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Phage hits not showing in NCBI but 100% to Gordonia wetsfalica

| posted 05 Feb, 2019 14:31
We are currently annotating a DM phage, Ashton. This cluster has few members and Ashton is from M. foliorum while the others are from Gordonia terrea. Ashton has some nucleotide similarity to SallySpecial and Emperor and there are high and low areas as you would expect. In the BLASTP analysis, we are not consistently seeing the genes from Emperor as hits but getting hits to proteins from Gordonia westfalica as the top match when we expect to see products from Emperor. When I do a BLASTP on the products from Emperor, they all hit with 100% alignment and 100% identity to Gordonia westfalica (the genes from Emperor are NOT showing as hits), even Emperor gene #9 listed as an orpham (see screen shot) hits to the westfalica! I can also manually align Ashton and Emperor products to show alignments that NCBI is not showing me vs giving me the Gordonia westfalica hits. Emperor is in Genbank, so I can find the sequences and accession numbers. Am I missing something here? Why is Emperor phage 100% matching to an annotated bacteria genome from a different Gordonia strain? We do see hits to the SallySpecial products even though they have much reduced identity vs. Emperor in some instances.
RS Pollenz
| posted 05 Feb, 2019 17:53
I believe the simple explanation is that the BLASTp database(s) have not incorporated the Emperor submission yet. Which, I agree seems odd.
| posted 05 Feb, 2019 19:49
On further review I was thinking Emperor could be a prophage…….this is posted on the Emperor Phages DB: Emperor was found as a prophage of Gordonia westfalica NRRL-B-24152. Liquid Gordonia westfalica was spotted on Gordonia terrae 3612, and the resulting phage release was picked and amplified, and called Emperor. So, now it make sense and perhaps since the Emperor genes are redundant to the Gordonia genome genes, they do not hot when doing a BLASTP.
RS Pollenz
| posted 05 Feb, 2019 20:00
You are right, because Emporer and the prophage in G. westfalica are identical sequences, the Emporer hit is buried. Check out the alignment, you will see +2 more titles. You will find Emporer there.
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