glgX

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004135 amylo-alpha-1,6-glucosidase activity	IBA GO_REF:0000033	MODIFY	Summary: amylo-alpha-1,6-glucosidase activity describes a different branch-glucose-releasing reaction than GlgX/EC 3.2.1.196. Reason: E. coli GlgX releases intact DP3-DP4 alpha-1,6 branches from phosphorylase limit dextrin, whereas GO:0004135/EC 3.2.1.33 releases free glucose from a single glucosyl stub; the precise GO:0120549 term should replace this wrong-reaction mapping. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000039997 · PANTHER:PTN000039997 SUPPORTS TRANSFER The PAINT node correctly covers bacterial GlgX debranching enzymes, but the propagated GO:0004135 term names the EC 3.2.1.33 glucosidase reaction rather than the EC 3.2.1.196 limit-dextrin branch hydrolase reaction. Proposed replacements: limit dextrin alpha-1,6-maltotetraose-hydrolase activity Supporting Evidence: PMID:15687211 debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues
GO:0005980 glycogen catabolic process	IBA GO_REF:0000033	ACCEPT	Summary: GlgX directly participates in glycogen catabolism by debranching the limit dextrin produced by glycogen phosphorylase. Reason: The genetic and biochemical evidence in PMID:15687211 supports the catabolic role: GlgX deletion overproduces glycogen with short external chains, and purified GlgX hydrolyzes short branches. Supporting Evidence: PMID:15687211 GlgX protein is predominantly involved in glycogen catabolism by selectively debranching the polysaccharide outer chains
GO:0004135 amylo-alpha-1,6-glucosidase activity	IEA GO_REF:0000002	MODIFY	Summary: amylo-alpha-1,6-glucosidase activity describes a different branch-glucose-releasing reaction than GlgX/EC 3.2.1.196. Reason: E. coli GlgX releases intact DP3-DP4 alpha-1,6 branches from phosphorylase limit dextrin, whereas GO:0004135/EC 3.2.1.33 releases free glucose from a single glucosyl stub; the precise GO:0120549 term should replace this wrong-reaction mapping. Proposed replacements: limit dextrin alpha-1,6-maltotetraose-hydrolase activity Supporting Evidence: PMID:15687211 debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds	IEA GO_REF:0000120	MODIFY	Summary: hydrolase activity, hydrolyzing O-glycosyl compounds is consistent with GlgX glycosidase chemistry but is less precise than the EC 3.2.1.196 limit-dextrin debranching term. Reason: This broad O-glycosyl hydrolase term is compatible with the GlgX reaction but is far less informative than the EC 3.2.1.196 term for hydrolysis of short alpha-1,6 branches from phosphorylase limit dextrin. Proposed replacements: limit dextrin alpha-1,6-maltotetraose-hydrolase activity
GO:0005975 carbohydrate metabolic process	IEA GO_REF:0000002	MODIFY	Summary: carbohydrate metabolic process captures glycogen/carbohydrate context but is broader than the GlgX catabolic step. Reason: GlgX participates specifically in glycogen breakdown after GlgP exposes short branch stubs, rather than in glycogen metabolism generally. Proposed replacements: glycogen catabolic process
GO:0005977 glycogen metabolic process	IEA GO_REF:0000002	MODIFY	Summary: glycogen metabolic process captures glycogen/carbohydrate context but is broader than the GlgX catabolic step. Reason: GlgX participates specifically in glycogen breakdown after GlgP exposes short branch stubs, rather than in glycogen metabolism generally. Proposed replacements: glycogen catabolic process
GO:0005980 glycogen catabolic process	IEA GO_REF:0000120	ACCEPT	Summary: GlgX directly participates in glycogen catabolism by debranching the limit dextrin produced by glycogen phosphorylase. Reason: The genetic and biochemical evidence in PMID:15687211 supports the catabolic role: GlgX deletion overproduces glycogen with short external chains, and purified GlgX hydrolyzes short branches. Supporting Evidence: PMID:15687211 GlgX protein is predominantly involved in glycogen catabolism by selectively debranching the polysaccharide outer chains
