gocentral
commented
15 years ago Er, not to whine or anything (well, OK, maybe a little), but why assign to me? I don't know anything in particular about these activities, and you've already done exactly what I would: look at EC because that must be where we got the synonyms. That said, we've deviated from EC elsewhere (yipe we're deviants!!!) for various reasons, and we can do so again.
I guess if you need to capture an NAD/NADP distinction for your annotations, let's remove the synonyms and add new terms. (If it didn't make any difference to annotation, we could just change the scope.)
(And, having got the whinging out of the way, I'm happy to do the edits if you don't want to. If you just want me to see an item, no need to assign it -- I see not only every new entry, but also every blasted comment, that comes in on this tracker. Don't I have a great job?)
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Original comment by: mah11
NAD+ diphosphatase activity
Def: Catalysis of the reaction: NAD+ + H2O = AMP + NMN.
Exact synonyms:
NADH pyrophosphatase activity NADP pyrophosphatase activity
Can that be right? The synonyms refer to compounds that are not in the definition, NAD+ != NADH and NAD+ != NADP.
I can trace the origin of the exact synonyms to the EC information:
http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/6/1/22.html
Also, when one looks at the BRENDA entry:
http://www.brenda-enzymes.org/php/result\_flat.php4?ecno=3.6.1.22
you see that substrates other than NAD+ (including NADPH) are given.
What do you think of this situation? The gene product I am annotating has been shown to have enzymatic activity in the presence of NADPH (and to a lesser extent NADH) and I'm wondering whether to annotate to this term or whether to create a new term 'NADPH pyrophosphatase activity' since activity towards NAD+ has NOT been demonstrate.
This is a ontology and annotation question rolled into one. Thought I'd air it on SF first.
Reported by: tberardini
Original Ticket: "geneontology/ontology-requests/5865":https://sourceforge.net/p/geneontology/ontology-requests/5865