{"cross_mech":[],"family":{"alphafold_models":24317,"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 small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).","domain_architectures":123,"interpro_id":"IPR002792","known_evidence_count":null,"matches":35074,"name":"TRAM domain","partial_evidence_count":null,"pfam_id":"PF01938","proteins":35071,"proteomes":19606,"short_name":"TRAM","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF01938","structures":18,"taxa":31439,"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/PF01938.yaml","record":{"characterization_status":"UNSCORED","counters":{"alphafold_models":24317,"domain_architectures":123,"matches":35074,"proteins":35071,"proteomes":19606,"structures":18,"taxa":31439},"curation_status":"SEEDED","description":"This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).","id":"Pfam:PF01938","interpro_id":"InterPro:IPR002792","name":"TRAM domain","pfam_id":"PF01938","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":"TRAM","source_url":"https://www.ebi.ac.uk/interpro/api/entry/pfam/PF01938"},"source":{"commit":"c8155abfcf881ad8662936343deb81e604e3a194","path":"data/families/PF01938.yaml","repository":"https://github.com/CultureBotAI/DUFMech","sha256":"4aa129f202d44fc17a6d80c0d29c5be6749cab407b09e78bc24c7eaf432771b9"}},"protein_examples":{"candidate_count":13,"discovery_scanned":true,"example_count":13,"examples":[{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Bacillus subtilis (strain 168)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/trma-1.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01230","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-1.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/trma-2.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01231","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-2.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.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:O31503","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF01938","PF05958"],"protein_name":"23S rRNA (uracil-C(5))-methyltransferase RlmCD","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"a591b92b3f39d09f36dc980c1883b8a966470d69c06e797ba3decdc2885d2bd8","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":"MKMKPPVEKNEYYDVTFEDLTHEGAGVAKVQGFPIFVPNALPEEKAQIKVTRVKKGFAFGRLIELKEESPHRTDAPCPIYKQCGGCQLQHMTYEGQLLFKQKQVKDVLERIGKLDLSKVTVHPTLGMEDPWNYRNKAQVPVGEREGGLVAGFYQQRSHDIIDMSACLIQQSKNDEAVQAVKDICANYGVKAYNEERHKGWLRHIMVRYGVVTGEMMIVFITRTSDFPHKAKIIEDITAQFPHVKSIVQNINPNKTNVIFGNETNVIWGEEYIYDLIGDVKFAISARSFYQVNPEQTKVLYDKALEYAELQGEETVIDAYCGIGTISLFLAKQAKKVYGVEIVPEAIEDAKRNAELNGNTNAEFAVGEAETVIPKWYEEGITADTLVVDPPRKGCDEALLRTIVEMKPKRVVYVSCNPGTLARDLRVLEDGGYVTREVQPVDMFPHTNHVECCVLIKLKE","sequence_length":459,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"a591b92b3f39d09f36dc980c1883b8a966470d69c06e797ba3decdc2885d2bd8","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/O31503.json","taxon_id":"224308","uniprot_accession":"O31503","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Bacillus subtilis (strain 168)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.