A0A3B6GK97

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0006629 lipid metabolic process	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO transfer from the PNPLA/patatin-like phospholipase domain (IPR002641) to the general biological process "lipid metabolic process". This is the exact and sole InterPro2GO mapping for IPR002641, and is biologically appropriate for a patatin-family lipid acyl hydrolase. Reason: The protein contains a well-defined PNPLA/patatin domain (PROSITE PS51635, residues 1-134; SUPFAM SSF52151; Gene3D 3.40.1090.10), and the patatin family is a family of lipid acyl hydrolases acting on glycerolipids. "Lipid metabolic process" is the correct, appropriately general BP given that only a domain match (not substrate-resolved experimental data) is available. The IEA evidence and InterPro2GO provenance are sound. (Caveat - in-repo bioinformatics shows the deposited model lacks the catalytic serine and may be a truncated gene model; the lipid-metabolic role is therefore a family/subfamily-level inference rather than confirmed for this sequence. Lipid metabolic process is deliberately retained as the substrate- and direction-neutral umbrella and is NOT sharpened to lipid catabolic process, since an acyl hydrolase may act in remodeling or signaling rather than degradation.) Supporting Evidence: GO_REF:0000002 GO:0006629 lipid metabolic process; IEA; WITH InterPro:IPR002641 (PNPLA domain) PMID:12779324 Patatin is a nonspecific lipid acyl hydrolase file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md A0A3B6GK97 belongs to the pPLAII subfamily file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md The best-supported plant functions are lipid mobilization during seed germination, initiation of storage-oil breakdown, membrane phospholipid turnover, and remodeling of LD surfaces to allow access of TAG lipases
GO:0016787 hydrolase activity	IEA GO_REF:0000117	MODIFY	Summary: ARBA machine-learning electronic annotation assigning the very general molecular function "hydrolase activity". This is correct in essence (patatin/PNPLA proteins are hydrolases) but is uninformatively broad given that the patatin domain reliably confers a specific class of activity, namely carboxylic ester (acyl) hydrolysis of lipids. Reason: The patatin/PNPLA domain is a lipid acyl hydrolase module that cleaves carboxylic ester bonds of glycerolipids using a Ser-Asp catalytic dyad [PMID:12779324]. "Hydrolase activity" (GO:0016787) is therefore correct but far too general; a more informative and equally well-supported term is "carboxylic ester hydrolase activity" (GO:0052689), the parent of the lipase/phospholipase/acylglycerol-lipase activities characteristic of this family. The UniProt entry's own family-level FUNCTION text describes non-specific lipolytic acyl hydrolase activity hydrolyzing phospholipids and galactolipids. More substrate-specific functions are in fact asserted for this protein by GO_Central as IBA (phylogenetic) annotations - glycerophospholipase activity (GO:0004620) and monoacylglycerol lipase activity (GO:0047372) - which are visible in AmiGO/GOlr but were not returned by the QuickGO GOA pull that seeded this review (see reference GO_REF:0000033 and the AmiGO record at http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A3B6GK97). Because those IBA lipase terms already capture the specific activity out of band, this generic ARBA "hydrolase activity" annotation is best modified to their immediate informative parent, "carboxylic ester hydrolase activity" (GO:0052689), rather than left at the root-level hydrolase term or duplicated into the specific IBA terms. IMPORTANT CAVEAT - the family-level MF may not hold for this specific deposited sequence. A reproducible bioinformatics analysis (file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md) shows that the modeled 302-aa protein places in the pPLAII subfamily but LACKS the entire N-terminal half of the patatin catalytic domain - both the oxyanion glycine-rich block (DGGG) and the catalytic-serine nucleophile elbow (G-T-S-T-G) are absent (the sequence has no G-x-S-x-G motif at all), although it retains the catalytic Asp. As modeled it is therefore predicted catalytically INACTIVE (no nucleophile), most likely reflecting an incomplete/incorrect gene model (~100-130 aa shorter than orthologs) rather than - but not excluding - a genuine degenerate pseudo-enzyme. The IBA lipase calls were propagated phylogenetically and do not verify active-site integrity. The MODIFY to carboxylic ester hydrolase activity is retained as the correct FAMILY-level term, but with this explicit caveat that the activity is not verifiable on, and may be absent from, the current sequence model. Proposed replacements: carboxylic ester hydrolase activity Supporting Evidence: PMID:12779324 Patatin is a nonspecific lipid acyl hydrolase GO_REF:0000033 Annotation inferences using phylogenetic trees file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md the modeled 302-aa protein places in the pPLAII subfamily but LACKS the entire N-terminal half of the patatin catalytic domain - both the oxyanion glycine-rich block (DGGG) and the catalytic-serine nucleophile elbow (G-T-S-T-G) are absent file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md PNPLA/patatin enzymes use a Ser-Asp catalytic dyad rather than the classical Ser-His-Asp triad of many alpha/beta-hydrolases

GO Term

Evidence

Action

Reason

GO:0006629 lipid metabolic process

IEA
GO_REF:0000002

Summary: InterPro2GO transfer from the PNPLA/patatin-like phospholipase domain (IPR002641) to the general biological process "lipid metabolic process". This is the exact and sole InterPro2GO mapping for IPR002641, and is biologically appropriate for a patatin-family lipid acyl hydrolase.

