Pathway: acyl-CoA metabolic process

[ValWood]

http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000251
broaden this pathway to "acyl-CoA metabolic process"

https://www.pombase.org/results/from/id/83cb2ae5-5821-42df-8771-18f5533d2ca7

16/32 are mitochondrial

You need to follow
geneontology/go-ontology#24350
see specifically geneontology/go-ontology#24350 (comment)
and
check out micropub-biology-001209.pdf

[ValWood]

I had a note for "acetyl-CoA biosynthetic process from pyruvate" that I need to find a source of the "mitochondria Matrix annotations, currently only have Mitochondrion"

[ValWood]

When an annotation is missing, I usually find an experimental source I can ISO to , or some review to TAS, or make an IC (for example if the MF is known to be in a specific location). It would be more useful if we find an EXP and ask Marc to PAINT it (I know Steven does this sometimes).

This will happen quite a lot during this project as we try to refine locations.

I use Helens tip to see if there are any existing EXP for any orthologs at the Alliance (you can retrieve all EXP annotations for orthologs)

For acetyl-CoA biosynthetic process from pyruvate,

I just checked pda1 (using human PDHA). SGD is annotated to nucleoid (which is part of matrix), so Marc might be able to PAINT based on this.

I suggest we link the PAINT tickets to these pathway tickets so that everyone can see that the request is in progress.
@PCarme I can show you this on Monday or Tuesday if unclear.

[ValWood]

PAINT REQUESTS

gene	PANTHER	term	ticket
S.p pda1 (human PDHA)	PTN008519424	mitochondrial matrix	geneontology/go-annotation#5485
-	-	-	-

[PCarme]

We should add [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity(GO:0004741) to https://www.pombase.org/gene/SPAC4A8.03c, based on ISO with https://www.yeastgenome.org/locus/S000002133

Note: the other PDHC phosphatase subunit, https://www.pombase.org/gene/SPAC10F6.17c, is annotated to this term with an IBA evidence.

[PCarme]

Also noticing that https://www.pombase.org/gene/SPCC794.07 has his gene product described as "e3 component", while his orthologs https://www.yeastgenome.org/locus/S000005015 https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:2896 are described as the E2 of PDHC.
https://www.pombase.org/gene/SPAC1002.09c is the E3.

[PCarme]

In the "acetyl-CoA biosynthetic process from panthotenate, need to add ptk1, hal3, cab4 and cab5 (IC with their respective molecular functions or with "CoA biosynthetic process"

[PCarme]

Also, should fas1 and fas2 be annotated to "long-chain fatty-acyl-CoA biosynthetic process" (GO:0035338) based on their MF annotation to https://www.pombase.org/term/GO:0004321