Pathway: oxidative phosphorylation (GO:0006119)

[ValWood]

Pathway: oxidative phosphorylation (GO:0006119)

Complete gene set https://www.pombase.org/term/GO:0006119

The model is missing the
proton-transporting ATP synthase complex (GO:0045259)/
proton motive force-driven mitochondrial ATP synthesis (GO:0042776) sub-part

because I don't have a COmplex Portal ID for proton-transporting ATP synthase complex (GO:0045259)
https://www.pombase.org/term/GO:0045259
(I could add it with the complex sub-parts)
See geneontology/go-ontology#29067

Model Link: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A663d668500000596

Current Model:

GOCAM viz

GOCAM viz complexes uncollapsed

[ValWood]

If we agree this is the way to model this process, the fly pathway should be identical, except ndi1 will be substituted by complex I

[ValWood]

@Antonialock

[hattrill]

Yikes - think if we are having to add components by has_part we could do with a bulk upload method....For complex I I have 44 members!

[hattrill]

Building the Fly version - not connected anything or filled in all the gaps yet: http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A67086be200000314

[hattrill]

Added some connections - think will have to add H+ input to complex V and add Cytochrome c and electron transferring flavoproteins somewhere in the mix

[hattrill]

Adding this note: CHEBI has electron entry....CHEBI:10545

[ValWood]

Yikes - think if we are having to add components by has_part we could do with a bulk upload method....For complex I I have 44 members!

That's why this ticket should be a priority, please add your voice!
geneontology/noctua#905

[ValWood]

Added some connections - think will have to add H+ input to complex V and add Cytochrome c and electron transferring flavoproteins somewhere in the mix

If you can add these parts I will copy them.

I will try to rationalize the assembly factors (I'll open a separate ticket)
we have a good start https://www.pombase.org/results/from/id/e5831c48-bd63-425d-92b1-c9dcd8aad95e
but there is some slightly wonky ontology ). I want to find out if these are really all assembly factors and, if so, what (i.e. chaperone) - some have turned out to be stabilizing the mRNA, so assembly is just a phenotype; this will take a while because I'm busy next week or so.

[ValWood]

PomBase Tim18 has
GO:0020037 heme bindingIBA with PTN001000243 , A5GZW8 GO_REF:0000033 19
GO:0048039 ubiquinone bindingIBA with A5GZW8 , PTN001000243 GO_REF:0000033 2
which looks incorerct for this subunit. @Antonialock coud you check this? (I think its from the complex)

@tim18 ignore- it has binding sites!

[hattrill]

1. Modified to show H+ output/input from complexes to complex V
2. Added cyt c
3. Very roughly added ETF complex and Etf-QO as place-holders - they mediate e- transfer from other mitochondrial pathways to ubiquinol for input for complex III. PMID: 33450351, but do not know what BP to add here as where boundary on oxphos chain is is unclear to me just now.