Obsoletion: compound electron transporter, transferring electrons from/within...terms

[ValWood]

We (PHI-BAse) are annotating a fungal protein that binds and inhibits plant TaISP https://www.uniprot.org/uniprot/Q7X9A6

We want to describe inhibition of the activity, but 3 are annotated:

1. GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity Enables the directed movement of electrons within the cytochrome b6/f complex of photosystem II.
   cytochrome | related cytochrome b/b6 | related cytochrome b6 | narrow cytochrome f | narrow

2. GO:0009496 plastoquinol--plastocyanin reductase activity Catalysis of the reaction: 2 H(+)[side 1] + 2 oxidized plastocyanin + plastoquinol-1 = 2 H(+)[side 2] + 2 reduced plastocyanin + plastoquinone. This reaction involves the concomitant transfer of 2 H+ ions across a membrane. plastoquinol-plastocyanin reductase activity | exact cytochrome b6f complex activity | related plastoquinol:oxidized-plastocyanin oxidoreductase activity | exact cytochrome b6-f complex activity | related cytochrome b6/f complex activity | related plastoquinol/plastocyanin oxidoreductase activity | exact cytochrome b6f | narrow

~3. GO:0008121 ubiquinol-cytochrome-c reductase activity Definition Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: CoQH2 + 2 ferricytochrome c = CoQ + 2 ferrocytochrome c + 2 H+.~ fixed by InterPro

Are 1&2 really the same activity. Both refer to b6/f

etc is described as Cytochrome b6-f complex iron-sulfur subunit, chloroplastic Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions

All the GO annotation to https://www.uniprot.org/uniprot/Q7X9A6 is by InterPro, The Rhea pathway is GO:0009496 plastoquinol--plastocyanin reductase activity

[ValWood]

https://en.wikipedia.org/wiki/Cytochrome_b6f_complex

2 is the correct reaction so the question

• [ ] is, is 2 the same thing as 1?

  • [x] I will ask InterPro to suppress 3 and wait to hear about 1 https://github.com/geneontology/go-annotation/issues/2857

[ValWood]

all annotation to GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity is IEA (InterPRO, UNirule)

[ValWood]

• [ ] Also please add parent 'photosynthesis' to GO:0009496 plastoquinol--plastocyanin reductase activity

(many are not annotated to photosynthesis including https://www.uniprot.org/uniprot/Q7X9A6

[ValWood]

3. has been removed

Only need to establish if 1&2 are the same thing

[ValWood]

Hi @hdrabkin . I am on a call with my collaborator @CuzickA

What is the best way to establish whether GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity

and GO:0009496 plastoquinol--plastocyanin reductase activity Catalysis of the reaction: 2 H(+)[side 1] + 2 oxidized plastocyanin + plastoquinol-1 = 2 H(+)[side 2] + 2 reduced plastocyanin + plastoquinone. This reaction involves the concomitant transfer of 2 H+ ions across a membrane.

are the same? Neither seems to have EC numbers

[ValWood]

Note to self Possibly to fix later PMID:31804478 depending on outcome of this ticket

[hdrabkin]

I have a list of things that maybe RHEA might help with. I'll ping @amorgat here

I have a spreadsheet that RHEA gave me with possible mappings GO:0009496 may map to RHEA:22148 This is based on metacyc2go + rhea2metacyc = (goid, metacyc, rheaid, rhea) and kegg_reaction2go + rhea2kegg_reaction = (goid, kegg, rheaid, rhea)

However, GO:0045158 is NOT in the spreadsheet (no data from any mapping files; the reference is to a textbook (8-( In Amigo, I see 4 annotations? a tas, an nas and a couple of IEAs. Am I reading that right? Maybe time to obsolete?

[ValWood]

that was what I was hoping, or a merge? hopefully @amorgat can advise

[ValWood]

Will close. The shared synonyms are related.

@tberardini
@lreiser

if you have any insight here, please reopen with instuctions.

[lreiser]

GO:0009496 seems to me to be precise whereas the electron transfer one is kinda generic

[ValWood]

so it seems that GO:0009496 should be a child of GO:0045158

[pgaudet]

I am not sure GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity is really a correct MF; it incorporates a MF and a CC.

[ValWood]

OK I can obsolete GO:0045158 and make GO:0009496 a child of GO:0009055 ?

[pgaudet]

Note that there are related terms, siblings of GO:0045158

• GO:0046028 electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity >> MF + CC
• GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity >> MF + BP
• GO:0045157 electron transporter, transferring electrons within the noncyclic electron transport pathway of photosynthesis activity >> MF + BP

They all have few (4 max) EXP annotations. I suggest we also obsolete these.

Thanks, Pascale

[ValWood]

OK< I'll get to this at some point, its a nice filler in ticket.

[lreiser]

agreed- the electron transfer terms are mish mosh

[ValWood]

Thanks @lreiser if you spot any others which don't have the "electron transfer activity' parent, me me know. I'll add those at the same time.

[ValWood]

I added GO:0009496 is_a GO:0009055

so this is now an obsoletion ticket for: GO:0046028 electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity MF + CC GO:0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity MF + BP GO:0045157 electron transporter, transferring electrons within the noncyclic electron transport pathway of photosynthesis activity MF + BP GO:0045158 electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity is really a correct MF MF + CC