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Conserved domains on  [gi|3402186]
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Chain A, TOBACCO RINGSPOT VIRUS CAPSID PROTEIN

Protein Classification

Nepo_coat and Nepo_coat_C domain-containing protein( domain architecture ID 10506154)

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 pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 177-342 9.89e-73

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: 228.03  E-value: 9.89e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    177 PTMTWPIQLGDTFAIDRYYEAKEIKLDGSTSMLSISYNFGGPVKHSKKHAISYSRAVMSRNLGWSGTISGSVKSVSSLFC 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    257 TASFVIFPWECEAPPTLRQVLWGPHQIMHGDGQFEIAIKTRLHSAAT-TEEGFGRLGILPLSGPIAPDAHVGSYEFIVHI 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATrFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 3402186    336 NTWRPDS 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 349-509 5.09e-53

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: 176.75  E-value: 5.09e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    349 FSSSELYNWFTLTNLKPDAntgvVNFDIPGYIHDFASKDATVTLASNPLSWLVAATGWHYGEVDLCISWSRSKQAQAQEG 428
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDA----LTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    429 SVSITTNYRDWGAYWQGQARI----YDLRRTEAEIPIFLGSYAGATPSGALGKQN-YVRISIVNAKDIVALRVCLRPKS- 502
Cdd:pfam03688  77 TVKIVTLVGDFGTGTDGESTIgdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEeWIRIKSDNAKSISSLRVSIEVLPg 156


                  ....*..
gi 3402186    503 IKFWGRS 509
Cdd:pfam03688 157 FSFYGRS 163
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 177-342 9.89e-73

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: 228.03  E-value: 9.89e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    177 PTMTWPIQLGDTFAIDRYYEAKEIKLDGSTSMLSISYNFGGPVKHSKKHAISYSRAVMSRNLGWSGTISGSVKSVSSLFC 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    257 TASFVIFPWECEAPPTLRQVLWGPHQIMHGDGQFEIAIKTRLHSAAT-TEEGFGRLGILPLSGPIAPDAHVGSYEFIVHI 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATrFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 3402186    336 NTWRPDS 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 349-509 5.09e-53

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: 176.75  E-value: 5.09e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    349 FSSSELYNWFTLTNLKPDAntgvVNFDIPGYIHDFASKDATVTLASNPLSWLVAATGWHYGEVDLCISWSRSKQAQAQEG 428
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDA----LTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    429 SVSITTNYRDWGAYWQGQARI----YDLRRTEAEIPIFLGSYAGATPSGALGKQN-YVRISIVNAKDIVALRVCLRPKS- 502
Cdd:pfam03688  77 TVKIVTLVGDFGTGTDGESTIgdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEeWIRIKSDNAKSISSLRVSIEVLPg 156


                  ....*..
gi 3402186    503 IKFWGRS 509
Cdd:pfam03688 157 FSFYGRS 163
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 177-342 9.89e-73

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: 228.03  E-value: 9.89e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    177 PTMTWPIQLGDTFAIDRYYEAKEIKLDGSTSMLSISYNFGGPVKHSKKHAISYSRAVMSRNLGWSGTISGSVKSVSSLFC 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    257 TASFVIFPWECEAPPTLRQVLWGPHQIMHGDGQFEIAIKTRLHSAAT-TEEGFGRLGILPLSGPIAPDAHVGSYEFIVHI 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVESDGQFEIKIQSPYHRTATrFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 3402186    336 NTWRPDS 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 349-509 5.09e-53

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: 176.75  E-value: 5.09e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    349 FSSSELYNWFTLTNLKPDAntgvVNFDIPGYIHDFASKDATVTLASNPLSWLVAATGWHYGEVDLCISWSRSKQAQAQEG 428
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDA----LTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3402186    429 SVSITTNYRDWGAYWQGQARI----YDLRRTEAEIPIFLGSYAGATPSGALGKQN-YVRISIVNAKDIVALRVCLRPKS- 502
Cdd:pfam03688  77 TVKIVTLVGDFGTGTDGESTIgdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEeWIRIKSDNAKSISSLRVSIEVLPg 156


                  ....*..
gi 3402186    503 IKFWGRS 509
Cdd:pfam03688 157 FSFYGRS 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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