CPS1

Summary: Phylogenetic ammonia-dependent synthetase activity is supported by target biochemistry.

Reason: The current IBD at PTN008517424 lies on the exact human target path in PTHR11405. Human CPS1 independently catalyzes ammonia-dependent carbamoyl-phosphate synthesis. Target experimental evidence among the descendants is legitimate grounding, not circularity; the short displayed donor list is not a measure of IBD quality.

Summary: The broad ancestral cytoplasmic location can be refined to the principal mitochondrial matrix location.

Reason: PTN000150222 is an actual ancestor of the human target, so the cytoplasmic IBD is not a mistaken tree join. The established human catalytic pool is mitochondrial matrix, which provides useful target-specific precision. This refinement does not deny the separately retained cytosolic, nucleolar, membrane-associated or nucleoid observations.

Proposed replacements: mitochondrial matrix

Summary: Broad glutamine-pathway participation remains unresolved despite established ammonia-specific catalysis.

Reason: The current PAINT IBD at PTN000150223 is on the human path and has actual experimental descendant support. Human CPS1 has lost direct glutamine hydrolysis and performs the independently demonstrated ammonia-dependent reaction. That resolves the molecular-function refinement, but the broader GO:0006541 definition includes multistep pathways. The unresolved question is whether the inherited source assertion represents a glutamine-metabolic pathway step actually performed by human CPS1, beyond the ancestral hydrolysis subactivity. The inspected evidence does not establish that role. A possible nitrogen origin is not positive participation evidence; UNDECIDED records this unresolved source-to-target scope rather than accepting the process.

Summary: Refine the composite glutamine-hydrolyzing activity to the demonstrated human ammonia reaction.

Reason: The exact PTN000150223 IBD and contributes_to qualifier are real. Bacterial carB and yeast CPA2 can contribute to a glutamine-dependent reaction without their own glutaminase, so loss of the catalytic cysteine alone is not sufficient to reject this assertion. Human single-chain CPS1 instead independently performs the ammonia reaction, and the assessed originals do not establish a human glutaminase-partner complex that supplies a composite glutamine-hydrolyzing activity. GO:0004087 is the supported target activity.

Proposed replacements: carbamoyl-phosphate synthase (ammonia) activity

Summary: Electronic ammonia-dependent catalytic activity matches direct human evidence.

Reason: Current ARBA00087481 branch 0 matches the target features, and the combined source also includes the correct Rhea/EC reaction and experimentally grounded rat and mouse orthologs. Independent native and recombinant human enzyme evidence establishes the ammonia-dependent reaction.

Summary: The shared-domain mapping needs the ammonia-dependent target subtype.

Reason: IPR006274 supports membership in the carbamoyl-phosphate-synthetase family, but human CPS1 uses ammonia rather than hydrolyzing glutamine. The shared architecture does not distinguish that mechanistic divergence. Replace the reaction subtype with the experimentally established ammonia activity; this does not exclude CPS1 from all glutamine-derived or pyrimidine pathway contexts.

Proposed replacements: carbamoyl-phosphate synthase (ammonia) activity

Summary: ATP binding is intrinsic to the two ATP-dependent phosphorylation steps.

Reason: Human kinetic experiments and the two nucleotide-binding phosphorylation domains support ATP utilization. The ligand-bound 2015 crystal structures contain ADP, not ATP; they complement the kinetic evidence rather than directly visualizing bound ATP.

Summary: Retain the reported nucleolar pool at the immunofluorescence source scope.

Reason: The current UniProt SL-0188 mapping is independently consistent with the HPA antibody-specific nucleolar or nucleolar-rim calls in A-431, U-251 MG and U2OS. These observations do not establish a nucleolar catalytic role or supplant the mitochondrial matrix core. No image-level reanalysis is claimed.

Summary: Mitochondrial localization is a well-supported broad electronic assertion.

Reason: The transit sequence, human mitochondrial proteomics and catalytic matrix evidence support this organelle. Current ARBA00026962 branch 85 matches the target; the other combined ortholog and subcellular-vocabulary sources converge on the same broad location.

Summary: Retain the ortholog-supported peripheral cell-surface pool as non-core.

Reason: The current mouse Q8C196 donor has IDA evidence from PMID:34799567. Nonpermeabilized primary mouse hepatocyte imaging and membrane-fraction pull-down/MS support a cell-surface CPS1 pool. Human HepG2 infection experiments in that study do not themselves image endogenous human surface CPS1. The transfer is retained at this qualified ortholog scope, without inferring a transmembrane topology, an autonomous receptor core or direct purified-human binding from the lysate assay.

