{
  "study_id": "STUDY-27-METAZOAN-VENOM-DISULFIDE-CONVERGENCE",
  "discovery_id": 104,
  "slug": "metazoan-venom-disulfide-scaffold",
  "validation_set_id": "VAL-SET-037-METAZOAN-VENOM-DISULFIDE-CONVERGENCE-32COHORT",
  "generated_at": "2026-11-04T05:59:00Z",
  "tier_trajectory": "Full Step-Up Trajectory (Tier 1 Exploratory -> Tier 2 Blinded Validation -> Tier 3 Scientific Synthesis)",
  "prior_beaker_depth": 5,
  "posterior_beaker_rating": 5,
  "posterior_z_score": 6.79,
  "runie_bootstrap_replicates": 50,
  "stage_1_tier1_exploratory": {
    "tier": 1,
    "taxa_count": 34,
    "sequence_volume_mb": 2.06,
    "disulfide_scaffolds_surveyed": [
      {
        "scaffold": "Cnidarian ShK-Like 3-Disulfide Helical Hairpins (C1-C6, C2-C4, C3-C5; PDB: 1BGK)",
        "unpartitioned_rcfv": 0.174,
        "partitioned_rcfv": 0.020,
        "rcfv_reduction_pct": 88.5,
        "signal_propeptide_dnds": 0.12,
        "mature_loop_dnds": 3.48,
        "key_finding": "Retaining the 22-aa ER signal peptide + 18-aa acidic propeptide KR cleavage SLiM in Track 1 while routing the Lys25-Tyr23 Kv1 pore-blocking dyad to Track 2 separates sea anemone BgK/ShK from convergent scorpion Charybdotoxin"
      },
      {
        "scaffold": "Molluscan & Arachnid Inhibitor Cystine Knots (ICK C1-C4, C2-C5, C3-C6; PDB: 1FU3)",
        "unpartitioned_rcfv": 0.186,
        "partitioned_rcfv": 0.021,
        "rcfv_reduction_pct": 88.7,
        "signal_propeptide_dnds": 0.11,
        "mature_loop_dnds": 3.92,
        "key_finding": "Conserved O-superfamily signal/propeptide SLiM (omega = 0.11) resolves Conus O1/O2/M/A superfamily phylogeny with 100% UFBoot, while Track 2 inter-cysteine loop vector distinguishes CaV2.2 (MVIIA) from NaV (TxVIA, 1FU3) modulators"
      },
      {
        "scaffold": "Reptilian Ly6/uPAR Three-Finger Scaffolds (3FTx 4-Disulfide Core; PDB: 1KBA)",
        "unpartitioned_rcfv": 0.172,
        "partitioned_rcfv": 0.019,
        "rcfv_reduction_pct": 89.0,
        "signal_propeptide_dnds": 0.14,
        "mature_loop_dnds": 2.96,
        "key_finding": "Retaining the 21-aa Ly6 signal peptide and C-terminal GPI-anchor deletion boundary roots elapid 3FTx (kappa-bungarotoxin, 1KBA) directly inside ancestral vertebrate LYNX1/SLURP1/CD59 housekeeping receptors"
      }
    ]
  },
  "stage_2_tier2_blinded_validation": {
    "tier": 2,
    "cohorts_total": 32,
    "dev_cohorts": 24,
    "reserve_cohorts": 8,
    "sequence_volume_mb": 3.52,
    "concordant_cohorts": 28,
    "mean_concordant_d_ctx": 0.08,
    "untouched_reserve_posterior_z": 6.46,
    "context_anomalies_isolated": [
      {
        "blind_token": "BLIND-VENOM-05",
        "taxa": "Bunodosoma granulifera BgK (Cnidaria, PDB: 1BGK) vs. Leiurus quinquestriatus Charybdotoxin (Arthropoda)",
        "repository_label": "Clustered Kv1 potassium-channel toxin family (88% unpartitioned bootstrap LBA lock)",
        "pass1_blinded_extrapolation": "Non-homologous disulfide topologies (ShK C1-C6/C2-C4/C3-C5 helical hairpin vs. CS-alpha/beta sheet); convergent Lys25-Tyr23/Phe6 pore-plugging dyad routed to Track 2",
        "z_blind": 6.42,
        "z_ctx": 0.46,
        "d_ctx": 5.96
      },
      {
        "blind_token": "BLIND-VENOM-12",
        "taxa": "Conus magus omega-Conotoxin MVIIA (CaV2.2 blocker) vs. Conus textile delta-Conotoxin TxVIA (NaV modulator, PDB: 1FU3)",
        "repository_label": "Unresolvable mature 26-27 aa ICK peptides under strict Pfam PF02950 core cropping (54% bootstrap split)",
        "pass1_blinded_extrapolation": "Track 1 O1-superfamily 22-aa signal + 24-aa propeptide KR SLiM (omega = 0.11) unites both in O1 superfamily (100% UFBoot); Track 2 Loop-2/Loop-4 hydrophobicity vector separates CaV2.2 vs. NaV pharmacology",
        "z_blind": 6.54,
        "z_ctx": 0.28,
        "d_ctx": 6.26
      },
      {
        "blind_token": "BLIND-VENOM-19",
        "taxa": "Bungarus multicinctus kappa-Bungarotoxin (PDB: 1KBA) vs. Homo sapiens Brain LYNX1 / Immune CD59",
        "repository_label": "Orphan reptile-specific three-finger neurotoxin family",
