{"cross_mech":[{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YiiS","reviewed":true,"short_name":"DUF406","source_category":"function/protein_family/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/function/protein_family/ncbifam/duf406-domain-containing-protein-nf007435.yaml","source_record_id":"NCBIfam:NF007435","source_record_label":"DUF406 domain-containing protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P32162","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YfcZ","reviewed":true,"short_name":"DUF406","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf406-pf04175.yaml","source_record_id":"Pfam:PF04175","source_record_label":"Protein of unknown function (DUF406)","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0AD33","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YfcZ","reviewed":true,"short_name":"DUF406","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf406-pf04175.yaml","source_record_id":"Pfam:PF04175","source_record_label":"Protein of unknown function (DUF406)","source_section":"canonical_examples","taxon_id":"NCBITaxon:199310","taxon_label":"Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)","uniprot_accession":"P0AD34","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":true,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YiiS","reviewed":true,"short_name":"DUF406","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf406-pf04175.yaml","source_record_id":"Pfam:PF04175","source_record_label":"Protein of unknown function (DUF406)","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P32162","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":null,"link_basis":["trait_identifier"],"pfam_id":"PF04175","protein_label":"","reviewed":null,"short_name":"DUF406","source_category":"sequence/family/pfam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/family/pfam/duf406-pf04175.yaml","source_record_id":"Pfam:PF04175","source_record_label":"Protein of unknown function (DUF406)","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":"PF04175","protein_label":"UPF0381 protein YfcZ","reviewed":true,"short_name":"DUF406","source_category":"sequence/homologous_superfamily/interpro","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml","source_record_id":"InterPro:IPR035571","source_record_label":"UPF0234-like, C-terminal","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0AD33","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YiiS","reviewed":true,"short_name":"DUF406","source_category":"sequence/homologous_superfamily/interpro","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml","source_record_id":"InterPro:IPR035571","source_record_label":"UPF0234-like, C-terminal","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P32162","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YfcZ","reviewed":true,"short_name":"DUF406","source_category":"sequence/homologous_superfamily/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml","source_record_id":"NCBIfam:TIGR00743","source_record_label":"DUF406 family protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0AD33","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YiiS","reviewed":true,"short_name":"DUF406","source_category":"sequence/homologous_superfamily/ncbifam","source_mech":"ProteinTraitsMech","source_path":"data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml","source_record_id":"NCBIfam:TIGR00743","source_record_label":"DUF406 family protein","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P32162","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YfcZ","reviewed":true,"short_name":"DUF406","source_category":"structure/homologous_superfamily/cath","source_mech":"ProteinTraitsMech","source_path":"data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.yaml","source_record_id":"CATH:3.30.70.860","source_record_label":"CATH homologous superfamily 3.30.70.860","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P0AD33","unknown_status":"UNKNOWN_CANDIDATE"},{"cited_uniprot_accession":"","family_mentioned_in_record":false,"link_basis":["canonical_example_family_classification"],"pfam_id":"PF04175","protein_label":"UPF0381 protein YiiS","reviewed":true,"short_name":"DUF406","source_category":"structure/homologous_superfamily/cath","source_mech":"ProteinTraitsMech","source_path":"data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.yaml","source_record_id":"CATH:3.30.70.860","source_record_label":"CATH homologous superfamily 3.30.70.860","source_section":"canonical_examples","taxon_id":"NCBITaxon:83333","taxon_label":"Escherichia coli (strain K12)","uniprot_accession":"P32162","unknown_status":"UNKNOWN_CANDIDATE"}],"family":{"alphafold_models":703,"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":5},"scanned":true},"curation_status":"SEEDED","demotion_reasons":[],"description":"Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterised enzyme specific for gamma proteobacteria.","domain_architectures":1,"interpro_id":"IPR005272","known_evidence_count":null,"matches":1083,"name":"Protein of unknown function (DUF406)","partial_evidence_count":null,"pfam_id":"PF04175","proteins":1083,"proteomes":977,"short_name":"DUF406","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04175","structures":3,"taxa":1360,"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/PF04175.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":703,"domain_architectures":1,"matches":1083,"proteins":1083,"proteomes":977,"structures":3,"taxa":1360},"curation_status":"SEEDED","description":"Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterised enzyme specific for gamma proteobacteria.","id":"Pfam:PF04175","interpro_id":"InterPro:IPR005272","name":"Protein of unknown function (DUF406)","pfam_id":"PF04175","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":"DUF406","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04175"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF04175.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"99f0c10c62b76df3bbc0e79896839fe02f8fcfd2a39e673fe5f1b8ef68290bbe"}},"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/duf406-pf04175.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04175","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf406-pf04175.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR035571","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00743","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.yaml","qualification_status":"NOT_ASSESSED","record_id":"CATH:3.30.70.860","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.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:P0AD33","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF04175"],"protein_name":"UPF0381 protein YfcZ","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"0e8c0f00cf1dd67717b890a46591e30777a544465118188345c6a857a2d67b0a","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":"MSKCSADETPVCCCMDVGTIMDNSDCTASYSRVFANRAEAEQTLAALTEKARSVESEPCKITPTFTEESDGVRLDIDFTFACEAEMLIFQLGLR","sequence_length":94,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"0e8c0f00cf1dd67717b890a46591e30777a544465118188345c6a857a2d67b0a","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P0AD33.json","taxon_id":"83333","uniprot_accession":"P0AD33","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/duf406-pf04175.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04175","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf406-pf04175.yaml"}],"pfam_ids":["PF04175"],"protein_name":"UPF0381 protein YfcZ","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MSKCSADETPVCCCMDVGTIMDNSDCTASYSRVFANRAEAEQTLAALTEKARSVESEPCKITPTFTEESDGVRLDIDFTFACEAEMLIFQLGLR","sequence_length":94,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"0e8c0f00cf1dd67717b890a46591e30777a544465118188345c6a857a2d67b0a","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P0AD34.json","taxon_id":"199310","uniprot_accession":"P0AD34","uniprot_release":"2026_03"},{"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/duf406-domain-containing-protein-nf007435.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF007435","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/duf406-domain-containing-protein-nf007435.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/duf406-pf04175.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF04175","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/duf406-pf04175.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR035571","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/homologous_superfamily/interpro/upf0234-like-c-terminal-ipr035571.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:TIGR00743","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/homologous_superfamily/ncbifam/duf406-family-protein-tigr00743.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.yaml","qualification_status":"NOT_ASSESSED","record_id":"CATH:3.30.70.860","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/structure/homologous_superfamily/cath/3-30-70-860-3-30-70-860.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:P32162","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF04175"],"protein_name":"UPF0381 protein YiiS","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"29fad3e72a8a80ccf333f903de848a322a98fe5b81dbe2790f3ec224077d0e6b","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":"MKDVVDKCSTKGCAIDIGTVIDNDNCTSKFSRFFATREEAESFMTKLKELAAATSSADEGASVAYKIKDLEGQVELDAAFTFSCQAEMIIFELSLRSLA","sequence_length":99,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"29fad3e72a8a80ccf333f903de848a322a98fe5b81dbe2790f3ec224077d0e6b","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P32162.json","taxon_id":"83333","uniprot_accession":"P32162","uniprot_release":"2026_03"}],"pfam_id":"PF04175","short_name":"DUF406","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
