[
  {
    "rank": 1,
    "gene": "Dic4",
    "accession": "Q9VVS1",
    "hypothesis": "The Drosophila melanogaster protein Q9VVS1 mediates uptake of thiamine pyrophosphate into mitochondria.",
    "source_prediction": {
      "accession": "Q9VVS1",
      "taxon_id": "7227",
      "type": "function",
      "id": "",
      "text": "Mitochondrial transporter that mediates uptake of thiamine pyrophosphate (ThPP) into mitochondria"
    },
    "current_assessment": "UNC",
    "selection_reason": "Mitochondrial carrier family membership establishes neither substrate nor direction. Comparative substrate-recognition analysis and experimentally characterized carrier subfamilies could resolve a transfer that the initial review could not.",
    "desired_resolution": "Determine whether the exact protein supports thiamine-pyrophosphate transport. Establish its placement among experimentally characterized mitochondrial carriers and compare substrate-recognition residues and transport mechanisms, including competing substrate assignments. Read the substrate panel and controls of any direct Dic4 reconstitution study; failure to transport a tested substrate does not exclude an untested one. Separate mitochondrial localization, transport competence, substrate specificity and uptake direction. Identify what structural/evolutionary evidence can resolve and what still needs transport measurements.",
    "prompt_file": "projects/PROTNLM_EVALUATION/fly-benchmark/openscientist-selection/01-Dic4-thiamine-pyrophosphate-transport-prompt.md",
    "prompt_sha256": "047e74e93e76d861bf9bb4192449f45da6dc487029b8507352e07188bc18e2ed",
    "sequence_sha256": "2f5383151315d764c10b9751f7af5754f60eb89416ded2ec518ea01bb71f6b5c",
    "sequence_length": 302,
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "DROME",
      "Dic4",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The Drosophila melanogaster protein Q9VVS1 mediates uptake of thiamine pyrophosphate into mitochondria.",
      "--slug",
      "fly41-thiamine-pyrophosphate-transport",
      "--context",
      "# Focused fly function hypothesis\n\nHypothesis: The Drosophila melanogaster protein Q9VVS1 mediates uptake of thiamine pyrophosphate into mitochondria.\n\nTarget: Drosophila melanogaster (NCBITaxon:7227), UniProt Q9VVS1. Gene label: Dic4. Verify identity and isoform independently; the gene label is not evidence for the hypothesis.\n\n## Original prediction\n\nMitochondrial transporter that mediates uptake of thiamine pyrophosphate (ThPP) into mitochondria\n\n## Decisive question\n\nDetermine whether the exact protein supports thiamine-pyrophosphate transport. Establish its placement among experimentally characterized mitochondrial carriers and compare substrate-recognition residues and transport mechanisms, including competing substrate assignments. Read the substrate panel and controls of any direct Dic4 reconstitution study; failure to transport a tested substrate does not exclude an untested one. Separate mitochondrial localization, transport competence, substrate specificity and uptake direction. Identify what structural/evolutionary evidence can resolve and what still needs transport measurements.\n\n## Identity and sequence\n\n- Target record: https://www.uniprot.org/uniprotkb/Q9VVS1/entry\n- FlyBase identifier(s) from the cohort identity mapping: FBgn0036808.\n- Frozen current UniProt sequence: 302 residues; SHA-256 `2f5383151315d764c10b9751f7af5754f60eb89416ded2ec518ea01bb71f6b5c`.\n- The sequence was frozen for the fly cohort on 2026-09-08. It is not established as the original prediction-time input. Analyze this sequence explicitly and document any alternate accession, version or isoform you analyze.\n\n```fasta\n>Q9VVS1 Drosophila melanogaster Dic4\nMPVFDDHFLGDCHDEPEGLLPRWWFGGFASMCVAFAVAPIDIVKTHMQIQRQKRSILGTV\nKRIHSLKGYLGFYDGFSAAILRQMTSTNIHFIVYDTGKKMEYVDRDSYLGKIILGCVAGA\nCGSAFGIPTDLINVRMQTDMKEPPYKRRNYKHVFDGLIRIPKEEGWKALYKGGSVAVFKS\nSLSTCSQIAFYDIIKTEVRKNISVNDGLPLHFLTSLGTSIISSAITHPLDVVRTIMMNSR\nPGEFRTVFQASVHMMRFGVMGPYRGFVPTIVRKAPATTLLFVLYEQLRLHFGICSLGGEK\nYN\n```\n\nPrimary literature lead to inspect (not a preassigned conclusion): https://pubmed.ncbi.nlm.nih.gov/21130726/\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. This is a focused mechanistic investigation, not a general gene overview. Seek supporting, contrary and competing explanations; an unresolved result is acceptable. Distinguish direct fly experiments, justified transfers and results on a different isoform. Do not equate missing target experiments with evidence of absence.