{"cross_mech":[],"family":{"alphafold_models":3348,"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 represents a group of bacterial, fungal and plant sequences, including 2-oxoadipate dioxygenase/decarboxylase (referred to as HGLS and YdcJ) from Escherichia coli. YdcJ, which is involved in D-lysine metabolism, catalyses a successive decarboxylation and intramolecular hydroxylation of 2-oxoadipate forming 2-hydroxyglutarate in a Fe(II) and oxygen-dependent manner. Members of this protein family are thought to belong to the the vicinal oxygen chelate (VOC) superfamily [[cite:PUB00102155],[cite:PUB00102156]]. The structure has been solved (PDB:3iuz, PDB:6w1g).","domain_architectures":39,"interpro_id":"IPR009770","known_evidence_count":null,"matches":5475,"name":"2-oxoadipate dioxygenase/decarboxylase","partial_evidence_count":null,"pfam_id":"PF07063","proteins":5110,"proteomes":4514,"short_name":"HGLS","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF07063","structures":6,"taxa":7095,"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/PF07063.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":3348,"domain_architectures":39,"matches":5475,"proteins":5110,"proteomes":4514,"structures":6,"taxa":7095},"curation_status":"SEEDED","description":"This entry represents a group of bacterial, fungal and plant sequences, including 2-oxoadipate dioxygenase/decarboxylase (referred to as HGLS and YdcJ) from Escherichia coli. YdcJ, which is involved in D-lysine metabolism, catalyses a successive decarboxylation and intramolecular hydroxylation of 2-oxoadipate forming 2-hydroxyglutarate in a Fe(II) and oxygen-dependent manner. Members of this protein family are thought to belong to the the vicinal oxygen chelate (VOC) superfamily [[cite:PUB00102155],[cite:PUB00102156]]. The structure has been solved (PDB:3iuz, PDB:6w1g).","id":"Pfam:PF07063","interpro_id":"InterPro:IPR009770","name":"2-oxoadipate dioxygenase/decarboxylase","pfam_id":"PF07063","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":"HGLS","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF07063"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF07063.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"f60bd403c5149c16c9993bf5ad4890ee8fc127c8a2f67a98ed44fd7b8e879e34"}},"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/2-oxoadipate-dioxygenase-decarboxylase-hgls-nf049974.yaml","qualification_status":"NOT_ASSESSED","record_id":"NCBIfam:NF049974","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/function/protein_family/ncbifam/2-oxoadipate-dioxygenase-decarboxylase-hgls-nf049974.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/cdd/uncharacterized-metal-dependent-enzyme-similar-to-shigella-flexneri-yd-cd16348.yaml","qualification_status":"NOT_ASSESSED","record_id":"CDD:cd16348","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/cdd/uncharacterized-metal-dependent-enzyme-similar-to-shigella-flexneri-yd-cd16348.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/hgls-pf07063.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF07063","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/hgls-pf07063.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/structure/homologous_superfamily/cath/uncharacterised-protein-pf07063-duf1338-3-10-180-80.yaml","qualification_status":"NOT_ASSESSED","record_id":"CATH:3.10.180.80","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/structure/homologous_superfamily/cath/uncharacterised-protein-pf07063-duf1338-3-10-180-80.yaml"}],"pfam_ids":["PF07063"],"protein_name":"2-oxoadipate dioxygenase/decarboxylase","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MANSITADEIREQFSQAMSAMYQQEVPQYGTLLELVADVNLAVLENNPQLHEKMVNADELARLNVERHGAIRVGTAQELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDASLARNPFRVFTSLLRLELIENEILRQKAAEILRQRDIFTPRCRQLLEEYEQQGGFNETQAQEFVQEALETFRWHQSATVDEETYRALHNEHRLIADVVCFPGCHINHLTPRTLDIDRVQSMMPECGIEPKILIEGPPRREVPILLRQTSFKALEETVLFAGQKQGTHTARFGEIEQRGVALTPKGRQLYDDLLRNAGTGQDNLTHQMHLQETFRTFPDSEFLMRQQGLAWFRYRLTPSGEAHRQAIHPGDDPQPLIERGWVVAQPITYEDFLPVSAAGIFQSNLGNETQTRSHGNASREAFEQALGCPVLDEFQLYQEAEERSKRRCGLL","sequence_length":447,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"0e34a3f54a82045a6ee58817c4406f3cfcfeb4a09647c24732b61702d4bca13a","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P76097.json","taxon_id":"83333","uniprot_accession":"P76097","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Oryza sativa subsp. japonica","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/hgls-pf07063.