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Conserved domains on  [gi|397776127|ref|YP_006546259|]
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VP0 [Pasivirus A1]

Protein Classification

capsid protein( domain architecture ID 10082122)

picornavirus capsid protein is a component of the capsid (protein coat) which encloses the viral genome; it may play roles in the infection cycle

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 81-244 8.79e-24

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich


:

Pssm-ID: 119412  Cd Length: 178  Bit Score: 94.00  E-value: 8.79e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  81 VLLDIVHFDNTWVWGGNDKLQLPlPKCFWKNRSFPAYG-TSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVYVPNdhYQSW 159
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWKLS-PALGFLLLQNTPLGaLLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP--GAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127 160 NNKDLILHTMFNWPHVIFNVATMTEADLYIPYINTHNLANTD------SSDCGWVVVTPFTHLEVASTTTNTLDIAVFGS 233
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgygpLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVR 165

                        170
                 ....*....|.
gi 397776127 234 LVDFQFQGPRP 244
Cdd:cd00205  166 AGDFELYGPRP 176
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 81-244 8.79e-24

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich


Pssm-ID: 119412  Cd Length: 178  Bit Score: 94.00  E-value: 8.79e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  81 VLLDIVHFDNTWVWGGNDKLQLPlPKCFWKNRSFPAYG-TSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVYVPNdhYQSW 159
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWKLS-PALGFLLLQNTPLGaLLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP--GAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127 160 NNKDLILHTMFNWPHVIFNVATMTEADLYIPYINTHNLANTD------SSDCGWVVVTPFTHLEVASTTTNTLDIAVFGS 233
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgygpLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVR 165

                        170
                 ....*....|.
gi 397776127 234 LVDFQFQGPRP 244
Cdd:cd00205  166 AGDFELYGPRP 176
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 118-200 1.34e-05

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.


Pssm-ID: 395026  Cd Length: 170  Bit Score: 44.22  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  118 GTSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVYVPNdHYQSWNNKDLILHTMFNwPHVIFNVATMTEADLYIPYINTHNL 197
Cdd:pfam00073  72 RLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPP-GAPPPGSRDYLWQATLN-PHQFWNLGLNSSARLSVPYISIAHY 149


                  ...
gi 397776127  198 ANT 200
Cdd:pfam00073 150 YST 152
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 81-244 8.79e-24

Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich


Pssm-ID: 119412  Cd Length: 178  Bit Score: 94.00  E-value: 8.79e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  81 VLLDIVHFDNTWVWGGNDKLQLPlPKCFWKNRSFPAYG-TSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVYVPNdhYQSW 159
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWKLS-PALGFLLLQNTPLGaLLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP--GAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127 160 NNKDLILHTMFNWPHVIFNVATMTEADLYIPYINTHNLANTD------SSDCGWVVVTPFTHLEVASTTTNTLDIAVFGS 233
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgygpLNSFGTLVVRVLTPLTVPSGAPTTVDITVYVR 165

                        170
                 ....*....|.
gi 397776127 234 LVDFQFQGPRP 244
Cdd:cd00205  166 AGDFELYGPRP 176
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 118-200 1.34e-05

picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.


Pssm-ID: 395026  Cd Length: 170  Bit Score: 44.22  E-value: 1.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  118 GTSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVYVPNdHYQSWNNKDLILHTMFNwPHVIFNVATMTEADLYIPYINTHNL 197
Cdd:pfam00073  72 RLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPP-GAPPPGSRDYLWQATLN-PHQFWNLGLNSSARLSVPYISIAHY 149


                  ...
gi 397776127  198 ANT 200
Cdd:pfam00073 150 YST 152
Nepo_coat pfam03391
Nepovirus coat protein, central domain; The members of this family are derived from ...
 109-197 1.59e-03

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: 38.13  E-value: 1.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 397776127  109 WKNRSFPAyGTSRYFQFFRGSFHIKIQVNAAAGSAGSFVVVyvpndhyQSWNNKDLILHTMFNWPHVIFNVATMTEADLY 188
Cdd:pfam03391  48 RIVYSFNA-ALLSHFLGWGGTIHGSVHSTSSAFVTCSLRVA-------SSWNGATPTLEQLFQRPHVIVESDGQFEIKIQ 119


                  ....*....
gi 397776127  189 IPYINTHNL 197
Cdd:pfam03391 120 SPYHRTATR 128
 
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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