Summary: CPS1 can supply pyrimidine nitrogen in a defined cancer context.

Reason: A shared CPS domain does not by itself establish pathway deployment, but PMID:28538732 directly tests CPS1 depletion and rescue in KRAS/LKB1-mutant lung-cancer cells, pyrimidine pools and incorporation of ammonia-derived nitrogen into thymidine. This supports performed precursor synthesis in that context rather than a blanket assignment of CAD function. PMID:31043737 corrects the claimed carbamoyl-phosphate LC-MS signal to phosphorylethanolamine; no measured carbamoyl-phosphate accumulation is asserted here. The separate tracing and pyrimidine results were not withdrawn.

Summary: Broad glutamine-pathway participation remains unresolved despite established ammonia-specific catalysis.

Reason: IPR006274 is an authentic shared carbamoyl-phosphate-synthetase domain mapping. Human CPS1 has lost direct glutamine hydrolysis and performs the independently demonstrated ammonia-dependent reaction. That resolves the molecular-function refinement, but the broader GO:0006541 definition includes multistep pathways. The unresolved question is whether the inherited source assertion represents a glutamine-metabolic pathway step actually performed by human CPS1, beyond the ancestral hydrolysis subactivity. The inspected evidence does not establish that role. A possible nitrogen origin is not positive participation evidence; UNDECIDED records this unresolved source-to-target scope rather than accepting the process.

Summary: The retired broad metal-binding source remains biologically sound.

Reason: This exact historical InterPro-only record is retired because the genuine current source combines InterPro and ARBA; retirement is not biological rejection. Catalytic magnesium and potassium binding are independently demonstrated. The source is preserved without retrofitting its omitted historical WITH/FROM.

Summary: Refine the broad biosynthetic mapping to the actual carbamoyl-phosphate product.

Reason: Current ARBA00029048 branches 17 and 76 match the target. CPS1 directly synthesizes carbamoyl phosphate, so GO:0070409 is the supported product-specific refinement of the broader organophosphate biosynthetic mapping. The original source identifier is preserved. The replacement rests on demonstrated chemistry, independently of the wording returned by ontology services.

Proposed replacements: carbamoyl phosphate biosynthetic process

Summary: Positive Raf-family interactions support MAP kinase kinase kinase binding.

Reason: The retired historical aggregate is preserved separately from the two current partner-specific assertions. The exact IntAct records report positive yeast two-hybrid interactions of a CPS1 420–771 fragment with defined RAF1 or ARAF regions. Both partners have independently supported MAP kinase kinase kinase activity, so GO:0031435 identifies the measured partner class without assigning kinase activity to CPS1. Fragment and assay context remain explicit; no full-length native mitochondrial interaction or signaling mechanism is inferred.

Proposed replacements: mitogen-activated protein kinase kinase kinase binding

Summary: The positive affinity-proteomics partner supports 14-3-3 protein binding.

Reason: The literal MINT record pairs CPS1 with P63104 in the GST-bait affinity-purification study, with peptide elution. The identified partner is 14-3-3 zeta, making GO:0071889 a supported class refinement. The available original abstract and curated experiment record do not establish a purified binary interface, but that is not a prerequisite for retaining positive association evidence. No CPS1 adaptor function is inferred.

Proposed replacements: 14-3-3 protein binding

Summary: The positive 14-3-3 zeta purification supports the specific binding class.

Reason: The original HeLa GFP–TAP–14-3-3 zeta experiment identifies mitochondrial CPS1 in the ceramide-treated preparation (Table 1); Table 2 assigns GI 4033707 to that identification but incorrectly discusses CAD biology. The literal MINT pair with P63104 is a positive spoke-expanded affinity association. GO:0071889 describes the identified partner class; neither this refinement nor the paper establishes a direct CPS1/14-3-3 interface, phosphorylation dependence of CPS1 binding, or a CPS1 apoptotic mechanism. The Methods explicitly allow recovery through a protein complex. The erroneous CAD background is not treated as evidence about CPS1 function, and expected compartment or abundance alone does not identify this measured association as contamination.

Proposed replacements: 14-3-3 protein binding

Summary: The rat ortholog transfer correctly captures the urea-cycle synthetic step.

Reason: The exact P07756 ortholog source is compatible with the independently established human reaction that generates the carbamoyl phosphate used by ornithine transcarbamylase. CPS1 performs a step of the cycle rather than merely being required for it.