        "pass1_blinded_extrapolation": "Retaining the 21-aa N-terminal ER signal SLiM + 4-disulfide Ly6 core + C-terminal GPI-transamidase loss scar roots 3FTx inside amniote LYNX1 allosteric nAChR modulators",
        "z_blind": 6.18,
        "z_ctx": 0.42,
        "d_ctx": 5.76
      },
      {
        "blind_token": "BLIND-VENOM-28",
        "taxa": "Nematostella vectensis 6x Tandem ShK-Domain Metalloprotease Scaffold vs. Secreted BgK Monomer (PDB: 1BGK)",
        "repository_label": "Misannotated 6-copy venom gland toxin polyprotein",
        "pass1_blinded_extrapolation": "Housekeeping extracellular matrix astacin-metalloprotease carrying 6 auxiliary ShK-like domains (dN/dS = 0.08, lacks prohormone KR cleavage SLiM)",
        "z_blind": 6.29,
        "z_ctx": 0.31,
        "d_ctx": 5.98
      }
    ]
  },
  "stage_3_tier3_scientific_synthesis": {
    "tier": 3,
    "taxa_count": 74,
    "sequence_volume_mb": 6.48,
    "cumulative_superfamilies": 31,
    "cumulative_taxa": 662,
    "cumulative_sequence_mb": 40.28,
    "hypotheses_ledger": [
      {
        "id": "H1",
        "system": "Cnidarian ShK Hairpin vs. Scorpion CS-alpha/beta Kv1 Dyad Convergence (PDB: 1BGK)",
        "rcfv_drop": "0.174 -> 0.020 (-88.5%)",
        "track2_receptor_mi_pct": 99.4,
        "delta_lnl": 548.2,
        "crown_ufboot_pct": 100.0,
        "posterior_z": 6.79
      },
      {
        "id": "H2",
        "system": "Conus ICK Conotoxin Signal/Propeptide SLiM (omega = 0.11) vs. Mature Loop (omega = 3.92; PDB: 1FU3)",
        "rcfv_drop": "0.186 -> 0.021 (-88.7%)",
        "track2_receptor_mi_pct": 99.5,
        "delta_lnl": 584.6,
        "crown_ufboot_pct": 100.0,
        "posterior_z": 6.64
      },
      {
        "id": "H3",
        "system": "Reptilian 3FTx Neofunctionalization from Housekeeping Ly6/LYNX1/CD59 (PDB: 1KBA)",
        "rcfv_drop": "0.172 -> 0.019 (-89.0%)",
        "track2_receptor_mi_pct": 99.2,
        "delta_lnl": 410.0,
        "crown_ufboot_pct": 99.8,
        "posterior_z": 6.32
      },
      {
        "id": "H4",
        "system": "B = 50 RuNIE Bootstrap Stability & Systematic LBA Lock Falsification Across 74 Taxa",
        "rcfv_drop": "0.178 -> 0.020 (-88.8%)",
        "track2_receptor_mi_pct": 99.4,
        "delta_lnl": 1542.8,
        "crown_ufboot_pct": 98.0,
        "posterior_z": 6.79
      }
    ],
    "runie_model_comparison": [
      {
        "rank": "1st (Best)",
        "architecture": "Minimizer Synteny -> Coupled Dual-Track Plan-7 HMM (Track 1: Signal/Propeptide KR SLiM + Phase-Locked Disulfide Core [+] Track 2: Inter-Cysteine Loop dN/dS & Pharmacophore Dyad Vector) -> Kabsch 3D (1BGK/1FU3/1KBA) -> Potts DCA -> Goldman-Yang dN/dS -> RP16 Supermatrix -> BIONJ ML Tree (LG+C60+F+R4)",
        "marginal_lnl": -174892.4,
        "delta_lnl": 0.0,
        "rcfv": 0.020,
        "runie_bootstrap_b50": "98.0% (49/50 • ±0.12 SD)",
        "posterior_z": 6.79
      },
      {
        "rank": "2nd (Nearest)",
        "architecture": "Single-Track Sub-Domain Partitioning (Track 1 Signal/Propeptide SLiM + Disulfide Core Kept; Hypervariable Loops Masked) -> *MAFFT L-INS-i -> *US-align 3D -> *IQ-TREE 2 (LG+F+G4)",
        "marginal_lnl": -175310.8,
        "delta_lnl": -418.4,
        "rcfv": 0.020,
        "runie_bootstrap_b50": "88.0% (44/50 • ±0.21 SD)",
        "posterior_z": 5.34
      },
      {
        "rank": "3rd (Medium)",
        "architecture": "*HMMER3 Strict Mature Pfam Domain-Only Cropping (22-aa Signal Peptide, Propeptide KR Cleavage SLiM & Ly6 GPI Boundary Stripped) -> *MAFFT -> *IQ-TREE 2",
        "marginal_lnl": -175577.0,
        "delta_lnl": -684.6,
        "rcfv": 0.026,
        "runie_bootstrap_b50": "56.0% Split (28/50 • ±0.68 SD)",
        "posterior_z": 3.24
      },
      {
        "rank": "4th (Rejected)",
        "architecture": "Unpartitioned Mature Peptide *MAFFT / Gotoh MSA (Cysteine-Frame Register Shifts & Convergent Kv1/NaV Dyad LBA Retained) -> *IQ-TREE 2 (LG+F+G4)",
        "marginal_lnl": -176435.2,
        "delta_lnl": -1542.8,
        "rcfv": 0.178,
        "runie_bootstrap_b50": "92.0% LBA Lock (46/50 Failed • ±0.17 SD)",
        "posterior_z": 1.06
      }
    ]
  }
}