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Conserved domains on  [gi|190643475|ref|YP_001976156|]
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coat protein Vp26 [Tomato marchitez virus]

Protein Classification

capsid protein( domain architecture ID 46111)

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

PubMed:  25184560|19925687

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rhv_like super family cl13999
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 20-179 1.11e-03

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


The actual alignment was detected with superfamily member cd00205:

Pssm-ID: 417456  Cd Length: 178  Bit Score: 38.53  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  20 VLLHYNWGTSSPMGTTLVSI-FSPSgiyESDGTLQPSLLGNIARNCKWWTGTCVFEICIEKTLFHSGSLAI----GLGTL 94
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWkLSPA---LGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVayvpPGAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  95 NTKMTNAHDIFNMPHVVCNLEMGRKFRFRC---SITNWngknlLSTgRKSSLPRPQHFSHLRLFatVMKPLVSTSIHLDS 171
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVpyvSPTPY-----RST-RYDGYGPLNSFGTLVVR--VLTPLTVPSGAPTT 157


                 ....*...
gi 190643475 172 VGVTVQLK 179
Cdd:cd00205  158 VDITVYVR 165
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 20-179 1.11e-03

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: 38.53  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  20 VLLHYNWGTSSPMGTTLVSI-FSPSgiyESDGTLQPSLLGNIARNCKWWTGTCVFEICIEKTLFHSGSLAI----GLGTL 94
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWkLSPA---LGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVayvpPGAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  95 NTKMTNAHDIFNMPHVVCNLEMGRKFRFRC---SITNWngknlLSTgRKSSLPRPQHFSHLRLFatVMKPLVSTSIHLDS 171
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVpyvSPTPY-----RST-RYDGYGPLNSFGTLVVR--VLTPLTVPSGAPTT 157


                 ....*...
gi 190643475 172 VGVTVQLK 179
Cdd:cd00205  158 VDITVYVR 165
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 20-179 1.11e-03

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: 38.53  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  20 VLLHYNWGTSSPMGTTLVSI-FSPSgiyESDGTLQPSLLGNIARNCKWWTGTCVFEICIEKTLFHSGSLAI----GLGTL 94
Cdd:cd00205    9 TTVGTNNWNSSASGTQLFQWkLSPA---LGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVayvpPGAPA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 190643475  95 NTKMTNAHDIFNMPHVVCNLEMGRKFRFRC---SITNWngknlLSTgRKSSLPRPQHFSHLRLFatVMKPLVSTSIHLDS 171
Cdd:cd00205   86 PTTGDTRWQATLNPHVIWDLGTNSSVTFVVpyvSPTPY-----RST-RYDGYGPLNSFGTLVVR--VLTPLTVPSGAPTT 157


                 ....*...
gi 190643475 172 VGVTVQLK 179
Cdd:cd00205  158 VDITVYVR 165
 
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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