Summary: Developmental expression is positive, but the specific developmental contribution is unresolved.

Reason: The current rat donor PMID:8690412 reports coordinated developmental and zonal expression of urea-cycle enzymes. That is genuine positive evidence, but the complete original was not recovered and the precise CPS1 contribution to liver development cannot be resolved from its abstract. The uncertainty concerns the functional interpretation at both donor and human scope, not a demonstrated donor-valid/target-invalid transfer.

Summary: A reported native CPS1 fragment has proteolytic activity, with unresolved transfer to human CPS1.

Reason: PMID:15304357 reports a native rat-liver fragment inferred to span approximately residues 418–1305 and peptide cleavage associated with a NIH3T3 extract. This positive evidence contradicts a blanket assertion that CPS1 cannot have such activity. Full original controls and a corresponding endogenous human fragment were not recovered, so neither autonomous full-length human endopeptidase activity nor a confident negative is established.

Summary: The reported calcium-binding band has unresolved CPS1 identity and human transfer scope.

Reason: PMID:9506839 reports a 45Ca-binding rat inner-membrane-fraction band of approximately 130 kDa, parenthetically identified as carbamoyl-phosphate synthetase. The accessed abstract does not state how that identity was established, and the full original was not recovered. The reported size is substantially below the approximately 165-kDa human precursor and 160-kDa mature CPS1, making an intact ortholog assignment uncertain without the identification or processing evidence. The positive rat observation is preserved, but a verified CPS1 fragment or intact-protein assignment and its human applicability remain unresolved. Calcium binding is distinct from catalytic activation; absence of a calcium site in selected structures is not used to disprove the assay.

Summary: Refine the phospholipid interaction to the specifically demonstrated cardiolipin ligand.

Reason: The complete accessed PMID:1898084 abstract reports selective interaction of purified rat liver CPS1 with cardiolipin, including inhibition and conformational effects, with weaker effects from other anionic phospholipids and negligible effects from the tested zwitterionic lipids. GO:1901612 is an actual is_a descendant of phospholipid binding and names this demonstrated ligand. The ortholog transfer remains restricted to this biochemical interaction; full original Methods and a direct human assay were not recovered. The refinement does not exclude the other reported anionic-phospholipid interactions or infer an obligatory catalytic cofactor.

Proposed replacements: cardiolipin binding

Summary: A peripheral inner-membrane-associated pool is compatible with matrix catalysis.

Reason: PMID:3680220 supplies positive rat biochemical membrane-association evidence. Human MitoCoP also identifies CPS1 and classifies it as peripheral rather than integral. Retain a conditional membrane-associated pool without asserting a transmembrane segment or replacing the principal soluble matrix location.

Summary: Retain the directly detected rat cytosolic CPS1 pool.

Reason: The full PMID:25684186 study identifies cytosolic CPS1 by mass spectrometry and antibody in rat liver during ethanol-associated protein damage. The isoaspartate/PIMT experiments concern damaged protein; they do not establish a cytosolic urea cycle or a beneficial response. A non-core location is nevertheless supported.

Summary: The developmental intestinal expression source does not resolve the full developmental claim.

Reason: The complete PMID:9544996 abstract reports spatial and temporal mRNA/protein distribution in rat intestine, including CPS1 in enterocytes and inferred citrulline synthesis. This supports metabolic differentiation but does not by itself settle CPS1 participation in progression of the midgut to mature structure. Full original text remains unavailable; the genuine experimental donor claim is not confidently rejected.

Summary: Retain the observed CPS1 expression response to a xenobiotic treatment.

Reason: PMID:19135993 reports that S35171 treatment restores liver mitochondrial CPS1 expression in hypertensive stroke-prone rats. GO:0009410 explicitly includes altered enzyme production and gene expression, so a separate CPS1-dependent protective mechanism is not required for this existing broad response annotation. The proposed contribution to protection remains an interpretation, not a demonstrated receptor or signaling activity.

Summary: Toxicant-associated CPS1 protein/transcript changes support the broad response scope.

Reason: PMID:14625847 reports changed rat CPS1 isoform abundance after toxic compounds, and PMID:20452409 directly measures decreased CPS1 transcript/protein after PFOA treatment. GO:0009636 includes these expression/state changes. Retain the contextual ortholog response without converting the marker data into a proven protective mechanism or CPS1-mediated toxicant metabolism.