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:O31778","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"46c67909de7441c5ba1944ee517d656d97ccb1f23f38f16d8398a490e216c53e","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":"MNEKQKLESGQVHPSDKKSEKDYSKYFEAVYIPPSLKDAKKRGKEAVTYHNDFKISEQFKGLGDGRKFYIRTYGCQMNEHDTEVMAGIFMALGYEATNSVDDANVILLNTCAIRENAENKVFGELGHLKALKKNNPDLILGVCGCMSQEESVVNRILKKHPFVDMIFGTHNIHRLPELLSEAYLSKEMVVEVWSKEGDVIENLPKVRNGKIKGWVNIMYGCDKFCTYCIVPYTRGKERSRRPEDIIQEVRRLASEGYKEITLLGQNVNAYGKDFEDMTYGLGDLMDELRKIDIPRIRFTTSHPRDFDDRLIEVLAKGGNLLDHIHLPVQSGSSEVLKLMARKYDRERYMELVRKIKEAMPNASLTTDIIVGFPNETDEQFEETLSLYREVEFDSAYTFIYSPREGTPAAKMKDNVPMRVKKERLQRLNALVNEISAKKMKEYEGKVVEVLVEGESKNNPDILAGYTEKSKLVNFKGPKEAIGKIVRVKIQQAKTWSLDGEMVGEAIEVK","sequence_length":509,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"46c67909de7441c5ba1944ee517d656d97ccb1f23f38f16d8398a490e216c53e","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/O31778.json","taxon_id":"224308","uniprot_accession":"O31778","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/sequence/pattern/mttase-radical.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01278","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/mttase-radical.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:P0AEI1","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"26bdd2566d710d030c2dc27ac3e2f2a1d372f29556e44d9ad3a1622431e517b3","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":"MTKKLHIKTWGCQMNEYDSSKMADLLDATHGYQLTDVAEEADVLLLNTCSIREKAQEKVFHQLGRWKLLKEKNPDLIIGVGGCVASQEGEHIRQRAHYVDIIFGPQTLHRLPEMINSVRGDRSPVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNKYCTYCVVPYTRGEEVSRPSDDILFEIAQLAAQGVREVNLLGQNVNAWRGENYDGTTGSFADLLRLVAAIDGIDRIRFTTSHPIEFTDDIIEVYRDTPELVSFLHLPVQSGSDRILNLMGRTHTALEYKAIIRKLRAARPDIQISSDFIVGFPGETTEDFEKTMKLIADVNFDMSYSFIFSARPGTPAADMVDDVPEEEKKQRLYILQERINQQAMAWSRRMLGTTQRILVEGTSRKSIMELSGRTENNRVVNFEGTPDMIGKFVDVEITDVYPNSLRGKVVRTEDEMGLRVAETPESVIARTRKENDLGVGYYQP","sequence_length":474,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"26bdd2566d710d030c2dc27ac3e2f2a1d372f29556e44d9ad3a1622431e517b3","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P0AEI1.json","taxon_id":"83333","uniprot_accession":"P0AEI1","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Saccharomyces cerevisiae (strain ATCC 204508 / S288c)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/trma-1.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01230","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-1.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/trma-2.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01231","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-2.yaml"}],"pfam_ids":["PF01938","PF05958"],"protein_name":"tRNA (uracil(54)-C(5))-methyltransferase","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MYEQFEFSFFFFENSDNKVKYKAHLISSIKRWSIITCMRCFWTVQKSIFKARFFACRNFVKKHNYKLISTMTGSTEMVPPTMKHTVDNKRLSSPLTDSGNRRTKKPKLRKYKAKKVETTSPMGVLEFEVNDLLKSQNLSREQVLNDVTSILNDKSSTDGPIVLQYHREVKNVKVLEITSNGNGLALIDNPVETEKKQVVIIPFGLPGDVVNIKVFKTHPYYVESDLLDVVEKSPMRRDDLIRDKYFGKSSGSQLEFLTYDDQLELKRKTIMNAYKFFAPRLVAEKLLPPFDTTVASPLQFGYRTKITPHFDMPKRKQKELSVRPPLGFGQKGRPQWRKDTLDIGGHGSILDIDECVLATEVLNKGLTNERRKFEQEFKNYKKGATILLRENTTILDPSKPTLEQLTEEASRDENGDISYVEVEDKKNNVRLAKTCVTNPRQIVTEYVDGYTFNFSAGEFFQNNNSILPIVTKYVRDNLQAPAKGDDNKTKFLVDAYCGSGLFSICSSKGVDKVIGVEISADSVSFAEKNAKANGVENCRFIVGKAEKLFESIDTPSENTSVILDPPRKGCDELFLKQLAAYNPAKIIYISCNVHSQARDVEYFLKETENGSAHQIESIRGFDFFPQTHHVESVCIMKRI","sequence_length":639,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"ff78b7f447ccc5f7be400547853f59731d3c0699bb84dd9fdccbcec8ef63e92d","sequence_version":2,"source_url":"https://rest.uniprot.org/uniprotkb/P33753.json","taxon_id":"559292","uniprot_accession":"P33753","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Bacillus subtilis (strain 168)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Threonylcarbamoyladenosine tRNA