resolve EC:1.14.13.- mappings about go-ontology HOT 9 OPEN

3-HSA hydroxylase activity EquivalentTo EC:1.14.13.- (most probable) 0.8

This is incorrect; this partial EC corresponds to GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen

I am removing all partial ECs, this leads to incorrect mappings, and see if others need to be obsoleted.
Annotations are here: geneontology/go-annotation#5221

from go-ontology.

-limonene monooxygenase activity :

• remove partial EC
• remove PMID:820855 reference, links to the wrong paper ("Long term changes in augmentation, potentiation, and depression of transmitter release as a function of repeated synaptic activity at the frog neuromuscular junction")
• other changes here: #27866

from go-ontology.

phenylacetate hydroxylase activity

• add EC:1.14.14.54
• add RHEA:53392
• fix def and term label to match RHEA and EC
• change parent to 'oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen'

from go-ontology.

2-hydroxy-phenylacetate hydroxylase activity

• removed partial EC; cannot find an EC or a RHEA for this reaction.
• added the reference cited by EAWAG-BBD , PMID: 8919815 - very weak evidence.

from go-ontology.

dimethyl sulfide monooxygenase activity

• Add EC:1.14.13.131
• Add RHEA:31355
• Add parent monooxygenase activity

from go-ontology.

• dimethylsulfoxide oxygenase activity (not in the list because the partial EC is on the def xref, not on the xref):
• add EC:1.14.13.245
• add RHEA:57960 - it only had a mapping to RHEA:57956 - this EC corresponds to both reactions.

Noting that there are no associated genes either in EC or in RHEA.

from go-ontology.

• phenanthrene 3,4-monooxygenase activity
• phenanthrene 1,2-monooxygenase activity
• phenanthrene 9,10-monooxygenase activity

Citing PMID:1599252 (via EAWAG-BBD )
No evidence that this specific activity exists; also phenanthrene seems to be a grouping class for many compounds, see https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:25961

• Removed the partial EC; added PMID:1599252

from go-ontology.

• 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase activity
• Removed partial EC
• The MetaCyc xref was incorrectly shared with 3-demethoxyubiquinol 3-hydroxylase activity; updated to MetaCyc:RXN-18458
• Changed parent from 'GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen' (1.14.13.-) to 'oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen' (1.14.99.-)
• Added parent monooxygenase activity

from go-ontology.

• GO:0052871 alpha-tocopherol omega-hydroxylase activity
• GO:0052870 tocopherol omega-hydroxylase activity
• GO:0052872 tocotrienol omega-hydroxylase activity

All 3 are referencing MetaCyc:RXN-11003

MetaCyc:RXN-11003 is

α-tocopherol + reduced [NADPH-hemoprotein reductase] + dioxygen → 13'-hydroxy-α-tocopherol + oxidized [NADPH-hemoprotein reductase] + H2O.
Note that this reaction equation differs from the official Enzyme Commission reaction equation for this EC entry, which can be found here.

(MetaCyc:LEUKOTRIENE-B4-20-MONOOXYGENASE-RXN corresponds to 1.14.14.94, ie leukotriene-B4 20-monooxygenase activity.

Email MetaCyc

I am struggling with this entry
(RXN-11003), that has a reaction:
α-tocopherol reduced [NADPH-hemoprotein reductase] dioxygen → 13'-hydroxy-α-tocopherol oxidized [NADPH-hemoprotein reductase] H2O
Note that this reaction equation differs from the official Enzyme Commission reaction equation for this EC entry, which can be found here.
The official EC reaction uses leukotriene B4. How are these two substrates related?

Reply from Ron Caspi

if you go to the actual MetaCyc page for this EC number,
http://metacyc.ai.sri.com/META/NEW-IMAGE?type=EC-NUMBER&object=EC-1.14.14.94
(you can get there by scrolling down in the page you referred, the table under the reaction diagram has a row for the EC number that is clickable),
you will see that the reaction with leukotriene B4 is listed as the official reaction, but there are 4 additional reactions (including the one you pointed out) that are listed as "unofficial reactions".
The justification can be found in the summary for the enzyme, CYP4F2 (http://metacyc.ai.sri.com/gene?orgid=META&id=HS02675-MONOMER), where it is explained that the enzyme catalyzes all of these reactions.
Even though the structures of leukotriene B4 and α-tocopherol are quite different, the enzyme catalyzes a pretty similar reaction - hydroxylation of the last carbon at the linear tail of the molecule. It is typical for P450s to catalyze similar reactions on a large number of different substrates.

DECISION

On the UniProt entry for https://www.uniprot.org/uniprotkb/P78329/entry, I found a RHEA reaction for GO:0052871 alpha-tocopherol omega-hydroxylase activity :
RHEA:45108
So, while this is a general P450, I will keep this in GO for now, since otherwise we need to annotate to the parent of the branch GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen

I also moved the term under that parent.

However I will obsolete

• GO:0052870 tocopherol omega-hydroxylase activity
• GO:0052872 tocotrienol omega-hydroxylase activity
  since these are not mentioned in the MetaCyc entry

from go-ontology.