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Conserved domains on  [gi|60115402|ref|YP_209239|]
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putative internal (I) ORF [Murine hepatitis virus strain JHM]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
embe-CoV_Protein-I_like cd21662
BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known ...
 5-119 1.08e-65

BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage) including murine hepatitis virus. The gene encoding protein I is included in the N gene as an alternative ORF. Protein I appears to have no homologous proteins in Sarbecovirus lineage B, which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. BECV-F15 protein I is not essential for viral replication. It is related to the ORF8b accessory protein of Middle East respiratory syndrome-related coronavirus (MERS-CoV) and other related merbecoviruses (C lineage); the gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a).


:

Pssm-ID: 394943  Cd Length: 115  Bit Score: 195.03  E-value: 1.08e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402   5 LHSKRDIGTDTTDVPLKHLMASRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGPLPILLKGTQVAMRLFL 84
Cdd:cd21662   1 LLKQRDIGIDTTDVLLKHLMASRSSCCPDGIFTILEQGPMLEPSMATALKESSGLLITRLTLIPLLTLLKGTQVAMRLFL 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 60115402  85 LGLRPVRYCLKVFMLKAQEGLHLLVDLVRGHNPVG 119
Cdd:cd21662  81 LGLRLVRYCLKAIMLKAQEGLHLLVDLVRGHNPVG 115
 
Name Accession Description Interval E-value
embe-CoV_Protein-I_like cd21662
BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known ...
 5-119 1.08e-65

BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage) including murine hepatitis virus. The gene encoding protein I is included in the N gene as an alternative ORF. Protein I appears to have no homologous proteins in Sarbecovirus lineage B, which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. BECV-F15 protein I is not essential for viral replication. It is related to the ORF8b accessory protein of Middle East respiratory syndrome-related coronavirus (MERS-CoV) and other related merbecoviruses (C lineage); the gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a).


Pssm-ID: 394943  Cd Length: 115  Bit Score: 195.03  E-value: 1.08e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402   5 LHSKRDIGTDTTDVPLKHLMASRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGPLPILLKGTQVAMRLFL 84
Cdd:cd21662   1 LLKQRDIGIDTTDVLLKHLMASRSSCCPDGIFTILEQGPMLEPSMATALKESSGLLITRLTLIPLLTLLKGTQVAMRLFL 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 60115402  85 LGLRPVRYCLKVFMLKAQEGLHLLVDLVRGHNPVG 119
Cdd:cd21662  81 LGLRLVRYCLKAIMLKAQEGLHLLVDLVRGHNPVG 115
Corona_I pfam03187
Corona nucleocapsid I protein;
1-136 9.42e-62

Corona nucleocapsid I protein;


Pssm-ID: 281216  Cd Length: 207  Bit Score: 188.38  E-value: 9.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402     1 MESQLHSKRDIGTDTTDVPLKHLMASRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGPLPILLKGTQVAM 80
Cdd:pfam03187  72 MESPLQSKRDIGIDTTAVLLKHLMGSRSNYCPDGIFTILAQGPMLEPVMETALKVSSGLQTAKRTPIPALILSKGTQAVM 151

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 60115402    81 RLFLLGLRPVRYCLKVFMLKAQEGLHLLVDLVRGHNPVGQIIALEAVPTSASLPLL 136
Cdd:pfam03187 152 RLFLLGLRPARYCLRAFMLKALEGLHLLADLVRGHNPVGQIIALEAVPTSASLPLL 207
 
Name Accession Description Interval E-value
embe-CoV_Protein-I_like cd21662
BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known ...
 5-119 1.08e-65

BECV protein I and related Embecovirus proteins; This subfamily includes protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage) including murine hepatitis virus. The gene encoding protein I is included in the N gene as an alternative ORF. Protein I appears to have no homologous proteins in Sarbecovirus lineage B, which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. BECV-F15 protein I is not essential for viral replication. It is related to the ORF8b accessory protein of Middle East respiratory syndrome-related coronavirus (MERS-CoV) and other related merbecoviruses (C lineage); the gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a).


