Annotation Conf. Call, May 27, 2014: Difference between revisions
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http://sourceforge.net/p/geneontology/ontology-requests/10635/ | http://sourceforge.net/p/geneontology/ontology-requests/10635/ | ||
* GO:0004839 ubiquitin activating enzyme activity | * GO:0004839 ubiquitin activating enzyme activity | ||
This term has had definition change. | ** This term has had definition change. | ||
** Synonym: E1 [currently in place] | ** Synonym: E1 [currently in place] | ||
** New definition: Catalysis of the reaction: E1 + ubiquitin + ATP --> E1-ubiquitin + AMP + PPi, where the E1-ubiquitin linkage is a thioester bond between the C-terminal glycine of Ub and a sulfhydryl side group of an E1 cysteine residue. This is the first step in a cascade of reactions in which ubiquitin is ultimately added to a protein substrate. | ** New definition: Catalysis of the reaction: E1 + ubiquitin + ATP --> E1-ubiquitin + AMP + PPi, where the E1-ubiquitin linkage is a thioester bond between the C-terminal glycine of Ub and a sulfhydryl side group of an E1 cysteine residue. This is the first step in a cascade of reactions in which ubiquitin is ultimately added to a protein substrate. |
Revision as of 01:55, 27 May 2014
Agenda
Punted from previous call
Alzheimer's Disease Annotation Project (Jane/Paola/Sejal)
http://wiki.geneontology.org/index.php/Alzheimer%27s_Disease_Annotation_Project
Extracellular branch of GO CC (David OS)
I've done some work on fixing a number of issues with the extracellular branch of GO CC. I'd like to get some feedback from annotators on my proposed changes before committing them. slides here
E2/E3 terms
The changes to the Ub terms have been made. http://sourceforge.net/p/geneontology/ontology-requests/10635/
- GO:0004839 ubiquitin activating enzyme activity
- This term has had definition change.
- Synonym: E1 [currently in place]
- New definition: Catalysis of the reaction: E1 + ubiquitin + ATP --> E1-ubiquitin + AMP + PPi, where the E1-ubiquitin linkage is a thioester bond between the C-terminal glycine of Ub and a sulfhydryl side group of an E1 cysteine residue. This is the first step in a cascade of reactions in which ubiquitin is ultimately added to a protein substrate.
- GO:0004842, ubiquitin-protein transferase activity" will change as follows, allowing for all current annotations to be correct as long as they were for 'E2' or 'E3' activities. Groups can choose to re-annotate as they wish.
- Definition: "Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages." http://amigo.geneontology.org/amigo/term/GO:0004842#display-lineage-tab
- two new children of GO:0004842, "ubiquitin-protein transferase activity"
- GO:0061631, Ubiquitin conjugating enzyme activity; Synonym E2, Hect E3
- GO:0061630, ubiquitin protein ligase activity; Synonym: E3
Annotation consistency exercise
MF vs BP annotations. Enzyme Regulator activity vs positive regulation of X terms