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Conserved domains on  [gi|25013729|ref|NP_733973|]
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capsid protein [Tomato ringspot virus]

Protein Classification

Nepo_coat_N and Nepo_coat_C domain-containing protein( domain architecture ID 10508561)

protein containing domains Nepo_coat_N, Nepo_coat, and Nepo_coat_C

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 ...
 177-342 6.08e-61

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: 198.76  E-value: 6.08e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   177 PFITLPHIFNRLDIGYWRGPTEIDLTSTPAPNAYRLLFGLSTVISGNMSTLNANQALLRFFQGSNGTLHGRIKKIGTALT 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   257 TCSLLLSLRHKDASLTLETAYQRPHYILA-DGQGAFSLPISTPHAATSFLEDMLRLEIFAIAGPFSPKDNKAKYQFMCYF 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVEsDGQFEIKIQSPYHRTATRFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 25013729   336 DHIELVE 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 348-507 1.26e-58

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: 192.55  E-value: 1.26e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   348 IAGEQQFNWCSFRNFKIDDWKFEWPARLPDILDDKSEVLLRQHPLSLLISSTGFFTGRAIFVFQWGLNTTAGNMKGSFSA 427
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDALTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   428 RLAFGKGVEEIEQTSTVQ---PLVGACEARIPVEFKTYTGYTTSGPPGSMEPYIYVRLTQAKLVDRLSVNVILQEGFSFY 504
Cdd:pfam03688  81 VTLVGDFGTGTDGESTIGdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEWIRIKSDNAKSISSLRVSIEVLPGFSFY 160


                  ...
gi 25013729   505 GPS 507
Cdd:pfam03688 161 GRS 163
Nepo_coat_N pfam03689
Nepovirus coat protein, N-terminal domain; The members of this family are derived from ...
 11-101 3.99e-31

Nepovirus coat protein, N-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: 397651  Cd Length: 91  Bit Score: 115.82  E-value: 3.99e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729    11 AYLGKVTCAKDAKGGTLLHTLDIIKECKSQNLLRYKEWQRQGFLHGKLRLRCFIPTNIFCGHSMMCSLDAFGRYDSNVlG 90
Cdd:pfam03689   2 AFVESITVPKDATAGTVLATLDIRAKIKETNSAVYYEWLRKGYVHPNLKVRIHLPTNIFAGITLGIVFDAYNRIPSDI-T 80

                          90
                  ....*....|.
gi 25013729    91 ASFPVKLASLL 101
Cdd:pfam03689  81 TTFPLSLAFSL 91
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 177-342 6.08e-61

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: 198.76  E-value: 6.08e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   177 PFITLPHIFNRLDIGYWRGPTEIDLTSTPAPNAYRLLFGLSTVISGNMSTLNANQALLRFFQGSNGTLHGRIKKIGTALT 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   257 TCSLLLSLRHKDASLTLETAYQRPHYILA-DGQGAFSLPISTPHAATSFLEDMLRLEIFAIAGPFSPKDNKAKYQFMCYF 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVEsDGQFEIKIQSPYHRTATRFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 25013729   336 DHIELVE 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 348-507 1.26e-58

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: 192.55  E-value: 1.26e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   348 IAGEQQFNWCSFRNFKIDDWKFEWPARLPDILDDKSEVLLRQHPLSLLISSTGFFTGRAIFVFQWGLNTTAGNMKGSFSA 427
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDALTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   428 RLAFGKGVEEIEQTSTVQ---PLVGACEARIPVEFKTYTGYTTSGPPGSMEPYIYVRLTQAKLVDRLSVNVILQEGFSFY 504
Cdd:pfam03688  81 VTLVGDFGTGTDGESTIGdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEWIRIKSDNAKSISSLRVSIEVLPGFSFY 160


                  ...
gi 25013729   505 GPS 507
Cdd:pfam03688 161 GRS 163
Nepo_coat_N pfam03689
Nepovirus coat protein, N-terminal domain; The members of this family are derived from ...
 11-101 3.99e-31

