{
  "pipeline_id": "bgc-mine-v1",
  "pipeline_cmd": "bio-suite bgc-mine --out runs/bgc-mine-report.json",
  "complexity_tier": "Low (Part 1 — Standardized High-Yield FASTA/MAG Miner)",
  "input_mag_or_genome": "Streptomyces_marinus_SCSIO64_MAG.fasta",
  "total_clusters_detected": 3,
  "known_clusters_dereplicated": 1,
  "novel_prioritized_clusters": 2,
  "total_duration_ms": 0,
  "step_trace": [
    {
      "step_index": 1,
      "stage_id": "bgc:prodigal_gv_antismash_gecco",
      "engine": "Tier 2 (bio-suite genome / antiSMASH 7 / GECCO)",
      "input_schema": "ActinomyceteDraftMAG<Streptomyces_marinus_SCSIO64>",
      "output_schema": "CandidateBgcSet[3]",
      "duration_ms": 0,
      "summary": "Scanned marine actinomycete MAG Streptomyces sp. SCSIO-64; detected 3 biosynthetic gene clusters (1 Erythromycin-like T1PKS, 1 Hybrid NRPS-PKS, and 1 cryptic 31-aa sORF RiPP/AMP cluster)."
    },
    {
      "step_index": 2,
      "stage_id": "bgc:mibig_bigscape_dereplication",
      "engine": "Tier 2 (bio-suite genome / BiG-SCAPE)",
      "input_schema": "CandidateBgcSet[3] x MIBiG_v3.1",
      "output_schema": "OrphanBgcSet[2] (1 Known Filtered)",
      "duration_ms": 0,
      "summary": "Dereplicated against MIBiG v3.1: filtered Cluster-01 (92.4% domain Jaccard similarity to BGC0000055 Erythromycin A); retained BGC-NRPS-02 (34.2% similarity) and BGC-RIPP-03 (18.5% similarity) as novel scaffolds."
    },
    {
      "step_index": 3,
      "stage_id": "bgc:arts_self_resistance_and_amp_folding",
      "engine": "Tier 2 (bio-suite target / ARTS / Macrel / ESMFold)",
      "input_schema": "OrphanBgcSet[2]",
      "output_schema": "Vec<BiosyntheticClusterDossier>[2]",
      "duration_ms": 0,
      "summary": "Identified embedded self-resistance gyrB paralog (Asp426Asn/Arg136His) inside BGC-NRPS-02 and verified amphipathic alpha-helical moment for cryptic sORF BGC-RIPP-03."
    }
  ],
  "novel_product_dossiers": [
    {
      "cluster_id": "BGC-NRPS-SCSIO64-02",
      "organism": "Streptomyces sp. SCSIO-64 (Marine Deep-Sea Sediment MAG)",
      "contig_region": "NODE_4:118,400..164,920 (46.5 kb)",
      "bgc_class": "Hybrid Non-Ribosomal Peptide Synthetase / Type-I Polyketide (NRPS-T1PKS)",
      "core_synthase_domains": [
        "A(Pip)-PCP-C",
        "A(dhb)-PCP-E",
        "KS-AT(mmal)-KR-ACP",
        "C-A(Orn)-PCP-TE"
      ],
      "nearest_mibig_compound": "BGC0001555 (Cinnabaramide A)",
      "mibig_domain_jaccard_similarity": 0.342,
      "passes_dereplication_novelty_gate": true,
      "self_resistance_hook": {
        "housekeeping_gene": "gyrB (DNA Gyrase Subunit B, Core Essential TIGR01059)",
        "canonical_locus_tag": "SCSIO64_00142 (Core Chromosomal Copy)",
        "bgc_duplicated_locus_tag": "SCSIO64_02189 (Embedded inside BGC-NRPS-02)",
        "copy_number_in_genome": 2,
        "divergence_from_core_pct": 19.8,
        "active_site_resistance_mutations": [
          "Asp426Asn (ATP-lid hydrogen bond network shift)",
          "Arg136His (Novobiocin/Coumermycin gatekeeper pocket)"
        ],
        "inferred_mechanism_of_action": "Competitive ATP-binding pocket inhibitor of bacterial DNA Gyrase Subunit B (GyrB), protected in the producer by an embedded Asn426/His136 self-resistant GyrB2 paralog."
      },
      "amp_structural_profile": null,
      "medicinal_chemistry_priority_score": 94.6,
      "dossier_summary": "Orphan 46.5 kb Hybrid NRPS-T1PKS cluster (MIBiG Jaccard = 0.342 < 0.80 dereplication gate) encoding a novel chlorinateddepsipeptide-polyketide scaffold co-localized with a diverged second copy of essential house-keeping gene gyrB (Asp426Asn/Arg136His), directly revealing DNA Gyrase B ATPase inhibition as its molecular mechanism of action."
    },
    {
      "cluster_id": "BGC-RIPP-SCSIO64-03",
      "organism": "Streptomyces sp. SCSIO-64 (Marine Deep-Sea Sediment MAG)",
      "contig_region": "NODE_11:42,100..51,850 (9.75 kb)",
      "bgc_class": "Short-ORF Ribosomally Synthesized Antimicrobial Peptide (sORF RiPP / AMP)",
      "core_synthase_domains": [
        "sORF_Precursor(31aa)",
        "YcaO_Cyclodehydratase",
        "ABC_Efflux_Transporter(BcrA/B)"
      ],
      "nearest_mibig_compound": "BGC0000581 (Microcin J25)",
      "mibig_domain_jaccard_similarity": 0.185,
      "passes_dereplication_novelty_gate": true,
      "self_resistance_hook": null,
      "amp_structural_profile": {
        "sorf_id": "SCSIO64_sORF_1942",
        "peptide_sequence": "GIGKFLHSAKKFGKAFVGEIMNSKWRKVGRK",
        "length_aa": 31,
        "net_charge_ph7": 8.1,
        "hydrophobic_moment_mu_h": 0.6862,
        "boman_interaction_index_kcal": 0.6194,
        "predicted_fold": "Amphipathic cationic alpha-helical hairpin (ESMFold pLDDT = 89.4)",
        "membrane_disruption_prob": 0.8511
      },
      "medicinal_chemistry_priority_score": 88.4,
      "dossier_summary": "Cryptic 31-aa sORF peptide (SCSIO64_sORF_1942) skipped by standard annotation callers; exhibits strong cationic charge (+8.1 at pH 7.4) and high Eisenberg amphipathic alpha-helical hydrophobic moment (mu_H = 0.6862), predicting potent Gram-negative outer-membrane permeabilization (P = 0.85)."
    }
  ],
  "emergent_findings": [
    {
      "finding_id": "EMERGENT-BGC-01",
      "title": "Embedded Self-Resistance GyrB Paralog De-Orphans Mechanism of Action for Novel Marine NRPS-PKS Scaffold",
      "engines_bridged": [
        "bio-suite genome (antiSMASH / BiG-SCAPE Dereplication)",
        "bio-suite target (ARTS Self-Resistance Target Seeker)",
        "bio-suite phylo (Core Paralog Divergence)"
      ],
      "statistic_name": "Medicinal Chemistry Priority Score",
      "statistic_value": 94.6,
      "biological_interpretation": "Orphan 46.5 kb Hybrid NRPS-T1PKS cluster (MIBiG Jaccard = 0.342 < 0.80 dereplication gate) encoding a novel chlorinateddepsipeptide-polyketide scaffold co-localized with a diverged second copy of essential house-keeping gene gyrB (Asp426Asn/Arg136His), directly revealing DNA Gyrase B ATPase inhibition as its molecular mechanism of action."
    }
  ]
}