Reason: The protein contains a well-defined PNPLA/patatin domain (PROSITE PS51635, residues 1-134; SUPFAM SSF52151; Gene3D 3.40.1090.10), and the patatin family is a family of lipid acyl hydrolases acting on glycerolipids. "Lipid metabolic process" is the correct, appropriately general BP given that only a domain match (not substrate-resolved experimental data) is available. The IEA evidence and InterPro2GO provenance are sound. (Caveat - in-repo bioinformatics shows the deposited model lacks the catalytic serine and may be a truncated gene model; the lipid-metabolic role is therefore a family/subfamily-level inference rather than confirmed for this sequence. Lipid metabolic process is deliberately retained as the substrate- and direction-neutral umbrella and is NOT sharpened to lipid catabolic process, since an acyl hydrolase may act in remodeling or signaling rather than degradation.)

Supporting Evidence:

GO_REF:0000002

GO:0006629 lipid metabolic process; IEA; WITH InterPro:IPR002641 (PNPLA domain)

PMID:12779324

Patatin is a nonspecific lipid acyl hydrolase

file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md

A0A3B6GK97 belongs to the pPLAII subfamily

file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md

The best-supported plant functions are lipid mobilization during seed germination, initiation of storage-oil breakdown, membrane phospholipid turnover, and remodeling of LD surfaces to allow access of TAG lipases

GO:0016787 hydrolase activity

IEA
GO_REF:0000117

MODIFY

Summary: ARBA machine-learning electronic annotation assigning the very general molecular function "hydrolase activity". This is correct in essence (patatin/PNPLA proteins are hydrolases) but is uninformatively broad given that the patatin domain reliably confers a specific class of activity, namely carboxylic ester (acyl) hydrolysis of lipids.

Reason: The patatin/PNPLA domain is a lipid acyl hydrolase module that cleaves carboxylic ester bonds of glycerolipids using a Ser-Asp catalytic dyad [PMID:12779324]. "Hydrolase activity" (GO:0016787) is therefore correct but far too general; a more informative and equally well-supported term is "carboxylic ester hydrolase activity" (GO:0052689), the parent of the lipase/phospholipase/acylglycerol-lipase activities characteristic of this family. The UniProt entry's own family-level FUNCTION text describes non-specific lipolytic acyl hydrolase activity hydrolyzing phospholipids and galactolipids. More substrate-specific functions are in fact asserted for this protein by GO_Central as IBA (phylogenetic) annotations - glycerophospholipase activity (GO:0004620) and monoacylglycerol lipase activity (GO:0047372) - which are visible in AmiGO/GOlr but were not returned by the QuickGO GOA pull that seeded this review (see reference GO_REF:0000033 and the AmiGO record at http://amigo.geneontology.org/amigo/gene_product/UniProtKB:A0A3B6GK97). Because those IBA lipase terms already capture the specific activity out of band, this generic ARBA "hydrolase activity" annotation is best modified to their immediate informative parent, "carboxylic ester hydrolase activity" (GO:0052689), rather than left at the root-level hydrolase term or duplicated into the specific IBA terms. IMPORTANT CAVEAT - the family-level MF may not hold for this specific deposited sequence. A reproducible bioinformatics analysis (file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md) shows that the modeled 302-aa protein places in the pPLAII subfamily but LACKS the entire N-terminal half of the patatin catalytic domain - both the oxyanion glycine-rich block (DGGG) and the catalytic-serine nucleophile elbow (G-T-S-T-G) are absent (the sequence has no G-x-S-x-G motif at all), although it retains the catalytic Asp. As modeled it is therefore predicted catalytically INACTIVE (no nucleophile), most likely reflecting an incomplete/incorrect gene model (~100-130 aa shorter than orthologs) rather than - but not excluding - a genuine degenerate pseudo-enzyme. The IBA lipase calls were propagated phylogenetically and do not verify active-site integrity. The MODIFY to carboxylic ester hydrolase activity is retained as the correct FAMILY-level term, but with this explicit caveat that the activity is not verifiable on, and may be absent from, the current sequence model.

