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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Wrong IntEnz xref on GO:0009033 trimethylamine-N-oxide reductase activity? #12192

Closed bmeldal closed 8 years ago

bmeldal commented 8 years ago

Proteins manually annotated to the above MF are also annotated to EC 1.7.2.3 in UniProt but the Go terms is linked to EC 1.6.6.9. It should probably be consistent...

Complex in question is Trimethylamine-N-oxide reductase TorAC complex, participants P33225 (TORA_ECOLI) & P33226 (TORC_ECOLI), annotated to GO:0009322 trimethylamine-N-oxide reductase complex, capable_of GO:0009033 trimethylamine-N-oxide reductase activity.

The complex is not yet released.

Birgit

tberardini commented 8 years ago

GO definition: "Catalysis of the reaction: NADH + H+ + trimethylamine-N-oxide = NAD+ + trimethylamine + H2O." [EC:1.6.6.9]

http://enzyme.expasy.org/EC/1.6.6.9 = Trimethylamine-N-oxide reductase.

NADH + trimethylamine N-oxide <=> NAD(+) + trimethylamine + H(2)O GO def: def: "Catalysis of the reaction: NADH + H+ + trimethylamine-N-oxide = NAD+ + trimethylamine + H2O." [EC:1.6.6.9]

http://enzyme.expasy.org/EC/1.7.2.3 = Trimethylamine-N-oxide reductase (cytochrome c).

Trimethylamine + 2 (ferricytochrome c)-subunit + H(2)O <=> trimethylamine N-oxide + 2 (ferrocytochrome c)-subunit + 2 H(+)

Are you sure it's GO that needs updating and not the "Proteins manually annotated to the above MF are also annotated to EC 1.7.2.3 in UniProt"?

bmeldal commented 8 years ago

Ah, I missed something: It's the ANNOTATIONS that probably need to be moved! Should this ticket be moved to the other tracker?

There are 4 proteins manually annotated to GO:0009033 http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009033. One is a SwissProt entry (http://www.uniprot.org/uniprot/Q9KRF0) and has EC 1.7.2.3 annotation in Uniprot. The other 3 are TrEMBL entries only. All GO annotations are by sequence alignment/similarity.

Similarly, the 2 manually annotated proteins to GO:0050626 trimethylamine-N-oxide reductase (cytochrome c) activity http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0050626 are SwissProt and also annotated to EC 1.7.2.3.

All these proteins are from the same protein family.

This leads me to believe that at least the SwissProt protein annotated to GO:0009033, and possible all 4 manually annotated protein here, should be annotated to GO:0050626. Then the 100s of inferred annotations will follow...

Apologies for the confusion!

Birgit

tberardini commented 8 years ago

Yes, please move the ticket to the annotation tracker and then close this one. Thanks. https://github.com/geneontology/go-annotation/issues

bmeldal commented 8 years ago

Moved to annotation tracker https://github.com/geneontology/go-annotation/issues/1340