I have protein sequences from STRING database: The amino acid sequence files are like this:


I want the corresponding nucleotide sequence for the same protein ID.


I tried emboss http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/ But emboss is based on codon usage and backtranslate and it doesn't give me the original nucleotide sequence.

Then I tried DDBJ http://getentry.ddbj.nig.ac.jp/top-e.html But DDBJ gives only amino acid sequences for corresponding Uniprot ID.

How do i get the original nucleotide sequence for the STRING protein sequences using STRING id or UniProt ID?

Any help in this regard is highly appreciated.

  • $\begingroup$ This should effectively clear your question uniprot.org/help/canonical_nucleotide $\endgroup$ Sep 10 '14 at 10:38
  • $\begingroup$ What is meant by canonical UniProtKB sequence? $\endgroup$ Sep 10 '14 at 10:46
  • $\begingroup$ @Raghavakrishna As it says, although most proteins derive from DNA translation, there isn't only a single way in which you can back translate the protein into nucleotide sequences. $\endgroup$
    – Vivek Rai
    Sep 10 '14 at 11:35
  • $\begingroup$ @VivekRai But emboss can be used to backtranslate? ebi.ac.uk/Tools/st/emboss_backtranseq $\endgroup$ Sep 11 '14 at 8:11

Google is not a bad resource for such a question.

In this case I find that the Yeast Genome site has a button which returns the nucleotide sequence. You can select the genomic sequence for the locus or the coding (CDS) sequence.


They also give a link to NCBI at the bottom of the page. I think the reason you were having such a hard time is that UniProt extracted the protein sequence from the mitochondrial genome record. Like many genome ORF predictions, Q0010 does not seem to have a distinct nucleotide record assigned yet.


In general you can do a web search for the uniprot id to start. In many cases, like this one you will find that the nucleotide seq is only a chromosomal sequence record. Biodatabases are a bit of a maze - there are scores of them out there, you may find that someone has clipped the nucleotide sequence of the gene out, which is helpful if there are introns!

  • $\begingroup$ OK for yeast,This is good.But for other organisms what is the way out? $\endgroup$ Sep 11 '14 at 7:32
  • $\begingroup$ i added a note to the post... $\endgroup$
    – shigeta
    Sep 11 '14 at 14:57

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.