Summary: Zinc deficiency alters the measured ureagenic enzyme response.

Reason: PMID:12840196 reports increased CPS1 activity in zinc-deficient rats in the context of altered protein/nitrogen metabolism. This is a measured enzymatic response, not merely expression of a marker. Retain it as a contextual ortholog-supported process without assigning zinc-binding or zinc-transport activity to CPS1.

Summary: Retain the measured CPS1 metabolic response in the dimethylnitrosamine model.

Reason: PMID:2864015 measures rat liver enzyme activities after dimethylnitrosamine exposure, including decreased ureagenic activities and altered proliferative metabolism. CPS1 is one metabolic effector of that response; this does not imply direct amine sensing or binding. The disease/exposure scope makes it non-core.

Summary: The demonstrated activating ligand is N-acetylglutamate.

Reason: The rat source PMID:8663466 concerns N-acetylglutamate-dependent regulation, and human structural evidence resolves the NAG pocket. GO:0072341 captures binding to this modified amino acid. This semantic correction is not a claim that the replacement is a typed child of free-glutamate binding or that CPS1 can never interact with free glutamate.

Proposed replacements: modified amino acid binding

Summary: Feeding-dependent ureagenic activity is a contextual CPS1 function.

Reason: PMID:15481768 examines measured CPS1/nitrogen-metabolic adaptation to feeding. The enzyme performs the ammonia-to-carbamoyl-phosphate step in the resulting metabolic adjustment, so a non-core response is defensible rather than treating every change in enzyme abundance as participation.

Summary: Rat endotoxin experiments measure reduced urea synthesis, distinct from release as a biomarker.

Reason: PMID:17539997 reports reduced urea-nitrogen synthesis rate/capacity and CPS1 mRNA after lipopolysaccharide, with preserved galactose elimination capacity. CPS1 is a metabolic effector in this impaired ureagenic response. Retain the ortholog claim as contextual; it is distinct from the serum-fragment observation supporting the separate human IDA row.

Summary: Retain membership in the conditional rat liver protein complex.

Reason: The complete PMID:17669278 study isolates an approximately 300-kDa preparation containing CPS1, formyltetrahydrofolate dehydrogenase and betaine-homocysteine methyltransferase after soybean trypsin inhibitor treatment/affinity purification. CPS1 can be predominantly monomeric in another preparation and still occur in this complex. No constitutive human complex or obligatory catalytic oligomer is inferred.

Summary: Glucagon-responsive ureagenic regulation is a secondary metabolic role.

Reason: PMID:3754512 reports the rat CPS1 expression response, while the separately assessed PMID:8460937 also measures increased CPS1 activity. Together these support a metabolic response rather than only an expression marker. The direct species and experimental contexts remain distinct.

Summary: Oleate-dependent CPS1 expression changes support the stated response term.

Reason: The complete PMID:8985169 abstract reports oleate suppression of dexamethasone-induced CPS1 mRNA in rat primary hepatocytes, with carnitine reversal and fatty-acid specificity. Both the organismal and cellular response definitions explicitly include gene-expression changes. A direct oleate-binding or protective function is not inferred, but is not a prerequisite for retaining this existing contextual response.

Summary: Starvation-associated changes in CPS1 activity support metabolic adaptation.

Reason: PMID:1979948 directly reports a starvation-dependent change in the rat hepatic CPS mRNA gradient, reversed by glucose refeeding. PMID:11577071 measures fatty acylation and inhibition of rat CPS1, then proposes nitrogen sparing during starvation as an interpretation; it does not directly test that physiological mechanism. Retain the existing contextual response at the measured expression-change scope, without assigning CPS1 a general starvation sensor or presenting the proposed mechanism as established.

Summary: Amino-acid-associated ureagenic output supports the contextual response.

Reason: PMID:11738098 measures rat CPS1 activity alongside blood urea nitrogen/ammonia in the amino-acid treatment context. CPS1 performs the ammonia-detoxifying step affected by the treatment. This is not evidence that every amino acid binds directly to the enzyme.

Summary: FGF4-induced hepatic marker expression supports a bounded cellular response.

Reason: PMID:12832696 reports CPS1 transcript expression among hepatic markers after rat embryonic stem-like cells are cultured with FGF4. GO:0044344 explicitly includes gene-expression changes after the stimulus. Retain that existing response at the differentiation-culture scope; it does not establish CPS1 as an FGF receptor, signaling factor or driver of hepatocyte differentiation.

