{
  "filename": "final_evidence_summary.png",
  "iteration": 3,
  "description": "Create final comprehensive evidence summary figure with all 12 lines of evidence and the decisive Faust et al. confirmation result",
  "timestamp": "2026-07-01 03:27:34",
  "code": "\nimport matplotlib.pyplot as plt\nimport matplotlib.patches as mpatches\nimport numpy as np\n\nfig, axes = plt.subplots(1, 2, figsize=(16, 8))\nfig.suptitle('Final Evidence Summary: Drosophila Acat1 (Q9W3N9) \u2014 GO:0005777 Peroxisome\\nVerdict: OVER-ANNOTATED (recommend removal)', \n             fontsize=13, fontweight='bold', y=0.98)\n\n# Panel A: Complete evidence scorecard\nax1 = axes[0]\nax1.axis('off')\n\nevidence_lines = [\n    (\"1. Experimental localization (LOPIT)\", \"Mitochondrion (HDA)\", \"#2ecc71\", \"STRONG\"),\n    (\"2. Phylogenetic inference (IBA)\", \"Mitochondrion\", \"#2ecc71\", \"MODERATE\"),\n    (\"3. C-terminal PTS1 signal (-EKL)\", \"Non-canonical, disfavored\", \"#e74c3c\", \"STRONG\"),\n    (\"4. N-terminal MTS (net charge +5)\", \"Matches human ACAT1 MTS\", \"#2ecc71\", \"STRONG\"),\n    (\"5. Functional context (thiolase II)\", \"Mitochondrial processes\", \"#2ecc71\", \"STRONG\"),\n    (\"6. Human ortholog localization\", \"Mito ONLY (no peroxisome)\", \"#e74c3c\", \"STRONG\"),\n    (\"7. Cholesterol synthesis in Drosophila\", \"Absent (auxotroph)\", \"#e74c3c\", \"STRONG\"),\n    (\"8. AlphaFold N-terminal structure\", \"Disordered MTS (pLDDT<64)\", \"#2ecc71\", \"HIGH\"),\n    (\"9. AlphaFold C-terminal structure\", \"Buried in fold (pLDDT>97)\", \"#e74c3c\", \"HIGH\"),\n    (\"10. Insect ortholog C-terminal cons.\", \"94% -EKL, 0% canonical PTS1\", \"#e74c3c\", \"HIGH\"),\n    (\"11. Faust et al. confirmed proteins\", \"Acat1 NOT among 6 confirmed\", \"#e74c3c\", \"DECISIVE\"),\n    (\"12. Active site conservation\", \"Thiolase II confirmed\", \"#2ecc71\", \"HIGH\"),\n]\n\ny_start = 0.95\nfor i, (label, finding, color, strength) in enumerate(evidence_lines):\n    y = y_start - i * 0.075\n    # Color indicator\n    ax1.add_patch(plt.Circle((0.02, y), 0.012, color=color, transform=ax1.transAxes))\n    ax1.text(0.05, y, label, transform=ax1.transAxes, fontsize=9, va='center', fontweight='bold')\n    ax1.text(0.52, y, finding, transform=ax1.transAxes, fontsize=8.5, va='center', color='#2c3e50')\n    ax1.text(0.88, y, f\"[{strength}]\", transform=ax1.transAxes, fontsize=8, va='center', \n             color='#7f8c8d', fontstyle='italic')\n\n# Legend\nax1.add_patch(plt.Circle((0.05, 0.04), 0.012, color='#2ecc71', transform=ax1.transAxes))\nax1.text(0.08, 0.04, \"= Supports mitochondrion\", transform=ax1.transAxes, fontsize=8, va='center')\nax1.add_patch(plt.Circle((0.45, 0.04), 0.012, color='#e74c3c', transform=ax1.transAxes))\nax1.text(0.48, 0.04, \"= Refutes peroxisome\", transform=ax1.transAxes, fontsize=8, va='center')\n\nax1.set_title('A. Complete Evidence Scorecard (12 lines of evidence)', fontsize=11, fontweight='bold', pad=15)\n\n# Panel B: Faust et al. confirmed proteins\nax2 = axes[1]\nax2.axis('off')\n\nconfirmed_text = \"\"\"FAUST et al. 2012 (PMID:22758915)\nExperimentally Confirmed Peroxisomal Proteins (IDA):\n\n  \u2605 Agps    \u2014 Alkylglycerone-phosphate synthase\n  \u2605 CRAT    \u2014 Carnitine acetyltransferase\n  \u2605 Ccs     \u2014 Copper chaperone for SOD\n  \u2605 CG17544 \u2014 Uncharacterized protein\n  \u2605 Mtpalpha \u2014 Mitochondrial trifunctional protein \u03b1\n  \u2605 Sod1    \u2014 Superoxide dismutase\n\nNOT confirmed (ISM prediction only):\n  \u2717 Acat1   \u2014 Acetoacetyl-CoA thiolase\n  \u2717 (and many other predicted proteins)\n\n\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\nCURATION RECOMMENDATION:\n\n  REMOVE:  GO:0005777 (peroxisome) [ISM]\n  RETAIN:  GO:0005739 (mitochondrion) [HDA]\n\n  Acat1 is a mitochondrial thiolase II.\n  The peroxisome ISM annotation is a\n  computational artifact that should be\n  removed from the gene record.\n\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n\"\"\"\n\nax2.text(0.05, 0.95, confirmed_text, transform=ax2.transAxes, fontsize=9.5,\n         fontfamily='monospace', verticalalignment='top',\n         bbox=dict(boxstyle='round,pad=0.8', facecolor='#fef9e7', alpha=0.9, edgecolor='#f39c12'))\nax2.set_title('B. Key Gap Closed: Faust et al. Confirmed Proteins', fontsize=11, fontweight='bold', pad=15)\n\nplt.tight_layout(rect=[0, 0, 1, 0.94])\nplt.savefig('final_evidence_summary.png', dpi=150, bbox_inches='tight')\nplt.show()\nprint(\"Final evidence summary figure saved.\")\n"
}