Blast2Go annotation question

Question

[mxlsherry1992]

Dear all,

I got some sequence, and I did uniprot annotation for these sequences, but some of them showed like uncharacterized protein LOC326903, it seems the function still unclear, but if these if any other method that I could know the annotation for these important sequences? I know Blast2Go could do annotation, but haven't used before, I just want to know if it a combination of many database? or I also need to choose a database one by one when using Blast2Go? please let me know if you have any suggestions.

Thank you!!

Answer 1

[Mensur Dlakic]

There are several reasons why a protein would have uncharacterized, unknown or hypothetical designation. For hypothetical proteins, it is not always clear that they are real proteins to begin with, either because of their unusual composition or relatively short length. Next, they may be truly uncharacterized and have no discernable sequence similarity to other characterized proteins. Or they may have distant homology to other characterized proteins, but one has to dig deep to uncover it as simple sequence comparisons (BLAST-like) will not detect it. Finally, a protein may have been in one of the above categories when the original annotation was done, and its annotation was never updated.

I am assuming that the link below is of your protein:

https://www.ncbi.nlm.nih.gov/protein/NP_001315129

If so, click on the link at the far right that says Identify Conserved Domains and you'll see that this protein has two domains that indicate a function in nucleic acid binding and integration. That may or may not help you directly, but it is better than not knowing anything.

[mxlsherry1992]

Got it !! Thank you so much!!