PMC:7335631 / 4938-8572 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T24","span":{"begin":23,"end":28},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T25","span":{"begin":81,"end":84},"obj":"http://purl.obolibrary.org/obo/CLO_0001319"},{"id":"T26","span":{"begin":675,"end":676},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T27","span":{"begin":696,"end":699},"obj":"http://purl.obolibrary.org/obo/CLO_0001562"},{"id":"T28","span":{"begin":696,"end":699},"obj":"http://purl.obolibrary.org/obo/CLO_0001563"},{"id":"T29","span":{"begin":714,"end":715},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T30","span":{"begin":1559,"end":1564},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T31","span":{"begin":1609,"end":1617},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T32","span":{"begin":1662,"end":1665},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T33","span":{"begin":2007,"end":2012},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T34","span":{"begin":3606,"end":3607},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"3 Results\nAmong these virus genomes from 3617 patients; 2588 were from the USA, 372 were from Asia, 287 were from Europe, 365 were from Oceania and 5 were from Africa. Here, we present the non-synonymous mutations of the E-protein protein over the available 3617 SARS-CoV2 genomes (Table 1 ). It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contained the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes. Changes of the R-group of each amino acid according to the mutations are also presented (Table-1). It is to be noted that the mutation of an amino acid A 1 to an amino acid A 2 is denoted by A 1 pA 2 where p denotes location in the reference amino acid sequence.• In less than 0.5% of the SARS-CoV2 genomes, the E-protein possesses the missense mutations as adumbrated in the Table 1. In TMD and C-terminus domain, there are nine different mutations where the R-group property changes. But only in QHZ00381, for the mutation L37H in the TMD of the envelope protein causes changes in amino acid from hydrophobic to hydrophilic.\n• TMD was also observed to be conserved over the SARS-CoV1 and COV2 genomes, but the protein sequences of QJA42107 (USA: VA), QJQ84222(USA: KENNER, LA), QHZ00381(South Korea) and QJS53352(Greece: Athens) possess four mutations A36V, L26F, L37H and L39M, respectively, in the TMD of the envelope protein. Change in the R-group property from Hydrophobic to Hydrophilic in the TMD of the envelope protein of the virus from South Korea may affect the ion channel activity of the envelope protein.\n• The motif ′DLLV′ has been changed to ′DFLV′ and ′YLLV′ in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) due to the mutations L73F and D72Y respectively. These mutations having changes in the motif ′DFLV′ may mis-target the PALS1 at Golgi and delaying TJ formation and accordingly may influence replication and/or infectivity of the virus [10].\n• In the C-terminus domain of the E-protein of SARS-CoV2 the amino acid S at 68th position changes to the amino acids F and C in the proteins {QKG87268, QKG88576} from the USA: Massachusetts and QKI36855 from China: Guangzhou respectively. Note that the mutation of the amino acid S to F keeps the R-group property unchanged (i.e. hydrophobic to hydrophilic) while that of the amino acid S to C changes the R-group from Hydrophilic to Hydrophobic. This would possibly make changes in protein functions and interactions.\nTable 1 Non- synonymous mutation in the E-protein of SARS-CoV2.\nProtein-ID Geo-location Mutation Domain Change of R-group\nQJA42107 USA: VA A36V TMDa Hydrophobic to Hydrophobic\nQJQ84222 USA: KENNER, LA L26F TMD Hydrophobic to Hydrophobic\nQHZ00381 South Korea L37H TMD Hydrophobic to Hydrophilic\nQJS53352 Greece: Athens L39M TMD Hydrophobic to Hydrophobic\nQJR88103 Australia: Victoria L73F C-terminus Hydrophobic to Hydrophobic\nQKE45838 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45886 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45898 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45910 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQJE38284 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQIU81527 USA: WA P71L C-terminus Hydrophobic to Hydrophobic\nQKG87268 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKG88576 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKI36831 China: Guangzhou D72Y C-terminus Hydrophilic to Hydrophobic\nQKI36855 China: Guangzhou S68C C-terminus Hydrophilic to Hydrophobic\na TMD: transmembrane domain."}