\n\nDo not consult the ai-gene-review repository's current reviews, generated research summaries or local bioinformatics analyses; these are held out for comparison. Agreement with ARBA or repeated prediction text does not validate the biology. Save executed methods/code, actual analysis outputs, sequence identifiers and primary-source URLs/DOIs/PMIDs. Report decisive evidence and limitations, not just a verdict. Do not fabricate computations or use docking/structural resemblance alone as experimental validation.\n"
    ],
    "expected_report": "genes/DROME/Dic4/Dic4-hypotheses/fly41-thiamine-pyrophosphate-transport/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "cc51f444-45ab-4933-b480-688ac83406d5",
    "submitted_at": "2026-09-09T04:52:12.822749Z"
  },
  {
    "rank": 2,
    "gene": "CG5611",
    "accession": "Q9VB17",
    "hypothesis": "The Drosophila melanogaster protein Q9VB17 contributes enzymatically to fatty-acid oxidation.",
    "source_prediction": {
      "accession": "Q9VB17",
      "taxon_id": "7227",
      "type": "function",
      "id": "",
      "text": "Could possibly oxidize fatty acids using specific components"
    },
    "current_assessment": "UNC",
    "selection_reason": "The crotonase superfamily includes diverse reactions. Resolving the narrower subfamily, catalytic apparatus and physiological substrate offers more information than repeating a tentative bacterial donor description.",
    "desired_resolution": "Identify the best-supported biochemical reaction of this exact protein and determine whether it participates in fatty-acid oxidation. Use experimentally characterized homologs, subfamily placement, active-site geometry and relevant targeting or pathway context. Compare credible alternative reactions and substrates within the same broad fold. The original wording is tentative and mechanistically ambiguous: do not silently strengthen it into direct oxidoreductase catalysis. An auxiliary hydratase/isomerase role in an oxidation pathway and direct fatty-acid oxidation are different claims. Report the best defensible specificity, including an unresolved result if necessary.",
    "prompt_file": "projects/PROTNLM_EVALUATION/fly-benchmark/openscientist-selection/02-CG5611-fatty-acid-oxidation-mechanism-prompt.md",
    "prompt_sha256": "94642084809c62ce00103e818af2392dd8ba996322b26c39c0ae8c164a85d16a",
    "sequence_sha256": "24288a1fe155fc15bd2f9f7ea8a64806adbbbb4e70d1086093e2b3aa14d5ece7",
    "sequence_length": 326,
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "DROME",
      "CG5611",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The Drosophila melanogaster protein Q9VB17 contributes enzymatically to fatty-acid oxidation.",
      "--slug",
      "fly41-fatty-acid-oxidation-mechanism",
      "--context",
      "# Focused fly function hypothesis\n\nHypothesis: The Drosophila melanogaster protein Q9VB17 contributes enzymatically to fatty-acid oxidation.\n\nTarget: Drosophila melanogaster (NCBITaxon:7227), UniProt Q9VB17. Gene label: CG5611. Verify identity and isoform independently; the gene label is not evidence for the hypothesis.\n\n## Original prediction\n\nCould possibly oxidize fatty acids using specific components\n\n## Decisive question\n\nIdentify the best-supported biochemical reaction of this exact protein and determine whether it participates in fatty-acid oxidation. Use experimentally characterized homologs, subfamily placement, active-site geometry and relevant targeting or pathway context. Compare credible alternative reactions and substrates within the same broad fold. The original wording is tentative and mechanistically ambiguous: do not silently strengthen it into direct oxidoreductase catalysis. An auxiliary hydratase/isomerase role in an oxidation pathway and direct fatty-acid oxidation are different claims. Report the best defensible specificity, including an unresolved result if necessary.\n\n## Identity and sequence\n\n- Target record: https://www.uniprot.org/uniprotkb/Q9VB17/entry\n- FlyBase identifier(s) from the cohort identity mapping: FBgn0039531.