IPR001047 Ribosomal protein S8E inc ribosome etc?

[gocentral]

according to SGD this is associated with the pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis, but not part of the cytoplasmic ribosome.

there is only 1 member of this family in S. cerevisiae

I wonder if this is actually a missannotation at SGD because these appear to ubiquitously annotated as cytoplasmic ribosome subunits, but hten again the ribosome ref in the swiss-prot entry is very old (1984)

what do you think?

http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YER126C

val

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/89":https://sourceforge.net/p/geneontology/annotation-issues/89

[gocentral]

• milestone: --> InterPro
• assigned_to: nobody --> orchard

Original comment by: mah11

[gocentral]

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by the way, I am basing all of these on the fact that SGD don't have these annotated to 'ribosome', and that they appear to only be annotated to nucleus or nucleolus/ but some could be missing annotations /annotation errors, so some may be incorrect...Its difficult to know because I can't see easily the source of the original annotations in uniprot.

Original comment by: ValWood

[gocentral]

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copied from duplicate entry (SF 1122317):

and another NSA2 is nucleur (nucleolar?) involved in ribosome biogensis

http://db.yeastgenome.org/cgi-bin/locus.pl?locus=YER126C

Original comment by: mah11

[gocentral]

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Not sure about this one. It is hitting TGF-beta inducible proteins, which don't have much annotation linking or not- linking them to ribosomal proteins that I can see, e.g. Q6T351, O95478, Q9CR47 etc. They are annotated as belonging to the ribosomal protein s8e family, but with no indication of function. To be safe should we remove all the GO mappings?

Original comment by: njmulder

[gocentral]

• status: open --> closed

Original comment by: njmulder

[gocentral]

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I have asked Rob Finn if it would be possible to break down this Pfam into the 2 representative families....see e-mail below.

For this one it may be better if the Pfam family was broken down into 2 separate families (It seems a shame to loose the distinction when there appear to be 2 orthologous groups, one which appears to represents the ribosomal proteins and one which relates to the nucleolar family involved in ribosome biogenesis which seems to have insertions relative to the ribosomal protein).

Rob, would it be possible to build Pfam hmms to distinguish between these families? This way they could both have the relevant mappings....

P05754 -cytoplasmic ribosomal Q9UU79 - nuclear involved in ribosome biogenesis

Val

Original comment by: ValWood

[gocentral]

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> > Hmmm, interesting point. So the answer to your question is, yes I could. > However, this is more subfamily annotation and not the philosophy of clans > etc. Subfamily annotation is something that we would like to do, but > there is enough work doing the hierarchy up :-). > > Sorry I can not be of more help, >

Thanks Rob, it was worth a try... Nicky, perhaps this can be broken down into subfamilies at the Interpro level, otherwise I guess the answer is yes the GO mappings will have to go.

thanks

Original comment by: ValWood

[gocentral]

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unfortunately we cannot create subfamilies in InterPro unless there are separate signatures describing the subfamilies, which there aren't. I will have to remove the mappings.

Original comment by: njmulder