Question: My translated A.A seq longer than my original Nucleotide seq!! Could someone explain the results?
0
gravatar for zaineb
7 months ago by
zaineb0
Orange County, California
zaineb0 wrote:

Hello everyone!

I am in the process of identifying an uncharacterized protein, when I convert my nucleotide sequence to Amino Acid using blastx, I get a long Amino Acid sequence. I am not sure if I am doing something wrong or missing a step or there is a biological explanation for it that I don't know of.

Nucleotide sequence / Accession Number X79334 region 333-548

GTTATTGTGTTCGCCGTTTTGCTGACGGCTTCTTGTCTGATGGTCTCCTTTGCCAACAGCTTTACGCTGC
TATTGCTGGACCGCGCCTGTCTTGGGTTGGCGCTGGACGGATTCTGGGCGATGTCGGCGTCGCTGACCAT
GCGACTGGTTCCCGCGCGTACCGTGCCGAAAGCGCTGTCGGTGATTTTTGGCGCGGTCTCCATCGCGTTA
GTGATC

Amino Acid Sequence / Protein accession number ERH37120.1

MNENIAEKFRADGVARPNWSAVFAVAFCVACLITVEFLPVSLLTPMAQDLGISEGIAGQSVTVTAFVAMF
SSLFITQIIQATDRRYIVILFAVLLTASCLMVSFANSFTLLLLGRACLGLALGGFWAMSASLTMRLVPAR
TVPKALSVIFGAVSIALVIAAPLGSFFGCXGISWSGRXALRPSAVMGVLC

I am new to Bioinformatics, but I am fascinated by this developing field. I was researching my question and came across this amazing website. I hope someone can help.

blast • 323 views
ADD COMMENTlink modified 7 months ago by Michael Dondrup43k • written 7 months ago by zaineb0
3
gravatar for Chris Miller
7 months ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

The search is returning the entire protein's sequence, just part of which matches your nucleotide sequence. If you translate your sequence using something like this site: http://web.expasy.org/translate/

You'll see that part of the sequence (starting with VSFANSFT...) is present in the aa sequence you pasted.

ADD COMMENTlink written 7 months ago by Chris Miller19k

Thank you for your prompt response! I used expasy website. interestingly when I run PSI-BLAST for the sequence obtained from expasy website, which is "MVSFANSFTLLLLDRACLGLALDGFWAMSASLTMRLVPARTVPKALSVIFGAVSIALVI" I get the same hypothetical protein as the one from blastx which is "MNENIAEKFRADGVARPNWSAVFAVAFCVACLITVEFLPVSLLTPMAQDLGISEGIAGQSVTVTAFVAMF SSLFITQIIQATDRRYIVILFAVLLTASCLMVSFANSFTLLLLGRACLGLALGGFWAMSASLTMRLVPAR TVPKALSVIFGAVSIALVIAAPLGSFFGCXGISWSGRXALRPSAVMGVLC"

I don't understand how do I get the same result from two different Amino acid sequences!

Thank you again

ADD REPLYlink written 7 months ago by zaineb0
1

You are not using 2 different AA sequences

Run a multiple sequence alignment on the AA input and output sequences using Clustal Omega

You will see the comparison between all your sequences...that might give you a better understanding.

More importantly....you may not want to focus on hypothetical proteins...these are not validated experimentally....and may or may not exist in reality...unless you have just produced it in the lab of course!

ADD REPLYlink modified 7 months ago • written 7 months ago by kennethcondon2007970

Thank you for the suggestion. Multiple alignment was a great tool for clarification

ADD REPLYlink written 7 months ago by zaineb0
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