Proposed replacements: carboxylic ester hydrolase activity

Supporting Evidence:

PMID:12779324

Patatin is a nonspecific lipid acyl hydrolase

GO_REF:0000033

Annotation inferences using phylogenetic trees

file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md

the modeled 302-aa protein places in the pPLAII subfamily but LACKS the entire N-terminal half of the patatin catalytic domain - both the oxyanion glycine-rich block (DGGG) and the catalytic-serine nucleophile elbow (G-T-S-T-G) are absent

file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md

PNPLA/patatin enzymes use a Ser-Asp catalytic dyad rather than the classical Ser-His-Asp triad of many alpha/beta-hydrolases

Core Functions

Predicted lipid acyl hydrolase of the plant patatin-related phospholipase A pPLAII subfamily (soluble acyl hydrolase / defense-stress clade), acting on glycerolipids in lipid metabolism. GO_Central IBA annotations specify glycerophospholipase (GO:0004620) and monoacylglycerol lipase (GO:0047372) activities; carboxylic ester hydrolase activity is used here as the unifying parent term. CAVEAT - this is the family/subfamily-level function; the deposited 302-aa model itself lacks the catalytic-serine nucleophile elbow (G-T-S-T-G) and oxyanion (DGGG) and is predicted inactive as modeled (likely a truncated gene model), so the activity is inferred for the gene/subfamily, not confirmed for the current sequence. Based on domain homology, phylogenetic (IBA) inference, and in-repo bioinformatics; no direct experimental data for this specific protein.

Molecular Function:

carboxylic ester hydrolase activity

Directly Involved In:

lipid metabolic process

Supporting Evidence:

PMID:12779324
Patatin is a nonspecific lipid acyl hydrolase
GO_REF:0000033
Annotation inferences using phylogenetic trees
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md
A0A3B6GK97 belongs to the pPLAII subfamily
file:WHEAT/A0A3B6GK97/A0A3B6GK97-deep-research-falcon.md
Plant PNPLA/patatin proteins function as calcium-independent phospholipases with lipase/phospholipase A-type activities acting on phospholipids, galactolipids, triacylglycerols, and lysophospholipids

ProtNLM2 External predictions

View prediction review YAML · A0A3B6GK97-protnlm-predictions-review.yaml · Review status: COMPLETE

The deposited patatin-like sequence lacks the catalytic serine region. Intrinsic lipase activity is contradicted for this sequence, and participation in lipid catabolism is unresolved.

Source documents: genes/WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt · genes/WHEAT/A0A3B6GK97/A0A3B6GK97-goa.tsv · publications/PMID_12779324.md · genes/WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0016298 lipase activity GO_MF

NPI — Nonparalog incorrect Review score: 0/2

Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot

DOMAIN ARCHITECTURE MISMATCH

Review rationale: The existing reproducible sequence alignment and motif scan place this protein with plant patatins but show a missing N-terminal catalytic region, including the serine nucleophile and oxyanion block. Structural and mutational work establishes the patatin Ser-Asp catalytic dyad (PMID:12779324), so the missing serine region argues against lipase activity in the deposited 302-residue sequence. This is target-specific contrary evidence despite the more specific lipase IBAs in the cached UniProt record. Whether the deficiency reflects an incomplete gene model or a biological inactive protein remains unresolved.

Supporting Evidence:

file:WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt: "ID A0A3B6GK97_WHEAT Unreviewed; 302 AA. ... DR GO; GO:0004620; F:glycerophospholipase activity; IBA:GO_Central. ... DR GO; GO:0047372; F:monoacylglycerol lipase activity; IBA:GO_Central. ... DR InterPro; IPR016035; Acyl_Trfase/lysoPLipase. ... DR InterPro; IPR002641; PNPLA_dom. ... FT DOMAIN 1..134 ... FT /note="PNPLA""
PMID:12779324: "Ser77 and Asp215 were critical for both esterase and bioactivity"
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md: "the modeled 302-aa sequence lacks the entire N-terminal half of the patatin catalytic domain ... serine nucleophile elbow (G-T-S-T-G)** are absent."

GO:0016042 lipid catabolic process GO_BP

UNC — Uncertain Review score: 1/2

Prediction method: ProtNLM2 · Version: UniProt 2024_06 pilot

Review rationale: The reproducible alignment supports a patatin-family relationship but shows that the deposited sequence lacks the catalytic serine region. Thus, lipid hydrolysis by the encoded protein cannot be assumed from family membership. The predicted biological process could still apply through a noncatalytic role or to a corrected full-length gene model, neither of which is established by the inspected evidence. Lipid catabolic process is not present as an equivalent annotation in the cached records and remains uncertain.

Supporting Evidence:

file:WHEAT/A0A3B6GK97/A0A3B6GK97-uniprot.txt: "ID A0A3B6GK97_WHEAT Unreviewed; 302 AA. ... DR GO; GO:0004620; F:glycerophospholipase activity; IBA:GO_Central. ... DR GO; GO:0047372; F:monoacylglycerol lipase activity; IBA:GO_Central. ... DR InterPro; IPR016035; Acyl_Trfase/lysoPLipase. ... DR InterPro; IPR002641; PNPLA_dom. ... FT DOMAIN 1..134 ... FT /note="PNPLA""
file:WHEAT/A0A3B6GK97/A0A3B6GK97-bioinformatics/RESULTS.md: "the modeled 302-aa sequence lacks the entire N-terminal half of the patatin catalytic domain ... serine nucleophile elbow (G-T-S-T-G)** are absent."

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Bioinformatics Results

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Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

External Prediction Reviews

ProtNLM2 External predictions

Deep Research

Falcon

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Notes

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