\n- Frozen current UniProt sequence: 326 residues; SHA-256 `24288a1fe155fc15bd2f9f7ea8a64806adbbbb4e70d1086093e2b3aa14d5ece7`.\n- The sequence was frozen for the fly cohort on 2026-09-08. It is not established as the original prediction-time input. Analyze this sequence explicitly and document any alternate accession, version or isoform you analyze.\n\n```fasta\n>Q9VB17 Drosophila melanogaster CG5611\nMSRFVYKLLQSANQTSSGCRRISLATVRNAESESQEGAPARTVLVEKDSHITLIGLNREQ\nQRNSIDANTAEQLTEAISQFEADDTSPVGVLYGIGGSFCAGYDLEELEAEAQRGSLNFLL\nRHEGSVGPTRRHLRKPLVCGISGFCVAGGLELALMCDLRVMEDTAVLGFFNRRLGVPLSD\nGGTVRLAAAVGYSNALEIIATGRRIYSGEARRIGLVNRVVATGTALGQAVNLAFSIAKFP\nMASLMHDRNAVLENANAYNKPGFHVASYNEIMNVTSDMITDMQEGVKRFKNSEIKGPKTD\nSWSIKEKTIPDWEKAEIEIEKQKQKT\n```\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. This is a focused mechanistic investigation, not a general gene overview. Seek supporting, contrary and competing explanations; an unresolved result is acceptable. Distinguish direct fly experiments, justified transfers and results on a different isoform. Do not equate missing target experiments with evidence of absence.\n\nDo not consult the ai-gene-review repository's current reviews, generated research summaries or local bioinformatics analyses; these are held out for comparison. Agreement with ARBA or repeated prediction text does not validate the biology. Save executed methods/code, actual analysis outputs, sequence identifiers and primary-source URLs/DOIs/PMIDs. Report decisive evidence and limitations, not just a verdict. Do not fabricate computations or use docking/structural resemblance alone as experimental validation.\n"
    ],
    "expected_report": "genes/DROME/CG5611/CG5611-hypotheses/fly41-fatty-acid-oxidation-mechanism/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "5f3a68b0-8473-4aca-b934-362c89e625b0",
    "submitted_at": "2026-09-09T04:52:13.867992Z"
  },
  {
    "rank": 3,
    "gene": "ttv",
    "accession": "D5SHU8",
    "hypothesis": "The Drosophila melanogaster protein D5SHU8 has glycosyltransferase activity.",
    "source_prediction": {
      "accession": "D5SHU8",
      "taxon_id": "7227",
      "type": "GO",
      "id": "GO:0016757",
      "text": "F:glycosyltransferase activity"
    },
    "current_assessment": "UNC",
    "selection_reason": "This native short isoform retains a catalytic region; loss of length alone cannot adjudicate activity. Structural completeness, donor/acceptor recognition and complex dependence could distinguish residual activity from an inactive fragment.",
    "desired_resolution": "Assess glycosyltransferase activity of the supplied exact sequence. Resolve its annotated transcript/isoform and compare it with structurally and biochemically characterized EXT-family proteins and relevant Drosophila partners. Determine which catalytic domain and substrate-binding architecture are present, whether the protein can fold into a functional catalytic unit, and whether partner interactions or targeting are required for intrinsic catalysis versus an in-vivo glycan-biosynthesis role. Neither short length nor a conserved catalytic residue alone settles the question. Distinguish experimentally demonstrated isolated-domain activity from structural plausibility.",
    "prompt_file": "projects/PROTNLM_EVALUATION/fly-benchmark/openscientist-selection/03-ttv-short-isoform-glycosyltransferase-prompt.md",
    "prompt_sha256": "e1dd86464cd14c2a501695c293d9f7368431a239caa6ce474b9b548c2a86fd22",
    "sequence_sha256": "76d919802eaf321c50ecd217e0e45d5f74f2ec9e6fb7a3806aa74f3433760493",
    "sequence_length": 299,
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "DROME",
      "ttv",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The Drosophila melanogaster protein D5SHU8 has glycosyltransferase activity.",
      "--slug",
      "fly41-short-isoform-glycosyltransferase",
      "--context",
