{"cross_mech":[],"family":{"alphafold_models":1465,"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 entry includes E3 ubiquitin-protein ligase APD1 to 4 from Arabidopsis. They are involved in pollen mitosis II (PMII) regulation during male gametogenesis [[cite:PUB00096500]]. This entry represents a functionally uncharacterised domain found in the middle of APD1-4 and in uncharacterised sequences mainly from arthropods. There are two completely conserved C residues that may be functionally important.","domain_architectures":56,"interpro_id":"IPR032010","known_evidence_count":null,"matches":1862,"name":"E3 ubiquitin-protein ligase APD1-4, middle domain","partial_evidence_count":null,"pfam_id":"PF16041","proteins":1852,"proteomes":646,"short_name":"APD1-4_M","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF16041","structures":0,"taxa":2179,"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/PF16041.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":1465,"domain_architectures":56,"matches":1862,"proteins":1852,"proteomes":646,"structures":0,"taxa":2179},"curation_status":"SEEDED","description":"This entry includes E3 ubiquitin-protein ligase APD1 to 4 from Arabidopsis. They are involved in pollen mitosis II (PMII) regulation during male gametogenesis [[cite:PUB00096500]]. This entry represents a functionally uncharacterised domain found in the middle of APD1-4 and in uncharacterised sequences mainly from arthropods. There are two completely conserved C residues that may be functionally important.","id":"Pfam:PF16041","interpro_id":"InterPro:IPR032010","name":"E3 ubiquitin-protein ligase APD1-4, middle domain","pfam_id":"PF16041","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":"APD1-4_M","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF16041"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF16041.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"63df95e98ce6ca19322a035104fcd25857ce5398b011022691749e6517aa8272"}},"protein_examples":{"candidate_count":4,"discovery_scanned":true,"example_count":4,"examples":[{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Arabidopsis thaliana","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032010","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032008","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF16041","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml","qualification_status":"NOT_ASSESSED","record_id":"Pfam:PF16040","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml"}],"pfam_ids":["PF13920","PF16040","PF16041"],"protein_name":"E3 ubiquitin-protein ligase APD3","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MGSIRGDLQPLFVMPPPPLDEDCDDIFNSDESSWGLLSLSCFGIIMGLWFFASVCLIFGVYGSETVWLGPNSSILVKPSSIFVKSIKVKELDFSKPGLQLYGFNGQSTPSGYFVNWTESRVLSVSQNSYKGWPYYLNRGTHMNISYNILPKGSAVRLVITEGSQVIGMPFFYRSSLKDIAFRDTAWSWNLIQGSGMIQLDISKSKGYYLTVANLKRKDIEVELDIDVKAVLYDTKQTSYNCSFSNGECSFKMNERYPVENYAVVTSPALGQGVSIDDEWYIELSYQPRLIAYGSFTGVLLSFMLVAIHFCNKLKCCGGEGFLSGDDSVRTCLLADKGDNDCCNDVEASNKSLCAICFDAPRDCCFLPCGHCVSCYQCGTKIKRTKGRCPICRKKMIHVKRIYTA","sequence_length":404,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"fe05712858031a5a48f11f679d72ffaf3f202eebc39176921aeff665b419fcfa","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/B3H754.json","taxon_id":"3702","uniprot_accession":"B3H754","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Arabidopsis thaliana","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032010","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032008","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF16041","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml","qualification_status":"NOT_ASSESSED","record_id":"Pfam:PF16040","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml"}],"pfam_ids":["PF13920","PF16040","PF16041"],"protein_name":"E3 