These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
NCBI PGAP External predictions
View prediction review YAML Β· glgE-pgap-predictions-review.yaml Β· Review status: COMPLETE
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.
Source documents: genes/PSEPK/glgE/glgE-pgap-prediction-evidence/WP_049588255.1.gp Β· genes/PSEPK/glgE/glgE-pgap-prediction-evidence/pgap_models.yaml
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
Prediction method: NCBI PGAP Β· Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record Β·
PMID:33270901 PARALOG OVERANNOTATION
Review rationale: 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.
Supporting Evidence: - PMID:24689960: "It catalyzes the Ξ±-retaining transfer of maltosyl units from Ξ±-maltose 1-phosphate to maltooligosaccharides"
- file:PSEPK/glgE/glgE-uniprot.txt: "Reaction=alpha-maltose 1-phosphate + [(1->4)-alpha-D-glucosyl](n) ="
Prediction method: NCBI PGAP Β· Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record Β·
PMID:33270901 Review rationale: 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).
Prediction method: NCBI PGAP Β· Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record Β·
PMID:33270901 PARALOG OVERANNOTATION
Review rationale: 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.
Supporting Evidence: - PMID:24689960: "It is the defining enzyme of a bacterial Ξ±-glucan biosynthetic pathway"
- PMID:33872310: "The first cluster consists of three genes, glgE, treS and glgB, that collectively code for the GlgE Ξ±-glucan biosynthetic pathway."
Prediction method: NCBI PGAP Β· Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record Β·
PMID:33270901 Review rationale: Correct and already in GOA (UniRule IEA), accepted by the main review: GlgE elongates alpha-1,4-glucan chains using maltose 1-phosphate.
Prediction method: NCBI PGAP Β· Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record Β·
PMID:33270901 Review rationale: 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.
Supporting Evidence: - PMID:24689960: "GlgE (EC 2.4.99.16) is an Ξ±-maltose 1-phosphate:(1β4)-Ξ±-d-glucan"