{"cross_mech":[{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ0678","reviewed":true,"short_name":"DUF389","source_category":"function/protein_family/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml","source_record_id":"NCBIfam:TIGR00341","source_record_label":"TIGR00341 family protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58091","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ1221","reviewed":true,"short_name":"DUF389","source_category":"function/protein_family/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml","source_record_id":"NCBIfam:TIGR00341","source_record_label":"TIGR00341 family protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58618","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ0678","reviewed":true,"short_name":"DUF389","source_category":"sequence/domain/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml","source_record_id":"NCBIfam:TIGR00271","source_record_label":"uncharacterized hydrophobic domain","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58091","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ1221","reviewed":true,"short_name":"DUF389","source_category":"sequence/domain/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml","source_record_id":"NCBIfam:TIGR00271","source_record_label":"uncharacterized hydrophobic domain","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58618","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ0678","reviewed":true,"short_name":"DUF389","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf389-pf04087.yaml","source_record_id":"Pfam:PF04087","source_record_label":"Domain of unknown function (DUF389)","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58091","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04087","protein_label":"Uncharacterized protein MJ1221","reviewed":true,"short_name":"DUF389","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf389-pf04087.yaml","source_record_id":"Pfam:PF04087","source_record_label":"Domain of unknown function (DUF389)","source_section":"canonical_examples","taxon_id":"NCBITaxon:243232","taxon_label":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","uniprot_accession":"Q58618","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":null,"link_basis":["trait_identifier"],"pfam_id":"PF04087","protein_label":"","reviewed":null,"short_name":"DUF389","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf389-pf04087.yaml","source_record_id":"Pfam:PF04087","source_record_label":"Domain of unknown function (DUF389)","source_section":"trait_identifier","taxon_id":"","taxon_label":"","uniprot_accession":"","unknown_status":"UNKNOWN_CANDIDATE"}],"family":{"alphafold_models":4748,"candidate_reasons":["short_name_matches_duf","name_says_unknown_function","domain_of_unknown_function"],"characterization_status":"","context_evidence_count":null,"cross_mech":{"example_proteins":2,"protein_traits_record":true,"records_by_mech":{"ProteinTraitsMech":3},"scanned":true},"curation_status":"SEEDED","demotion_reasons":[],"description":"Family of hypothetical bacterial proteins with an undetermined function.","domain_architectures":25,"interpro_id":"IPR005240","known_evidence_count":null,"matches":7185,"name":"Domain of unknown function (DUF389)","partial_evidence_count":null,"pfam_id":"PF04087","proteins":7177,"proteomes":5575,"short_name":"DUF389","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04087","structures":0,"taxa":9165,"unknown_status":"UNKNOWN_CANDIDATE"},"inputs":{"cross_mech":"cross-mech-duf-examples-2026-10-10","members":"pfam-uniprot-uniref90-2026-10-07","protein_examples":"duf-protein-examples-2026-10-13","worklist":"interpro-pfam-duf-2026-10-10"},"members":[],"metadata":{"curation_status":"SEEDED","local_source":"source/data/families/PF04087.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":4748,"domain_architectures":25,"matches":7185,"proteins":7177,"proteomes":5575,"structures":0,"taxa":9165},"curation_status":"SEEDED","description":"Family of hypothetical bacterial proteins with an undetermined function.","id":"Pfam:PF04087","interpro_id":"InterPro:IPR005240","name":"Domain of unknown function (DUF389)","pfam_id":"PF04087","provenance":{"generated_at":"2026-10-10T07:44:21.614711Z","path":"data/worklists/interpro-pfam-duf-2026-10-10.json","sha256":"17fb625876c9326ed284263a47bcd84e0d7844a31c040dc06cd2260c36f1c383","snapshot_id":"interpro-pfam-duf-2026-10-10","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/"},"seed_status":"UNKNOWN_CANDIDATE","short_name":"DUF389","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04087"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF04087.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"c252710162877cfd2da199825ad4ec432c3352af1641e2a106fb0b6055c682f3"}},"protein_examples":{"candidate_count":2,"discovery_scanned":true,"example_count":2,"examples":[{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00341","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00271","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/family/pfam/duf389-pf04087.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04087","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf389-pf04087.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_registry_exact_uniprot_pfam_xref"],"mech":"ProteinTraitsMech","path":"data/grounding/protein_registry.jsonl","qualification_status":"NOT_ASSESSED_FOR_THIS_FAMILY","record_id":"UniProtKB:Q58091","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF04087"],"protein_name":"Uncharacterized protein MJ0678","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"7c6178d7ab1ba28b9defe9aaee226bf15aeb2192d6d7f1f15cbcb037bbaeedc0","sequence_version":1,"sha256":"1be0cf02b76b03a8fe9b80bcead9cd4a419157116eb8da038f266bcc33015eb9","uniprot_release":"2026_03","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"},"registry_status":"EXACT_SEQUENCE_VERSION_MATCH","reviewed":true,"sequence":"MKLRFIECHIPKHLFMGIDEIREWDGVIWANVKTNGTISTIQILTTLKDSEKIVDKLKEMYGGANYRVVVFEPTMTYPPIEEEEEKEEPERLIREELYNIASDIANLSKENMLMLILSTIVAIAGIYKDDVALLIASMIIAPLLGPNIALSLSITVADYKLALKSIKTLIAELIFVIILSMIAGHYLPISLDNPQIHSRITLDFWSIIIALSAGIAGSLSTVSNISSIAVGVMIAIALLPPLAVFGLLIGAGYVEQSFSALILFLINMIAINLSAIVIFSAYGISPYRWWKKEEARKYTLYAILLWVTLFIAIFVLIIYH","sequence_length":320,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"7c6178d7ab1ba28b9defe9aaee226bf15aeb2192d6d7f1f15cbcb037bbaeedc0","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q58091.json","taxon_id":"243232","uniprot_accession":"Q58091","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00341","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/tigr00341-family-protein-tigr00341.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00271","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/ncbifam/uncharacterized-hydrophobic-domain-tigr00271.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/family/pfam/duf389-pf04087.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04087","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf389-pf04087.yaml"}],"pfam_ids":["PF04087"],"protein_name":"Uncharacterized protein MJ1221","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MWFGERMRYMKIIIPKKFLNTVEEILKKNNAYSISIIEPLKTSIEDGIIITCNADARDAEKIVLELKKLGLGEKGHGSVTIMPANITFSCREEGIASTSLSPLELYYKAKTMVKITKNVIIKVILASIMGVIGLIEHNIPTLIGAMIIAPLVDTVMGSAIGTVLGDKELFIQGMKKELLCSGIVIVCAFIPSLFFVSKELVLQYLSETSIILSAIVAIIAGISGGMSIASGKEYEIIGVTIDVSILIPALLMGMALATMDLYLIYITFILLAINIVLLDVGGYIGLKYKVGKINQKIKY","sequence_length":299,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"31119593457a96c54aedfbcc0bc0f4d52f78c87e3704baaf6039a384bee4dc3d","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q58618.json","taxon_id":"243232","uniprot_accession":"Q58618","uniprot_release":"2026_03"}],"pfam_id":"PF04087","short_name":"DUF389","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