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF07063","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/hgls-pf07063.yaml"}],"pfam_ids":["PF07063"],"protein_name":"2-oxoadipate dioxygenase/decarboxylase, chloroplastic/amyloplastic","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MAVALAGARSPGAGAILSLRRLAPAAAAPVRLGGSGTPGTRRRRGIAMAAAASAPPAPADALPKGADSFFRTVISNMEKVYLSRNPTAKTILELVRSYDGDHICYDHFAFRTFGVDGYGIKSLAEFFTDFGYVPREELRFPAKKLRALWFSPPTNDGYTGTGVYGPLPRIFISELLVDELSPQSQDIIQKYIRTSGKGNKHATLASTSGELTWEKPIYSDFQVLSRESEYAAWTLVNGYALNHTTISTHRLISDIRSINKFNKFVEDNGFKLNSEGGILKVSPDGLLQQSSTVADSALFTFADGITESIPRSYIEFAERLVLPQFKDLPNDEVNEHHRRDGFEVGNADKIFESTSNDQLTRRSA","sequence_length":364,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"5b341120384c739143b96c02b56ccdb70e014dff121bd2735c1619f8a4e8f2e0","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q337M4.json","taxon_id":"39947","uniprot_accession":"Q337M4","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification","ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/hgls-pf07063.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF07063","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/hgls-pf07063.yaml"}],"pfam_ids":["PF07063"],"protein_name":"2-oxoadipate dioxygenase/decarboxylase","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MPANDFVSPDSIRAQFSAAMSLMYKQEVPLYGTLLELVSEINQQVMAQQPEVAEALRWTGEIERLDQERHGAIRVGTAEELATIARLFAVMGMQPVGYYDLSSAGVPVHSTAFRAVHEQSLHVSPFRVFTSLLRLELIDNPQLRELAQSILAKRQIFTSRALELIAQCEREGGLDAADAETFVQEALHTFRWHQDATVTAEQYQQLHDQHRLIADVVAFKGPHINHLTPRTLDIDAIQLGMPAKGIPPKAVVEGPPTRRHPILLRQTSFKALQETVAFRDQQGREGSHTARFGEIEQRGAALTPKGRQLYDKLLDATRVALGGAPAEANAERYMALLQANFAEFPDDLAQMREQGLAYFRYFATEKGLAARDQEGRPTTLQGLIDAGHVHFEALVYEDFLPVSAAGIFQSNLGDDAQAEYGSNANREAFEAALGLQVQDELALYAQSERRSLQACAQALNLGSM","sequence_length":464,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"659c4c8b8b6ae501f44f65fe45302646241004c2e674b8e68f8de1fbffd7df57","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q88CC1.json","taxon_id":"160488","uniprot_accession":"Q88CC1","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/cdd/uncharacterized-subfamily-of-the-vicinal-oxygen-chelate-voc-family-the-cd16350.yaml","qualification_status":"NOT_ASSESSED","record_id":"CDD:cd16350","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/cdd/uncharacterized-subfamily-of-the-vicinal-oxygen-chelate-voc-family-the-cd16350.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/structure/homologous_superfamily/cath/3-10-180-50-3-10-180-50.yaml","qualification_status":"NOT_ASSESSED","record_id":"CATH:3.10.180.50","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/structure/homologous_superfamily/cath/3-10-180-50-3-10-180-50.yaml"}],"pfam_ids":["PF07063"],"protein_name":"2-oxoadipate dioxygenase/decarboxylase, chloroplastic","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MISLHSSAIKASLYGSFPSSLRSTLSVSFSAGSLIRLPSVGKRNLSVVVSSGRDSSMSSNNVSRGSSSKVAAESFFRSVLGQMETVYLNRNPTPKSVLELVRSVDDQQLCYDHLAFRTFGIGGYGIDSLASFFLDYGYTPMDELKFPAKKLRALWFAPPNASAVPGGSGVNGPLPRVFISELLVDQMSSQTQDVIRKYTEASPNGKKYAGLSSALGTLTWEKPLSSEFEQLARESEYAAWTLVNGYALNHVTISVHRLKSHLNKIKKLNQFLEEKGIKLNSEGGVLKVSPDGGLQQSSTVADSISFKFADGVTKSIPCSYIEFAERLVLPQYQNIPESEIQESHRRDGFEVGNADKIFESTFQEQLSRRTG","sequence_length":371,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"4e48f23ed2610c4b7d03b30092bcaed0230736be06a67b8b03c4565f98cd2138","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q9LMJ7.json","taxon_id":"3702","uniprot_accession":"Q9LMJ7","uniprot_release":"2026_03"}],"pfam_id":"PF07063","short_name":"HGLS","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}