GAMT

Summary: The BioPlex GAMT–FARS2 association is real but does not specify a molecular function.

Reason: The retained original BioPlex2 table contains the exact Q14353–O95363 pair at line 19992. The inspected source describes tagged human ORFeome proteins and affinity-purification mass spectrometry in HEK293T cells; this establishes a candidate co-complex association, not direct binary binding or a functional GAMT–FARS2 mechanism. Remove the uninformative protein-binding annotation under the current policy while preserving the positive pair evidence; no specific replacement activity is justified by this screen alone.

Summary: The HuRI GAMT–RAB24 pair does not establish a more informative GAMT function.

Reason: The authentic retained HuRI dataset contains Q14353-1 with Q969Q5 in array, prey-pooling and validated two-hybrid records. Human ORFs were tested in a yeast host; the target clone suffix is preserved as source provenance without rewriting the unsuffixed incoming GOA target. These positive binary interaction records do not establish GAMT as a GTPase regulator, cargo adapter or another defined functional activity. Remove generic protein binding as uninformative, not because the interaction is false.

Summary: The tested GAMT–TRIM39-2 pair supports binding without a defined GAMT molecular role.

Reason: Original HuRI records explicitly pair Q14353-1 with Q9HCM9-2 and preserve the TRIM39 isoform suffix, with array, prey-pooling and validated two-hybrid records from screens 2 and 4. These human ORF interactions in yeast do not demonstrate that GAMT performs ubiquitin transfer, substrate recognition or another specific molecular function. Remove the bare protein-binding annotation for lack of functional information while retaining the exact positive pair and construct scope.

Summary: BioPlex3 supports a GAMT–FARS2 co-association without defining a functional role.

Reason: The original BioPlex3 293T table contains Q14353–O95363 at line 63913. The exact pair is absent from the inspected HCT116 network, which is a dataset observation rather than proof of biological absence. Tagged-bait affinity-purification mass spectrometry detects co-associations and does not by itself establish a direct binding interface or a specific GAMT activity. Remove generic protein binding as uninformative while preserving the positive 293T evidence; do not invent a catalytic-regulatory replacement.

Summary: Curated phylogenetic evidence supports a nonexclusive nuclear localization, retained as non-core.

Reason: The actual nuclear IBD at PTN001282244 lies on the exact human Q14353 lineage. Its literal yeast RMT2 donor has experimental nuclear-localization records, including an authentic abstract reporting immunofluorescence and subcellular fractionation. This positive ancestral placement supports retention; GO_REF:0000033 identifies the inference method rather than supplying a human localization experiment. A central biochemical role for a human nuclear GAMT pool is not established, so retain the nuclear annotation as non-core while the verified cytosolic reaction defines the core. Fungal donor substrate specialization does not by itself demonstrate target-specific loss of the inherited compartment, and cytosolic evidence is nonexclusive.

Summary: GAMT’s verified cytosolic reaction supports refinement of the broad cytoplasmic location.

Reason: GAMT is explicitly assigned to cytosol in the resolved human Reactome catalyst R-HSA-71276. Refine the broad cytoplasm annotation to GO:0005829 cytosol, which has a verified direct part_of relationship to GO:0005737. The actual PTN001282244 cytoplasmic IBD lies on the human target lineage and its experimental fungal donors remain legitimate; the refinement uses specific target evidence and does not allege faulty ancestry or localization loss. Cytosolic activity is nonexclusive, so the separately supported nuclear annotation is retained.

Proposed replacements: cytosol

Summary: The human Reactome catalyst is explicitly located in the cytosol.

Reason: The official R-HSA-71286 reaction identifies GAMT catalyst entity R-HSA-71276, linked to human UniProt Q14353 and assigned to cytosol. The location belongs to the resolved enzyme participant, not only the reaction compartment. This is a supported site of GAMT creatine synthesis and does not imply an exclusive location or activity for every natural splice product.

Summary: GAMT performs the biosynthetic methyl-transfer step of creatine metabolism.

Reason: R-HSA-71288 includes the two-reaction synthesis of creatine before transport, phosphorylation and spontaneous creatinine formation. GAMT itself catalyses guanidinoacetate methylation in the linked human R-HSA-71286 reaction; the other downstream metabolic operations are not GAMT activities. Refine the broad process to GO:0006601 creatine biosynthetic process, a verified is_a descendant of GO:0006600.

Proposed replacements: creatine biosynthetic process

Summary: The ancestral assertion supports GAMT participation in creatine synthesis.

