GCDH’s central role is mitochondrial glutaryl-CoA oxidation and decarboxylation. The single catalytic core links amino-acid catabolism to direct crotonyl-CoA production. The review distinguishes this chemistry from unresolved physiological fatty-acid oxidation and from the contextual nuclear pool. This is a manually authored source synthesis; it does not claim a new research-provider run.
The current review contains all 25 original contexts: 17 ACCEPT, three MODIFY, two MARK_AS_OVER_ANNOTATED, one TOO_GENERAL, one UNDECIDED and one KEEP_AS_NON_CORE. There are no NEW assertions, extension atoms or negations. The broad enzyme-class rows are refined through actual is_a paths to GO:0004361. The two beta-oxidation claims are marked over-annotated after resolving their source scope; the separate rat-derived fatty-acid-oxidation claim remains unresolved. The mitochondrial organelle claims are retained alongside the more precise matrix evidence.
The 38 reference assessments state the actual reading limits. PMID:8541831(https://pubmed.ncbi.nlm.nih.gov/8541831/) and PMID:17176108(https://pubmed.ncbi.nlm.nih.gov/17176108/) anchor human catalytic and kinetic interpretation; their available abstracts are not represented as complete Methods readings. The measured alternative-substrate result in PMID:11024031(https://pubmed.ncbi.nlm.nih.gov/11024031/) remains visible in the enzyme-class review without adding a physiological pathway. Its full original Methods and tables were not recovered.
PMID:25416781(https://pmc.ncbi.nlm.nih.gov/articles/PMC4281744/) now has a selected original protocol reading, detailed once in its reference assessment. The cache remains unchanged.
The exact mitochondrial-proteome target group in PMID:34800366(https://pubmed.ncbi.nlm.nih.gov/34800366/) is identified in its reference assessment. Grouped natural-product accessions, inherited GO matrix labels and functional-category labels are kept distinct from directly measured localization and physiological flux. The selected original reading of PMID:37198486(https://pubmed.ncbi.nlm.nih.gov/37198486/) distinguishes GCDH acyl-donor production from CBP-mediated histone transfer and engineered reagents from natural products.
The actual Reactome reaction R-HSA-71046 resolves through its catalyst to human Q92947 residues 45–438 in the mitochondrial matrix. R-HSA-71064 supplies the lysine-pathway context. The participant chain, rather than the pathway name alone, establishes the target and compartment. Auxiliary sequence, clinical and proteomic references are retained at their actual evidential scope; no target-specific peptide or cleavage-site claim is inferred from a study’s global coverage.
The two official natural sequences are Q92947-1, 438 residues, and Q92947-2, 428 residues. Direct FASTAs agree with the VSP_000145 reconstruction. The alternative-product descriptions separate those sequence facts from historical reagent identity and the source of the short-product inactivity assignment. The transit coordinate remains a curated prediction rather than a newly verified cleavage site.
The actual PTHR42807 tree, alignment, sequence file and node attributes place the exact displayed target at AN28/PTN002533783. All five incoming IBD assertions join to AN3/PTN005130278. No retained negative record blocks those target paths. Valid inheritance mechanics do not resolve excessive process scope; the beta-oxidation judgment concerns the inherited claim, and target self-donor evidence is not circularity.
The compact evidence archive retains all current raw fields and explicit original-to-native joins. It also records the immutable original 26-row review and its 43 quotation associations by commit, blob, JSON pointer and excerpt hash. Three original history records, the 7,006-byte journal prefix and all four generated hypothesis artifacts are preserved. Unmatched historical source keys remain in that archive; they are not converted into synthetic NEW assertions.
The prior OpenScientist report is preserved as generated. Its specific self-IBA and wrong-paper premises are disputed in the current bibliography; the physiological process uncertainty is still considered independently. The four prior publication excerpts remain exact, with source hashes and UTF-8 byte offsets. The 20-word human UniProt FUNCTION anchor remains once in the core with its record section and normalized-source locator. One additional short introductory clause from PMID:25416781 is attached once to its inherited beta-oxidation review; the prior ETF-assay excerpt remains unchanged. The earlier authentic PubMed abstract coordinates for PMID:11024031 remain separately recorded; its excerpt has only native line wrapping adjusted.
Genuine target fetching and source acquisition are complete. The untouched native seed contains 25 keys for all 25 originals, with no collision restoration needed. The actual source union contains 24 publications, two Reactome entries and three family files: 17 unchanged main objects and 12 missing-only publication acquisitions. All new publication caches are abstract-only. Machine joins, factual access flags and all four quotation offsets have been reconciled. Default validation and strict GOA matching passed with no annotation advisories. The published c29e80 amendment also passed default validation, strict GOA matching and computed-status checks without annotation advisories. The generic record-section dry run reported no changes; because it skips UniProtKB citations, the 20-word FUNCTION anchor was separately verified with direct quote-matching and section-parser calls against the unchanged local record. Status remains COMPLETE with one explicit rat-derived oxidation uncertainty. Genuine EDIT history and private rendering/link checks passed. The PR remains draft pending renewed substantive review and CI.
The amino-acid parent is refined to L-lysine catabolism and L-tryptophan catabolism, both verified is_a descendants. Hydroxylysine remains explicit in the core description. Acyl-CoA metabolism is TOO_GENERAL because the already accepted fatty-acyl-CoA biosynthesis term entails it through two verified is_a paths. This does not reject direct product formation within catabolism. The three core process facets have no ancestor/descendant relationship to one another.
GO:0046949 covers direct fatty-acyl-CoA formation. Its children include isovaleryl-CoA and methylbut(en)oyl-CoA biosynthesis, showing that formation of an amino-acid-catabolic intermediate is not categorically excluded. The specified human ACAD comparators lack this annotation in the inspected official snapshot; that absence does not negate GCDH’s direct crotonyl-CoA production or its verified ancestral assertion. No new process annotation is introduced.
Four original human annotations retain FlyBase as their assigning database. The literal target/taxon and experimentally inspected human contexts are preserved; the organization name alone does not establish a source defect.
The two added source assessments link the actual originals, PMID:32446361(https://pmc.ncbi.nlm.nih.gov/articles/PMC7248122/) and PMID:41196119(https://pmc.ncbi.nlm.nih.gov/articles/PMC13066932/), and state their experimental limits. They inform the unresolved broad oxidation question; they do not establish an additional human process annotation. The rat source remains abstract-only. The broader electron-removal process and the narrower iterative beta-oxidation pathway are assessed independently.
This successor preserves all 29 existing source files and adds two genuinely acquired full-XML publication caches, for 31 sources in total. Their titles and availability flags match the native records. Default validation and strict GOA matching passed without annotation advisories; computed status remains COMPLETE with one explicit uncertainty. Genuine EDIT history, private rendering/local links and scoped authored whitespace passed. The added excerpt matches its exact source byte slice. The PR remains draft outside the queue pending renewed substantive review and CI; earlier results above belong to the published parent.