LitCovid-PD-CHEBI

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T2","span":{"begin":911,"end":914},"obj":"Phenotype"},{"id":"T3","span":{"begin":1060,"end":1063},"obj":"Phenotype"},{"id":"T4","span":{"begin":1152,"end":1155},"obj":"Phenotype"},{"id":"T5","span":{"begin":1425,"end":1428},"obj":"Phenotype"},{"id":"T6","span":{"begin":1524,"end":1527},"obj":"Phenotype"},{"id":"T7","span":{"begin":2746,"end":2749},"obj":"Phenotype"},{"id":"T8","span":{"begin":2803,"end":2806},"obj":"Phenotype"},{"id":"T9","span":{"begin":2863,"end":2866},"obj":"Phenotype"},{"id":"T10","span":{"begin":3608,"end":3611},"obj":"Phenotype"}],"attributes":[{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A4","pred":"hp_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A5","pred":"hp_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A6","pred":"hp_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A7","pred":"hp_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A8","pred":"hp_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A9","pred":"hp_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/HP_0005534"},{"id":"A10","pred":"hp_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/HP_0005534"}],"text":"3 Results\nAmong these virus genomes from 3617 patients; 2588 were from the USA, 372 were from Asia, 287 were from Europe, 365 were from Oceania and 5 were from Africa. Here, we present the non-synonymous mutations of the E-protein protein over the available 3617 SARS-CoV2 genomes (Table 1 ). It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contained the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes. Changes of the R-group of each amino acid according to the mutations are also presented (Table-1). It is to be noted that the mutation of an amino acid A 1 to an amino acid A 2 is denoted by A 1 pA 2 where p denotes location in the reference amino acid sequence.• In less than 0.5% of the SARS-CoV2 genomes, the E-protein possesses the missense mutations as adumbrated in the Table 1. In TMD and C-terminus domain, there are nine different mutations where the R-group property changes. But only in QHZ00381, for the mutation L37H in the TMD of the envelope protein causes changes in amino acid from hydrophobic to hydrophilic.\n• TMD was also observed to be conserved over the SARS-CoV1 and COV2 genomes, but the protein sequences of QJA42107 (USA: VA), QJQ84222(USA: KENNER, LA), QHZ00381(South Korea) and QJS53352(Greece: Athens) possess four mutations A36V, L26F, L37H and L39M, respectively, in the TMD of the envelope protein. Change in the R-group property from Hydrophobic to Hydrophilic in the TMD of the envelope protein of the virus from South Korea may affect the ion channel activity of the envelope protein.\n• The motif ′DLLV′ has been changed to ′DFLV′ and ′YLLV′ in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) due to the mutations L73F and D72Y respectively. These mutations having changes in the motif ′DFLV′ may mis-target the PALS1 at Golgi and delaying TJ formation and accordingly may influence replication and/or infectivity of the virus [10].\n• In the C-terminus domain of the E-protein of SARS-CoV2 the amino acid S at 68th position changes to the amino acids F and C in the proteins {QKG87268, QKG88576} from the USA: Massachusetts and QKI36855 from China: Guangzhou respectively. Note that the mutation of the amino acid S to F keeps the R-group property unchanged (i.e. hydrophobic to hydrophilic) while that of the amino acid S to C changes the R-group from Hydrophilic to Hydrophobic. This would possibly make changes in protein functions and interactions.\nTable 1 Non- synonymous mutation in the E-protein of SARS-CoV2.\nProtein-ID Geo-location Mutation Domain Change of R-group\nQJA42107 USA: VA A36V TMDa Hydrophobic to Hydrophobic\nQJQ84222 USA: KENNER, LA L26F TMD Hydrophobic to Hydrophobic\nQHZ00381 South Korea L37H TMD Hydrophobic to Hydrophilic\nQJS53352 Greece: Athens L39M TMD Hydrophobic to Hydrophobic\nQJR88103 Australia: Victoria L73F C-terminus Hydrophobic to Hydrophobic\nQKE45838 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45886 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45898 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45910 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQJE38284 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQIU81527 USA: WA P71L C-terminus Hydrophobic to Hydrophobic\nQKG87268 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKG88576 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKI36831 China: Guangzhou D72Y C-terminus Hydrophilic to Hydrophobic\nQKI36855 China: Guangzhou S68C C-terminus Hydrophilic to Hydrophobic\na TMD: transmembrane domain."