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180 | def query_uniprot(uniprot_id: str) -> Response | None:
"""Fetch the data from a specified UniProtID from the UniProt REST API
Args:
uniprot_id: The formatted UniProtID which consists of either a 6 or 10 character code
Returns:
The UniProtID entry JSON as a dictionary if query was successful
"""
# Typical response fields from Q9HIA7 (PDB ID: 1NOG)
# {'entryType': 'UniProtKB unreviewed (TrEMBL)', 'primaryAccession': 'Q9HIA7', 'uniProtkbId': 'Q9HIA7_THEAC',
# 'entryAudit': {'firstPublicDate': '2001-03-01', 'lastAnnotationUpdateDate':
# '2021-06-02', 'lastSequenceUpdateDate': '2001-03-01', 'entryVersion': 97, 'sequenceVersion': 1},
# 'annotationScore': 15.100000000000001,
# 'organism': {'scientificName':
# 'Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)',
# 'taxonId': 273075,
# 'evidences': [{'evidenceCode': 'ECO:0000313', 'source': 'Proteomes', 'id': 'UP000001024'}],
# 'lineage': ['Archaea', 'Candidatus Thermoplasmatota', 'Thermoplasmata', 'Thermoplasmatales',
# 'Thermoplasmataceae', 'Thermoplasma']},
# 'proteinExistence': '1: Evidence at protein level',
# 'proteinDescription': {'recommendedName': {'fullName': {'evidences': [{'evidenceCode': 'ECO:0000259', 'source':
# 'Pfam', 'id': 'PF01923'}],
# 'value': 'Cob_adeno_trans domain-containing protein'}}},
# 'genes': [{'orderedLocusNames': [{'evidences': [{'evidenceCode': 'ECO:0000313', 'source': 'EMBL',
# 'id': 'CAC12554.1'}],
# 'value': 'Ta1434'}]}],
# 'comments': [{'texts': [{'evidences': [{'evidenceCode': 'ECO:0000256', 'source': 'ARBA', 'id': 'ARBA00007487'}],
# 'value': 'Belongs to the Cob(I)alamin adenosyltransferase family'}],
# 'commentType': 'SIMILARITY'}],
# 'features': [
# {'type': 'Domain',
# 'location': {'start': {'value': 2, 'modifier': 'EXACT'},
# 'end': {'value': 158, 'modifier': 'EXACT'}},
# 'description': 'Cob_adeno_trans',
# 'evidences': [{'evidenceCode': 'ECO:0000259', 'source': 'Pfam', 'id': 'PF01923'}]
# }],
# 'keywords': [{'evidences': [{'evidenceCode': 'ECO:0007829', 'source': 'PDB', 'id': '1NOG'}],
# 'id': 'KW-0002', 'category': 'Technical term', 'name': '3D-structure'},
# {'evidences': [{'evidenceCode': 'ECO:0000256', 'source': 'ARBA',
# 'id': 'ARBA00022840'}],
# 'id': 'KW-0067', 'category': 'Ligand', 'name': 'ATP-binding'},
# {'evidences': [{'evidenceCode': 'ECO:0000256', 'source': 'ARBA',
# 'id': 'ARBA00022741'}],
# 'id': 'KW-0547', 'category': 'Ligand', 'name': 'Nucleotide-binding'},
# {'evidences': [{'evidenceCode': 'ECO:0000313', 'source': 'Proteomes',
# 'id': 'UP000001024'}],
# 'id': 'KW-1185', 'category': 'Technical term', 'name': 'Reference proteome'},
# {'evidences': [{'evidenceCode': 'ECO:0000256', 'source': 'ARBA',
# 'id': 'ARBA00022679'}],
# 'id': 'KW-0808', 'category': 'Molecular function', 'name': 'Transferase'}],
# 'references': [
# {'citation': {'id': '11029001', 'citationType': 'journal article',
# 'authors': ['Ruepp A.', 'Graml W.', 