{
  "about": "Biopython ProtParam MW + Pace e280 and Ikai aliphatic index for the construct tag model the CSO ruled on 20 October 2026 (memo 2026-10-20-cso-audit-fixes.md, section 2 item 2): an explicit protease per tag, AviTag-His6 not cleavable and allowed at either terminus with no cleaved species, a protease tag refused at the C-terminus, and an initiator Met prepended when the construct would not start with Met. Masses hold to the v1 tolerance (within 1 Da of Biopython; e280 and the aliphatic index exact). construct-cropper-v1.json is unchanged and still checked.",
  "recordedOn": "2026-10-20",
  "oracle": "pipeline/protein-explorer/construct-cropper/reference.py",
  "environment": {
    "python": "3.13.16",
    "biopython": "1.88"
  },
  "refusalCodes": {
    "cTerminalProtease": "c-terminal-cleavage-not-modelled"
  },
  "tagModel": {
    "none": {
      "sequence": "",
      "protease": null,
      "cleavable": false,
      "termini": [],
      "postCleavageScarN": null
    },
    "his6": {
      "sequence": "MGSSHHHHHH",
      "protease": null,
      "cleavable": false,
      "termini": [
        "n-term",
        "c-term"
      ],
      "postCleavageScarN": null
    },
    "his6-tev": {
      "sequence": "MGSSHHHHHHSSGENLYFQG",
      "protease": "TEV",
      "cleavable": true,
      "termini": [
        "n-term"
      ],
      "postCleavageScarN": "G"
    },
    "his6-thrombin": {
      "sequence": "MGSSHHHHHHSSGLVPRGS",
      "protease": "thrombin",
      "cleavable": true,
      "termini": [
        "n-term"
      ],
      "postCleavageScarN": "GS"
    },
    "his6-3c": {
      "sequence": "MGSSHHHHHHSSGLEVLFQGP",
      "protease": "HRV 3C",
      "cleavable": true,
      "termini": [
        "n-term"
      ],
      "postCleavageScarN": "GP"
    },
    "strep-ii": {
      "sequence": "MASWSHPQFEKGA",
      "protease": null,
      "cleavable": false,
      "termini": [
        "n-term",
        "c-term"
      ],
      "postCleavageScarN": null
    },
    "flag": {
      "sequence": "MDYKDDDDK",
      "protease": null,
      "cleavable": false,
      "termini": [
        "n-term",
        "c-term"
      ],
      "postCleavageScarN": null
    },
    "avi-his6": {
      "sequence": "MGLNDIFEAQKIEWHEGHHHHHH",
      "protease": null,
      "cleavable": false,
      "termini": [
        "n-term",
        "c-term"
      ],
      "postCleavageScarN": null
    }
  },
  "aviTagBiotinylation": {
    "aviTagSequence": "GLNDIFEAQKIEWHE",
    "aviTagLength": 15,
    "lysineInAviTag": 10,
    "lysineInStoredTag": 11,
    "storedTagSequence": "MGLNDIFEAQKIEWHEGHHHHHH",
    "biotinAdductFormula": "C10H14N2O2S",
    "note": "BirA biotinylates the AviTag's single lysine; the extent of biotinylation is not predicted here and no biotinylated mass is reported."
  },
  "cases": {
    "ubq_avihis6_nterm": {
      "tagId": "avi-his6",
      "terminus": "n-term",
      "wt": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "startResidue1Based": 1,
      "endResidue1Based": 76,
      "refused": null,
      "coreSequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "initiatorMetAdded": false,
      "assembledTagged": "MGLNDIFEAQKIEWHEGHHHHHHQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "assembledCleaved": null,
      "wildType": {
        "length": 76,
        "molecularWeightDa": 8564.74,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 100.0
      },
      "tagged": {
        "length": 98,
        "molecularWeightDa": 11255.58,
        "extinctionReduced": 6990,
        "extinctionCystines": 6990,
        "aliphaticIndex": 90.5
      },
      "cleaved": null
    },
    "ubq_avihis6_cterm": {
      "tagId": "avi-his6",
      "terminus": "c-term",
      "wt": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "startResidue1Based": 1,
      "endResidue1Based": 76,
      "refused": null,
      "coreSequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "initiatorMetAdded": false,
      "assembledTagged": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGLNDIFEAQKIEWHEGHHHHHH",
      "assembledCleaved": null,
      "wildType": {
        "length": 76,
        "molecularWeightDa": 8564.74,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 100.0
      },
      "tagged": {
        "length": 98,
        "molecularWeightDa": 11255.58,
        "extinctionReduced": 6990,
        "extinctionCystines": 6990,
        "aliphaticIndex": 90.5
      },
      "cleaved": null
    },
    "ubq_his6tev_cterm_refused": {
      "tagId": "his6-tev",
      "terminus": "c-term",
      "wt": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "startResidue1Based": 1,
      "endResidue1Based": 76,
      "refused": "c-terminal-cleavage-not-modelled"
    },
    "ubq_untagged_10_70_initiator_met": {
      "tagId": "none",
      "terminus": "n-term",
      "wt": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "startResidue1Based": 10,
      "endResidue1Based": 70,
      "refused": null,
      "coreSequence": "GKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV",
      "initiatorMetAdded": true,
      "assembledTagged": "MGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV",
      "assembledCleaved": null,
      "wildType": {
        "length": 76,
        "molecularWeightDa": 8564.74,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 100.0
      },
      "tagged": {
        "length": 62,
        "molecularWeightDa": 6980.82,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 92.7
      },
      "cleaved": null
    },
    "ubq_untagged_full_length": {
      "tagId": "none",
      "terminus": "n-term",
      "wt": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "startResidue1Based": 1,
      "endResidue1Based": 76,
      "refused": null,
      "coreSequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "initiatorMetAdded": false,
      "assembledTagged": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG",
      "assembledCleaved": null,
      "wildType": {
        "length": 76,
        "molecularWeightDa": 8564.74,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 100.0
      },
      "tagged": {
        "length": 76,
        "molecularWeightDa": 8564.74,
        "extinctionReduced": 1490,
        "extinctionCystines": 1490,
        "aliphaticIndex": 100.0
      },
      "cleaved": null
    },
    "gfp_his6tev_nterm": {
      "tagId": "his6-tev",
      "terminus": "n-term",
      "wt": "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK",
      "startResidue1Based": 1,
      "endResidue1Based": 238,
      "refused": null,
      "coreSequence": "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK",
      "initiatorMetAdded": false,
      "assembledTagged": "MGSSHHHHHHSSGENLYFQGSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK",
      "assembledCleaved": "GSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK",
      "wildType": {
        "length": 238,
        "molecularWeightDa": 26885.99,
        "extinctionReduced": 21890,
        "extinctionCystines": 22015,
        "aliphaticIndex": 74.9
      },
      "tagged": {
        "length": 257,
        "molecularWeightDa": 29023.14,
        "extinctionReduced": 23380,
        "extinctionCystines": 23505,
        "aliphaticIndex": 70.9
      },
      "cleaved": {
        "length": 238,
        "molecularWeightDa": 26811.85,
        "extinctionReduced": 21890,
        "extinctionCystines": 22015,
        "aliphaticIndex": 74.9
      }
    }
  }
}