Pssm-ID: 394943  Cd Length: 115  Bit Score: 195.03  E-value: 1.08e-65
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402   5 LHSKRDIGTDTTDVPLKHLMASRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGPLPILLKGTQVAMRLFL 84
Cdd:cd21662   1 LLKQRDIGIDTTDVLLKHLMASRSSCCPDGIFTILEQGPMLEPSMATALKESSGLLITRLTLIPLLTLLKGTQVAMRLFL 80

                        90       100       110
                ....*....|....*....|....*....|....*
gi 60115402  85 LGLRPVRYCLKVFMLKAQEGLHLLVDLVRGHNPVG 119
Cdd:cd21662  81 LGLRLVRYCLKAIMLKAQEGLHLLVDLVRGHNPVG 115
Corona_I pfam03187
Corona nucleocapsid I protein;
1-136 9.42e-62

Corona nucleocapsid I protein;


Pssm-ID: 281216  Cd Length: 207  Bit Score: 188.38  E-value: 9.42e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402     1 MESQLHSKRDIGTDTTDVPLKHLMASRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGPLPILLKGTQVAM 80
Cdd:pfam03187  72 MESPLQSKRDIGIDTTAVLLKHLMGSRSNYCPDGIFTILAQGPMLEPVMETALKVSSGLQTAKRTPIPALILSKGTQAVM 151

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 60115402    81 RLFLLGLRPVRYCLKVFMLKAQEGLHLLVDLVRGHNPVGQIIALEAVPTSASLPLL 136
Cdd:pfam03187 152 RLFLLGLRPARYCLRAFMLKALEGLHLLADLVRGHNPVGQIIALEAVPTSASLPLL 207
embe-merbe_CoV_ORF8b_protein-I-like cd21654
MERS-CoV ORF8b, BECV protein I, and related Embecovirus and Merbecovirus proteins; This family ...
 5-111 2.47e-42

MERS-CoV ORF8b, BECV protein I, and related Embecovirus and Merbecovirus proteins; This family includes the ORF8b accessory protein from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and related merbecoviruses (C lineage), and protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage). The gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a), and the gene encoding protein I is included in the N gene as an alternative ORF. ORF8b and protein I appear to have no homologous proteins in Sarbecovirus (lineage B), which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. MERS-CoV ORF8b and BECV-F15 protein I are not essential for viral replication.


Pssm-ID: 394941  Cd Length: 104  Bit Score: 135.46  E-value: 2.47e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402   5 LHSKRDIGTDTTDVPLKHLMasRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPRLGpLPILLKGTQVAMRLFL 84
Cdd:cd21654   1 LRKMLGIGGDRTEKLIKHME--RSSWLPGGISTTLEQDPKLASSSALISMESSGSMKNRPRLL-LPLLGRGTLTMMQLLL 77

                        90       100
                ....*....|....*....|....*..
gi 60115402  85 LGLRPVRYCLKVFMLKAQEGLHLLVDL 111
Cdd:cd21654  78 LGSRPVLSFLKTSTLKALEALVNHLQL 104
merbe_CoV_ORF8b-like cd21661
MERS-CoV ORF8b protein and related Merbecovirus proteins; This subfamily includes the ORF8b ...
 5-108 1.45e-07

MERS-CoV ORF8b protein and related Merbecovirus proteins; This subfamily includes the ORF8b accessory protein from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and related merbecoviruses (C lineage). The gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a). ORF8b appear to have no homologous proteins in Sarbecovirus (lineage B), which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. MERS-CoV ORF8b is not essential for viral replication. It is related to protein I (also known as accessory protein N2) of bovine enteritic coronavirus-F15 strain (BECV-F15) and other related Embecoviruses; the gene encoding protein I is included in the N gene as an alternative ORF.


Pssm-ID: 394942  Cd Length: 104  Bit Score: 46.45  E-value: 1.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 60115402   5 LHSKRDIGTDTTDVPLKHLmaSRSSYCPDGIFTILEQGPMLAQSMATISKELSGSQANRPrLGPLPILLKGTQVAMRLFL 84
Cdd:cd21661   1 LRKMLGIGGDRTEKLIQGM--ELSNWLPGGTSTTLELDPKQTSHSELSRMASFGSMKMVP-LMLLQLLGRGTLTMIQLLL 77

                        90       100
                ....*....|....*....|....*.
gi 60115402  85 LGLRPVRYCLKVFMLKAQEGL--HLL 108
Cdd:cd21661  78 HSSLPVLSFLKTSTLRGLEAIvnHLQ 103
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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