      "# Focused fly function hypothesis\n\nHypothesis: The Drosophila melanogaster protein D5SHU8 has glycosyltransferase activity.\n\nTarget: Drosophila melanogaster (NCBITaxon:7227), UniProt D5SHU8. Gene label: ttv. Verify identity and isoform independently; the gene label is not evidence for the hypothesis.\n\n## Original prediction\n\nF:glycosyltransferase activity\n\n## Decisive question\n\nAssess glycosyltransferase activity of the supplied exact sequence. Resolve its annotated transcript/isoform and compare it with structurally and biochemically characterized EXT-family proteins and relevant Drosophila partners. Determine which catalytic domain and substrate-binding architecture are present, whether the protein can fold into a functional catalytic unit, and whether partner interactions or targeting are required for intrinsic catalysis versus an in-vivo glycan-biosynthesis role. Neither short length nor a conserved catalytic residue alone settles the question. Distinguish experimentally demonstrated isolated-domain activity from structural plausibility.\n\n## Identity and sequence\n\n- Target record: https://www.uniprot.org/uniprotkb/D5SHU8/entry\n- FlyBase identifier(s) from the cohort identity mapping: FBgn0265974.\n- Frozen current UniProt sequence: 299 residues; SHA-256 `76d919802eaf321c50ecd217e0e45d5f74f2ec9e6fb7a3806aa74f3433760493`.\n- The sequence was frozen for the fly cohort on 2026-09-08. It is not established as the original prediction-time input. Analyze this sequence explicitly and document any alternate accession, version or isoform you analyze.\n\n```fasta\n>D5SHU8 Drosophila melanogaster ttv\nMPFLLNSMGAEPRHNYTAVIYVQIGAALGPNAALYKLVRTITKSQFVERILVLWAADRPL\nPLKKRWPPTSHIPLHVISLGGSTRSQGAGPTSQTTEGRPSISQRFLPYDEIQTDAVLSLD\nEDAILNTDELDFAYTVWRDFPERIVGYPARAHFWDDSKNAWGYTSKWTNYYSIVLTGAAF\nYHRYYNYLYTNWLSLLLLKTVQQSSNCEDILMNLLVSHVTRKPPIKVTQRKGYKDRETGR\nSPWNDPDHFIQRQSCLNTFAAVFGYMPLIRSNLRMDPMLYRDPVSNLRKKYRQIELVGS\n```\n\nPrimary literature lead to inspect (not a preassigned conclusion): https://pubmed.ncbi.nlm.nih.gov/36593275/\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. This is a focused mechanistic investigation, not a general gene overview. Seek supporting, contrary and competing explanations; an unresolved result is acceptable. Distinguish direct fly experiments, justified transfers and results on a different isoform. Do not equate missing target experiments with evidence of absence.\n\nDo not consult the ai-gene-review repository's current reviews, generated research summaries or local bioinformatics analyses; these are held out for comparison. Agreement with ARBA or repeated prediction text does not validate the biology. Save executed methods/code, actual analysis outputs, sequence identifiers and primary-source URLs/DOIs/PMIDs. Report decisive evidence and limitations, not just a verdict. Do not fabricate computations or use docking/structural resemblance alone as experimental validation.\n",
      "--term-id",
      "GO:0016757",
      "--term-label",
      "glycosyltransferase activity"
    ],
    "expected_report": "genes/DROME/ttv/ttv-hypotheses/fly41-short-isoform-glycosyltransferase/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "939966e3-12ee-4a0a-8311-48cd73058c14",
    "submitted_at": "2026-09-09T04:52:13.273582Z"
  },
  {
    "rank": 4,
    "gene": "TyrRS",
    "accession": "Q9VV60",
    "hypothesis": "The Drosophila melanogaster protein Q9VV60 binds resveratrol.",
    "source_prediction": {
      "accession": "Q9VV60",
      "taxon_id": "7227",
      "type": "GO",
      "id": "GO:1905594",
      "text": "F:resveratrol binding"
    },
    "current_assessment": "UNC",
    "selection_reason": "A mammalian ligand-bound structure offers a concrete pocket-level comparison. Conserved aminoacylation does not automatically establish resveratrol recognition or its downstream signaling effects.",
    "desired_resolution": "Evaluate biochemical resveratrol recognition by the supplied fly TyrRS sequence using verified ligand-bound structures, experimentally tested contact residues and conformational requirements in characterized TyrRS proteins. Establish the transferability of the binding pocket rather than relying on whole-protein similarity. Assess assay conditions, controls and compound isomer where reported. If docking is used, include meaningful controls and treat scores as hypotheses, not measured binding or evidence of physiological function. Separate binding from downstream stress signaling and from whether this interaction merits a GO molecular-function annotation; check the current status and scope of the emitted term independently.",
