{"cross_mech":[{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF06288","protein_label":"Protein YihD","reviewed":true,"short_name":"DUF1040","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf1040-pf06288.yaml","source_record_id":"Pfam:PF06288","source_record_label":"Protein of unknown function (DUF1040)","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0ADP9","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF06288","protein_label":"Protein YihD","reviewed":true,"short_name":"DUF1040","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf1040-pf06288.yaml","source_record_id":"Pfam:PF06288","source_record_label":"Protein of unknown function (DUF1040)","source_section":"canonical_examples","taxon_id":"NCBITaxon:199310","taxon_label":"Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)","uniprot_accession":"P0ADQ0","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF06288","protein_label":"Uncharacterized protein HI_0845","reviewed":true,"short_name":"DUF1040","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf1040-pf06288.yaml","source_record_id":"Pfam:PF06288","source_record_label":"Protein of unknown function (DUF1040)","source_section":"canonical_examples","taxon_id":"NCBITaxon:71421","taxon_label":"Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)","uniprot_accession":"P44900","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":null,"link_basis":["trait_identifier"],"pfam_id":"PF06288","protein_label":"","reviewed":null,"short_name":"DUF1040","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf1040-pf06288.yaml","source_record_id":"Pfam:PF06288","source_record_label":"Protein of unknown function (DUF1040)","source_section":"trait_identifier","taxon_id":"","taxon_label":"","uniprot_accession":"","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF06288","protein_label":"Protein YihD","reviewed":true,"short_name":"DUF1040","source_category":"sequence/homologous_superfamily/interpro","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/homologous_superfamily/interpro/yihd-like-superfamily-ipr038134.yaml","source_record_id":"InterPro:IPR038134","source_record_label":"YihD-like superfamily","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0ADP9","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF06288","protein_label":"Protein YihD","reviewed":true,"short_name":"DUF1040","source_category":"structure/homologous_superfamily/cath","source_mech":"ProteinTraitsMech","source_path":"data/traits/structure/homologous_superfamily/cath/protein-of-unknown-function-duf1040-1-10-1580-20.yaml","source_record_id":"CATH:1.10.1580.20","source_record_label":"Protein of unknown function DUF1040","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0ADP9","unknown_status":"UNKNOWN_CANDIDATE"}],"family":{"alphafold_models":595,"candidate_reasons":["short_name_matches_duf","name_says_unknown_function","description_says_unknown_function"],"characterization_status":"","context_evidence_count":null,"cross_mech":{"example_proteins":3,"protein_traits_record":true,"records_by_mech":{"ProteinTraitsMech":3},"scanned":true},"curation_status":"SEEDED","demotion_reasons":[],"description":"This family consists of several bacterial YihD proteins of unknown function [[cite:PUB00009964]].","domain_architectures":3,"interpro_id":"IPR009383","known_evidence_count":null,"matches":889,"name":"Protein of unknown function (DUF1040)","partial_evidence_count":null,"pfam_id":"PF06288","proteins":888,"proteomes":887,"short_name":"DUF1040","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF06288","structures":1,"taxa":1261,"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/PF06288.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":595,"domain_architectures":3,"matches":889,"proteins":888,"proteomes":887,"structures":1,"taxa":1261},"curation_status":"SEEDED","description":"This family consists of several bacterial YihD proteins of unknown function [[cite:PUB00009964]].","id":"Pfam:PF06288","interpro_id":"InterPro:IPR009383","name":"Protein of unknown function (DUF1040)","pfam_id":"PF06288","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":"DUF1040","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF06288"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF06288.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"d9da7fb964b4848c2696f732011f99a6ad62e6d1fa6975c420cf2a6094f79f75"}},"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","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/family/pfam/duf1040-pf06288.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF06288","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf1040-pf06288.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/homologous_superfamily/interpro/yihd-like-superfamily-ipr038134.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR038134","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/homologous_superfamily/interpro/yihd-like-superfamily-ipr038134.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/structure/homologous_superfamily/cath/protein-of-unknown-function-duf1040-1-10-1580-20.yaml","qualification_status":"NOT_ASSESSED","record_id":"CATH:1.10.1580.20","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/structure/homologous_superfamily/cath/protein-of-unknown-function-duf1040-1-10-1580-20.yaml"}],"pfam_ids":["PF06288"],"protein_name":"Protein YihD","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKCKRLNEVIELLQPAWQKEPDLNLLQFLQKLAKESGFDGELADLTDDILIYHLKMRDSAKDAVIPGLQKDYEEDFKTALLRARGVIKE","sequence_length":89,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"b974f3b11a82818ab212228bc7afb60e4c0af62418e3287e9099f3da1f9ae5f4","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P0ADP9.json","taxon_id":"83333","uniprot_accession":"P0ADP9","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)","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/duf1040-pf06288.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF06288","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf1040-pf06288.yaml"}],"pfam_ids":["PF06288"],"protein_name":"Protein YihD","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKCKRLNEVIELLQPAWQKEPDLNLLQFLQKLAKESGFDGELADLTDDILIYHLKMRDSAKDAVIPGLQKDYEEDFKTALLRARGVIKE","sequence_length":89,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"b974f3b11a82818ab212228bc7afb60e4c0af62418e3287e9099f3da1f9ae5f4","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P0ADQ0.json","taxon_id":"199310","uniprot_accession":"P0ADQ0","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)","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/duf1040-pf06288.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF06288","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf1040-pf06288.yaml"}],"pfam_ids":["PF06288"],"protein_name":"Uncharacterized protein HI_0845","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKCKRLNEVLELLQSYWSKDSDLSLMEILQKIANESGFQKPLNELTDEVIIYQLKMDGTDKYEPIPGLKKDYEEDFKTALLRARGIIK","sequence_length":88,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"5802e5e7180b8bff00f7249931f00f4e0d201876cb9e552160da4e635bea58a0","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P44900.json","taxon_id":"71421","uniprot_accession":"P44900","uniprot_release":"2026_03"}],"pfam_id":"PF06288","short_name":"DUF1040","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