Summary: Complex membership does not resolve binding to an assembled protein complex.

Reason: PMID:17669278 provides positive CPS1-containing complex isolation. Its Figure 4 binding experiment specifically concerns FDH and soybean trypsin inhibitor, while CPS1 recruitment is inferred; Figure 5 detects anti-SBTI signal after injection. This is insufficient to identify a CPS1-specific interaction with the assembled complex, but it does not justify a confident negative.

Summary: Hormonal regulation of ureagenic capacity supports a contextual response.

Reason: The rat PMID:9688877 study measures urea-nitrogen synthesis capacity, nitrogen balance and CPS1 expression during hormonal treatment. CPS1 performs the affected synthetic step, so this is more than use of the protein as a developmental marker. Retain the source-specific endocrine/metabolic context without adding a hormone receptor or signaling core.

Summary: Retain hormone/cAMP-dependent regulation of CPS1 metabolic output.

Reason: PMID:17397987 characterizes rat CPS1 promoter regulation; PMID:6092398 separately measures hormonally restored enzyme/function and ornithine-dependent growth. These complementary experiments support regulation of the performed CPS1 reaction, while promoter responsiveness alone would not establish every downstream biological process. No direct cAMP binding or autonomous signal-transduction activity is inferred.

Summary: Retain hormone/cAMP-dependent regulation of CPS1 metabolic output.

Reason: PMID:17397987 characterizes rat CPS1 promoter regulation; PMID:6092398 separately measures hormonally restored enzyme/function and ornithine-dependent growth. These complementary experiments support regulation of the performed CPS1 reaction, while promoter responsiveness alone would not establish every downstream biological process. No direct cAMP binding or autonomous signal-transduction activity is inferred.

Summary: The specific monoatomic-anion homeostasis claim is unresolved.

Reason: The current rat donor PMID:4062872 concerns cafeteria diet, urea-nitrogen excretion and metabolic enzyme changes. GO:0055081 explicitly concerns monoatomic anions; general nitrogen disposal or bicarbonate utilization is not an exact substitute. The complete original was not recovered and the required source-specific anion mechanism remains unresolved, so the annotation is neither accepted by term association nor removed as a proven error.

Summary: Hormonal regulation of ureagenic capacity supports a contextual response.

Reason: The rat PMID:9688877 study measures urea-nitrogen synthesis capacity, nitrogen balance and CPS1 expression during hormonal treatment. CPS1 performs the affected synthetic step, so this is more than use of the protein as a developmental marker. Retain the source-specific endocrine/metabolic context without adding a hormone receptor or signaling core.

Summary: The differentiation source establishes marker expression while the target contribution remains unresolved.

Reason: PMID:12939595 uses CPS1 and other markers to follow maturation and hepatocyte-to-biliary transitions after fetal rat cell transplantation. The complete abstract is positive about marker changes; full original details were not recovered. The precise CPS1 role in acquisition of hepatocyte features remains unresolved rather than disproven or accepted merely from marker expression.

Summary: Retain hormone/cAMP-dependent regulation of CPS1 metabolic output.

Reason: PMID:17397987 characterizes rat CPS1 promoter regulation; PMID:6092398 separately measures hormonally restored enzyme/function and ornithine-dependent growth. These complementary experiments support regulation of the performed CPS1 reaction, while promoter responsiveness alone would not establish every downstream biological process. No direct cAMP binding or autonomous signal-transduction activity is inferred.

Summary: Glucagon changes measured cellular CPS1 activity.

Reason: PMID:8460937 reports rat CPS1 transcript and enzyme-activity increases. CPS1 is therefore a metabolic effector of the cellular hormonal response, not merely an abundance marker in this experiment. This remains a contextual annotation rather than the primary catalytic core.

Summary: Oleate-dependent CPS1 expression changes support the stated response term.

Reason: The complete PMID:8985169 abstract reports oleate suppression of dexamethasone-induced CPS1 mRNA in rat primary hepatocytes, with carnitine reversal and fatty-acid specificity. Both the organismal and cellular response definitions explicitly include gene-expression changes. A direct oleate-binding or protective function is not inferred, but is not a prerequisite for retaining this existing contextual response.

Summary: Retain CPS1 expression in the glucocorticoid-induced cellular-state change.