'Santos-Martinez M.L.',
# 'Koretke K.K.', 'Volker C.', 'Mewes H.W.', 'Frishman D.',
# 'Stocker S.', 'Lupas A.N.', 'Baumeister W.'],
# 'citationCrossReferences': [{'database': 'PubMed', 'id': '11029001'},
# {'database': 'DOI', 'id': '10.1038/35035069'}],
# 'title': 'The genome sequence of the thermoacidophilic scavenger '
# 'Thermoplasma acidophilum.',
# 'publicationDate': '2000',
# 'journal': 'Nature',
# 'firstPage': '508', 'lastPage': '513', 'volume': '407'},
# 'referencePositions': ['NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]'],
# 'referenceComments': [{'evidences': [{'evidenceCode': 'ECO:0000313',
# 'source': 'Proteomes', 'id': 'UP000001024'}],
# 'value': 'ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AM'
# 'RC-C165',
# 'type': 'STRAIN'}],
# 'evidences': [{'evidenceCode': 'ECO:0000313', 'source': 'EMBL', 'id': 'CAC12554.1'},
# {'evidenceCode': 'ECO:0000313', 'source': 'Proteomes', 'id': 'UP000001024'}]},
# {'citation': {'id': '15044458', 'citationType': 'journal article',
# 'authors': ['Saridakis V.', 'Yakunin A.', 'Xu X.', 'Anandakumar P.',
# 'Pennycooke M.', 'Gu J.', 'Cheung F.', 'Lew J.M.',
# 'Sanishvili R.', 'Joachimiak A.', 'Arrowsmith C.H.',
# 'Christendat D.', 'Edwards A.M.'],
# 'citationCrossReferences': [{'database': 'PubMed', 'id': '15044458'},
# {'database': 'DOI',
# 'id': '10.1074/jbc.M401395200'}],
# 'title': 'The structural basis for methylmalonic aciduria. The '
# 'crystal structure of archaeal ATP:cobalamin '
# 'adenosyltransferase.',
# 'publicationDate': '2004', 'journal': 'J. Biol. Chem.',
# 'firstPage': '23646', 'lastPage': '23653', 'volume': '279'},
# 'referencePositions': ['X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS)'],
# 'evidences': [{'evidenceCode': 'ECO:0007829', 'source': 'PDB', 'id': '1NOG'}]}
# ],
# 'uniProtKBCrossReferences': [{'database': 'EMBL', 'id': 'AL445067',
# 'properties': [{'key': 'ProteinId', 'value': 'CAC12554.1'},
# {'key': 'Status', 'value': '-'},
# {'key': 'MoleculeType', 'value': 'Genomic_DNA'}]},
# {'database': 'RefSeq', 'id': 'WP_010901837.1',
# 'properties': [{'key': 'NucleotideSequenceId', 'value': 'NC_002578.1'}]},
# {'database': 'PDB', 'id': '1NOG',
# 'properties': [{'key': 'Method', 'value': 'X-ray'},
# {'key': 'Resolution', 'value': '1.55 A'},
# {'key': 'Chains', 'value': 'A=1-177'}]},
# {'database': 'PDBsum', 'id': '1NOG',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'SMR', 'id': 'Q9HIA7',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'STRING', 'id': '273075.Ta1434',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'DNASU', 'id': '1456890',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'EnsemblBacteria', 'id': 'CAC12554',
# 'properties': [{'key': 'ProteinId', 'value': 'CAC12554'},
# {'key': 'GeneId', 'value': 'CAC12554'}]},
# {'database': 'GeneID', 'id': '1456890',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'KEGG', 'id': 'tac:Ta1434',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'eggNOG', 