Summary: Phylogenetic inference that ATG-5 participates in autophagosome assembly.

Reason: Core process, supported by C. elegans evidence that loss of atg-5 abolishes LGG-1 lipidation and puncta formation (PMID:24185444).

Summary: Zhang et al. showed that atg-5 loss of function abolishes LGG-1 lipidation and the formation of LGG-1 puncta.

Reason: Direct C. elegans loss-of-function evidence for the core process.

Summary: Author statement in the same paper; duplicates the IMP row.

Reason: Correct; redundant with the IMP annotation from the same paper.

Summary: Phylogenetic inference of mitophagy, from yeast and S. pombe Atg5.

Reason: Cargo-specific output of general autophagy machinery; untested for atg-5 in C. elegans. Non-core.

Summary: Pull-down/yeast two-hybrid interactions of ATG-5 with ATG-16.1 (Q19124) and ATG-16.2 (Q09406).

Reason: The interactions are real and important (removal does not mean the interaction is false), but protein binding is uninformative. They define membership of the Atg12-Atg5-Atg16 complex (GO:0034274), which is annotated separately and captures them informatively; no more specific binding MF term fits.

Summary: Pull-down/yeast two-hybrid interactions of ATG-5 with ATG-16.1 (Q19124) and ATG-16.2 (Q09406).

Reason: The interactions are real and important (removal does not mean the interaction is false), but protein binding is uninformative. They define membership of the Atg12-Atg5-Atg16 complex (GO:0034274), which is annotated separately and captures them informatively; no more specific binding MF term fits.

Summary: InterPro (Atg5 family) mapping to cytoplasm.

Reason: Correct general location for a cytoplasmic autophagy protein.

Summary: Author statement of cytoplasmic localization.

Reason: Correct; cytosol (also annotated) is the more precise term.

Summary: Phylogenetic inference that ATG-5 is active at the autophagosome.

Reason: The Atg12-Atg5-Atg16 complex acts on the forming phagophore and largely dissociates on completion; phagophore (GO:0061908, also annotated) is the precise location of the core activity. Not wrong under the broad GO autophagosome term, so retained as non-core.

Summary: Author statement of cytosolic localization.

Reason: Atg5 orthologs exist as a cytosolic pool of the conjugate complex; correct.

Summary: InterPro (Atg5 family) mapping to autophagy.

Reason: Correct, general; specific process captured by autophagosome assembly.

Summary: WormBook review of C. elegans autophagy; the cached copy is abstract-only and the underlying atg-5 phenotype is not visible.

Reason: The assertion is correct and consistent with later direct atg-5 data (PMID:24185444); deferring to the curator on the specific evidence in the full WormBook chapter.

Summary: Author statement; ATG-5 is part of the autophagy machinery.

Reason: Correct, general.

Summary: Phylogenetic inference of response to nitrogen starvation, from Dictyostelium atg5.

Reason: Unicellular starvation framing not tested in C. elegans; non-core inherited annotation.

Summary: ARBA machine-learning annotation to vacuole organization.

Reason: Vacuole organization is an ancestor of autophagosome assembly (via autophagosome organization); it is true but far too general. Replace with the specific process.

Proposed replacements: autophagosome assembly

Summary: Loss of atg-5 abolishes LGG-1 lipidation and puncta formation (curated as regulation of autophagy).

Reason: The phenotype is sound, but ATG-5 is a core structural/E3-like component of the conjugation machinery, not a regulator of autophagy. The direct process is autophagosome assembly (and the lipidation step).

Proposed replacements: autophagosome assembly

Summary: ARBA annotation to macroautophagy.

Reason: Correct.

Summary: Author statement; ATG-5 functions in macroautophagy.

Reason: Correct.

Summary: Phylogenetic inference that ATG-5 contributes to Atg8-family ligase (E3-like) activity as part of the Atg12-Atg5-Atg16 complex.

Reason: Core molecular function, correctly qualified as contributes_to: the E3-like activity belongs to the LGG-3-ATG-5 conjugate within the complex. C. elegans data show atg-5 is required for LGG-1 lipidation.

Summary: Phylogenetic inference to phagophore assembly site membrane, a term now obsolete in GO (QuickGO: replaced_by GO:7770114 phagophore membrane, because the PAS is not a membrane-bounded compartment).

Reason: The intended location, the membrane of the forming autophagosome, is correct for the Atg12-Atg5-Atg16 complex; update to the replacement term.

Proposed replacements: phagophore membrane

Summary: UniProt SubCell mapping (preautophagosomal structure membrane) to the now-obsolete PAS membrane term.

Reason: Update to the GO replacement term phagophore membrane.

Proposed replacements: phagophore membrane

Summary: Author statement mapped to the now-obsolete PAS membrane term.

Reason: Update to the GO replacement term phagophore membrane.

Proposed replacements: phagophore membrane

Summary: Phylogenetic inference that ATG-5 is part of the Atg12-Atg5-Atg16 complex.

Reason: Core complex membership; supported in C. elegans by direct binding of ATG-5 to ATG-16.1 and ATG-16.2.

Summary: Author statement of complex membership.

Reason: Correct, consistent with the binding data in the same paper.

Summary: Phylogenetic inference of piecemeal microautophagy of the nucleus from the eukaryotic ATG5 node PANTHER:PTN000315667 (S. cerevisiae Atg5, SGD:S000006070).

Reason: Piecemeal microautophagy of the nucleus (GO:0034727) is a budding-yeast process at nucleus-vacuole junctions (Nvj1-Vac8) not documented in C. elegans. While some reviews (human/ATG2A, ATG2B, ATG12, ULK1) left GO:0034727 UNDECIDED on whether macroautophagic nuclear turnover could be treated as a functional equivalent, GO's ontology hierarchy places the general parent term GO:0044804 (nucleophagy) under GO:0016236 (macroautophagy) for autophagosome-mediated nuclear cargo degradation, whereas GO:0034727 (piecemeal microautophagy of the nucleus) is its GO:0016237 (microautophagy)-scoped child (defined by direct endosomal, lysosomal, or vacuolar membrane invagination without prior autophagosome sequestration). Placing GO:0034727 at the eukaryotic ATG5 root node PANTHER:PTN000315667 over-propagates a yeast-specific organelle topology to nematode ATG-5, whose conserved role is LGG-3/ATG12 conjugation and LGG-1/LGG-2 lipidation in autophagosome assembly (GO:0000045). Marked as over-annotated for consistency with human/ATG5, SCHPO/atg5, worm/atg-2, worm/atg-4.1, worm/atg-9, worm/atg-13, and worm/unc-51.

Summary: Phylogenetic inference of aggrephagy.

Reason: Aggrephagy of embryonic protein aggregates (PGL granules, SQST-1) is the principal assay of basal autophagy in C. elegans, and loss of atg-5 blocks LGG-1 lipidation and puncta formation needed for it. Accepted as a key physiological process of ATG-5 in worms.

Summary: Phylogenetic inference that ATG-5 is active at the phagophore.

Reason: Precise location of the E3-like activity of the Atg12-Atg5-Atg16 complex.

Summary: Author statement mapped to transferase complex.

Reason: Transferase complex is a parent (via catalytic complex) of the Atg12-Atg5-Atg16 complex; correct but uninformative. Use the specific complex.

Proposed replacements: Atg12-Atg5-Atg16 complex