methylthiotransferase MtaB","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MATVAFHTLGCKVNHYETEAIWQLFKEAGYERRDFEQTADVYVINTCTVTNTGDKKSRQVIRRAIRQNPDGVICVTGCYAQTSPAEIMAIPGVDIVVGTQDREKMLGYIDQYREERQPINGVSNIMKARVYEELDVPAFTDRTRASLKIQEGCNNFCTFCIIPWARGLLRSRDPEEVIKQAQQLVDAGYKEIVLTGIHTGGYGEDMKDYNFAKLLSELDTRVEGVKRIRISSIEASQITDEVIEVLDRSDKIVNHLHIPIQSGSNTVLKRMRRKYTMEFFADRLNKLKKALPGLAVTSDVIVGFPGETEEEFMETYNFIKEHKFSELHVFPYSKRTGTPAARMEDQVDENVKNERVHRLIALSDQLAKEYASQYENEVLEIIPEEAFKETEEENMFVGYTDNYMKVVFKGTEDMIGKIVKVKILKAGYPYNEGQFVRVVEDEITEHMRLSS","sequence_length":451,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"00bcb775d7ce84725cbb760cd07245902d3f5d2f566d61fadf86ad6a9c8b06e2","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/P54462.json","taxon_id":"224308","uniprot_accession":"P54462","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/sequence/pattern/trma-1.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01230","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-1.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/trma-2.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01231","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/trma-2.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:P55135","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF01938","PF05958"],"protein_name":"23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"ff260d7755b448fb61fbaf85125216fe8b6491633fb647ee3384aa6cbdba150f","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":"MAQFYSAKRRTTTRQIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSRVK","sequence_length":433,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"ff260d7755b448fb61fbaf85125216fe8b6491633fb647ee3384aa6cbdba150f","sequence_version":3,"source_url":"https://rest.uniprot.org/uniprotkb/P55135.json","taxon_id":"83333","uniprot_accession":"P55135","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","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/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF01938"],"protein_name":"Uncharacterized protein MJ0660","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MFNNKGRRNVRNNEVRRNVPVKEGETYTVTIEDMGRGGDGIARVEGFVVFVPETQKGETVNVKITAVKSKFAFAEKI","sequence_length":77,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"0b99b016ab8e26b7ee753d735f920663a954706bf451910a24795a903ed83ded","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q58074.json","taxon_id":"243232","uniprot_accession":"Q58074","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Probable threonylcarbamoyladenosine tRNA methylthiotransferase","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MWLYYLQVVMDMRVYVEGYGCVLNTADTEIIKNSLKKHGFEVVNNLEEADIAIINTCVVRLETENRMIYRINELKNLGKEVVVAGCLPKALKNKVKGFLHIYPREAHKAGEILKNYVEKHYRMPYIEEDINKTLYKKLDYLKPSLITPLPICEGCIGNCSYCIVKIARGGLISYPREKIVNKAKELINKGAKCLLITAQDTACYGFDIGDNLANLLNELTQIKGEFIMRVGMMHAKNAELILDELIEVYQNEKVGKFLHLPLQSGDDEILKRMKRGYTVDEFKDIVNEFRRKIKNLCFTTDIIVGFPGETEEQFQNTLEVLRELKPDYIHGAKYSQRKGTEAAKMKQIDTKIRKRRSEILDKLRRELSYLNNKKYIGKAMKVLVLDEGKGYTDNFKVVKFEGGEVGEFRKVKITDAKTFGLKGELIL","sequence_length":427,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"c3072c9a2e3ccf540bf423c348bade1b5924875f85de34a474ded0f1e592ae92","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q58277.json","taxon_id":"243232","uniprot_accession":"Q58277","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF01938","PF02310","PF04055"],"protein_name":"Uncharacterized protein