'id': 'arCOG00489',
# 'properties': [{'key': 'ToxonomicScope', 'value': 'Archaea'}]},
# {'database': 'HOGENOM', 'id': 'CLU_083486_0_1_2',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'OMA', 'id': 'HQACTVV',
# 'properties': [{'key': 'Fingerprint', 'value': '-'}]},
# {'database': 'OrthoDB', 'id': '98914at2157',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'BRENDA', 'id': '2.5.1.17',
# 'properties': [{'key': 'OrganismId', 'value': '6324'}]},
# {'database': 'EvolutionaryTrace', 'id': 'Q9HIA7',
# 'properties': [{'key': 'Description', 'value': '-'}]},
# {'database': 'Proteomes', 'id': 'UP000001024',
# 'properties': [{'key': 'Component', 'value': 'Chromosome'}]},
# {'database': 'GO', 'id': 'GO:0005524',
# 'properties': [{'key': 'GoTerm', 'value': 'F:ATP binding'},
# {'key': 'GoEvidenceType', 'value': 'IEA:UniProtKB-KW'}]},
# {'database': 'GO', 'id': 'GO:0016740',
# 'properties': [{'key': 'GoTerm', 'value': 'F:transferase activity'},
# {'key': 'GoEvidenceType', 'value': 'IEA:UniProtKB-KW'}]},
# {'database': 'Gene3D', 'id': '1.20.1200.10',
# 'properties': [{'key': 'EntryName', 'value': '-'},
# {'key': 'MatchStatus', 'value': '1'}]},
# {'database': 'InterPro', 'id': 'IPR016030',
# 'properties': [{'key': 'EntryName', 'value': 'CblAdoTrfase-like'}]},
# {'database': 'InterPro', 'id': 'IPR036451',
# 'properties': [{'key': 'EntryName', 'value': 'CblAdoTrfase-like_sf'}]},
# {'database': 'InterPro', 'id': 'IPR029499',
# 'properties': [{'key': 'EntryName', 'value': 'PduO-typ'}]},
# {'database': 'PANTHER', 'id': 'PTHR12213',
# 'properties': [{'key': 'EntryName', 'value': 'PTHR12213'},
# {'key': 'MatchStatus', 'value': '1'}]},
# {'database': 'Pfam', 'id': 'PF01923',
# 'properties': [{'key': 'EntryName', 'value': 'Cob_adeno_trans'},
# {'key': 'MatchStatus', 'value': '1'}]},
# {'database': 'SUPFAM', 'id': 'SSF89028',
# 'properties': [{'key': 'EntryName', 'value': 'SSF89028'},
# {'key': 'MatchStatus', 'value': '1'}]},
# {'database': 'TIGRFAMs', 'id': 'TIGR00636',
# 'properties': [{'key': 'EntryName', 'value': 'PduO_Nterm'},
# {'key': 'MatchStatus', 'value': '1'}]}
# ],
# 'sequence': {'value': 'MFTRRGDQGETDLANRARVGKDSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVLGEDVSTGGKG'
# 'RTVTREMIDYLEARVKEMKAEIGKIELFVVPGGSIESASLHMARAVSRRLERRIVAASKLTEINKNVLIYANRLS'
# 'SILFMHALLSNKRLNIPEKIWSIHRVS', 'length': 177, 'molWeight': 20013,
# 'crc64': '13D3B46CB3ED92F6', 'md5': '5D8AFDAE2BFCB93431C348E2A0172D96'},
# 'extraAttributes': {'countByCommentType': {'SIMILARITY': 1}, 'countByFeatureType': {'Domain': 1},
# 'uniParcId': 'UPI000006403F'}
# }
if uniprot_id and len(uniprot_id) in [6, 10]:
# query_url = f'https://rest.uniprot.org/uniprotkb/{uniprot_id}.json'
return connection_exception_handler(f'https://rest.uniprot.org/uniprotkb/{uniprot_id}.json')
else:
# logger.warning('UniProt ID "%s" is not of the required format and will not be found with the UniProt API'
# % uniprot_id)
return None
|