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60ad85f700003288 de novo UMP biosynthetic process Mouse

Let me review the specific GO-CAM model 60ad85f700003288. Based on the model information I've retrieved, this GO-CAM represents the "'de novo' UMP biosynthetic process" in mouse (NCBITaxon:10090). The model describes several molecular functions carried out by different proteins that are part of this biosynthetic pathway.

Here's my review of the model:

GO-CAM Model Review: gomodel:60ad85f700003288

Basic Information

  • Title: "'de novo' UMP biosynthetic process (Mouse)"
  • Taxon: NCBITaxon:10090 (Mouse)
  • Status: Production
  • Comments: Sourced from gomodel:R-HSA-500753

Pathway Overview

This model represents the de novo UMP biosynthetic pathway in mouse, where several enzymes catalyze sequential reactions leading to UMP synthesis.

Model Structure

The model includes three key proteins: 1. MGI:MGI:1916969 (Cad) - multifunctional protein with three activities: - Carbamoyl-phosphate synthase (GO:0004088) - Aspartate carbamoyltransferase (GO:0004070)
- Dihydroorotase (GO:0004151)

  1. MGI:MGI:1928378 (Dhodh) - with activity:

  2. Dihydroorotate dehydrogenase (GO:0004152)

  3. MGI:MGI:1298388 (Umps) - with two activities:

  4. Orotate phosphoribosyltransferase (GO:0004588)
  5. Orotidine-5'-phosphate decarboxylase (GO:0004590)

Pathway Flow

The causal flow in the model is: 1. Cad carbamoyl-phosphate synthase → Cad aspartate carbamoyltransferase → Cad dihydroorotase → Dhodh dihydroorotate dehydrogenase → Umps orotate phosphoribosyltransferase → Umps orotidine-5'-phosphate decarboxylase

All causal connections use the predicate RO:0002413 "provides input for", which correctly represents the sequential enzymatic reactions in a biosynthetic pathway.

Evidence

The model includes appropriate evidence for each assertion: - Evidence from direct assays (ECO:0000314) - Mutant phenotype evidence (ECO:0000315) - Sequence orthology evidence (ECO:0000266)

Each assertion is backed by PMIDs, indicating proper literature support.

Strengths

  1. The model correctly represents the known enzymatic activities in the de novo UMP biosynthetic pathway
  2. The causal connections accurately reflect the flow of intermediates in the pathway
  3. All activities are appropriately linked to the overall process (GO:0044205)
  4. The model uses appropriate evidence codes with literature references
  5. The use of multifunctional proteins (Cad, Umps) accurately reflects the biology

Potential Issues

  1. There's a "part_of" relationship from GO:0004151 to GO:0004152 in one of the activities which seems incorrect - dihydroorotase activity shouldn't be part of dihydroorotate dehydrogenase activity as these are distinct enzymatic functions
  2. There's a BFO:0000050 causal association which is inconsistent with the rest of the causal associations that use RO:0002413 - this should be standardized
  3. One evidence reference has a space before the PMID (" PMID:6154574"), which should be fixed

Overall Assessment

This GO-CAM model provides a good representation of the UMP biosynthetic pathway in mouse with appropriate proteins, activities, and causal connections. The few minor issues identified should be addressed for complete consistency, but they don't detract from the biological accuracy of the model.

The model is parsimonious, focused on the essential activities of the pathway, and maintains a clear linear flow that is easily interpretable. The evidence citations are appropriate and support the assertions made in the model.