Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: GmhA is predicted to be a soluble cytoplasmic enzyme. Reason: The location is compatible with soluble nucleotide-sugar biosynthesis but is not the defining function. Supporting Evidence: file:PSEPK/gmhA/gmhA-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0005975 carbohydrate metabolic process	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Phosphoheptose isomerization is carbohydrate metabolism. Reason: GO:2001061 identifies the relevant heptose-biosynthetic process more precisely.
GO:0008270 zinc ion binding	IEA GO_REF:0000104	KEEP AS NON CORE	Summary: The GmhA-family assignment predicts one catalytic zinc ion per subunit. Reason: Zinc binding supports catalysis but does not replace the exact phosphoheptose isomerase activity. Supporting Evidence: file:PSEPK/gmhA/gmhA-uniprot.txt Binds 1 zinc ion per subunit
GO:0008968 D-sedoheptulose 7-phosphate isomerase activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the exact GmhA reaction converting sedoheptulose 7-phosphate to phosphoheptose anomers. Reason: HAMAP, UniRule, EC 5.3.1.28, and Rhea 27489 consistently support this catalytic assignment. Supporting Evidence: file:PSEPK/gmhA/gmhA-uniprot.txt EC=5.3.1.28
GO:0030246 carbohydrate binding	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Binding to a sugar-phosphate substrate is implicit in the catalytic reaction. Reason: The generic binding term adds no useful information beyond GO:0008968.
GO:0097367 carbohydrate derivative binding	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: The SIS-domain protein binds a phosphorylated carbohydrate substrate. Reason: This broad domain mapping is less informative than the exact catalytic term.
GO:1901135 carbohydrate derivative metabolic process	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: The GmhA reaction is a carbohydrate-derivative metabolic step. Reason: The pathway-specific GO:2001061 annotation should carry the core process assertion.
GO:2001061 D-glycero-D-manno-heptose 7-phosphate biosynthetic process	IEA GO_REF:0000041	ACCEPT	Summary: GmhA directly produces both anomers of D-glycero-D-manno-heptose 7-phosphate. Reason: The UniPathway and HAMAP assignments match the exact reaction product and pathway position. Supporting Evidence: file:PSEPK/gmhA/gmhA-uniprot.txt D-glycero-D-manno-heptose 7-phosphate biosynthesis

Core Functions

Zinc-dependent D-sedoheptulose 7-phosphate isomerase (EC 5.3.1.28; Rhea 27489) producing alpha- and beta-D-glycero-D-manno-heptose 7-phosphate for ADP-heptose precursor biosynthesis.

Molecular Function:

D-sedoheptulose 7-phosphate isomerase activity

Directly Involved In:

D-glycero-D-manno-heptose 7-phosphate biosynthetic process

Supporting Evidence:

file:PSEPK/gmhA/gmhA-uniprot.txt
Catalyzes the isomerization of sedoheptulose 7-phosphate

References

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Suggested Experiments

Experiment: Assay purified PP_1323 for Rhea 27489 activity and test whether deletion alters ADP-heptose or LPS-core composition.

Type: enzyme assay and targeted glycomics

📚 Additional Documentation

Notes

(gmhA-notes.md)

gmhA curation notes

Q88N89 carries the exact phosphoheptose-isomerase reaction, EC 5.3.1.28, and
GmhA-specific HAMAP/InterPro signatures
[file:PSEPK/gmhA/gmhA-uniprot.txt, "Catalyzes the isomerization of
sedoheptulose 7-phosphate"].
The same record maps Q88N89 to PTHR30390:SF6 with the label "DNAA
INITIATOR-ASSOCIATING PROTEIN DIAA", but this conflicts with the exact
catalytic, pathway, and GmhA-family evidence
[file:PSEPK/gmhA/gmhA-uniprot.txt, "PTHR30390:SF6; DNAA
INITIATOR-ASSOCIATING PROTEIN DIAA"]. The module therefore uses the
GmhA-specific InterPro selector rather than transferring a DiaA role.
The broad carbohydrate-binding rows are not used as core functions; the
exact GO:0008968 reaction and GO:2001061 product process carry the biological
assertions.

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