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Conserved domains on  [gi|294861828|gb|ADF45573|]
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nucleocapsid protein, partial [Bovine coronavirus cow/WDBR-923/BRA/2003]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CoV_N-NTD super family cl47273
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 12-85 2.86e-30

N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.


The actual alignment was detected with superfamily member cd21554:

Pssm-ID: 439219  Cd Length: 123  Bit Score: 103.43  E-value: 2.86e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294861828  12 PYYSWFSGITQFQKGKeFEFAEGQGVPIAPGVPATEAKGYWYRHNRRSFKTadGNQRQLLPRWYFYYLGTGPHA 85
Cdd:cd21554    1 IPLSWFAPITQTGKNK-PFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK--GGRKPLPPRWYFYYLGTGPHA 71
 
Name Accession Description Interval E-value
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 12-85 2.86e-30

N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.


Pssm-ID: 439219  Cd Length: 123  Bit Score: 103.43  E-value: 2.86e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294861828  12 PYYSWFSGITQFQKGKeFEFAEGQGVPIAPGVPATEAKGYWYRHNRRSFKTadGNQRQLLPRWYFYYLGTGPHA 85
Cdd:cd21554    1 IPLSWFAPITQTGKNK-PFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK--GGRKPLPPRWYFYYLGTGPHA 71
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 4-85 2.15e-25

Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).


Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 95.88  E-value: 2.15e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294861828    4 QPSGGNVVPYYSWFSGITQFQKGKEFEFAEGQGVPIAPGvPATEAKGYWYRHNRrsFKTADGNQRQLLPRWYFYYLGTGP 83
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPR--YRMGKGQRKQLPPRWYFYYLGTGP 77


                  ..
gi 294861828   84 HA 85
Cdd:pfam00937  78 HA 79
 
Name Accession Description Interval E-value
CoV_N-NTD cd21554
N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) ...
 12-85 2.86e-30

N-terminal domain of nucleocapsid (N) protein of coronavirus; The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.


Pssm-ID: 439219  Cd Length: 123  Bit Score: 103.43  E-value: 2.86e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 294861828  12 PYYSWFSGITQFQKGKeFEFAEGQGVPIAPGVPATEAKGYWYRHNRRSFKTadGNQRQLLPRWYFYYLGTGPHA 85
Cdd:cd21554    1 IPLSWFAPITQTGKNK-PFFKVPQGVPPNGGGPKDQQIGYWNRQPRWRMGK--GGRKPLPPRWYFYYLGTGPHA 71
CoV_nucleocap pfam00937
Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved ...
 4-85 2.15e-25

Coronavirus nucleocapsid; Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs).


Pssm-ID: 460005 [Multi-domain]  Cd Length: 343  Bit Score: 95.88  E-value: 2.15e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 294861828    4 QPSGGNVVPYYSWFSGITQFQKGKEFEFAEGQGVPIAPGvPATEAKGYWYRHNRrsFKTADGNQRQLLPRWYFYYLGTGP 83
Cdd:pfam00937   1 MAPRRNGRVPLSWFQPITQQGKKNFWKVMPGNGVPKGKG-NKDQQIGYWNRQPR--YRMGKGQRKQLPPRWYFYYLGTGP 77


                  ..
gi 294861828   84 HA 85
Cdd:pfam00937  78 HA 79
 
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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