Question

What are the possible explanations for the result shown below?

1. The BLASTX query sequence was translated in all six reading frames, and the top hit was found in a different reading frame than the correct one.
2. The BLASTX database contained a pseudogene.
3. The BLASTP database contained a protein sequence that was more closely related to the query sequence than any of the protein sequences in the 4. BLASTX database.
4. The BLASTX search was performed using a different scoring matrix than the BLASTP search.
5. The BLASTX search was performed using a different e-value cutoff than the BLASTP search.

Answer 1

The possible explanations include incorrect reading frame, presence of a pseudogene, closer protein sequence match in BLASTP database, different scoring matrix, and different e-value cutoff.

Step-by-step explanation:

The possible explanations for the result shown below are as follows:

1. The BLASTX query sequence was translated in all six reading frames, and the top hit was found in a different reading frame than the correct one.
2. The BLASTX database contained a pseudogene.
3. The BLASTP database contained a protein sequence that was more closely related to the query sequence than any of the protein sequences in the BLASTX database.
4. The BLASTX search was performed using a different scoring matrix than the BLASTP search.
5. The BLASTX search was performed using a different e-value cutoff than the BLASTP search.