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

4932.Q0010 (Saccharomyces cerevisiae) MYYIMFLYNMLLIIILIFYSIVGVPIIIFNNNYYWDPDIFLFIIYYFIKFIIIFNLYLYYMINYIVYTPSGSPPGRGTYI LLYNMLYSYNMFIDYVMKFITCVTYMYLMFWLLSPTPSPYYVSEVPVS

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

4932.Q0010

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.

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  • $\begingroup$ This should effectively clear your question uniprot.org/help/canonical_nucleotide $\endgroup$ – The Last Word Sep 10 '14 at 10:38
  • $\begingroup$ What is meant by canonical UniProtKB sequence? $\endgroup$ – Raghavakrishna 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 $\endgroup$ – Raghavakrishna Sep 11 '14 at 8:11
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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.

http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=Q0010

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.

Summary:

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!

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

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