Reason: PMID:19446026 reports CPS1-positive hepatocyte-like cells after glucocorticoid treatment and associated changes in a pancreatic cell model. GO:0071548 covers expression and cellular-state responses, so the marker evidence can support this broad contextual annotation without establishing a CPS1-performed differentiation mechanism or direct hormone sensing. The literal donor links the experiment to dexamethasone; the accessed abstract describes glucocorticoid exposure.

Summary: Alcohol exposure changes cytosolic CPS1 abundance as well as protein damage.

Reason: The actual PMID:25684186 Results report a significant 2.27-fold CPS1 protein increase after eight weeks of ethanol feeding. That observed state/abundance change supports the broad response-to-alcohol definition. Separate isoaspartate-damage and PIMT-substrate experiments do not establish that CPS1 catalyzes repair or protects against ethanol; the functional consequence of the damage remains unresolved.

Summary: CPS1 performs the first synthetic reaction of the curated urea cycle.

Reason: The live R-HSA-70635 hierarchy reaches target-labelled CPS1 catalyst entities in the ammonia/bicarbonate-to-carbamoyl-phosphate reaction. The function is independently supported by human biochemistry, not merely by pathway membership.

Summary: Native human liver enzyme experiments support the ammonia reaction.

Reason: The complete PMID:6249820 abstract describes stabilization, purification and kinetic characterization of human liver CPS1, including ammonia, bicarbonate, MgATP and NAG. Full original Methods were not recovered; the positive experimental annotation is retained with curator deference and independent recombinant/structural confirmation.

Summary: Retain the experimental nucleolar imaging call without inventing a nucleolar function.

Reason: The actual HPA target record reports nucleolar/nucleolar-rim staining in A-431, U-251 MG and U2OS. The source is antibody- and cell-context specific; no original image pixels were inspected. It supports a secondary location without demonstrating a nucleolar CPS1 reaction.

Summary: The variant reaction places the target-derived CPS1 entities in mitochondrial matrix.

Reason: The actual R-HSA-9955543 graph reaches CPS1 variant entities and the P31327 reference entity in the matrix. This is a location assertion in a deficient-reaction model, not evidence that every variant lacks all activity. The established wild-type matrix pool is independently supported.

Summary: The deglutarylation reaction places CPS1 substrate in the matrix.

Reason: The actual R-HSA-9955504 graph identifies CPS1 as the modified substrate acted on by SIRT5. PMID:24703693 provides the original glutarylation/deglutarylation and activity context. This supports CPS1 location, not deglutarylase activity or a NEW protein-deglutarylation process for CPS1.

Summary: Recombinant mature human CPS1 performs the ammonia-dependent reaction.

Reason: Actual author-uploaded Methods/Results describe human residues 40–1500 with a 28-residue His tag and coupled/partial-reaction kinetic assays. These are not tests of registered products 2 or 3. A listed corrigendum, PMID:30740827, was authenticated but its operative text was not recovered; its scope is not assumed harmless. Independent 2015 and native-enzyme evidence also establish the activity.

Summary: Retain the positive recombinant-human activity annotation with explicit access limits.

Reason: The complete PMID:24813853 abstract and publisher Introduction describe recombinant human CPS1 and functional effects of central-domain variants. Full Methods/Results were not recovered. The existing experimental annotation is consistent with independent human biochemical evidence, so incomplete access is not grounds to remove it.

Summary: Retain the ortholog-supported peripheral cell-surface pool as non-core.

Reason: The current mouse Q8C196 donor has IDA evidence from PMID:34799567. Nonpermeabilized primary mouse hepatocyte imaging and membrane-fraction pull-down/MS support a cell-surface CPS1 pool. Human HepG2 infection experiments in that study do not themselves image endogenous human surface CPS1. The transfer is retained at this qualified ortholog scope, without inferring a transmembrane topology, an autonomous receptor core or direct purified-human binding from the lysate assay.

Summary: Human mitochondrial proteomics directly identifies CPS1.

Reason: The authentic MitoCoP workbook contains CPS1 in sheets A and B, including the P31327/-3/-2 majority-protein group and mitochondrial classification. The pooled peptide assignment does not resolve which alternative product was measured. This supports the organelle-level HTP annotation without assigning equal localization or activity to every product.

Summary: Potassium binding supports the human CPS1 catalytic architecture.

Reason: The human structural and biochemical source explicitly identifies potassium at the functional site. This is distinct from incidental crystallization ions and from the independently supported catalytic magnesium.

Summary: N-acetylglutamate is the defined allosteric small-molecule ligand.

