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Conserved domains on  [gi|495027912|ref|YP_007969873|]
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capsid protein VP0 [avihepatovirus 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 ...
 80-252 2.19e-28

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: 106.33  E-value: 2.19e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912  80 SRLVHLVTGQWVPNDDYYACLRWLATPACFFQNNTQPAYGQ-TRYFRFIRCGFHFRLLVNAPSGSAGALMLVWMPYpycr 158
Cdd:cd00205    6 DRPTTVGTNNWNSSASGTQLFQWKLSPALGFLLLQNTPLGAlLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP---- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912 159 vlsGTNQIHANVERRSLMNLPYAILDLRTNTEIDLVVPYVNYRNYVEITTSDTTG----GAICVIVLGKYRHGNGTSNTV 234
Cdd:cd00205   82 ---GAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPlnsfGTLVVRVLTPLTVPSGAPTTV 158

                        170
                 ....*....|....*...
gi 495027912 235 DFTLFGELLETDLQCPRP 252
Cdd:cd00205  159 DITVYVRAGDFELYGPRP 176
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 80-252 2.19e-28

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: 106.33  E-value: 2.19e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912  80 SRLVHLVTGQWVPNDDYYACLRWLATPACFFQNNTQPAYGQ-TRYFRFIRCGFHFRLLVNAPSGSAGALMLVWMPYpycr 158
Cdd:cd00205    6 DRPTTVGTNNWNSSASGTQLFQWKLSPALGFLLLQNTPLGAlLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP---- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912 159 vlsGTNQIHANVERRSLMNLPYAILDLRTNTEIDLVVPYVNYRNYVEITTSDTTG----GAICVIVLGKYRHGNGTSNTV 234
Cdd:cd00205   82 ---GAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPlnsfGTLVVRVLTPLTVPSGAPTTV 158

                        170
                 ....*....|....*...
gi 495027912 235 DFTLFGELLETDLQCPRP 252
Cdd:cd00205  159 DITVYVRAGDFELYGPRP 176
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 122-203 2.19e-04

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: 40.76  E-value: 2.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912  122 RYFRFIRCGFHFRLLVNAPSGSAGALMLVWMPyPYCRVlsgtnqihaNVERRSLMNL---PYAILDLRTNTEIDLVVPYV 198
Cdd:pfam00073  75 RYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVP-PGAPP---------PGSRDYLWQAtlnPHQFWNLGLNSSARLSVPYI 144


                  ....*
gi 495027912  199 NYRNY 203
Cdd:pfam00073 145 SIAHY 149
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 80-252 2.19e-28

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: 106.33  E-value: 2.19e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912  80 SRLVHLVTGQWVPNDDYYACLRWLATPACFFQNNTQPAYGQ-TRYFRFIRCGFHFRLLVNAPSGSAGALMLVWMPYpycr 158
Cdd:cd00205    6 DRPTTVGTNNWNSSASGTQLFQWKLSPALGFLLLQNTPLGAlLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPP---- 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912 159 vlsGTNQIHANVERRSLMNLPYAILDLRTNTEIDLVVPYVNYRNYVEITTSDTTG----GAICVIVLGKYRHGNGTSNTV 234
Cdd:cd00205   82 ---GAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPlnsfGTLVVRVLTPLTVPSGAPTTV 158

                        170
                 ....*....|....*...
gi 495027912 235 DFTLFGELLETDLQCPRP 252
Cdd:cd00205  159 DITVYVRAGDFELYGPRP 176
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 122-203 2.19e-04

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: 40.76  E-value: 2.19e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495027912  122 RYFRFIRCGFHFRLLVNAPSGSAGALMLVWMPyPYCRVlsgtnqihaNVERRSLMNL---PYAILDLRTNTEIDLVVPYV 198
Cdd:pfam00073  75 RYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVP-PGAPP---------PGSRDYLWQAtlnPHQFWNLGLNSSARLSVPYI 144


                  ....*
gi 495027912  199 NYRNY 203
Cdd:pfam00073 145 SIAHY 149
 
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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