{"cross_mech":[],"family":{"alphafold_models":2152,"candidate_reasons":["pfam_previous_unknown_name"],"characterization_status":"","context_evidence_count":null,"cross_mech":{"example_proteins":0,"protein_traits_record":false,"records_by_mech":{},"scanned":false},"curation_status":"SEEDED","demotion_reasons":[],"description":"Amidase_YiiX is a family of permuted papain-like amidases. It has amidase specificity for the amide bond between a lipid and an amino acid (or peptide). From the structure, a tetramer, each monomer is made up of a layered alpha-beta fold with a central, 6-stranded, antiparallel beta-sheet that is protected by helices on either side. The catalytic Cys154 in UniProtKB:Q74NK7, PDB:3kw0, is located on the N-terminus of helix alphaF. The two additional helices located above Cys154 contribute to the formation of the active site, where the lysine ligand is bound [[cite:PUB00075488]].","domain_architectures":32,"interpro_id":"IPR024453","known_evidence_count":null,"matches":3260,"name":"Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family","partial_evidence_count":null,"pfam_id":"PF05708","proteins":3259,"proteomes":2690,"short_name":"Peptidase_C92","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF05708","structures":2,"taxa":4781,"unknown_status":"EX_DUF"},"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/PF05708.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":2152,"domain_architectures":32,"matches":3260,"proteins":3259,"proteomes":2690,"structures":2,"taxa":4781},"curation_status":"SEEDED","description":"Amidase_YiiX is a family of permuted papain-like amidases. It has amidase specificity for the amide bond between a lipid and an amino acid (or peptide). From the structure, a tetramer, each monomer is made up of a layered alpha-beta fold with a central, 6-stranded, antiparallel beta-sheet that is protected by helices on either side. The catalytic Cys154 in UniProtKB:Q74NK7, PDB:3kw0, is located on the N-terminus of helix alphaF. The two additional helices located above Cys154 contribute to the formation of the active site, where the lysine ligand is bound [[cite:PUB00075488]].","id":"Pfam:PF05708","interpro_id":"InterPro:IPR024453","name":"Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family","pfam_id":"PF05708","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":"EX_DUF","short_name":"Peptidase_C92","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF05708"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF05708.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"3ae4e1e8dc9278f9a5f203d420636f03a175eb4e8a2276a33e18bbc386d079c7"}},"protein_examples":{"candidate_count":4,"discovery_scanned":true,"example_count":4,"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/yebb-family-permuted-papain-like-enzyme-nf008547.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF008547","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/yebb-family-permuted-papain-like-enzyme-nf008547.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/peptidase-c92-pf05708.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF05708","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/peptidase-c92-pf05708.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:P24238","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF05708"],"protein_name":"Uncharacterized protein YebB","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"4a11aba2f17eeb1f007a6734cb3ffa0270a79960e90246bd6f21d40d12cfd87b","sequence_version":2,"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":"MNINYPAEYEIGDIVFTCIGAALFGQISAASNCWSNHVGIIIGHNGEDFLVAESRVPLSTITTLSRFIKRSSNQRYAIKRLDAGLTERQKQRIVEQVPSRLRKLYHTGFKYESSRQFCSKFVFDIYKEALCIPVGEIETFGELLNSNPNAKLTFWKFWFLGSIPWERKTVTPASLWHHPGLVLIHAEGVETPQPELTEAV","sequence_length":200,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"4a11aba2f17eeb1f007a6734cb3ffa0270a79960e90246bd6f21d40d12cfd87b","sequence_version":2,"source_url":"https://rest.uniprot.org/uniprotkb/P24238.json","taxon_id":"83333","uniprot_accession":"P24238","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/yiix-family-permuted-papain-like-enzyme-nf007458.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF007458","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/yiix-family-permuted-papain-like-enzyme-nf007458.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/peptidase-c92-pf05708.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF05708","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/peptidase-c92-pf05708.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:P32167","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF05708"],"protein_name":"Uncharacterized protein YiiX","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"2384f1400aaade6814db807ccaaf652d45145a5e73ce83cf4ccdf007ea2cd3df","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":"MKNRLLILSLLVSVPAFAWQPQTGDIIFQISRSSQSKAIQLATHTDYSHTGMLVIRNKKPYVFEAVGPVKYTPLKQWIAHGEKGKYVVRRVEGGLSVEQQQKLAQTAKRYLGKPYDFSFSWSDDRQYCSEVVWKVYQNALGMRVGEQQKLKEFDLSSPQVQAKLKERYGKNIPLEETVVSPQAVFDAPQLTTVAKEWPLFSW","sequence_length":202,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"2384f1400aaade6814db807ccaaf652d45145a5e73ce83cf4ccdf007ea2cd3df","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P32167.json","taxon_id":"83333","uniprot_accession":"P32167","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/yaef-family-permuted-papain-like-enzyme-nf008552.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF008552","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/yaef-family-permuted-papain-like-enzyme-nf008552.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/peptidase-c92-pf05708.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF05708","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/peptidase-c92-pf05708.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:P37056","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF05708"],"protein_name":"Probable lipoprotein peptidase YaeF","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"ec8286d1ae04bf681552830aeecf326962d31fb4b6d892bc71c8bbfbe0b66c64","sequence_version":3,"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":"MDKPKAYCRLFLPSFLLLSACTVDISQPDPSATAVDAEAKTWAVKFQHQSSFTEQSIKEITAPDLKPGDLLFSSSLGVTSFGIRVFSTSSVSHVAIFLGDNNVAEATGAGVQIVSLKKAMKHSDKLFVLRVPDLTPQQATDITAFANKIKDSGYNYRGIVEFIPFMVTRQMCSLNPFSEDFRQQCVSGLAKAQLSSVGEGDKKSWFCSEFVTDAFAKAGHPLTLAQSGWISPADLMHMRIGDVSAFKPETQLQYVGHLKPGIYIKAGRFVGLTR","sequence_length":274,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"ec8286d1ae04bf681552830aeecf326962d31fb4b6d892bc71c8bbfbe0b66c64","sequence_version":3,"source_url":"https://rest.uniprot.org/uniprotkb/P37056.json","taxon_id":"83333","uniprot_accession":"P37056","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Bacillus subtilis (strain 168)","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/peptidase-c92-pf05708.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF05708","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/family/pfam/peptidase-c92-pf05708.yaml"}],"pfam_ids":["PF05708"],"protein_name":"Uncharacterized protein YycO","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKLKKRVSMFLVALTMCGGLFVTPAKAVKTTNYAEEIAALQPGTTPEEIMKSASQIAKQQHVKQDVILKQFYKEITADKAEGDRLAKESGMSIMGGSSGTKKLPTSAKGNIYYTNSYTAYYNHGHVGMYSAADKIVESVPSDGVRQIAYNARDVEDNSIVQTVSVSSSQKTAAADWAVSKVGDPYSFNFVNNRNTGHDGAKNCSKLLWSAFLLKAGIDIDSNGGLGVYPRDITSSSYTTTIMTIY","sequence_length":245,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"5f4c504fe1db591eb88abdee272131d654f1303096f5bb2b21aa462441a4856b","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q45607.json","taxon_id":"224308","uniprot_accession":"Q45607","uniprot_release":"2026_03"}],"pfam_id":"PF05708","short_name":"Peptidase_C92","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}