Reason: The ligand-bound human structures resolve NAG in the C-terminal activation pocket. GO:0072341 specifies the modified-amino-acid interaction more informatively than generic small-molecule binding; the replacement is a semantic ligand refinement, not an asserted typed child relationship.

Proposed replacements: modified amino acid binding

Summary: Refine experimentally resolved metal binding to catalytic magnesium.

Reason: The actual human structural entries identify catalytic magnesium, and GO:0000287 is an authenticated direct child of GO:0046872. Potassium is independently represented by the existing source-specific row. This does not assert that magnesium is the only ion that CPS1 can bind.

Proposed replacements: magnesium ion binding

Summary: The vascular association is positive but its exact CPS1 participation remains unresolved.

Reason: The complete PMID:14718356 abstract reports human T1405N genotype associations with nitric-oxide metabolites and measured forearm-blood-flow responses to bradykinin and nitroprusside. These are positive functional vascular observations, not merely a gene-expression marker. The full original Methods/Results were not recovered, and the accessed evidence does not separate a CPS1-performed contribution to smooth-muscle relaxation from an indirect metabolic or vascular-reactivity association. UNDECIDED records that unresolved source-to-process scope; it neither accepts vasodilation participation nor infers that every genotype association is overannotation.

Summary: Human CPS1 deficiency supports the performed carbamoyl-phosphate synthesis step.

Reason: The actual clinical cohort and structural discussion in PMID:21120950 link CPS1 defects with impaired nitrogen disposal and the established reaction. They do not show complete catalytic abolition for every reported variant. CPS1 nevertheless directly performs the biosynthetic step, independently verified with recombinant human enzyme.

Summary: CPS1 contributes to cellular ammonia handling through its own catalytic reaction.

Reason: The source is a human deficiency/variant cohort rather than a controlled acute ammonium-exposure experiment. CPS1 consumes ammonia in its synthetic reaction, and defective activity causes hyperammonemia. This supports a bounded metabolic-response interpretation, but the broad response term is secondary to the precisely established biosynthetic reaction.

Summary: The CPS1 catalytic reaction is explicitly localized to mitochondrial matrix.

Reason: The live R-HSA-70555 reaction identifies the target CPS1 catalyst and matrix compartment. This is direct reaction-location context and agrees with human biochemical and targeting evidence.

Summary: Retain the location of the CPS1 product in its expression model.

Reason: R-HSA-9959874 reaches the target-labelled mitochondrial CPS1 product. The assertion concerns that product location; it does not mean CPS1 catalyzes its own gene expression.

Summary: The demonstrated female-specific genotype–homocysteine association does not establish CPS1 participation in a homocysteine reaction or pathway.

Reason: The accessed PMID:20031578 Results report a genotype–plasma-homocysteine association in 13,974 women, including independent female-specific replication. Its complete available Discussion explicitly leaves the underlying biological processes for further experiments. Those positive observations identify an association, not a CPS1-performed homocysteine-metabolic step; assigning GO:0050667 therefore exceeds the experimentally resolved scope. This judgment follows the reported Results and their stated limitation, not a requirement to refute the association or a categorical exclusion of mitochondrial enzymes. Full Methods were not recovered, so no claim is made to have excluded every possible full-paper experiment. The original IDA source code remains unchanged; its more specific assay interpretation is unresolved.

Summary: N-acetylglutamate binding is independently established, while this citation remains limited.

Reason: NAG is a modified amino acid directly bound by human CPS1. The accessed PMID:20031578 text discusses the NAG-binding-site context as background rather than supplying a new CPS1 binding assay, and full Methods remain unavailable. Retain the biologically correct existing annotation using the independently read human structural evidence while explicitly qualifying the original source attribution.

Summary: Reduced patient enzyme activity supports the carbamoyl-phosphate synthesis role.

Reason: The complete PMID:7416778 abstract reports approximately half the mean control CPS1 activity in a duodenal biopsy, not complete loss. Native enzyme measurements and the independently established reaction support the process despite unavailable full original text.

Summary: The human cloning paper supports CPS1 participation in ureagenesis.

Reason: The complete PMID:1840546 abstract identifies the human CPS1 precursor and its urea-cycle context. Direct human catalytic work independently resolves the step, so the NAS assertion is retained without treating cloning alone as a complete mechanistic assay.

Summary: The splice defect reduces, rather than abolishes, measured human CPS1 activity.

Reason: The actual PMID:8486760 original reports approximately 11% of control liver CPS1 activity, reduced protein/RNA and abnormal splicing. This is positive evidence for the catalytic role and a disease-associated impairment; complete abolition is not claimed.

