PMC:7376845 / 13979-14838 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7376845","sourcedb":"PMC","sourceid":"7376845","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7376845","text":"S protein reference sequences for SARS-CoV-1, SARS-CoV-2, batRaTG13, Middle East respiratory syndrome (MERS) and human common-cold coronaviruses 229E, NL63, OC43 and HKU1 were downloaded from the National Center for Biotechnology Information (NCBI). A multiple sequence alignment was created with multiple alignment using fast Fourier transform (MAFFT) using the slow but accurate L-INS-I parameter settings [24] and the alignment curated, cut to the target region 1029–1192 (SARS-CoV-1 numbering) and visualised with Jalview [25]. We used Molecular Evolutionary Genetics Analysis (MEGA) X [26] to calculate the number of amino-acid differences for all sequence pairs in the alignment of the mAb target region and the full S protein normalised by the length of the aligned sequence of the respective reference protein to obtain per cent amino acid identities.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T87","span":{"begin":2,"end":9},"obj":"Body_part"},{"id":"T88","span":{"begin":622,"end":632},"obj":"Body_part"},{"id":"T89","span":{"begin":725,"end":732},"obj":"Body_part"},{"id":"T90","span":{"begin":810,"end":817},"obj":"Body_part"},{"id":"T91","span":{"begin":837,"end":847},"obj":"Body_part"}],"attributes":[{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A91","pred":"fma_id","subj":"T91","obj":"http://purl.org/sig/ont/fma/fma82739"},{"subj":"T87","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T88","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T89","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T90","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T91","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"341","span":{"begin":34,"end":42},"obj":"Species"},{"id":"342","span":{"begin":46,"end":56},"obj":"Species"},{"id":"343","span":{"begin":113,"end":118},"obj":"Species"},{"id":"344","span":{"begin":131,"end":144},"obj":"Species"},{"id":"345","span":{"begin":476,"end":484},"obj":"Species"},{"id":"346","span":{"begin":145,"end":149},"obj":"Species"},{"id":"347","span":{"begin":151,"end":155},"obj":"Species"},{"id":"348","span":{"begin":157,"end":161},"obj":"Species"},{"id":"349","span":{"begin":166,"end":170},"obj":"Species"},{"id":"350","span":{"begin":69,"end":101},"obj":"Disease"},{"id":"351","span":{"begin":103,"end":107},"obj":"Disease"}],"attributes":[{"id":"A341","pred":"tao:has_database_id","subj":"341","obj":"Tax:694009"},{"id":"A342","pred":"tao:has_database_id","subj":"342","obj":"Tax:2697049"},{"id":"A343","pred":"tao:has_database_id","subj":"343","obj":"Tax:9606"},{"id":"A344","pred":"tao:has_database_id","subj":"344","obj":"Tax:11118"},{"id":"A345","pred":"tao:has_database_id","subj":"345","obj":"Tax:694009"},{"id":"A346","pred":"tao:has_database_id","subj":"346","obj":"Tax:11137"},{"id":"A347","pred":"tao:has_database_id","subj":"347","obj":"Tax:277944"},{"id":"A348","pred":"tao:has_database_id","subj":"348","obj":"Tax:31631"},{"id":"A349","pred":"tao:has_database_id","subj":"349","obj":"Tax:290028"},{"id":"A350","pred":"tao:has_database_id","subj":"350","obj":"MESH:D018352"},{"id":"A351","pred":"tao:has_database_id","subj":"351","obj":"MESH:D018352"},{"subj":"341","pred":"source","obj":"LitCovid-PubTator"},{"subj":"342","pred":"source","obj":"LitCovid-PubTator"},{"subj":"343","pred":"source","obj":"LitCovid-PubTator"},{"subj":"344","pred":"source","obj":"LitCovid-PubTator"},{"subj":"345","pred":"source","obj":"LitCovid-PubTator"},{"subj":"346","pred":"source","obj":"LitCovid-PubTator"},{"subj":"347","pred":"source","obj":"LitCovid-PubTator"},{"subj":"348","pred":"source","obj":"LitCovid-PubTator"},{"subj":"349","pred":"source","obj":"LitCovid-PubTator"},{"subj":"350","pred":"source","obj":"LitCovid-PubTator"},{"subj":"351","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T123","span":{"begin":34,"end":42},"obj":"Disease"},{"id":"T124","span":{"begin":34,"end":38},"obj":"Disease"},{"id":"T125","span":{"begin":46,"end":54},"obj":"Disease"},{"id":"T126","span":{"begin":46,"end":50},"obj":"Disease"},{"id":"T127","span":{"begin":119,"end":130},"obj":"Disease"},{"id":"T128","span":{"begin":476,"end":484},"obj":"Disease"},{"id":"T129","span":{"begin":476,"end":480},"obj":"Disease"}],"attributes":[{"id":"A123","pred":"mondo_id","subj":"T123","