GO:0120549 limit dextrin alpha-1,6-maltotetraose-hydrolase activity	IEA GO_REF:0000120	ACCEPT	Summary: The EC 3.2.1.196 mapping exactly captures GlgX limit-dextrin alpha-1,6-maltotetraose hydrolase activity. Reason: This is the specific GlgX molecular function and is supported by direct E. coli deletion/substrate-specificity evidence and the curated EC reaction. Supporting Evidence: PMID:15687211 debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues
GO:0120549 limit dextrin alpha-1,6-maltotetraose-hydrolase activity	EXP PMID:15687211 Role of the Escherichia coli glgX gene in glycogen metabolis...	ACCEPT	Summary: The EC 3.2.1.196 mapping exactly captures GlgX limit-dextrin alpha-1,6-maltotetraose hydrolase activity. Reason: Dauvillée et al. experimentally established that E. coli GlgX preferentially hydrolyzes alpha-1,6 branches of three or four glucose residues, matching EC 3.2.1.196. Supporting Evidence: PMID:15687211 debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues
GO:0120549 limit dextrin alpha-1,6-maltotetraose-hydrolase activity	EXP PMID:779849 Purification and properties of a debranching enzyme from Esc...	ACCEPT	Summary: The EC 3.2.1.196 mapping exactly captures GlgX limit-dextrin alpha-1,6-maltotetraose hydrolase activity. Reason: The 1976 purified debranching enzyme hydrolyzed alpha-1,6 linkages in phosphorylase and beta-amylase limit dextrins, consistent with the limit-dextrin hydrolase activity later assigned to glgX; its weak activity on glycogen itself is treated cautiously in the reference review below. Supporting Evidence: PMID:779849 The enzyme hydrolyzed 1,6-alpha-glucosidic linkages in phosphorylase and beta-amylase limit dextrins
GO:0120549 limit dextrin alpha-1,6-maltotetraose-hydrolase activity	EXP PMID:8576033 Coordinate genetic regulation of glycogen catabolism and bio...	ACCEPT	Summary: The EC 3.2.1.196 mapping exactly captures GlgX limit-dextrin alpha-1,6-maltotetraose hydrolase activity. Reason: Romeo and colleagues assigned the glycogen debranching enzyme to the glgX gene, supporting the gene-to-enzyme mapping that UniProt uses for this experimentally supported EC annotation. Supporting Evidence: PMID:8576033 which is now shown to be encoded by the gene glgX
GO:0005980 glycogen catabolic process	IMP PMID:15687211 Role of the Escherichia coli glgX gene in glycogen metabolis...	ACCEPT	Summary: GlgX directly participates in glycogen catabolism by debranching the limit dextrin produced by glycogen phosphorylase. Reason: The genetic and biochemical evidence in PMID:15687211 supports the catabolic role: GlgX deletion overproduces glycogen with short external chains, and purified GlgX hydrolyzes short branches. Supporting Evidence: PMID:15687211 GlgX protein is predominantly involved in glycogen catabolism by selectively debranching the polysaccharide outer chains
GO:0006974 DNA damage response	IEP PMID:11967071 Over 1000 genes are involved in the DNA damage response of E...	MARK AS OVER ANNOTATED	Summary: This row comes from a mitomycin-C expression study rather than direct evidence that GlgX executes the DNA damage response. Reason: Changed glgX transcript abundance after DNA damage is not evidence that the glycogen debranching enzyme performs a step in DNA repair or DNA-damage signalling. Supporting Evidence: PMID:11967071 number of genes (nearly 30% of all genes) displayed significant changes in their expression level
GO:0004135 amylo-alpha-1,6-glucosidase activity	IDA PMID:15687211 Role of the Escherichia coli glgX gene in glycogen metabolis...	MODIFY	Summary: amylo-alpha-1,6-glucosidase activity describes a different branch-glucose-releasing reaction than GlgX/EC 3.2.1.196. Reason: E. coli GlgX releases intact DP3-DP4 alpha-1,6 branches from phosphorylase limit dextrin, whereas GO:0004135/EC 3.2.1.33 releases free glucose from a single glucosyl stub; the precise GO:0120549 term should replace this wrong-reaction mapping. Proposed replacements: limit dextrin alpha-1,6-maltotetraose-hydrolase activity Supporting Evidence: PMID:15687211 debranching enzyme with high specificity for hydrolysis of chains consisting of three or four glucose residues