PAINT: PANTHER PTN000185192 (should not get through, have NOT label)

[ValWood]

Can the following PAINT annotations for fission yeast SPAC1B3.15c

	Term ID	Term name	Evidence	Qualifiers	Reference	Count

• | GO:0015878 | biotin transport | IBA with PTN000185192 , vht1 |   | Gaudet P et al. (2011) | 2
• | GO:1905039 | carboxylic acid transmembrane transport | IBA with vht1 , PTN000185192 |   | Gaudet P et al. (2011) | 66
• | GO:0035461 | vitamin transmembrane transport | IBA with PTN000185192 , vht1 |   | Gaudet P et al. (2011) | 8

be removed. SPAC1B3.15 has been tested and appears to have no role in biotin transport
see:

• | GO:1905135 | NOT biotin import across plasma membrane | IGI with S000003297 | heterologous_system | Stolz J (2003) | 1

second biotin transporter in Sz. pombe, I investigated whether SPAC1B3.15p can complement a disruption in the S. cerevisiae vht1 gene. As shown in Figure 4C, expression of SPAC1B3.15c does not rescue the growth defect of the JSYΔvht1 on low concentrations of biotin. As this assay is extremely sensitive, I propose that SPAC1B3.15c has no function in biotin uptake. It is possible that SPAC1B3.15c is functionally related to the S. cerevisiae VHT1 homologue SEO1. seo1 mutants are resistant against the toxic methionine analogue ethionine sulphoxide (Isnard et al., 1996), implying that Seo1p mediates the plasma membrane transport of the drug. However, the natural substrate of Seo1p has yet to be identified.

Taken together these results demonstrate that SpVht1p mediates biotin and desthiobiotin uptake and that no other biotin transporter is encoded in the Sz. pombe genome.

[ValWood]

Also

SPAC1B3.15c | transmembrane transporter (predicted) |   | biotin transmembrane transporter activity |   | GO_Central | Schizosaccharomyces pombe | IBA | PANTHER:PTN000185192PomBase:SPAC1B3.15cPomBase:SPAC1B3.16c | family not named pthr43791 | protein |   | PMID:21873635 | 20170228

  | SPAC1B3.15c | transmembrane transporter (predicted) |   | dethiobiotin transmembrane transporter activity |   | GO_Central | Schizosaccharomyces pombe | IBA | PANTHER:PTN000185192PomBase:SPAC1B3.16c | family not named pthr43791 | protein |   | PMID:21873635 | 20181004

[pgaudet]

I don't understand - again we have both positive and negative annotations. This should not be the case - @dustine32 can you check what is going on ?

Also, the same annotation is duplicated, with 2 different dates:

Any idea what is happening ?

Thanks, Pascale

[dustine32]

@pgaudet I believe the conflicting qualifier is an example of the issue here pantherdb/fullgo_paint_update#30. At first glance, we may need to add some additional structure to our DB schema to handle this. I'll do some testing with this and try to get it fixed soon. More detail will be added in that ticket.

For the duplicated annotations I'll add some code to the IBA creation script to collapse these together. Separate ticket coming soon!

[dustine32]

@pgaudet And pantherdb/fullgo_paint_update#35 is the duplicated annotation ticket.

[pgaudet]

Great, thanks !

[dustine32]

@pgaudet I'm close to fixing the larger conflicting qualifier issue in our DB but, for this specific case, I think some curator intervention may be necessary. Can you see how this GO:0015225 (biotin transmembrane transporter activity) to PTN000185192 annotation looks in the PAINT tool (PTHR43791)? In the DB, I see three of these duplicate annotations and none of them have a NOT qualifier.

So in order for the positive GO:0015225 to SPAC1B3.15c IBA(s) to go away, either these PAINT annotations will need to be obsoleted or an IKR/IRD NOT could be annotated on or above the SPAC1B3.15c leaf. Does this sound sane?

[pgaudet]

Hi @dustine32

I see the same in PAINT:

I removed 2 of the 3 annotations. Let me know what it now looks like in the database.

Thanks, Pascale

[dustine32]

Hi @pgaudet ! @huaiyumi is manually fixing the redundant IBD for this in PAINT but one step remains to prevent PomBase:SPAC1B3.15c getting a positive GO:0015225 IBA. We still need a GO:0015225 IKR or IRD PAINT annotation on or above SPAC1B3.15c. There is a NOT experimental GO annotation on PomBase:SPAC1B3.15c, which you can see in amigo and the PAINT tool, but that's not enough to block the IBD from being propagated to it.

Lemme know if you wanna skype about this.

[marcfeuermann]

I've reviewed this family. Was still a correction to do, but should be okay now.