Talk:RefGenome Electronic Jamboree 2008-10 PFKL

<iframe_embed> coveritlive 23c5dca960 </iframe_embed>

Issues

1. Inconsistency of annotations to Fructose 6-P metaoblism. Should all groups have annotated to this if there is an assay for PFK

2. inter-ontology link between F6P metabolism and PKF activity?

4. Annotation to Glycolysis: when can you annotate this process with IDA/IMP to PFKL?

5. Does PFK really bind fructose? Fructose is not the same as fructose-6-P or fructose 1,6 bisP.

• Is it good to have fructose binding as a GO term vs fructose or other ligand as a with from CheBI?

--JimHu 18:56, 8 October 2008 (UTC)

--Ruth In CheBI fructose-6-P and fructose 1,6 bisP are child terms of fructose, revisit GO definition? http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3a32968&viewTermLineage=true&structureView=image#termLineage

After talking with Jane, because of the CheBI hierarchy, it is not incorrect to annotate to fructose binding but we will request a new term for F-6-P binding to give a more granular annotation.

6. Should we be annotating to negative regulation of glycolysis and positive regulation of glycolysis based on known allosteric regulation of the enzyme, but in the absence of evidence that this regulation is happening in vivo? --JimHu 08:20, 10 October 2008 (UTC)

- however most enzymes have this capacity?

- I don't think so - JH

-UK group sorry we misread your point. We were thinking that most enzymes catalyse both forward and backward reactions.

7. based on just enzyme activity should we annotate to product/substrate binding (fructose/ATP/ADP binding). If so, which evidence code to use?

- I thought that after the last jamboree we were going to not annotate product/substrate binding. ADP should be there (at least for E. coli - not sure about the others) because it's an allosteric ligand as well as a product. But we should definitely discuss this. - JH

8. Usefulness of annotating to protein binding as well as the cc complex term.

9. Can papers be used for annotation when they have not clearly identified the genes that encode the gene products. For example, PFK complex in S. cerevisiae is an alpha4, beta4 heteromer. PFK1 = alpha, PFK2 = beta. Older papers that characterize kinetics and binding do not have this level of detail. Are they ok to use? -EH
- If there is no doubt it is the gene product(s) they were looking at (especially if there is only one gene) I think old papers can be used. PF

Test chat

<iframe_embed> coveritlive 063cc87b71 </iframe_embed>