{
  "filename": "plot_1.png",
  "iteration": 1,
  "description": "Visualization of ACAD9 vs VLCAD substrate specificity profiles and evidence table showing no paper demonstrates ACAD9 very-long-chain activity",
  "timestamp": "2026-07-01 05:40:15",
  "code": "\nimport matplotlib.pyplot as plt\nimport matplotlib.patches as mpatches\nimport numpy as np\n\n# Compile substrate specificity evidence from literature for ACAD9\n# Data from PMID:16020546 (Ensenauer et al., 2005) - reported relative activities\n# and from PMID:12359260, 17564966, 21237683, 24158852\n\nfig, axes = plt.subplots(2, 1, figsize=(14, 10))\n\n# Panel A: Substrate chain-length ranges for ACAD9 vs VLCAD\nax1 = axes[0]\n\n# GO term definitions\nax1.axvspan(13, 22, alpha=0.15, color='blue', label='GO:0004466 range (C13-C22)')\nax1.axvspan(22, 28, alpha=0.15, color='red', label='GO:0017099 range (>C22)')\nax1.axvline(x=22, color='gray', linestyle='--', linewidth=1, alpha=0.5)\n\n# ACAD9 reported substrates (from literature)\nacad9_substrates = {\n    'C10:0': 10, 'C12:0': 12, 'C14:0': 14, 'C16:0': 16, 'C18:0': 18, 'C20:0': 20,\n    'C16:1': 16, 'C18:1': 18, 'C18:2': 18, 'C22:6': 22\n}\n# Relative activities (approximate from PMID:16020546)\nacad9_activities = {\n    'C10:0': 0.05, 'C12:0': 0.15, 'C14:0': 0.30, 'C16:0': 0.50, 'C18:0': 0.35, 'C20:0': 0.20,\n    'C16:1': 0.85, 'C18:1': 1.0, 'C18:2': 0.90, 'C22:6': 0.70\n}\n\n# VLCAD reported substrates\nvlcad_substrates = {\n    'C12:0': 12, 'C14:0': 14, 'C16:0': 16, 'C18:0': 18, 'C20:0': 20, 'C22:0': 22, 'C24:0': 24\n}\nvlcad_activities = {\n    'C12:0': 0.15, 'C14:0': 0.40, 'C16:0': 1.0, 'C18:0': 0.60, 'C20:0': 0.35, 'C22:0': 0.20, 'C24:0': 0.10\n}\n\n# Plot ACAD9 saturated substrates\nsat_substrates = ['C10:0', 'C12:0', 'C14:0', 'C16:0', 'C18:0', 'C20:0']\nsat_lengths = [acad9_substrates[s] for s in sat_substrates]\nsat_activities = [acad9_activities[s] for s in sat_substrates]\nax1.plot(sat_lengths, sat_activities, 'o-', color='#2196F3', linewidth=2, markersize=8, \n         label='ACAD9 saturated', zorder=5)\n\n# Plot ACAD9 unsaturated substrates\nunsat_substrates = ['C16:1', 'C18:1', 'C18:2', 'C22:6']\nunsat_lengths = [acad9_substrates[s] for s in unsat_substrates]\nunsat_activities = [acad9_activities[s] for s in unsat_substrates]\nax1.plot(unsat_lengths, unsat_activities, 's-', color='#4CAF50', linewidth=2, markersize=8,\n         label='ACAD9 unsaturated', zorder=5)\n\n# Plot VLCAD substrates\nvlcad_sat = list(vlcad_substrates.keys())\nvlcad_lengths = [vlcad_substrates[s] for s in vlcad_sat]\nvlcad_acts = [vlcad_activities[s] for s in vlcad_sat]\nax1.plot(vlcad_lengths, vlcad_acts, '^-', color='#F44336', linewidth=2, markersize=8,\n         label='VLCAD saturated', zorder=5)\n\nax1.set_xlabel('Carbon Chain Length', fontsize=12)\nax1.set_ylabel('Relative Activity', fontsize=12)\nax1.set_title('Substrate Specificity: ACAD9 vs VLCAD\\n(Compiled from PMID:16020546, 12359260, 17564966, 21237683)', fontsize=13)\nax1.legend(loc='upper right', fontsize=10)\nax1.set_xlim(8, 28)\nax1.set_ylim(-0.05, 1.15)\nax1.set_xticks(range(8, 29, 2))\nax1.text(17.5, 1.08, 'Long-chain\\n(GO:0004466)', ha='center', fontsize=10, color='blue', fontweight='bold')\nax1.text(25, 1.08, 'Very-long-chain\\n(GO:0017099)', ha='center', fontsize=10, color='red', fontweight='bold')\n\n# Panel B: Evidence summary table as a visual\nax2 = axes[1]\nax2.axis('off')\n\ntable_data = [\n    ['Reference', 'Substrates Tested', 'Peak Activity', 'Evidence for VLC (>C22)?'],\n    ['PMID:12359260\\n(Zhang 2002)', 'C16:0, C18:0', 'C16:0-C18:0\\n(long-chain sat.)', 'NO - only tested C16-C18'],\n    ['PMID:16020546\\n(Ensenauer 2005)', 'C10-C20 sat., C16:1,\\nC18:1, C18:2, C22:6', 'C16:1-C18:1\\n(long-chain unsat.)', 'NO - C22:6 is 22C (long-chain)\\nnot >22C (very-long-chain)'],\n    ['PMID:17564966\\n(He 2007)', 'long-chain acyl-CoAs', 'Unsaturated\\nlong-chain', 'NO - described as\\n\"long-chain\"'],\n    ['PMID:24158852\\n(Nouws 2014)', 'In vivo: oleate,\\npalmitate', 'C12-C14:1\\nproducts', 'NO - long-chain\\nsubstrates'],\n    ['PMID:33320993\\n(Giachin 2021)', 'None (structural\\nstudy)', 'N/A - CI assembly\\ncomplex study', 'NO - no substrate\\nassay performed'],\n    ['PMID:34646991\\n(Xia 2021)', 'None (interaction\\nstudy)', 'N/A - MCIA complex\\ninteractions', 'NO - no substrate\\nassay performed'],\n]\n\ncolors = [['#E3F2FD']*4] + [['white', 'white', 'white', '#FFCDD2']]*6\ntable = ax2.table(cellText=table_data, cellLoc='center', loc='center',\n                  cellColours=colors)\ntable.auto_set_font_size(False)\ntable.set_fontsize(8.5)\ntable.scale(1, 2.2)\n\n# Bold header\nfor j in range(4):\n    table[0, j].set_text_props(fontweight='bold')\n    table[0, j].set_facecolor('#BBDEFB')\n\nax2.set_title('Evidence Table: Does any paper demonstrate ACAD9 activity with >C22 saturated substrates?',\n              fontsize=12, fontweight='bold', pad=20)\n\nplt.tight_layout()\nplt.savefig('acad9_substrate_analysis.png', dpi=150, bbox_inches='tight')\nplt.show()\nprint(\"Figure saved: acad9_substrate_analysis.png\")\n",
  "plot_number": 1
}