Annotation Conf. Call December 10, 2013

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Agenda

ubiquitin hydrolase

Pascale

  • Confusion between use of:

GO:0004221 ubiquitin thiolesterase activity

and

GO:0004843 ubiquitin-specific protease activity


1) ubiquitin thiolesterase activity: Catalysis of the reaction: ubiquitin C-terminal thioester + H2O = ubiquitin + a thiol (mapped to EC:3.1.2.15)

2) ubiquitin-specific protease activity: Catalysis of the hydrolysis of various forms of polymeric ubiquitin sequences (not mapped to any EC term).

However my understanding is that, although the reaction is sulfur-dependent, it's still a protease, and NOT a thiolesterase. Is this right ?

Those annotations are also in the following InterPro families:

IPR001394 IPR001578 IPR006615 IPR018200

I have the feeling the ubiquitin thiolesterase activity is not a real reaction. See http://sourceforge.net/p/geneontology/ontology-requests/10519/ for request to obsolete. I am waiting for the Swiss-Prot enzyme expert for input (Kristian Axelsen)

Kristian agrees that ubiquitin thiolesterase activity is not a real reaction - it's an unfortunate error in the name that has seemingly never been caught and that resulted in two separate EC entries.

Histone kinase terms (mentioning specific residues in term names)

Continued from last call: There are some histone kinase terms that include the name of the residue that is being phosphorylated in the term name itself (http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0035174#lineage). Although histones are very well conserved, there are still some differences in the sequence and the serine is always not in the same position in all organisms, but often the context is the same (i.e it is +/- one or two residues).

  • It is not clear if curators should request granular term with specific residues in the term name.
  • how do we capture functional equivalence in GO term name?

UniProt-GOA species-specific files

We plan to stop submitting the GOA species-specific GAFs if the species is one owned by another group, that is the following files;

  • gene_association.goa_arabidopsis
  • gene_association.goa_mouse
  • gene_association.goa_rat
  • gene_association.goa_zebrafish

Users will still be able to get these files from the UniProt-GOA ftp site, or from the UniProt multispecies file.

We will announce this in our next release (10th December) and probably stop providing them early next year.

However, if you are one of the groups above, could you ensure that you are picking up annotations from other groups for your species so that you have a full set of annotations (remembering to consider the annotation extension column, your database may have the same annotation but without an annotation extension that another group has provided).

If your group is using Protein2GO then you will be getting the full set of annotations back from us anyway.