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A124","pred":"mondo_id","subj":"T124","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A125","pred":"mondo_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A126","pred":"mondo_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0005709"},{"id":"A128","pred":"mondo_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A129","pred":"mondo_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T123","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T124","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T125","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T126","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T127","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T128","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T129","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T165","span":{"begin":113,"end":118},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T166","span":{"begin":250,"end":251},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T165","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T166","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T125","span":{"begin":2,"end":9},"obj":"Chemical"},{"id":"T126","span":{"begin":582,"end":586},"obj":"Chemical"},{"id":"T127","span":{"begin":622,"end":627},"obj":"Chemical"},{"id":"T128","span":{"begin":628,"end":632},"obj":"Chemical"},{"id":"T129","span":{"begin":725,"end":732},"obj":"Chemical"},{"id":"T130","span":{"begin":810,"end":817},"obj":"Chemical"},{"id":"T131","span":{"begin":837,"end":847},"obj":"Chemical"},{"id":"T132","span":{"begin":837,"end":842},"obj":"Chemical"},{"id":"T133","span":{"begin":843,"end":847},"obj":"Chemical"}],"attributes":[{"id":"A125","pred":"chebi_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A126","pred":"chebi_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/CHEBI_6617"},{"id":"A127","pred":"chebi_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A130","pred":"chebi_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A133","pred":"chebi_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"subj":"T125","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T126","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T127","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T128","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T129","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T130","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T131","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T132","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T133","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T100","span":{"begin":0,"end":249},"obj":"Sentence"},{"id":"T101","span":{"begin":250,"end":531},"obj":"Sentence"},{"id":"T102","span":{"begin":532,"end":859},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T100","pred":"source","obj":"LitCovid-sentences"},{"subj":"T101","pred":"source","obj":"LitCovid-sentences"},{"subj":"T102","pred":"source","obj":"LitCovid-sentences"}]},{"project":"2_test","denotations":[{"id":"32700671-29506019-29327479","span":{"begin":409,"end":411},"obj":"29506019"},{"id":"32700671-19151095-29327480","span":{"begin":527,"end":529},"obj":"19151095"},{"id":"32700671-29722887-29327481","span":{"begin":591,"end":593},"obj":"29722887"}],"attributes":[{"subj":"32700671-29506019-29327479","pred":"source","obj":"2_test"},{"subj":"32700671-19151095-29327480","pred":"source","obj":"2_test"},{"subj":"32700671-29722887-29327481","pred":"source","obj":"2_test"}]},{"project":"MyTest","denotations":[{"id":"32700671-29506019-29327479","span":{"begin":409,"end":411},"obj":"29506019"},{"id":"32700671-19151095-29327480","span":{"begin":527,"end":529},"obj":"19151095"},{"id":"32700671-29722887-29327481","span":{"begin":591,"end":593},"obj":"29722887"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"attributes":[{"subj":"32700671-29506019-29327479","pred":"source","obj":"MyTest"},{"subj":"32700671-19151095-29327480","pred":"source","obj":"MyTest"},{"subj":"32700671-29722887-29327481","pred":"source","obj":"MyTest"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#e193ec","default":true},{"id":"LitCovid-PubTator","color":"#93ecc7"},{"id":"LitCovid-PD-MONDO","color":"#ecad93"},{"id":"LitCovid-PD-CLO","color":"#9393ec"},{"id":"LitCovid-PD-CHEBI","color":"#acec93"},{"id":"LitCovid-sentences","color":"#ec93c6"},{"id":"2_test","color":"#93e0ec"},{"id":"MyTest","color":"#ecdd93"}]}]}}