GO terms with EC:1.5.3.17 xref

sjm41 commented 1 year ago

Relates to #24701.

We have several specific GO terms with EC:1.5.3.17 ("non-specific polyamine oxidase") as an xref and synonym attribution (listed below). I think:

these current EC:1.5.3.17 xrefs should be removed (or at least marked as 'broad' xrefs)
the EC:1.5.3.17-related synonyms should be removed
consider adding EC:1.5.3.17 as an xref to the parent grouping term in GO (GO:0046592 polyamine oxidase activity) instead

id: GO:0052899 name: N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity def: "Catalysis of the reaction: H2O + N(1),N(12)-diacetylspermine + O2 = 3-acetamidopropanal + H2O2 + N(1)-acetylspermidine." [RHEA:25868] synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13] synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17] xref: EC:1.5.3.13 xref: MetaCyc:RXN-10460 xref: RHEA:25868 is_a: GO:0046592 ! polyamine oxidase activity

id: GO:0052904 name: N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity def: "Catalysis of the reaction: H2O + N(1)-acetylspermidine + O2 = 3-acetamidopropanal + H2O2 + putrescine." [RHEA:25812] synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13] synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17] synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17] xref: EC:1.5.3.13 xref: EC:1.5.3.17 xref: KEGG_REACTION:R09074 xref: MetaCyc:RXN-12091 xref: MetaCyc:RXN-9942 xref: RHEA:25812 is_a: GO:0046592 ! polyamine oxidase activity

id: GO:0052903 name: N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity def: "Catalysis of the reaction: H2O + N(1)-acetylspermine + O2 = 3-acetamidopropanal + H2O2 + spermidine." [RHEA:25800] synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13] synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17] synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17] xref: EC:1.5.3.13 xref: EC:1.5.3.17 xref: KEGG_REACTION:R03899 xref: MetaCyc:RXN-12090 xref: MetaCyc:RXN-9940 xref: RHEA:25800 is_a: GO:0046592 ! polyamine oxidase activity

id: GO:0052902 name: spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity def: "Catalysis of the reaction: H2O + O2 + spermidine = 3-aminopropanal + H2O2 + putrescine." [RHEA:25808] synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13] synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17] synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17] xref: EC:1.5.3.13 xref: EC:1.5.3.17 xref: KEGG_REACTION:R09077 xref: MetaCyc:RXN-10461 xref: MetaCyc:RXN-12089 xref: RHEA:25808 is_a: GO:0046592 ! polyamine oxidase activity

id: GO:0052901 name: spermine:oxygen oxidoreductase (spermidine-forming) activity def: "Catalysis of the reaction: H2O + O2 + spermine = 3-aminopropanal + H2O2 + spermidine." [RHEA:25804] synonym: "N(1)-acetylpolyamine oxidase activity" BROAD [EC:1.5.3.13] synonym: "non-specific polyamine oxidase activity" BROAD [EC:1.5.3.17] synonym: "polyamine oxidase activity" BROAD [EC:1.5.3.13, EC:1.5.3.17] synonym: "spermine oxidase activity" BROAD [EC:1.5.3.16] xref: EC:1.5.3.13 xref: EC:1.5.3.16 xref: EC:1.5.3.17 xref: KEGG_REACTION:R09076 xref: MetaCyc:1.5.3.17-RXN xref: MetaCyc:RXN-9015 xref: RHEA:25804 is_a: GO:0046592 ! polyamine oxidase activity

sjm41 commented 6 months ago

@pgaudet OK if I proceed with this one?

pgaudet commented 6 months ago

Do we need the children?

Looking at the annotations, there are many instances of the same protein, it seems this may represent specific substrates?

sjm41 commented 6 months ago

Ah, yes I agree they children could just go. The only EXP annotations to the children are to 5 rice proteins from 3 papers:

39947 Oryza sativa subsp. japonica UniProt UniProtKB:Q0J290 PAO7 enables GO:0052894 norspermine:oxygen oxidoreductase activity PMID:24634478
UniProtKB:Q0J290 PAO7 enables GO:0052901 spermine:oxygen oxidoreductase (spermidine-forming) activity PMID:24634478
UniProtKB:Q0J290 PAO7 enables GO:0052903 N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity PMID:24634478
UniProtKB:Q0J290 PAO7 enables GO:0052904 N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity PMID:24634478

UniProtKB:Q0J954 PAO5 enables GO:0052894 norspermine:oxygen oxidoreductase activity PMID:21796433
UniProtKB:Q0J954 PAO5 enables GO:0052901 spermine:oxygen oxidoreductase (spermidine-forming) activity PMID:21796433

UniProtKB:Q5NAI7 PAO1 enables GO:0052894 norspermine:oxygen oxidoreductase activity PMID:24105034
UniProtKB:Q5NAI7 PAO1 enables GO:0052901 spermine:oxygen oxidoreductase (spermidine-forming) activity PMID:24105034
UniProtKB:Q5NAI7 PAO1 enables GO:0052903 N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity PMID:24105034

UniProtKB:Q7X809 PAO3 enables GO:0052894 norspermine:oxygen oxidoreductase activity PMID:21796433
UniProtKB:Q7X809 PAO3 enables GO:0052901 spermine:oxygen oxidoreductase (spermidine-forming) activity PMID:21796433
UniProtKB:Q7X809 PAO3 enables GO:0052903 N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity PMID:21796433

UniProtKB:Q7XR46 PAO4 enables GO:0052894 norspermine:oxygen oxidoreductase activity PMID:21796433
UniProtKB:Q7XR46 PAO4 enables GO:0052901 spermine:oxygen oxidoreductase (spermidine-forming) activity PMID:21796433

geneontology / go-ontology

GO terms with EC:1.5.3.17 xref #25837