sib2 sib1 - Githubissues

Antonialock commented 7 years ago

sib2 is annotated to iron assimilation by chelation and transport "A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors."

sib1 and sib2 make the siderophore (pombe siderophore is known as "ferrichrome") it sounds like this is upstream of "iron assimilation by chelation and transport"?

They are also annotated to ferrichrome biosynthetic process The chemical reactions and pathways resulting in the formation of a ferrichrome. Ferrichromes are any of a group of growth-promoting Fe(III) chelates formed by various genera of microfungi. They are homodetic cyclic hexapeptides made up of a tripeptide of glycine (or other small neutral amino acids) and a tripeptide of an N'acyl-N4-hydroxy-L-ornithine (this sounds fine)

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ValWood commented 7 years ago

Agreed and deleted.

[x] Can you see a way to get an experimental annotation for "ferrichrome biosynthetic process" ? I have a TAS in artemis but it is currently the IEA which is not filtered....

(this might be done already as part of iron metabolism project?)

Antonialock commented 7 years ago

They will get this from PMID:20435771

Antonialock commented 7 years ago

I can\t see the sib2 iron assimilation by chelation and transport in artemis? maybe I already deleted?

ValWood commented 7 years ago

That would make sense if you have processed PMID: 16963626 as its a TAS from this...

Antonialock commented 7 years ago

oh I just saw that you agreed with me here :-P I'm leaning towards putting it back.. @mah11 do you think making the siderophore is part of 'iron assimilation by chelation and transport' "A process in which iron (Fe3+) is solubilized by ferric iron-specific chelators, known as siderophores, excreted by a cell; the iron-siderophore complex is then transported into the cell by specific cell surface receptors."

ValWood commented 7 years ago

I would say it isn't part_of "iron assimilation by chelation and transport", but it might be "positive regulation of iron assimilation by chelation and transport" if the pathway is regulated by the production of ferrichrome?

mah11 commented 7 years ago

@mah11 do you think making the siderophore is part of 'iron assimilation by chelation and transport'

No; I think it fits LEGO's "causally upstream of". I don't know enough about the process(es) to say whether it's regulating assimilation.

Antonialock commented 7 years ago

ok i'll leave out the regulation for the time being.

pombase / curation

sib2 sib1 #1099