Skip to content

6516135700001077 Heme B biosynthetic process Mouse

Now, let me review the GO-CAM model for "Heme B biosynthetic process (Mouse)" based on the information provided and best practices.

Review of GO-CAM Model gomodel:6516135700001077

Model Overview

This GO-CAM model represents the heme B biosynthetic process in mouse (Mus musculus), showing the complete pathway from initial substrates to the final heme B product. The model includes 9 activities carried out by different enzymes, with appropriate causal connections between them.

Strengths of the Model

  1. Complete Pathway Representation: The model captures the entire heme B biosynthesis pathway from the initial synthesis of 5-aminolevulinate through to the formation of ferroheme b.

  2. Detailed Molecular Context: Each activity correctly specifies:

  3. The molecular function (MF) of the enzyme
  4. The biological process (BP) it's part of (heme B biosynthetic process)
  5. The cellular component (CC) where it occurs
  6. Input and output molecules with proper CHEBI identifiers

  7. Appropriate evidence with PMID references

  8. Causal Connections: The model uses the "provides input for" (RO:0002413) predicate appropriately to connect activities in a sequential manner that reflects the biological flow of the pathway.

  9. Cellular Localization: The model correctly represents the subcellular locations where each step occurs (cytosol, mitochondrial matrix, mitochondrial intermembrane space, mitochondrial membrane).

  10. Species Specificity: The model is properly specified for mouse, using MGI IDs for gene products.

  11. Evidence Support: Each activity is well-supported by multiple evidence codes (ECO terms) and literature references (PMIDs).

Specific Aspects to Note

  1. Transporter Activity: The model includes a heme B transmembrane transporter activity (GO:0170003) enabled by PR:B2RXV4-2 (mFLVCR1/isom2 Mmus) that occurs in the mitochondrial membrane, which follows the proper pattern for annotating transporters.

  2. Input/Output Annotation: The model properly uses the has_input and has_output relations to show the substrates and products of each enzymatic reaction.

  3. Subcellular Compartments: The model accurately represents the compartmentalization of the pathway across mitochondrial and cytosolic compartments, which is crucial for heme biosynthesis.

Areas for Improvement

  1. Transport Steps: While the model includes the final heme B transport step, it could potentially benefit from explicitly modeling the transport of intermediates between cellular compartments, if supported by evidence.

  2. Complex Representation: If any of these enzymes function as part of complexes, that information could be represented according to the complex annotation guidelines.

  3. Regulatory Processes: The model focuses on the core enzymatic steps but doesn't include regulatory aspects of heme biosynthesis. Adding these if evidence exists would enhance the model's comprehensiveness.

Scientific Accuracy

The model accurately represents the canonical heme B biosynthetic pathway as described in biochemistry textbooks and the scientific literature. The sequence of reactions, enzyme activities, substrates/products, and cellular locations align with current knowledge of this pathway.

Overall Assessment

This is a high-quality GO-CAM model that accurately represents the heme B biosynthetic process in mice. It follows GO-CAM best practices and provides a comprehensive and well-evidenced representation of this important metabolic pathway. The model is parsimonious while capturing the essential features of the pathway, making it easy for humans to understand.

The model passes QC review and is appropriate for production status.