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60d5209a00001406 de novo XMP biosynthetic process Mouse

Now, let's review the GO-CAM model "gomodel:60d5209a00001406" titled "'de novo' XMP biosynthetic process (Mouse)". This is a production-status model for the mouse (NCBITaxon:10090).

Model Overview

This GO-CAM represents the 'de novo' XMP biosynthetic process in mouse, detailing the enzymatic activities and molecular functions involved in this pathway. The model was sourced from gomodel:R-HSA-73817 and was created/contributed by ORCID:0000-0001-7476-6306 on July 7, 2021.

Pathway Structure and Connectivity

The model accurately represents the 'de novo' XMP biosynthetic pathway with: - 11 distinct activities representing different enzymatic steps - All activities are properly connected via causal associations using the appropriate "RO:0002413" predicate (provides input for) - The activities form a coherent, linear pathway where each enzymatic step feeds into the next

The pathway flow appears to be: 1. PPAT (amidophosphoribosyltransferase) → 2. GART (phosphoribosylamine-glycine ligase) → 3. GART (phosphoribosylglycinamide formyltransferase) → 4. PFAS (phosphoribosylformylglycinamidine synthase) → 5. GART (phosphoribosylformylglycinamidine cyclo-ligase) → 6. PAICS (phosphoribosylaminoimidazole carboxylase) → 7. PAICS (phosphoribosylaminoimidazolesuccinocarboxamide synthase) → 8. ADSL ((S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase) → 9. ATIC (phosphoribosylaminoimidazolecarboxamide formyltransferase) → 10. ATIC (IMP cyclohydrolase) → 11. IMPDH1/IMPDH2 (IMP dehydrogenase)

Evidence and References

The model includes appropriate evidence codes with references: - ECO:0000314 (direct assay evidence) - ECO:0000315 (mutant phenotype evidence) - ECO:0000266 (sequence orthology evidence)

Each activity is supported by at least one reference, primarily from peer-reviewed publications (PMIDs).

Strengths of the Model

  1. The activities are properly placed in the context of the biological process "GO:0097294" ('de novo' XMP biosynthetic process)
  2. Appropriate molecular functions are assigned to each gene product
  3. The causal connections between activities form a coherent pathway
  4. Subcellular localization (cytosol) is specified where relevant
  5. Multi-functional proteins (like GART with three distinct activities) are properly represented

Conformance to GO-CAM Best Practices

The model appears to follow GO-CAM best practices: - Each activity is properly enabled by a specific gene product - The correct causal relationship predicate (RO:0002413 "provides input for") is used throughout - Each connection has appropriate evidence - The activities accurately represent the known enzymatic steps in this pathway

Potential Issues and Recommendations

I did not identify any significant issues with the model. It represents a well-characterized metabolic pathway and adheres to GO-CAM best practices. The pathway is complete from the initial steps through to XMP production.

For additional thoroughness, the curator might consider: 1. Checking if any newer literature has emerged since 2021 that might further validate or refine this pathway 2. Ensuring that all relevant cellular compartments are correctly specified for each activity (currently only cytosol is mentioned for some activities)

Conclusion

This is a high-quality GO-CAM model that accurately represents the 'de novo' XMP biosynthetic process in mouse. The activities are properly connected, each with appropriate evidence, and the model provides a clear illustration of this metabolic pathway. No significant revisions appear necessary.

You can view this model at: https://bioregistry.io/go.model:60d5209a00001406