Checking whether protein sequences have start and stop codon

Question

[lukhanyomakhabane]

Hello guys

I did NCBI Blastp analysis, and got hit protein sequences. So someone told me I should check whether the protein sequences have start and stop codon. How can I do this, I'm lost please assist me. Your help would be greatly appreciated.

Best

[Asaf]

Since input to blastp is protein sequence it will not have codons but amino acids. You will not see a stop codon but you might look for the initial Methionine (although not necessarily).

[lukhanyomakhabane]

Thank you guys, you the best!

Answer 1

[Jeremy]

I agree with Asaf's comment. Also keep in mind that NCBI blastp does a local alignment (as opposed to global), so you are likely getting partial protein sequences as hits, which would not include start and stop codons even if done at the nucleotide level. You can use the accession number to get the full-length sequence of a hit, which will include the start codon (methionine) and exclude the stop codon, since it is not translated. The bottom line is that the accession numbers of your results will have full-length sequences with the start codon included and the stop codon implied, so you don't need to check to make sure that they're there.

[Mensur Dlakic]

The bottom line is that the accession numbers of your results will have full-length sequences with the start codon included and the stop codon implied, so you don't need to check to make sure that they're there.

This works in theory, but not always in practice. The absence of stop codon from translation doesn't mean there is one in the sequence. It could be a partial sequence, so the translation just stops because the sequence runs out.

A start codon could be a GTG (normally codes for valine) in many GC-rich bacteria, but it is translated as methionine. Or it can be a TTG (normally leucine) in AT-rich microbes. A starting methionine in protein sequence is not a guarantee of an ATG codon. The only way to know for sure that a protein sequence is complete and has both start and stop codons is to look back into DNA from which the translation was made.

[Jeremy]

Thanks for the clarification Mensur. I learned something new today!