Question: Hypothetical proteins in NCBI protein Reseq records what annotation to consider??
0
gravatar for bionicstar
3.5 years ago by
bionicstar0
bionicstar0 wrote:

Hi all,

I have a query regarding protein entries in the Refseq NCBI protein pages.

For example an entry as such:

enter image description here

When the attribute "definition" says hypothetical and the protein product ="hypothetical protein" but the "region" information under 'FEATURES', specifies certain regions of the sequence as some particular protein type or domain. Should the protein be considered as hypothetical or should it be referred to as the name of the protein mentioned in the "region note"?.

Any help to clarify this would be appreciated!

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by bionicstar0
1

This is not a RefSeq record. Validated RefSeq entries would start with a N* accession, where as predicted would be X*,Z*.
This type of a record comes from predictive analysis. The region referred to above must show a good similarity/identity to known Glycosyltransferase_GTB_type but until someone proves that function experimentally it is safer to call it hypothetical.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax73k

Thank you very much for the response!

Are records with accession numbers starting with WP_ considered to be validated RefSeq entries?

For comparative genomics purposes can we call the protein to be annotated as glycosyltransferase?

ADD REPLYlink written 3.5 years ago by bionicstar0

WP_ records are non-redundant RefSeq entries. See this for more.
Is there a reason you want to include this hypothetical protein? There must be several other RefSeq entries that must qualify.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by genomax73k

Ok thanks. No I used this just as an example. The proteins that I am studying have WP_ accession numbers.

ADD REPLYlink written 3.5 years ago by bionicstar0
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