{"cross_mech":[],"family":{"alphafold_models":623,"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":"This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches [[cite:PUB00044133]]. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction [[cite:PUB00044133]]. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme [[cite:PUB00044133]].","domain_architectures":8,"interpro_id":"IPR007505","known_evidence_count":null,"matches":972,"name":"PD-(D/E)XK nuclease superfamily","partial_evidence_count":null,"pfam_id":"PF04411","proteins":970,"proteomes":917,"short_name":"PDDEXK_7","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04411","structures":0,"taxa":1891,"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/PF04411.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":623,"domain_architectures":8,"matches":972,"proteins":970,"proteomes":917,"structures":0,"taxa":1891},"curation_status":"SEEDED","description":"This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches [[cite:PUB00044133]]. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction [[cite:PUB00044133]]. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme [[cite:PUB00044133]].","id":"Pfam:PF04411","interpro_id":"InterPro:IPR007505","name":"PD-(D/E)XK nuclease superfamily","pfam_id":"PF04411","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":"PDDEXK_7","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF04411"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF04411.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"466e24468793c1cbf3c08456d31044e256466bbb03e72c1d2f5862916baca98d"}},"protein_examples":{"candidate_count":0,"discovery_scanned":true,"example_count":0,"examples":[],"pfam_id":"PF04411","short_name":"PDDEXK_7","status":"NO_SIBLING_CANDIDATE","unresolved":[]}}
