expression

Is it expected that a protein with the exact same amino acid sequence will be expressed by the cells?

sequencing sequence genome gene • 455 views
ADD COMMENTlink modified 12 months ago by WouterDeCoster41k • written 12 months ago by alexille564010
2

UniProtKB encompasses several individual protein sequence resources that are depicted on this page. If you are talking about a sequence that is from SwissProt (manually reviewed/curated sequences) or UniRef100 clusters then that sequence is likely perfectly accurate. Every SwissProt record should have a corresponding nucleotide entry so you should not need to do any sequence manipulation (but there may be an exon/intron model to consider).

That said it is unclear what is the aim of this question. Do you wish to express a protein that is not normally present in that host?

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax73k

Sorry for my lack of knowledge, but how do you access the corresponding nucleotide entry of for example: Mus musculus Actin Beta entry from uniprot (https://www.uniprot.org/uniprot/P60710).

ADD REPLYlink written 12 months ago by alexille564010

If you scroll down to the Sequence Databases section on the page you linked you will find this information.

ADD REPLYlink written 12 months ago by genomax73k
1

Yes (for SwissProt), assuming ceteris paribus. Question is, can we ensure ceteris paribus?

ADD REPLYlink modified 12 months ago • written 12 months ago by RamRS24k
1

How do you propose to reverse translate the amino acid sequence? The number of resulting possibilities are astronomical...just using the most frequent codon or something?

ADD REPLYlink modified 12 months ago • written 12 months ago by Joe14k

Yes, relying on the degeneracy of codons, I'm assuming "Sequence Manipulation Suite: Reverse Translate" is sufficient.

ADD REPLYlink written 12 months ago by alexille564010

relying on the degeneracy of codons?

What do you mean by that?

ADD REPLYlink written 12 months ago by RamRS24k

The degeneracy, used to describe how one Amino Acid can be encoded by multiple codons.

Codon Table

ADD REPLYlink written 12 months ago by alexille564010

I am aware of the concept of codon degeneracy. I was asking what you meant by "relying on" codon degeneracy for picking the most frequent codon. Without codon degeneracy one wouldn't encounter any form of frequency, so I was trying to understand the point you were making.

ADD REPLYlink written 12 months ago by RamRS24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2436 users visited in the last hour