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60ad85f700002947 de novo IMP biosynthetic process Mouse

Now let me review the GO-CAM model for 'de novo' IMP biosynthetic process (Mouse) with ID gomodel:60ad85f700002947 based on all the information I've gathered.

GO-CAM Model Review: 'de novo' IMP biosynthetic process (Mouse)

Model Summary

  • Model ID: gomodel:60ad85f700002947
  • Title: 'de novo' IMP biosynthetic process (Mouse)
  • Taxon: Mouse (NCBITaxon:10090)
  • Status: Production
  • Sourced from: gomodel:R-HSA-73817

Review of Biological Content

This GO-CAM model represents the 'de novo' IMP (inosine monophosphate) biosynthetic process in mouse. The model depicts the pathway for purine biosynthesis, specifically focusing on the enzymatic steps leading to IMP production.

Pathway Representation

The model correctly captures the sequence of enzymatic reactions in the 'de novo' IMP biosynthetic pathway. Each enzyme is properly annotated with its molecular function and is shown to participate in the GO:0006189 ('de novo' IMP biosynthetic process). The causal connections between activities use the appropriate predicate "RO:0002413" (provides input for), showing the sequential nature of the pathway.

The pathway includes the following key enzymes: 1. Ppat (amidophosphoribosyltransferase activity) 2. Gart (phosphoribosylamine-glycine ligase, phosphoribosylglycinamide formyltransferase, and phosphoribosylformylglycinamidine cyclo-ligase activities) 3. Pfas (phosphoribosylformylglycinamidine synthase activity) 4. Paics (phosphoribosylaminoimidazolesuccinocarboxamide synthase activity) 5. Adsl (adenylosuccinate lyase activity) 6. Atic (phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase activities)

Evidence Quality

The model uses appropriate evidence codes for the assertions: - ECO:0000314 (direct assay evidence used in manual assertion) - ECO:0000315 (mutant phenotype evidence used in manual assertion) - ECO:0000266 (sequence orthology evidence used in manual assertion)

All assertions are supported by literature references, primarily from the following publications: - PMID:6480832 - Studies on adenylosuccinate lyase and muscle function - PMID:26588576 - Referenced for orthology-based assertions - PMID:26144885 - Evidence for ATIC function - PMID:6327016 - Evidence for amidophosphoribosyltransferase - PMID:8299947 - Evidence for GART activity - PMID:27590927 - Evidence for PFAS and PAICS functions - PMID:2183217 - Evidence for GART function

Molecular Functions and Biological Process

All entities in the model are correctly annotated with appropriate molecular function terms: - GO:0004044 - amidophosphoribosyltransferase activity - GO:0004637 - phosphoribosylamine-glycine ligase activity - GO:0004644 - phosphoribosylglycinamide formyltransferase activity - GO:0004641 - phosphoribosylformylglycinamidine cyclo-ligase activity - GO:0004642 - phosphoribosylformylglycinamidine synthase activity - GO:0004639 - phosphoribosylaminoimidazolesuccinocarboxamide synthase activity - GO:0070626 - (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity - GO:0004643 - phosphoribosylaminoimidazolecarboxamide formyltransferase activity - GO:0003937 - IMP cyclohydrolase activity

All activities are properly connected to the biological process GO:0006189 ('de novo' IMP biosynthetic process).

Technical Quality Assessment

Model Structure

  1. Activity Flow: The model correctly represents the sequential flow of enzymatic activities with appropriate causal connections using "RO:0002413" (provides input for).

  2. Cellular Location: Two of the enzymes (Gart activities) are correctly annotated with the cellular location GO:0005829 (cytosol), which is consistent with what is known about this pathway.

  3. Gene Products: The model uses the correct MGI IDs for the mouse gene products:

  4. MGI:MGI:2387203 (Ppat)
  5. MGI:MGI:95654 (Gart)
  6. MGI:MGI:2684864 (Pfas)
  7. MGI:MGI:1914304 (Paics)
  8. MGI:MGI:103202 (Adsl)

  9. MGI:MGI:1351352 (Atic)

  10. Bifunctional Enzymes: The model correctly represents bifunctional enzymes. Particularly noteworthy is the representation of Atic, which has two distinct molecular functions (phosphoribosylaminoimidazolecarboxamide formyltransferase and IMP cyclohydrolase activities) that catalyze the last two steps of the pathway.

  11. Causal Relationships: All causal relationships between activities are properly represented with the appropriate predicate "RO:0002413" (provides input for).

Compliance with GO-CAM Best Practices

The model follows GO-CAM best practices by:

  1. Using appropriate molecular function terms for each enzyme
  2. Connecting all molecular functions to the relevant biological process
  3. Using appropriate evidence codes and citations
  4. Properly representing spatial information where known (cytosol location)
  5. Correctly handling multi-functional enzymes

Suggestions for Improvement

While the model is already of high quality, there are a few minor suggestions for potential improvement:

  1. Additional Cellular Locations: Consider annotating all enzymes with their subcellular locations if this information is available.

  2. Chemical Entities: The model could be enhanced by including the chemical entities (substrates and products) for each reaction step, which would make the pathway more understandable to users.

  3. Regulation Information: If known, regulatory information about how this pathway is controlled could be added using appropriate causal predicates like "RO:0002629" (directly positively regulates) or "RO:0002630" (directly negatively regulates).

Conclusion

The GO-CAM model gomodel:60ad85f700002947 accurately represents the 'de novo' IMP biosynthetic process in mouse. The model correctly depicts the sequential enzymatic steps in this pathway, with appropriate molecular functions, biological process annotations, and causal connections. The evidence provided supports the assertions in the model, and the model complies with GO-CAM best practices. The model is clear, scientifically accurate, and provides a useful representation of this important metabolic pathway.