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T6","span":{"begin":1597,"end":1617},"obj":"http://purl.obolibrary.org/obo/GO_0005216"},{"id":"T7","span":{"begin":1601,"end":1617},"obj":"http://purl.obolibrary.org/obo/GO_0015267"},{"id":"T8","span":{"begin":1929,"end":1938},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"3 Results\nAmong these virus genomes from 3617 patients; 2588 were from the USA, 372 were from Asia, 287 were from Europe, 365 were from Oceania and 5 were from Africa. Here, we present the non-synonymous mutations of the E-protein protein over the available 3617 SARS-CoV2 genomes (Table 1 ). It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contained the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes. Changes of the R-group of each amino acid according to the mutations are also presented (Table-1). It is to be noted that the mutation of an amino acid A 1 to an amino acid A 2 is denoted by A 1 pA 2 where p denotes location in the reference amino acid sequence.• In less than 0.5% of the SARS-CoV2 genomes, the E-protein possesses the missense mutations as adumbrated in the Table 1. In TMD and C-terminus domain, there are nine different mutations where the R-group property changes. But only in QHZ00381, for the mutation L37H in the TMD of the envelope protein causes changes in amino acid from hydrophobic to hydrophilic.\n• TMD was also observed to be conserved over the SARS-CoV1 and COV2 genomes, but the protein sequences of QJA42107 (USA: VA), QJQ84222(USA: KENNER, LA), QHZ00381(South Korea) and QJS53352(Greece: Athens) possess four mutations A36V, L26F, L37H and L39M, respectively, in the TMD of the envelope protein. Change in the R-group property from Hydrophobic to Hydrophilic in the TMD of the envelope protein of the virus from South Korea may affect the ion channel activity of the envelope protein.\n• The motif ′DLLV′ has been changed to ′DFLV′ and ′YLLV′ in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) due to the mutations L73F and D72Y respectively. These mutations having changes in the motif ′DFLV′ may mis-target the PALS1 at Golgi and delaying TJ formation and accordingly may influence replication and/or infectivity of the virus [10].\n• In the C-terminus domain of the E-protein of SARS-CoV2 the amino acid S at 68th position changes to the amino acids F and C in the proteins {QKG87268, QKG88576} from the USA: Massachusetts and QKI36855 from China: Guangzhou respectively. Note that the mutation of the amino acid S to F keeps the R-group property unchanged (i.e. hydrophobic to hydrophilic) while that of the amino acid S to C changes the R-group from Hydrophilic to Hydrophobic. This would possibly make changes in protein functions and interactions.\nTable 1 Non- synonymous mutation in the E-protein of SARS-CoV2.\nProtein-ID Geo-location Mutation Domain Change of R-group\nQJA42107 USA: VA A36V TMDa Hydrophobic to Hydrophobic\nQJQ84222 USA: KENNER, LA L26F TMD Hydrophobic to Hydrophobic\nQHZ00381 South Korea L37H TMD Hydrophobic to Hydrophilic\nQJS53352 Greece: Athens L39M TMD Hydrophobic to Hydrophobic\nQJR88103 Australia: Victoria L73F C-terminus Hydrophobic to Hydrophobic\nQKE45838 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45886 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45898 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45910 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQJE38284 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQIU81527 USA: WA P71L C-terminus Hydrophobic to Hydrophobic\nQKG87268 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKG88576 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKI36831 China: Guangzhou D72Y C-terminus Hydrophilic to Hydrophobic\nQKI36855 China: Guangzhou S68C C-terminus Hydrophilic to Hydrophobic\na TMD: transmembrane domain."}