MJ1620","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MKALIIDCLASGDGKRILARDVIGAGPRTVKGILQSEGIEAKITPVEDLDIKDIKKYNLIFISAMTSDFKCVKKLVERIRLKTDSKIIVGGPIANDINILEKIEADISIVGEGEITIRELIKKDFDAEDVKGTTYWDYNEDELKINPLREILTDLKLITPSTEIKDYKNYFSARVYVEVVRGCSNFKRPLLLCTNKKCNLCENGTLKCPLNINPGCGFCSVPSVFGYARSRDEEDILKEVEALLKEGVNRIVLSAPDFLDYKRGEKLINPYFPEPNYEAIESLLSKCKDLADKYNANVLIENIKANLFNEKVAEIFSKYLKTPIYIGCESGDKNHCKLLGRPTTPDDVLKAVKIAKKYNLKAQVYFIYGLPGENEETAKNTVNFMHKIKNYIDKITVYKFRPLPMSAFQNFKPNITKYSLLIRETANKINLEIKKKYIGRVLEVIISERHFRNKRDAIGYLPDSGLMVVVKDGAKFIGKTKKVKIIKAYEKYLEGRILKTWLCKY","sequence_length":505,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"7bdc5a86467264f6648e5e13bfd491b5fd40f112e871b95f56447f98eddda07d","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q59015.json","taxon_id":"243232","uniprot_accession":"Q59015","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Homo sapiens","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/mttase-radical.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01278","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/mttase-radical.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:Q5VV42","section":"protein_registry","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/grounding/protein_registry.jsonl"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Threonylcarbamoyladenosine tRNA methylthiotransferase","registry_source":{"commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","path":"data/grounding/protein_registry.jsonl","repository":"https://github.com/CultureBotAI/proteintraitsmech","sequence_sha256":"953bb915470572d6fcacec27790b3308fcde3109b505eda96a209a3c847f7d76","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":"MPSASCDTLLDDIEDIVSQEDSKPQDRHFVRKDVVPKVRRRNTQKYLQEEENSPPSDSTIPGIQKIWIRTWGCSHNNSDGEYMAGQLAAYGYKITENASDADLWLLNSCTVKNPAEDHFRNSIKKAQEENKKIVLAGCVPQAQPRQDYLKGLSIIGVQQIDRVVEVVEETIKGHSVRLLGQKKDNGRRLGGARLDLPKIRKNPLIEIISINTGCLNACTYCKTKHARGNLASYPIDELVDRAKQSFQEGVCEIWLTSEDTGAYGRDIGTNLPTLLWKLVEVIPEGAMLRLGMTNPPYILEHLEEMAKILNHPRVYAFLHIPVQSASDSVLMEMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKMEQVPAQVKKQRTKDLSRVFHSYSPYDHKIGERQQVLVTEESFDSKFYVAHNQFYEQVLVPKNPAFMGKMVEVDIYESGKHFMKGQPVSDAKVYTPSISKPLAKGEVSGLTKDFRNGLGNQLSSGSHTSAASQCDSASSRMVLPMPRLHQDCALRMSVGLALLGLLFAFFVKVYN","sequence_length":579,"sequence_origin":"PTM_REGISTRY_MIRROR","sequence_sha256":"953bb915470572d6fcacec27790b3308fcde3109b505eda96a209a3c847f7d76","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q5VV42.json","taxon_id":"9606","uniprot_accession":"Q5VV42","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Mus musculus","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/mttase-radical.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01278","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/mttase-radical.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Mitochondrial tRNA methylthiotransferase CDK5RAP1","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MHPLRCVLQVQRLSAPFTSMCWVLLRTCRAQSSVSSTPCPSPEAKSSEAQKDFSSRLATGPTFQHFLRSASVPQEKPSSPEVEDPPPYLSGDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRSRVPLRIGILGCMAERLKGEILNREKMVDLLAGPDAYRDLPRLLAVVESGQQAANVLLSLDETYADIMPVQTSPSATSAFVSIMRGCDNMCSYCIVPFTRGRERSRPVASILDEVRKLSEQGLKEVTLLGQNVNSFRDNSEVQFNNAGSANLSRGFTTNYKPKQGGLRFSHLLDQVSRIDPEMRIRFTSPHPKDFPDEVLQLIRERHNICKQIHLPAQSGSSRVLDAMRRGYSREAYVALVHHVRETIPGVSLSSDFITGFCGETEDDHRQTVSLLREVQYNTGFLFAYSMRQKTRAYHRLKDDVPEEVKLRRLEELITVFREEASKANKTSVGCSQLVLVEGFSKRSTTDLCGRNDANLKVIFPDAEVEDITNPGLKVRAQPGDYVLVKITSASSQTLKGHILCRTTMKDSLTYCTT","sequence_length":588,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"adf9c7c99a38ecdfca54f8c1d94b50de0f560689f40d52d20ffccb333df2401a","sequence_version":2,"source_url":"https://rest.uniprot.org/uniprotkb/Q8BTW8.json","taxon_id":"10090","uniprot_accession":"Q8BTW8","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Mus musculus","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/mttase-radical.