{"cross_mech":[{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04340","protein_label":"Uncharacterized protein YigA","reviewed":true,"short_name":"DUF484","source_category":"function/protein_family/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/function/protein_family/ncbifam/hypothetical-protein-nf008203.yaml","source_record_id":"NCBIfam:NF008203","source_record_label":"hypothetical protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P23305","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04340","protein_label":"Uncharacterized protein YigA","reviewed":true,"short_name":"DUF484","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","source_record_id":"Pfam:PF04340","source_record_label":"Protein of unknown function, DUF484","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P23305","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04340","protein_label":"Uncharacterized protein YigA","reviewed":true,"short_name":"DUF484","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","source_record_id":"Pfam:PF04340","source_record_label":"Protein of unknown function, DUF484","source_section":"canonical_examples","taxon_id":"NCBITaxon:99287","taxon_label":"Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)","uniprot_accession":"P55886","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04340","protein_label":"Uncharacterized protein YigA","reviewed":true,"short_name":"DUF484","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","source_record_id":"Pfam:PF04340","source_record_label":"Protein of unknown function, DUF484","source_section":"canonical_examples","taxon_id":"NCBITaxon:623","taxon_label":"Shigella flexneri","uniprot_accession":"Q83IW8","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":null,"link_basis":["trait_identifier"],"pfam_id":"PF04340","protein_label":"","reviewed":null,"short_name":"DUF484","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","source_record_id":"Pfam:PF04340","source_record_label":"Protein of unknown function, DUF484","source_section":"trait_identifier","taxon_id":"","taxon_label":"","uniprot_accession":"","unknown_status":"UNKNOWN_CANDIDATE"}],"family":{"alphafold_models":3267,"candidate_reasons":["short_name_matches_duf","name_says_unknown_function"],"characterization_status":"","context_evidence_count":null,"cross_mech":{"example_proteins":3,"protein_traits_record":true,"records_by_mech":{"ProteinTraitsMech":2},"scanned":true},"curation_status":"SEEDED","demotion_reasons":[],"description":"This family consists of several proteins of uncharacterised function.","domain_architectures":6,"interpro_id":"IPR007435","known_evidence_count":null,"matches":5092,"name":"Protein of unknown function, DUF484","partial_evidence_count":null,"pfam_id":"PF04340","proteins":5088,"proteomes":4716,"short_name":"DUF484","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04340","structures":1,"taxa":6409,"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/PF04340.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":3267,"domain_architectures":6,"matches":5092,"proteins":5088,"proteomes":4716,"structures":1,"taxa":6409},"curation_status":"SEEDED","description":"This family consists of several proteins of uncharacterised function.","id":"Pfam:PF04340","interpro_id":"InterPro:IPR007435","name":"Protein of unknown function, DUF484","pfam_id":"PF04340","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":"DUF484","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04340"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF04340.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"cc4baf139dc1485df61d95e75d47a1ff14681356aaa0c3a39e7b4d73561326e3"}},"protein_examples":{"candidate_count":3,"discovery_scanned":true,"example_count":3,"examples":[{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Escherichia coli (strain K12)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/function/protein_family/ncbifam/hypothetical-protein-nf008203.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF008203","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/hypothetical-protein-nf008203.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/duf484-pf04340.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04340","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf484-pf04340.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:P23305","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF04340"],"protein_name":"Uncharacterized protein YigA","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"27be98f5ed627b4dbc2aa4e08d7390fcee4dfdf024e641a98693ea85b1e6c3f8","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":"MKQPGEELQETLTELDDRAVVDYLIKNPEFFIRNARAVEAIRVPHPVRGTVSLVEWHMARARNHIHVLEENMALLMEQAIANEGLFYRLLYLQRSLTAASSLDDMLMRFHRWARDLGLAGASLRLFPDRWRLGAPSNHTHLALSRQSFEPLRIQRLGQEQHYLGPLNGPELLVVLPEAKAVGSVAMSMLGSDADLGVVLFTSRDASHYQQGQGTQLLHEIALMLPELLERWIERV","sequence_length":235,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"27be98f5ed627b4dbc2aa4e08d7390fcee4dfdf024e641a98693ea85b1e6c3f8","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P23305.json","taxon_id":"83333","uniprot_accession":"P23305","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04340","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf484-pf04340.yaml"}],"pfam_ids":["PF04340"],"protein_name":"Uncharacterized protein YigA","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKQPEEELQETLTELDDRAVVDYLRHHPEFFIRNAHAVEAMRVPHPVRGTVSLVEWHMARARNHINVLEENMTLLMEQAHANESLFYRLLHLQSRLVAADSLDEMLVRFHRWARDLGLAGATLRLFPDRWRLGAPSRYTHLALNRQAFEPLRIQRLGQSQHYLGPLNGPELLVVLPEAKAVGSVAMSMMGSDGGLGVILFSSRDPHHYQPGQGTQLLQEIALMLPELLERWIKRV","sequence_length":235,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"abca8c43478efd9495e28cfdad8965105d7972eaf02863e594a4bf1a53476dfd","sequence_version":2,"source_url":"https://rest.uniprot.org/uniprotkb/P55886.json","taxon_id":"99287","uniprot_accession":"P55886","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Shigella flexneri","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/family/pfam/duf484-pf04340.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04340","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf484-pf04340.yaml"}],"pfam_ids":["PF04340"],"protein_name":"Uncharacterized protein YigA","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKQPGEELQETLTELDDRAVVDYLIKNPEFFIRNARAVEAIRVPHPVRGTISLVEWHMARARNHIHVLEENMALLMEQAIANEGLFYRLLYLQRSLTAASSLDDMLMRFHRWARDLGLAGASLRLFPDRWRLGAPSNHTHLALSRQSFEPLRIQRLGQEQHYLGPLNGPELLVVLPEAKAVGSVAMSMLGSDADLGVVLFTSRDASHYQQGQGTQLLHEIALMLPELLERWIERV","sequence_length":235,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"bce7cf0651f12a0428dc1ebdd771b4359f7db3037675af8dded878f197a1f8fc","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q83IW8.json","taxon_id":"623","uniprot_accession":"Q83IW8","uniprot_release":"2026_03"}],"pfam_id":"PF04340","short_name":"DUF484","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
