Q53353

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0010436 carotenoid dioxygenase activity	IEA GO_REF:0000118	REMOVE	Summary: Automated (IEA / TreeGrafter) carotenoid dioxygenase activity - wrong substrate class and directly contradicted by this gene's own experimental annotation to lignostilbene alpha,beta-dioxygenase activity (GO:0050054, IDA). A TreeGrafter over-propagation from the mixed CCO family. Reason: LSD-I is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same substrate-class error as LSD-III, NOV1/NOV2, Rco1, and cao-1.
GO:0016121 carotene catabolic process	IEA GO_REF:0000118	REMOVE	Summary: Automated (IEA / TreeGrafter) carotene catabolic process. Wrong substrate class; LSD-I's real process is lignin/stilbene catabolism, already captured experimentally (GO:0046274, IDA). Reason: Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation.
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based (IEA) dioxygenase MF term; correct general parent of the specific lignostilbene activity. Reason: Accurate general dioxygenase MF.
GO:0050054 lignostilbene alpha beta-dioxygenase activity	IEA GO_REF:0000120	ACCEPT	Summary: Automated (IEA) annotation of the specific lignostilbene alpha,beta-dioxygenase activity, also supported by IDA. The correct, specific MF term for LSD-I. Reason: Core molecular function, corroborated by IDA.
GO:0046274 lignin catabolic process	IDA PMID:7763880 Structural and enzymatical comparison of lignostilbene-alpha...	ACCEPT	Summary: Direct experimental (IDA) annotation of lignin catabolic process; LSD cleaves lignin-derived stilbene (lignostilbene) to vanillin. Reason: Core biological process, experimentally supported; the correct (non-carotenoid) process. Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
GO:0050054 lignostilbene alpha beta-dioxygenase activity	IDA PMID:7763880 Structural and enzymatical comparison of lignostilbene-alpha...	ACCEPT	Summary: Direct experimental (IDA) annotation of lignostilbene alpha,beta-dioxygenase activity from the purification/characterization of the LSD isozymes. Core, correct molecular function of LSD-I. Reason: Core catalytic function (EC 1.13.11.43), directly demonstrated. The specific term the TreeGrafter carotenoid annotations should never have overridden. Supporting Evidence: PMID:7763880 Three isozymes of lignostilbene-alpha,beta-dioxygenase (LSD) from Pseudomonas
GO:0005506 iron ion binding	IDA DOI:10.1271/bbb1961.53.2757	ACCEPT	Summary: Direct experimental (IDA) annotation of iron binding from the original LSD-I purification. LSD/SCO enzymes use a non-heme mononuclear iron center. Reason: Bona fide cofactor of this non-heme iron dioxygenase, experimentally supported.
GO:0046274 lignin catabolic process	IDA DOI:10.1271/bbb1961.53.2757	ACCEPT	Summary: Direct experimental (IDA) annotation of lignin catabolic process from the original LSD-I characterization. Reason: Core biological process, experimentally supported (duplicate term from a distinct reference).
GO:0050054 lignostilbene alpha beta-dioxygenase activity	IDA DOI:10.1271/bbb1961.53.2757	ACCEPT	Summary: Direct experimental (IDA) annotation of lignostilbene alpha,beta-dioxygenase activity from the original LSD-I purification and characterization. Reason: Core catalytic function, experimentally supported (the founding LSD-I characterization).