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01278","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/mttase-radical.yaml"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Threonylcarbamoyladenosine tRNA methylthiotransferase","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MPSASCDVLLDDIEDIISQEDSKPQDRQFSRKHVFPKVRRRNTQKYLQEEPRPPSDSTIPGIQKIWIRTWGCSHNNSDGEYMAGQLAAYGYKITENASDADLWLLNSCTVKNPAEDHFRNSIKKAQEENKKVVLAGCVPQAQPRQDYLKGLSIIGVQQIDRVVEVVEETIKGHSVRLLGQKKDNGKRLGGARLDLPKIRKNPLIEIISINTGCLNACTYCKTKHARGNLASYPIDELVERAKQSFQEGVCEIWLTSEDTGAYGRDIGTDLPTLLWKLVEVIPEGAMLRLGMTNPPYILEHLEEMAKILNHPRVYAFLHIPVQSASDSVLMDMKREYCVADFKRVVDFLKEKVPGITIATDIICGFPGETDQDFQETVKLVEEYKFPSLFINQFYPRPGTPAAKAEQVPAHVKKQRTKDLSRVFHSYNPYDHKIGERQQVLVTEESFDSKFYVAHNRFYEQVLVPKNPAFMGKMVEVDIYESGKHFLKGQPVSETRVYTPSISKPLAKGEVSGLTKEFRNRLGNHPNGTSDTCPATQHGSAYSRMVLQMSQYDCALKVATGLALLALLLHFWPDSLLTM","sequence_length":578,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"ffcd62b5429543a2d5fc384546d6cdd5757e3a47bf0e0302dafdba898f5c7f1d","sequence_version":1,"source_url":"https://rest.uniprot.org/uniprotkb/Q91WE6.json","taxon_id":"10090","uniprot_accession":"Q91WE6","uniprot_release":"2026_03"},{"evidence_scope":"FAMILY_MEMBERSHIP_NOT_FUNCTION","organism":"Homo sapiens","origins":[{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["canonical_example_family_classification"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/pattern/mttase-radical.yaml","qualification_status":"NOT_ASSESSED","record_id":"PROSITE:PS01278","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/pattern/mttase-radical.yaml"},{"cited_uniprot_accession":"","commit":"70edd6f8458845f7d7783ac4f416df519f5e1de6","link_basis":["ptm_own_pfam_record_example"],"mech":"ProteinTraitsMech","path":"data/traits/sequence/domain/pfam/tram-pf01938.yaml","qualification_status":"LEGACY_OR_UNSPECIFIED","record_id":"Pfam:PF01938","section":"canonical_examples","url":"https://github.com/CultureBotAI/proteintraitsmech/blob/70edd6f8458845f7d7783ac4f416df519f5e1de6/data/traits/sequence/domain/pfam/tram-pf01938.yaml"}],"pfam_ids":["PF00919","PF01938","PF04055"],"protein_name":"Mitochondrial tRNA methylthiotransferase CDK5RAP1","registry_status":"NOT_IN_REGISTRY","reviewed":true,"sequence":"MHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLAAGPTFQHFLKSASAPQEKLSSEVEDPPPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPLRIGILGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMPVQTSASATSAFVSIMRGCDNMCSYCIVPFTRGRERSRPIASILEEVKKLSEQVFLPPRPPKVLGLQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQVSRVDPEMRIRFTSPHPKDFPDEVLQLIHERDNICKQIHLPAQSGSSRVLEAMRRGYSREAYVELVHHIRESIPGVSLSSDFIAGFCGETEEDHVQTVSLLREVQYNMGFLFAYSMRQKTRAYHRLKDDVPEEVKLRRLEELITIFREEATKANQTSVGCTQLVLVEGLSKRSATDLCGRNDGNLKVIFPDAEMEDVNNPGLRVRAQPGDYVLVKITSASSQTLRGHVLCRTTLRDSSAYC","sequence_length":601,"sequence_origin":"UNIPROT_FETCH","sequence_sha256":"1d322390e9e68338b2f72f2714eb5d7b1348014580179634fd32b6a8522aaaa3","sequence_version":2,"source_url":"https://rest.uniprot.org/uniprotkb/Q96SZ6.json","taxon_id":"9606","uniprot_accession":"Q96SZ6","uniprot_release":"2026_03"}],"pfam_id":"PF01938","short_name":"TRAM","status":"HAS_SEQUENCE_EXAMPLE","unresolved":[]}}
