Skip to content

6516135700000380 Heme A biosynthetic process Mouse

Now I have a good understanding of the model. Let me review the GO-CAM model for "Heme A biosynthetic process (Mouse)" with ID gomodel:6516135700000380.

Review of GO-CAM Model: Heme A biosynthetic process (Mouse)

Model Overview

This model represents the heme A biosynthetic pathway in mouse (NCBITaxon:10090). It includes ten connected activities performed by different gene products, including the conversion of various metabolites in the pathway leading to the synthesis of heme A.

Biological Content Assessment

The model accurately represents the heme A biosynthetic pathway, which begins with the synthesis of 5-aminolevulinate and proceeds through multiple enzymatic steps to form heme A, an essential cofactor for cytochrome c oxidase in the mitochondrial respiratory chain.

The pathway flow appears to be correctly represented, with appropriate causal connections (RO:0002413 - provides input for) between the activities in the expected sequential order:

  1. ALAS1 (5-aminolevulinate synthase) → ALAD (porphobilinogen synthase)
  2. ALAD → HMBS (hydroxymethylbilane synthase)
  3. HMBS → UROS (uroporphyrinogen-III synthase)
  4. UROS → UROD (uroporphyrinogen decarboxylase)
  5. UROD → CPOX (coproporphyrinogen oxidase)
  6. CPOX → PPOX (protoporphyrinogen oxidase)
  7. PPOX → FECH (ferrochelatase)
  8. FECH → COX10 (protoheme IX farnesyltransferase)
  9. COX10 → COX15 (oxidoreductase)

Evaluation of GO-CAM Best Practices

  1. Molecular Functions: Each activity has an appropriate molecular function term assigned:
  2. GO:0003870 (5-aminolevulinate synthase activity)
  3. GO:0004655 (porphobilinogen synthase activity)
  4. GO:0004418 (hydroxymethylbilane synthase activity)
  5. GO:0004852 (uroporphyrinogen-III synthase activity)
  6. GO:0004853 (uroporphyrinogen decarboxylase activity)
  7. GO:0004109 (coproporphyrinogen oxidase activity)
  8. GO:0004729 (oxygen-dependent protoporphyrinogen oxidase activity)
  9. GO:0004325 (ferrochelatase activity)
  10. GO:0008495 (protoheme IX farnesyltransferase activity)

  11. GO:0016627 (oxidoreductase activity, acting on the CH-CH group of donors)

  12. Cellular Components: Each activity is assigned an appropriate cellular component:

  13. Mitochondrial matrix (GO:0005759)
  14. Cytosol (GO:0005829)

  15. Mitochondrial intermembrane space (GO:0005758)

  16. Biological Process: All activities are correctly part of the heme A biosynthetic process (GO:0006784).

  17. Molecule Inputs and Outputs: The model appropriately represents substrates and products for each reaction:

  18. Chemical entities are correctly represented as CHEBI terms

  19. Inputs and outputs are connected in a logical way between sequential reactions

  20. Evidence: Each activity has appropriate evidence codes and references:

  21. ECO:0000314 (direct assay evidence used in manual assertion)
  22. ECO:0000315 (mutant phenotype evidence used in manual assertion)
  23. ECO:0000266 (sequence orthology evidence used in manual assertion)

  24. ECO:0000316 (genetic interaction evidence used in manual assertion)

  25. Causal Relations: Appropriate causal connections (RO:0002413 - provides input for) are used to connect sequential activities in the pathway.

Areas for Improvement

  1. Visual Complexity: This model has no obvious issues, but with 10 activities and numerous molecular inputs/outputs, it could potentially be complex to visualize. However, the sequential nature makes it understandable.

  2. Evidence Documentation: All activities have evidences attached, which is excellent. Most evidence is supported by primary literature (PMIDs).

  3. Complex Representation: No protein complexes appear to be involved in this pathway, so the complex annotation guidelines do not apply directly to this model.

Conclusion

The GO-CAM model for "Heme A biosynthetic process (Mouse)" (gomodel:6516135700000380) is a high-quality representation of the heme A biosynthetic pathway. It follows all the GO-CAM best practices, with:

  • Accurate representation of the biological process
  • Appropriate molecular functions for each gene product
  • Correct cellular locations
  • Well-documented evidence
  • Logical causal connections between activities
  • Appropriate molecule inputs and outputs

The model is biologically accurate and appears to be consistent with the literature on heme A biosynthesis. No significant issues or improvements are needed.

You can view this model at: https://bioregistry.io/go.model:6516135700000380