id: Q88FM9 gene_symbol: glgE taxon: id: NCBITaxon:160488 label: Pseudomonas putida KT2440 status: COMPLETE locus_tag: PP_4060 description: >- NCBI PGAP names WP_049588255.1 "alpha-1,4-glucan--maltose-1-phosphate maltosyltransferase" from the SPARCLE CDD domain architecture 10571012 (GlgE N-terminal domain plus a GlgE-like alpha-amylase catalytic domain) and passes on EC 2.4.99.16 and four GO terms. The name, the EC number, hexosyltransferase activity and alpha-glucan biosynthetic process are correct and match the main review. The other two terms come from the catabolic, hydrolytic majority of glycoside hydrolase family 13 and are wrong for GlgE. Hydrolase activity on O-glycosyl compounds is removed by the main review, because GlgE transfers maltosyl units from maltose 1-phosphate to glucan rather than hydrolysing them. Oligosaccharide catabolic process inverts GlgE's role: it is the polymer-elongating enzyme of the TreS-Pep2-GlgE-GlgB alpha-glucan biosynthetic pathway. Both errors lie on the architecture's GO mapping, so they reach every GlgE named by it. references: - id: PMID:33270901 title: 'RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.' - id: PMID:24689960 title: Structural insight into how Streptomyces coelicolor maltosyl transferase GlgE binds α-maltose 1-phosphate and forms a maltosyl-enzyme intermediate. - id: PMID:33872310 title: Trehalose and α-glucan mediate distinct abiotic stress responses in Pseudomonas aeruginosa. - id: file:PSEPK/glgE/glgE-uniprot.txt title: UniProtKB entry for glgE (Q88FM9) - id: file:PSEPK/glgE/glgE-pgap-prediction-evidence/WP_049588255.1.gp title: RefSeq GenPept record WP_049588255.1 - id: file:PSEPK/glgE/glgE-pgap-prediction-evidence/pgap_models.yaml title: PGAP naming model and matched NCBI HMMs for glgE source_documents: - genes/PSEPK/glgE/glgE-pgap-prediction-evidence/WP_049588255.1.gp - genes/PSEPK/glgE/glgE-pgap-prediction-evidence/pgap_models.yaml predictions: - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0004553 label: hydrolase activity, hydrolyzing O-glycosyl compounds predicted_term_type: GO_MF review: assessment: NPI confidence_score: 0 error_type: PARALOG_OVERANNOTATION summary: >- Wrong, and consistent with the main review, which REMOVEs the same term (InterPro IEA) from GOA. GlgE belongs to the GH13 fold, but its reaction is an alpha-retaining maltosyl transfer from alpha-maltose 1-phosphate onto an alpha-1,4-glucan acceptor, releasing phosphate. That is a transferase reaction, not hydrolysis. The term is the activity of the hydrolytic GH13 amylases, wrongly carried over to the GlgE subfamily. NCBI's PfamAutoEq model NF023324 (PF11896) maps to the same term, so the mapping error is not confined to the PGAP architecture. supported_by: - reference_id: PMID:24689960 supporting_text: "It catalyzes the α-retaining transfer of maltosyl units from α-maltose 1-phosphate to maltooligosaccharides" - reference_id: file:PSEPK/glgE/glgE-uniprot.txt supporting_text: "Reaction=alpha-maltose 1-phosphate + [(1->4)-alpha-D-glucosyl](n) =" - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0016758 label: hexosyltransferase activity predicted_term_type: GO_MF review: assessment: CNN confidence_score: 2 summary: >- Correct and already in GOA (UniRule IEA), accepted by the main review as the most specific GO term available for the GlgE maltosyltransferase reaction (GO has no GlgE-specific function term). supported_by: - reference_id: file:PSEPK/glgE/glgE-uniprot.txt supporting_text: "FUNCTION: Maltosyltransferase that uses maltose 1-phosphate (M1P) as" - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0009313 label: oligosaccharide catabolic process predicted_term_type: GO_BP review: assessment: NPI confidence_score: 0 error_type: PARALOG_OVERANNOTATION summary: >- Wrong. GlgE uses maltooligosaccharides and glucans as acceptors and lengthens them; it is the defining enzyme of a biosynthetic pathway that builds branched alpha-glucan from trehalose via maltose 1-phosphate. In Pseudomonas, glgE clusters with treS and glgB in that pathway. Breaking down oligosaccharides is the role of the catabolic GH13 amylases and glucosidases, not of the GlgE subfamily. The term is not in GOA, and the accepted process, alpha-glucan biosynthetic process, is also on the PGAP record. None of the three InterPro-matched NCBI HMMs for this protein carries the catabolic term, so it enters through the PGAP architecture's GO mapping. supported_by: - reference_id: PMID:24689960 supporting_text: "It is the defining enzyme of a bacterial α-glucan biosynthetic pathway" - reference_id: PMID:33872310 supporting_text: "The first cluster consists of three genes, glgE, treS and glgB, that collectively code for the GlgE α-glucan biosynthetic pathway." - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: GO:0030979 label: alpha-glucan biosynthetic process predicted_term_type: GO_BP review: assessment: CNN confidence_score: 2 summary: >- Correct and already in GOA (UniRule IEA), accepted by the main review: GlgE elongates alpha-1,4-glucan chains using maltose 1-phosphate. supported_by: - reference_id: file:PSEPK/glgE/glgE-uniprot.txt supporting_text: "the sugar donor to elongate linear or branched alpha-(1->4)-glucans." - source_method: NCBI PGAP source_version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record source_reference_id: PMID:33270901 predicted_term: id: EC:2.4.99.16 label: EC 2.4.99.16 predicted_term_type: EC review: assessment: CNN confidence_score: 2 summary: >- Correct and not novel: EC 2.4.99.16 is on the UniProt entry (HAMAP MF_02124) and is the EC number of characterized GlgE. supported_by: - reference_id: PMID:24689960 supporting_text: "GlgE (EC 2.4.99.16) is an α-maltose 1-phosphate:(1→4)-α-d-glucan"