Summary: The human CPS1 variant supports the established enzymatic role.

Reason: PMID:9711878 identifies the Thr544Met disease-associated variant. The complete abstract does not report the later recombinant bicarbonate-Km experiment, which belongs to PMID:23649895. Retain the positive catalytic annotation with that source distinction and without assuming every patient allele is catalytically null.

Summary: CPS1 supplies carbamoyl phosphate to the citrulline biosynthetic pathway.

Reason: GO:0019240 covers a pathway, not only the final ornithine-transcarbamylase reaction. CPS1 performs the upstream synthesis that supplies carbamoyl phosphate, and PMID:21120950 explicitly describes intestinal citrulline production. The original PMID:14718356 is available only as a complete abstract describing vascular/genotype associations, so it is not represented as a direct pathway assay. The positive physiological pathway role is retained as secondary to the hepatic urea-cycle core.

Summary: The triglyceride-catabolism annotation cannot be resolved from the available clinical abstract.

Reason: The complete PMID:9711878 abstract foregrounds CPS1 deficiency and a missense variant. Full original clinical/biochemical details were not recovered. That is insufficient to conclude that the curator misattributed a triglyceride observation or that the complete paper excludes it; the inherited confident removal is replaced with explicit uncertainty.

Summary: Retain the observed LPS-induced CPS1 change and release at the experimental scope.

Reason: The complete PMID:15897806 abstract reports N-terminal fragmentation in baboon liver and LPS-induced circulating CPS1 in healthy humans and baboons. GO:0032496 includes changes in state, secretion and enzyme production; the existing positive response annotation therefore need not imply a protective or signaling action. Fragment release as a biomarker is retained distinctly from the separate rat ureagenic-output response.

Summary: Retain the positive CPS1 association with native and crosslinked human nucleoids.

Reason: The actual PMID:18063578 Methods, Results and Table 1 identify CPS1 NP_001866 as a class-I protein: peptide counts 5/21 in native TFAM/mtSSB preparations and 21/0 in crosslinked preparations. The earlier claim that CPS1 was not recovered with crosslinked nucleoids is incorrect. The authors discuss abundant metabolic proteins and possible indirect association; a non-core nucleoid location does not imply autonomous DNA binding or a proven maintenance mechanism.

Summary: The nitric-oxide association leaves the precise target contribution unresolved.

Reason: PMID:14718356 reports a positive human T1405N genotype association with nitric-oxide metabolites and agonist-induced vascular responses. CPS1 performs precursor synthesis upstream of citrulline/arginine, while GO:0046209 includes pathways as well as individual reactions. The complete original was not recovered, leaving unresolved whether the experimentally assigned role represents that performed precursor contribution within the nitric-oxide pathway or an indirect genotype/metabolite association. Neither direct NO-synthase activity nor pathway participation based only on a possible nitrogen origin is asserted. UNDECIDED preserves the specific uncertainty rather than declaring the positive measurements false.

Summary: Positive Raf-family interactions support MAP kinase kinase kinase binding.

Reason: The exact IntAct records report positive yeast two-hybrid interactions of a CPS1 420–771 fragment with defined RAF1 or ARAF regions. Both partners have independently supported MAP kinase kinase kinase activity, so GO:0031435 identifies the measured partner class without assigning kinase activity to CPS1. Fragment and assay context remain explicit; no full-length native mitochondrial interaction or signaling mechanism is inferred.

Proposed replacements: mitogen-activated protein kinase kinase kinase binding

Summary: Positive Raf-family interactions support MAP kinase kinase kinase binding.

Reason: The exact IntAct records report positive yeast two-hybrid interactions of a CPS1 420–771 fragment with defined RAF1 or ARAF regions. Both partners have independently supported MAP kinase kinase kinase activity, so GO:0031435 identifies the measured partner class without assigning kinase activity to CPS1. Fragment and assay context remain explicit; no full-length native mitochondrial interaction or signaling mechanism is inferred.

Proposed replacements: mitogen-activated protein kinase kinase kinase binding

Summary: Broad metal binding is correct despite an unresolved current ARBA branch match.

Reason: The genuine current combined record cites ARBA00028199 and IPR011761. No present ARBA condition set matches the target features, so that branch provenance remains unresolved rather than being reconstructed from a guessed historical rule. The domain mapping and directly read human magnesium/potassium evidence independently support the broad biological assertion.