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Based on my examination of the GO-CAM model and relevant literature, let me provide a thorough review.

Review of GO-CAM Model: gomodel:6246724f00000078

Model Overview

Title: Glucuronate catabolic process to xylulose 5-phosphate (Mouse)
Taxon: Mouse (NCBITaxon:10090)
Status: Production
Source: Derived from gomodel:R-HSA-5661270

Pathway Description

This GO-CAM model represents the D-glucuronate catabolic pathway that converts D-glucuronate to D-xylulose 5-phosphate in mouse. This is a well-documented metabolic pathway that consists of a series of enzymatic reactions catalyzed by specific proteins.

Chain of Activities

The model correctly shows the following sequential enzymatic reactions:

  1. Akr1a1 (MGI:MGI:1929955) - L-glucuronate reductase activity (GO:0047939)
  2. Converts D-glucuronate to L-gulonate
  3. Located in cytosol (GO:0005829)

  4. Provides input for the next reaction (Cryl1)

  5. Cryl1 (MGI:MGI:1915881) - L-gulonate 3-dehydrogenase activity (GO:0050104)

  6. Converts L-gulonate to 3-dehydro-L-gulonate

  7. Located in cytosol (GO:0005829)

  8. Dcxr (MGI:MGI:1915130) - L-xylulose reductase (NADPH) activity (GO:0050038)

  9. Converts to xylitol
  10. Located in cytosol (GO:0005829)

  11. Provides input for the next reaction (Sord)

  12. Sord (MGI:MGI:98266) - D-xylulose reductase activity (GO:0046526)

  13. Converts to D-xylulose
  14. Located in cytosol (GO:0005829)

  15. Provides input for the next reaction (Xylb)

  16. Xylb (MGI:MGI:2142985) - D-xylulokinase activity (GO:0004856)

  17. Phosphorylates D-xylulose to produce D-xylulose 5-phosphate (CHEBI:57737)
  18. Located in cytosol (GO:0005829)

Quality Check

Strengths of the Model:

  1. Complete pathway representation: The model correctly represents all the key enzymatic steps in the glucuronate catabolic pathway from D-glucuronate to D-xylulose 5-phosphate.

  2. Correct molecular functions: All proteins have been assigned the appropriate molecular functions based on their enzymatic activities.

  3. Evidence citations: Each activity is supported by appropriate evidence codes and literature references.

  4. Proper cellular locations: All activities are correctly annotated to occur in the cytosol.

  5. Causal relationships: The model correctly uses the "provides input for" (RO:0002413) relationship to connect the sequential enzymatic reactions.

  6. Output annotation: The final product D-xylulose 5-phosphate is correctly annotated as the output of the Xylb enzyme.

Areas for Improvement:

  1. Missing reaction intermediates: While the model correctly shows the activity chain, it does not explicitly annotate all the intermediate metabolites in the pathway. For completeness, it could include:
  2. The conversion of 3-dehydro-L-gulonate to L-xylulose (spontaneous decarboxylation)

  3. The specific annotation of xylitol as an intermediate

  4. Incomplete evidence: Some of the causal associations lack explicit evidence codes and references. While the individual activities have evidence, the connections between them would benefit from literature support.

  5. Compartmentalization details: While all activities are correctly placed in the cytosol, for more complex models, additional details about potential membrane associations or protein-protein interactions could be valuable.

Biological Accuracy

The model is biologically accurate and consistent with the current understanding of the D-glucuronate catabolic pathway in mammals. The enzymes and their activities are correctly represented, and the sequential flow of reactions is properly modeled.

This pathway is part of the uronic acid metabolism and represents an important route for the catabolism of D-glucuronate, which can be derived from the breakdown of proteoglycans, glycosaminoglycans, and other carbohydrates.

Conclusion

This GO-CAM model (gomodel:6246724f00000078) accurately represents the D-glucuronate catabolic pathway leading to D-xylulose 5-phosphate in mouse. The model follows GO-CAM best practices in terms of structure and annotation quality. Each enzymatic step is properly represented, with appropriate molecular functions assigned to the correct gene products, and the sequential flow of the pathway is correctly modeled using causal relationships.

The model is ready for production use and provides a valuable resource for researchers interested in carbohydrate metabolism. Minor improvements could be made by annotating intermediate metabolites more explicitly and providing additional evidence for the causal relationships between activities.