LitCovid-sentences

2_test

{"project":"2_test","denotations":[{"id":"32640274-30712672-44882429","span":{"begin":2014,"end":2016},"obj":"30712672"}],"text":"3 Results\nAmong these virus genomes from 3617 patients; 2588 were from the USA, 372 were from Asia, 287 were from Europe, 365 were from Oceania and 5 were from Africa. Here, we present the non-synonymous mutations of the E-protein protein over the available 3617 SARS-CoV2 genomes (Table 1 ). It is to be noted that 10 (0.386%) out of 2588 genomes from USA, 3 (0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania) contained the missense mutations (Table 1) in the envelope proteins of SARS-CoV2 genomes. Changes of the R-group of each amino acid according to the mutations are also presented (Table-1). It is to be noted that the mutation of an amino acid A 1 to an amino acid A 2 is denoted by A 1 pA 2 where p denotes location in the reference amino acid sequence.• In less than 0.5% of the SARS-CoV2 genomes, the E-protein possesses the missense mutations as adumbrated in the Table 1. In TMD and C-terminus domain, there are nine different mutations where the R-group property changes. But only in QHZ00381, for the mutation L37H in the TMD of the envelope protein causes changes in amino acid from hydrophobic to hydrophilic.\n• TMD was also observed to be conserved over the SARS-CoV1 and COV2 genomes, but the protein sequences of QJA42107 (USA: VA), QJQ84222(USA: KENNER, LA), QHZ00381(South Korea) and QJS53352(Greece: Athens) possess four mutations A36V, L26F, L37H and L39M, respectively, in the TMD of the envelope protein. Change in the R-group property from Hydrophobic to Hydrophilic in the TMD of the envelope protein of the virus from South Korea may affect the ion channel activity of the envelope protein.\n• The motif ′DLLV′ has been changed to ′DFLV′ and ′YLLV′ in the proteins QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) due to the mutations L73F and D72Y respectively. These mutations having changes in the motif ′DFLV′ may mis-target the PALS1 at Golgi and delaying TJ formation and accordingly may influence replication and/or infectivity of the virus [10].\n• In the C-terminus domain of the E-protein of SARS-CoV2 the amino acid S at 68th position changes to the amino acids F and C in the proteins {QKG87268, QKG88576} from the USA: Massachusetts and QKI36855 from China: Guangzhou respectively. Note that the mutation of the amino acid S to F keeps the R-group property unchanged (i.e. hydrophobic to hydrophilic) while that of the amino acid S to C changes the R-group from Hydrophilic to Hydrophobic. This would possibly make changes in protein functions and interactions.\nTable 1 Non- synonymous mutation in the E-protein of SARS-CoV2.\nProtein-ID Geo-location Mutation Domain Change of R-group\nQJA42107 USA: VA A36V TMDa Hydrophobic to Hydrophobic\nQJQ84222 USA: KENNER, LA L26F TMD Hydrophobic to Hydrophobic\nQHZ00381 South Korea L37H TMD Hydrophobic to Hydrophilic\nQJS53352 Greece: Athens L39M TMD Hydrophobic to Hydrophobic\nQJR88103 Australia: Victoria L73F C-terminus Hydrophobic to Hydrophobic\nQKE45838 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45886 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45898 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQKE45910 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQJE38284 USA: CA P71L C-terminus Hydrophobic to Hydrophobic\nQIU81527 USA: WA P71L C-terminus Hydrophobic to Hydrophobic\nQKG87268 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKG88576 USA: Massachusetts S68F C-terminus Hydrophobic to Hydrophobic\nQKI36831 China: Guangzhou D72Y C-terminus Hydrophilic to Hydrophobic\nQKI36855 China: Guangzhou S68C C-terminus Hydrophilic to Hydrophobic\na TMD: transmembrane domain."}

LitCovid-PMC-OGER-BB

PMC:7335631 / 4938-8572 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7335631 / 4938-8572 JSON TXT