ubiquitin-protein ligase APD4","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MGSIRGDLQPLFVMPPPPLDEDCDDIFNSDESSWGLLSLSCFGIIMGLWFFASVCLIFGVYGSETVWLGPNSSILVKPSSIFVKSINAKELDFSKPGLQLYGFNGQSTPSGYFVNWTESRVLSVSQNSYKGWPYYLNRGTHMNISYNILPKGSAVRLVITEGMPFFYRSSLKDIAFRDTAWSWNLIQGSGMIQLDISKSKGYYLTVANLKRKDVEVELDIDVKVVLYDTKQSSYNCSFSNGECSFKMNERSPVENYAVVTSPALGQGVSIDDEWYIELSYQPRLIAYGSFTGVLLSFMLVAIHFCNKLKCCGGEGFLSEDDSVRTCLLADKGDNDCCNDVEASNKSLCAICFDAPRDCCFLPCGHCVSCYQCGTKIKRTKGRCPICRKKIMHVKRIYTA","sequence_length":399,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"bdf6b8ffb97cbcfbc7cc257f513cabadb5b09c9edaeb53c241883bb7702ca83a","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/F4ISV9.json","taxon_id":"3702","uniprot_accession":"F4ISV9","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Arabidopsis thaliana","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032010","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032008","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF16041","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-m-pf16041.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml","qualification_status":"NOT_ASSESSED","record_id":"Pfam:PF16040","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/apd1-4-n-pf16040.yaml"}],"pfam_ids":["PF13920","PF16040","PF16041"],"protein_name":"E3 ubiquitin-protein ligase APD1","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MDSAPSPSSLDFELSPPVLVTMTSTSSSASDNVEGADDDANTHGIFNWRDFSSCWRVSESNLYCFSLALLIWFFASFILIENLYGPKNVWLGPSSSILVEPSSIFVKSIKVKVLDYSEPGLQLYGFYRTPALDCFVNWSESRVLSISHESYKGWPYYLNSGSLLNITYTVKPQGSAVQLVVDEGHQGVPQSVLNDPAYRYNVWSWNLIEGSGMIQLEIRKSSSYYLAVANLKSKDVEVELNIDVKAVLYDTKQSFYNCNFSNGECTFNAMSLVGNSVVVTSPAASQGVSIEDEWYIRFSYQPREIAYVIGTGVVICFMLVAIQFCNRFQCSGGEGHLTEDDSARTRLLADKDDDGSSMGSCDDSYANDDADLEEFMGNDGEASNRSRRLCAICFDVPRDCFFLPCGHSVSCYECGTTMQEADGSCPICRRKMKKVKRIYTV","sequence_length":441,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"14ca7e9b1c7167878a4212fa44c32281621dbeafa93083c3088a76c58cca0dd3","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q0WS06.json","taxon_id":"3702","uniprot_accession":"Q0WS06","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Arabidopsis thaliana","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032010","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-middle-domain-ipr032010.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml","qualification_status":"NOT_ASSESSED","record_id":"InterPro:IPR032008","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/interpro/e3-ubiquitin-protein-ligase-apd1-4-n-terminal-ipr032008.yaml"}],"pfam_ids":["PF13920","PF16040","PF16041"],"protein_name":"E3 ubiquitin-protein ligase APD2","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MSLPDSLPSSSSSPPVTREETGFHRFEHHGNDSGFDHRDRPPWNRSEYDYRHGSVVASENVRNNSTSEDPWSCVVVVATFCIFVSMTLILGLYGTTNVWLGPNSSFLIKPTSVFVQNVIVEELGNKGSGLILYGLNQAPQLDVLTKWSEVHYLAVPNDSYKYWIQYLNKGSRVKVSYNVESVGSSLYLVIAQGVDGLSEWVQDPTRPDTTLSWHIISDSGYIEQDITKSSSYYVAVGNVYLNEVKATIDIQVEGVLYDTTNAYYNCSFPNDKCTLSVPLFGTNAAVLTSPGPKLNNSKNEFCAKLSYEPRWIAYIVCMGVVTALLLIVSSLFNKRQPVTEDETVDENDDVAPLIPGKDDDNSSWCSSYSSILTSTEELEGAHGEGHSSTRYLCAICYDAPRDCFFLSCGHCVACFQCGTRIAETSGFCPVCRKKIRKVKKIFNV","sequence_length":444,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"e523d97676115df9e3612d3db4902ed03d9289e76ffc3fe0573ae82aa303d569","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q6DBH0.json","taxon_id":"3702","uniprot_accession":"Q6DBH0","uniprot_release":"2026_03"}],"pfam_id":"PF16041","short_name":"APD1-4_M","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
