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Conserved domains on  [gi|2108669259|gb|UCJ00930|]
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polyprotein [Raspberry ringspot virus]

Protein Classification

Nepo_coat and Nepo_coat_C domain-containing protein( domain architecture ID 10263765)

Nepo_coat and Nepo_coat_C domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nepo_coat super family cl04041
Nepovirus coat protein, central domain; The members of this family are derived from ...
 768-934 1.96e-58

Nepovirus coat protein, central domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


The actual alignment was detected with superfamily member pfam03391:

Pssm-ID: 397456  Cd Length: 167  Bit Score: 198.37  E-value: 1.96e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  768 PTFVWPPKSTDISLLKEVWGPYRFTLDGTEARESFSLMPGMAITHGKQTVRTFPRVIAAHFRSWTGKVKISIQEVSSIFL 847
Cdd:pfam03391    1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  848 TGTYMVGVSWN-ASAELTDITTRKHWIVKSGEVFELDLYCPYGENPTFTGLVNGMPYIIVhkLGGIVGPKDSVGTFGFFI 926
Cdd:pfam03391   81 TCSLRVASSWNgATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATRFGDDGSRFYISS--LSGPIAPKDMEAKYQFMI 158


                   ....*...
gi 2108669259  927 HIHGLTGV 934
Cdd:pfam03391  159 HIEGIVAV 166
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 945-1103 4.16e-51

Nepovirus coat protein, C-terminal domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


:

Pssm-ID: 397650  Cd Length: 163  Bit Score: 177.14  E-value: 4.16e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  945 RSVGSAWFRVTNIIDDNLTFNIPGRIEDMAAvvGKYDVTNYVNPTSLLFSVTGLHGGIIRLHITWCPNTSLGESRGTLKY 1024
Cdd:pfam03688    3 YSQRFNWFTLSNFTVDALTFKIPSRISDITS--KDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259 1025 MQYLYH----TPTENFFGDqaTRGIIDQDGFTVDLACGDFFGATRVGLKGEVER-LGIYSSNAKSIAEIRVSFEILS-MN 1098
Cdd:pfam03688   81 VTLVGDfgtgTDGESTIGD--TNGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEwIRIKSDNAKSISSLRVSIEVLPgFS 158


                   ....*
gi 2108669259 1099 FYGST 1103
Cdd:pfam03688  159 FYGRS 163
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 768-934 1.96e-58

Nepovirus coat protein, central domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


Pssm-ID: 397456  Cd Length: 167  Bit Score: 198.37  E-value: 1.96e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  768 PTFVWPPKSTDISLLKEVWGPYRFTLDGTEARESFSLMPGMAITHGKQTVRTFPRVIAAHFRSWTGKVKISIQEVSSIFL 847
Cdd:pfam03391    1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  848 TGTYMVGVSWN-ASAELTDITTRKHWIVKSGEVFELDLYCPYGENPTFTGLVNGMPYIIVhkLGGIVGPKDSVGTFGFFI 926
Cdd:pfam03391   81 TCSLRVASSWNgATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATRFGDDGSRFYISS--LSGPIAPKDMEAKYQFMI 158


                   ....*...
gi 2108669259  927 HIHGLTGV 934
Cdd:pfam03391  159 HIEGIVAV 166
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 945-1103 4.16e-51

Nepovirus coat protein, C-terminal domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


Pssm-ID: 397650  Cd Length: 163  Bit Score: 177.14  E-value: 4.16e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  945 RSVGSAWFRVTNIIDDNLTFNIPGRIEDMAAvvGKYDVTNYVNPTSLLFSVTGLHGGIIRLHITWCPNTSLGESRGTLKY 1024
Cdd:pfam03688    3 YSQRFNWFTLSNFTVDALTFKIPSRISDITS--KDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259 1025 MQYLYH----TPTENFFGDqaTRGIIDQDGFTVDLACGDFFGATRVGLKGEVER-LGIYSSNAKSIAEIRVSFEILS-MN 1098
Cdd:pfam03688   81 VTLVGDfgtgTDGESTIGD--TNGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEwIRIKSDNAKSISSLRVSIEVLPgFS 158


                   ....*
gi 2108669259 1099 FYGST 1103
Cdd:pfam03688  159 FYGRS 163
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 768-934 1.96e-58

Nepovirus coat protein, central domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


Pssm-ID: 397456  Cd Length: 167  Bit Score: 198.37  E-value: 1.96e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  768 PTFVWPPKSTDISLLKEVWGPYRFTLDGTEARESFSLMPGMAITHGKQTVRTFPRVIAAHFRSWTGKVKISIQEVSSIFL 847
Cdd:pfam03391    1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  848 TGTYMVGVSWN-ASAELTDITTRKHWIVKSGEVFELDLYCPYGENPTFTGLVNGMPYIIVhkLGGIVGPKDSVGTFGFFI 926
Cdd:pfam03391   81 TCSLRVASSWNgATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATRFGDDGSRFYISS--LSGPIAPKDMEAKYQFMI 158


                   ....*...
gi 2108669259  927 HIHGLTGV 934
Cdd:pfam03391  159 HIEGIVAV 166
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 945-1103 4.16e-51

Nepovirus coat protein, C-terminal domain; The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure.


Pssm-ID: 397650  Cd Length: 163  Bit Score: 177.14  E-value: 4.16e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259  945 RSVGSAWFRVTNIIDDNLTFNIPGRIEDMAAvvGKYDVTNYVNPTSLLFSVTGLHGGIIRLHITWCPNTSLGESRGTLKY 1024
Cdd:pfam03688    3 YSQRFNWFTLSNFTVDALTFKIPSRISDITS--KDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2108669259 1025 MQYLYH----TPTENFFGDqaTRGIIDQDGFTVDLACGDFFGATRVGLKGEVER-LGIYSSNAKSIAEIRVSFEILS-MN 1098
Cdd:pfam03688   81 VTLVGDfgtgTDGESTIGD--TNGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEwIRIKSDNAKSISSLRVSIEVLPgFS 158


                   ....*
gi 2108669259 1099 FYGST 1103
Cdd:pfam03688  159 FYGRS 163
 
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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