id: P80505
gene_symbol: gap2
taxon:
  id: NCBITaxon:1111708
  label: Synechocystis sp. PCC 6803 substr. Kazusa
status: COMPLETE
locus_tag: sll1342
description: >-
  NCBI PGAP names WP_010874115.1 (Gap2, sll1342) with the NCBIfam equivalog NF005641.0 (PRK07403,
  "type I glyceraldehyde-3-phosphate dehydrogenase"), which supplies the product name and EC 1.2.1.-
  but no GO terms. PGAP passes on GO only from the naming model, so the protein receives no GO
  annotation at all. The second matching equivalog, TIGR01534, has the same product name and maps
  GO:0006006, GO:0016620, GO:0050661 and GO:0051287, but its GO is discarded because it was not the
  naming model. The single PGAP prediction, EC 1.2.1.-, is correct but less precise than the
  experimentally supported EC 1.2.1.59 (NAD(P)-dependent phosphorylating GAPDH) curated in UniProt
  from PMID:9226260. Neither PGAP model distinguishes the NADP-using Calvin-cycle Gap2 from the
  NAD-specific glycolytic Gap1, although EC 1.2.1.59 could be assigned at the cyanobacterial/plastid
  Gap2-subfamily level.
source_documents:
- genes/SYNY3/gap2/gap2-pgap-prediction-evidence/WP_010874115.1.gp
- genes/SYNY3/gap2/gap2-pgap-prediction-evidence/pgap_models.yaml
predictions:
- source_method: NCBI PGAP
  source_version: GCF_000009725.1-RS_2026_01_07 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: EC:1.2.1.-
    label: EC 1.2.1.-
  predicted_term_type: EC
  review:
    assessment: LSP
    confidence_score: 2
    summary: >-
      EC 1.2.1.- (oxidoreductase acting on aldehydes, NAD+ or NADP+ acceptor) is correct for Gap2 but
      less precise than its known activity. Purified native and recombinant Gap2 catalyse the
      phosphorylating oxidation of glyceraldehyde 3-phosphate with either NAD+ or NADP+, which is EC
      1.2.1.59, and UniProt curates both reactions with experimental evidence. The incomplete EC comes
      from the naming model NF005641, which carries EC 1.2.1.- because the type I GAPDH family includes
      NAD-specific (EC 1.2.1.12), NADP-specific (EC 1.2.1.13) and dual-specificity (EC 1.2.1.59)
      members. No error type applies, because the prediction is not wrong, only underspecified.
    supported_by:
    - reference_id: file:SYNY3/gap2/gap2-pgap-prediction-evidence/WP_010874115.1.gp
      supporting_text: /EC_number="1.2.1.-"
    - reference_id: file:SYNY3/gap2/gap2-pgap-prediction-evidence/pgap_models.yaml
      supporting_text: 'WP_010874115.1: HMM:NF005641.0'
    - reference_id: file:SYNY3/gap2/gap2-uniprot.txt
      supporting_text: EC=1.2.1.59 {ECO:0000269|PubMed:9226260};
    - reference_id: file:SYNY3/gap2/gap2-uniprot.txt
      supporting_text: can use both NADP and NAD. {ECO:0000269|PubMed:9226260}.
    - reference_id: PMID:9226260
      supporting_text: The recombinant GAPDH2 showed the dual pyridine nucleotide specificity characteristic
        of the native cyanobacterial enzyme
references:
- id: file:SYNY3/gap2/gap2-pgap-prediction-evidence/WP_010874115.1.gp
  title: RefSeq GenPept record WP_010874115.1
- id: file:SYNY3/gap2/gap2-pgap-prediction-evidence/pgap_models.yaml
  title: PGAP naming model and matched NCBI HMMs for WP_010874115.1
- id: file:SYNY3/gap2/gap2-uniprot.txt
  title: UniProt record P80505 (G3P2_SYNY3)
- id: PMID:9226260
  title: Functional complementation of an Escherichia coli gap mutant supports an amphibolic role
    for NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase of Synechocystis sp. strain PCC 6803.