Nepovirus coat protein, N-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: 397651  Cd Length: 91  Bit Score: 115.82  E-value: 3.99e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729    11 AYLGKVTCAKDAKGGTLLHTLDIIKECKSQNLLRYKEWQRQGFLHGKLRLRCFIPTNIFCGHSMMCSLDAFGRYDSNVlG 90
Cdd:pfam03689   2 AFVESITVPKDATAGTVLATLDIRAKIKETNSAVYYEWLRKGYVHPNLKVRIHLPTNIFAGITLGIVFDAYNRIPSDI-T 80

                          90
                  ....*....|.
gi 25013729    91 ASFPVKLASLL 101
Cdd:pfam03689  81 TTFPLSLAFSL 91
 
Name Accession Description Interval E-value
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 177-342 6.08e-61

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: 198.76  E-value: 6.08e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   177 PFITLPHIFNRLDIGYWRGPTEIDLTSTPAPNAYRLLFGLSTVISGNMSTLNANQALLRFFQGSNGTLHGRIKKIGTALT 256
Cdd:pfam03391   1 PTLTYPIKFGDLSLLFLRLPPKFIALGGTTALKSPLLLAGQTVSHGGRIVYSFNAALLSHFLGWGGTIHGSVHSTSSAFV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   257 TCSLLLSLRHKDASLTLETAYQRPHYILA-DGQGAFSLPISTPHAATSFLEDMLRLEIFAIAGPFSPKDNKAKYQFMCYF 335
Cdd:pfam03391  81 TCSLRVASSWNGATPTLEQLFQRPHVIVEsDGQFEIKIQSPYHRTATRFGDDGSRFYISSLSGPIAPKDMEAKYQFMIHI 160


                  ....*..
gi 25013729   336 DHIELVE 342
Cdd:pfam03391 161 EGIVAVP 167
Nepo_coat_C pfam03688
Nepovirus coat protein, C-terminal domain; The members of this family are derived from ...
 348-507 1.26e-58

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: 192.55  E-value: 1.26e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   348 IAGEQQFNWCSFRNFKIDDWKFEWPARLPDILDDKSEVLLRQHPLSLLISSTGFFTGRAIFVFQWGLNTTAGNMKGSFSA 427
Cdd:pfam03688   1 INYSQRFNWFTLSNFTVDALTFKIPSRISDITSKDATVTNYVNPFALLIASTGMHRGSVTLHFSWSLNTELGKSKGTVKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729   428 RLAFGKGVEEIEQTSTVQ---PLVGACEARIPVEFKTYTGYTTSGPPGSMEPYIYVRLTQAKLVDRLSVNVILQEGFSFY 504
Cdd:pfam03688  81 VTLVGDFGTGTDGESTIGdtnGLIQAGSFSIPLEFGDFAGPTTSGGLGLEEEWIRIKSDNAKSISSLRVSIEVLPGFSFY 160


                  ...
gi 25013729   505 GPS 507
Cdd:pfam03688 161 GRS 163
Nepo_coat_N pfam03689
Nepovirus coat protein, N-terminal domain; The members of this family are derived from ...
 11-101 3.99e-31

Nepovirus coat protein, N-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: 397651  Cd Length: 91  Bit Score: 115.82  E-value: 3.99e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 25013729    11 AYLGKVTCAKDAKGGTLLHTLDIIKECKSQNLLRYKEWQRQGFLHGKLRLRCFIPTNIFCGHSMMCSLDAFGRYDSNVlG 90
Cdd:pfam03689   2 AFVESITVPKDATAGTVLATLDIRAKIKETNSAVYYEWLRKGYVHPNLKVRIHLPTNIFAGITLGIVFDAYNRIPSDI-T 80

                          90
                  ....*....|.
gi 25013729    91 ASFPVKLASLL 101
Cdd:pfam03689  81 TTFPLSLAFSL 91
 
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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