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Can anyone explain me, why I don't find a specific protein with a blast that was took before from the NCBI refseq database?

Specifically, I was trying to blast the protein with the accession number "NP_420767" and its sequence, respectively, however that protein does not show up in the results. It not only happens when the standard options are chosen, but also, when "Reference proteins (refseq_protein)" as database in the blast options is selected.

I am really puzzled by that.. Shouldn't blast show the initial refseq entry in the results list as it is part of the refseq database and has the same sequence?

Matthias F.
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1 Answers1

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NP_420767 is represented by the non-redundant refSeq protein WP_010919826, which has the same amino acid sequence. This is not very clearly annotated, but if you scroll down to the sequence in the GenPept entry for NP_420767, you'll see the following:

CONTIG      join(WP_010919826.1:1..799)

See here for more info.

heathobrien
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  • Ah, I understand.. And in the list after clicking on "identical proteins" on the "WP_010919826.1" site, "NP_420767" gets listed. – Matthias F. Jul 25 '17 at 12:00