    "prompt_file": "projects/PROTNLM_EVALUATION/fly-benchmark/openscientist-selection/04-TyrRS-resveratrol-recognition-prompt.md",
    "prompt_sha256": "0295a1ef7e8792bbbb309375ebe99665266eab4b3715b595907799ce88887899",
    "sequence_sha256": "94682a9b94b943a5eca242d7bb960b2787dc2557781933a8d5849bd5e371a01f",
    "sequence_length": 525,
    "launch_argv": [
      "just",
      "gene-hypothesis-research",
      "openscientist",
      "DROME",
      "TyrRS",
      "--focus-type",
      "function-assignment",
      "--hypothesis",
      "The Drosophila melanogaster protein Q9VV60 binds resveratrol.",
      "--slug",
      "fly41-resveratrol-recognition",
      "--context",
      "# Focused fly function hypothesis\n\nHypothesis: The Drosophila melanogaster protein Q9VV60 binds resveratrol.\n\nTarget: Drosophila melanogaster (NCBITaxon:7227), UniProt Q9VV60. Gene label: TyrRS. Verify identity and isoform independently; the gene label is not evidence for the hypothesis.\n\n## Original prediction\n\nF:resveratrol binding\n\n## Decisive question\n\nEvaluate biochemical resveratrol recognition by the supplied fly TyrRS sequence using verified ligand-bound structures, experimentally tested contact residues and conformational requirements in characterized TyrRS proteins. Establish the transferability of the binding pocket rather than relying on whole-protein similarity. Assess assay conditions, controls and compound isomer where reported. If docking is used, include meaningful controls and treat scores as hypotheses, not measured binding or evidence of physiological function. Separate binding from downstream stress signaling and from whether this interaction merits a GO molecular-function annotation; check the current status and scope of the emitted term independently.\n\n## Identity and sequence\n\n- Target record: https://www.uniprot.org/uniprotkb/Q9VV60/entry\n- FlyBase identifier(s) from the cohort identity mapping: FBgn0027080.\n- Frozen current UniProt sequence: 525 residues; SHA-256 `94682a9b94b943a5eca242d7bb960b2787dc2557781933a8d5849bd5e371a01f`.\n- The sequence was frozen for the fly cohort on 2026-09-08. It is not established as the original prediction-time input. Analyze this sequence explicitly and document any alternate accession, version or isoform you analyze.\n\n```fasta\n>Q9VV60 Drosophila melanogaster TyrRS\nMVGITPAEKKALITRNLQETLGDDKLTKILAERDLKIYWGTATTGKPHVAYFVPMSKIAD\nFLKAGCEVTILFADLHAYLDNMKAPWSLLELRTKYYEQVIKAMLSSIGVPLEKLKFVKGS\nDYQLSKEYTLDVYKLSSVVTQHDAKKAGAEVVKQVEYPLLSGLLYPGLQALDEEYLKVDA\nQFGGVDQRKIFTFSEKYLPQLGYEKRIHFMNPMVPGLAGGKMSSSEEDSKIDLLDSPANV\nKKKLKKAFCEPGNIADNGLLSFVKHVLFSLFKEGEGFEVNREAEHGGDVTFLKYEDLEKY\nYAEDKLHPGDLKATVEKYINRLLDPIRKAFENPELQKLSAAAYPPPAKVKAGAAPAAGAD\nEDAPHRLDIRVGKVVEVARHPDADTLYVLKIDLAEAQPRTIISGLVKFVTEEELNQRLVA\nVLCNLKPSKMRGILSEGMVLCTSNADHTVVEPIVLPATATAGSRLSFEGFSGTPDEQLNP\nKKKVWEKLSADFKTNSDGLAVWKDNFLLTPEGEKLSSKLANCSIK\n```\n\nPrimary literature lead to inspect (not a preassigned conclusion): https://pubmed.ncbi.nlm.nih.gov/25533949/\n\n## Evidence and deliverable\n\nUse primary literature and public sequence, structural and genomic resources. This is a focused mechanistic investigation, not a general gene overview. Seek supporting, contrary and competing explanations; an unresolved result is acceptable. Distinguish direct fly experiments, justified transfers and results on a different isoform. Do not equate missing target experiments with evidence of absence.\n\nDo not consult the ai-gene-review repository's current reviews, generated research summaries or local bioinformatics analyses; these are held out for comparison. Agreement with ARBA or repeated prediction text does not validate the biology. Save executed methods/code, actual analysis outputs, sequence identifiers and primary-source URLs/DOIs/PMIDs. Report decisive evidence and limitations, not just a verdict. Do not fabricate computations or use docking/structural resemblance alone as experimental validation.\n",
      "--term-id",
      "GO:1905594",
      "--term-label",
      "resveratrol binding"
    ],
    "expected_report": "genes/DROME/TyrRS/TyrRS-hypotheses/fly41-resveratrol-recognition/openscientist.md",
    "status": "SUBMITTED",
    "dry_run": "PASSED",
    "job_id": "30831c8b-4d81-4e64-a72f-8a3a97a9605d",
    "submitted_at": "2026-09-09T04:52:12.487562Z"
  }
]