Reason: GAMT performs the second chemical step of creatine biosynthesis by methylating guanidinoacetate, rather than merely being necessary for an indirect clinical outcome. The actual biosynthesis IBD at PTN001285367 lies on the exact human lineage and its current/main/literal mouse, rat and human donors agree. Direct human reaction/product evidence independently supports the process; the human self-donor is valid.

Summary: The human assay detects the product of GAMT-mediated creatine synthesis.

Reason: The original PMID:8651275 activity experiment separates and measures radiolabeled creatine formed by methyl transfer to guanidinoacetate in human liver preparations. This directly places GAMT in creatine biosynthesis. The reduced patient activity supports the defect, while the reaction/product assay supplies the positive process evidence.

Summary: The electronic pathway assignment agrees with direct creatine-product formation.

Reason: The ARBA00087325/UniPathway UPA00104 assignment describes the established biosynthetic role of GAMT. The human enzyme directly makes creatine from guanidinoacetate using SAM, demonstrated in the human liver assay and represented as a catalyst in the official human Reactome reaction. This is catalytic process participation, not an inference from disease necessity alone.

Summary: The cited human GAMT record explicitly describes its creatine-synthesis reaction.

Reason: The complete authentic abstract of PMID:9325156 identifies GAMT as the SAM-dependent guanidinoacetate-to-creatine enzyme and maps the human gene. This traceable statement agrees with directly inspected human activity in PMID:8651275 and the human Reactome catalytic step. The mouse jittery candidate analysis does not show a coding GAMT mutation and is not being used as additional human functional evidence.

Summary: The specific evidence underlying the contraction TAS remains unresolved.

Reason: The complete accessible PMID:8547310 abstract describes cloned human GAMT cDNA and a child with low creatine, hypotonia and a movement disorder. It does not expose the experiment or interpretation underlying this muscle-contraction TAS. The independently demonstrated GAMT reaction supplies creatine for energy buffering; that chemistry and the clinical phenotype alone do not settle whether the original source supports participation in GO-defined force generation. Because the full original supporting the assignment was not recovered, retain source-specific uncertainty. This is not a confident negative about GAMT participation or a claim that no experiment could occur in a cloning paper.

Summary: The established reaction is specifically guanidinoacetate N-methylation.

Reason: The authentic PMID:9325156 abstract explicitly identifies SAM-dependent conversion of guanidinoacetate to creatine. The accessible source therefore supports the specific activity, corroborated by the directly inspected human-liver radiomethyl-transfer assay in PMID:8651275. Replace the broad methyltransferase term with its verified is_a descendant GO:0030731; subscription Methods of 9325156 were not independently read.

Proposed replacements: guanidinoacetate N-methyltransferase activity

Summary: The Reactome reaction identifies the specific GAMT catalytic activity.

Reason: The official human R-HSA-71286 record explicitly consumes SAM and guanidinoacetate and produces SAH, creatine and a proton, with catalyst R-HSA-71276 resolving to Q14353. This is more specific than methyltransferase activity. GO:0030731 describes exactly this reaction and is a verified is_a descendant of GO:0008168. The event was read through official HTML, not an unavailable ContentService JSON response.

Proposed replacements: guanidinoacetate N-methyltransferase activity

Summary: GAMT conserves the SAM-dependent methylation of guanidinoacetate to creatine.

Reason: The human liver assay directly measures radiolabeled methyl transfer from SAM to guanidinoacetate and chromatographically identifies creatine; patient/control and substrate-free measurements support the specific reaction. The actual PAINT activity assertion at PTN001285367 lies on the exact human Q14353 target lineage, and current incoming, literal IBD and retained-main donor contexts agree. The target self-donor is legitimate experimental grounding, not circularity.

Summary: The electronic catalytic annotation agrees with the verified human reaction.

Reason: The IEA combines InterPro IPR016550, RHEA:10656 and EC:2.1.1.2. The official GO:0030731 definition specifies SAM + guanidinoacetate to SAH + creatine + H+, which is directly supported by the human-liver activity/product assay in PMID:8651275 and the official human Reactome reaction. No contradictory enzymatic mapping was identified.

Summary: Patient and control liver assays directly support guanidinoacetate methyltransferase activity.

Reason: The inspected original pages 915–917 describe fractionated/dialysed human liver extracts, radiolabeled SAM, guanidinoacetate-dependent methyl transfer and chromatographic separation of creatine. The two deficient patients had strongly reduced activity relative to controls; substrate-free blanks, reference enzymes, cautery effects and mixing controls were considered. This directly establishes the molecular reaction without inferring it solely from clinical creatine deficiency.