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Conserved domains on  [gi|2133186835|gb|UEP63842|]
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VP1 [Norovirus GII]

Protein Classification

capsid protein VP1( domain architecture ID 10256749)

capsid protein VP1 may play a role in viral immunoevasion

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Calici_coat_C pfam08435
Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) ...
317-541 9.01e-130

Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) C-terminal region.


:

Pssm-ID: 429995  Cd Length: 224  Bit Score: 377.74  E-value: 9.01e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 317 LDNLNGTPYDPAEDiPAPLGTPDFQGKVFGVASQRNPD-GTTRAHEAKVDTTSGRFTPKLGSLEIITES-GDFNPNMPTK 394
Cdd:pfam08435   1 LTELDGSPFDPTED-PAPLGFPDFGGCDWGVESQRNTNnGATRAHEAVIATNSAKFTPKLGSVQFSTWStGDFLGNQPWR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 395 FTPVGVGVDtdEEFQQWVLPRYSGQVTHNMNLAPAVAPNFPGEQLLFFRSQLPSSGGTSSGTLDCLVPQEWVQHFYQESA 474
Cdd:pfam08435  80 FTPVGIAGD--DWFPQWTIPDYGGSLTLNTNLAPAVAPPGPGEQLLFFRSYIPGAGGVNPGAIDCLLPQEWVQHFYQEQA 157
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2133186835 475 PAQTQVALVRYVNPDTGRVLFEAKLHKLGFITIAKNGDSPITVPPNGYFRFESWVNPFYTLAPMGTG 541
Cdd:pfam08435 158 PSQSDVALLRYVNPDTGRNLFEAKLYPEGFITVNSSGSGPQVLPTNGYFRFVSWVSRFYQLAPVGTG 224
Calici_coat super family cl03015
Calicivirus coat protein;
8-274 1.70e-73

Calicivirus coat protein;


The actual alignment was detected with superfamily member pfam00915:

Pssm-ID: 459994  Cd Length: 291  Bit Score: 235.56  E-value: 1.70e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835   8 AAPSSDGAAG---LVPEIN-NEAMALEPVAGAAIAAPLTGQQNIID-PWIMNNFVQAPGGEFTVSPrnsPGEVLLNLELG 82
Cdd:pfam00915  13 ATSESDGASGtgiLVPEVGaSVPLAMAPVSGSSATAATAGQGKSVDqEWITNFSYHTSQNWSTIEP---QGKVLFDQSLG 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  83 PEINPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNfpIDNLSAAQITMCPHVIVDVRQLEPINLPMPDVR 162
Cdd:pfam00915  90 PHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPG--VEPITSASMLQFPHVLFDARQLEPVIFTIPDLR 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 163 NNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP--TVESKTKP-FTLPILTISEMSN 239
Cdd:pfam00915 168 NTLFHNMDRNTDTTRLVIMVYNPLINPGGTGDSSVCAVTVETRPSPDFNFLLLKPPgsTVEHGSRPsDTIPNLSLSWLGN 247
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 2133186835 240 sRFPVPIDSLHTSPTdnvIVQCQNGRVTLDGELMG 274
Cdd:pfam00915 248 -RWWSPISGFGISPQ---VFQFQNRHFDLDGRTVG 278
 
Name Accession Description Interval E-value
Calici_coat_C pfam08435
Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) ...
317-541 9.01e-130

Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) C-terminal region.


Pssm-ID: 429995  Cd Length: 224  Bit Score: 377.74  E-value: 9.01e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 317 LDNLNGTPYDPAEDiPAPLGTPDFQGKVFGVASQRNPD-GTTRAHEAKVDTTSGRFTPKLGSLEIITES-GDFNPNMPTK 394
Cdd:pfam08435   1 LTELDGSPFDPTED-PAPLGFPDFGGCDWGVESQRNTNnGATRAHEAVIATNSAKFTPKLGSVQFSTWStGDFLGNQPWR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 395 FTPVGVGVDtdEEFQQWVLPRYSGQVTHNMNLAPAVAPNFPGEQLLFFRSQLPSSGGTSSGTLDCLVPQEWVQHFYQESA 474
Cdd:pfam08435  80 FTPVGIAGD--DWFPQWTIPDYGGSLTLNTNLAPAVAPPGPGEQLLFFRSYIPGAGGVNPGAIDCLLPQEWVQHFYQEQA 157
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2133186835 475 PAQTQVALVRYVNPDTGRVLFEAKLHKLGFITIAKNGDSPITVPPNGYFRFESWVNPFYTLAPMGTG 541
Cdd:pfam08435 158 PSQSDVALLRYVNPDTGRNLFEAKLYPEGFITVNSSGSGPQVLPTNGYFRFVSWVSRFYQLAPVGTG 224
Calici_coat pfam00915
Calicivirus coat protein;
8-274 1.70e-73

Calicivirus coat protein;


Pssm-ID: 459994  Cd Length: 291  Bit Score: 235.56  E-value: 1.70e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835   8 AAPSSDGAAG---LVPEIN-NEAMALEPVAGAAIAAPLTGQQNIID-PWIMNNFVQAPGGEFTVSPrnsPGEVLLNLELG 82
Cdd:pfam00915  13 ATSESDGASGtgiLVPEVGaSVPLAMAPVSGSSATAATAGQGKSVDqEWITNFSYHTSQNWSTIEP---QGKVLFDQSLG 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  83 PEINPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNfpIDNLSAAQITMCPHVIVDVRQLEPINLPMPDVR 162
Cdd:pfam00915  90 PHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPG--VEPITSASMLQFPHVLFDARQLEPVIFTIPDLR 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 163 NNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP--TVESKTKP-FTLPILTISEMSN 239
Cdd:pfam00915 168 NTLFHNMDRNTDTTRLVIMVYNPLINPGGTGDSSVCAVTVETRPSPDFNFLLLKPPgsTVEHGSRPsDTIPNLSLSWLGN 247
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 2133186835 240 sRFPVPIDSLHTSPTdnvIVQCQNGRVTLDGELMG 274
Cdd:pfam00915 248 -RWWSPISGFGISPQ---VFQFQNRHFDLDGRTVG 278
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
86-219 3.46e-16

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: 76.67  E-value: 3.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  86 NPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNFPI--DNLSAAQITMCPHVIVDVRQLEPINLPMPDVRN 163
Cdd:cd00205    41 NTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAptTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2133186835 164 NFFHYNQGSDSRL-----RLIAMLYTPLRANNSGDDvfTVSCRVLTRPSpDFSFNFLVPPT 219
Cdd:cd00205   121 TPYRSTRYDGYGPlnsfgTLVVRVLTPLTVPSGAPT--TVDITVYVRAG-DFELYGPRPPR 178
 
Name Accession Description Interval E-value
Calici_coat_C pfam08435
Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) ...
317-541 9.01e-130

Calicivirus coat protein C-terminal; This is the calicivirus coat protein (pfam00915) C-terminal region.


Pssm-ID: 429995  Cd Length: 224  Bit Score: 377.74  E-value: 9.01e-130
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 317 LDNLNGTPYDPAEDiPAPLGTPDFQGKVFGVASQRNPD-GTTRAHEAKVDTTSGRFTPKLGSLEIITES-GDFNPNMPTK 394
Cdd:pfam08435   1 LTELDGSPFDPTED-PAPLGFPDFGGCDWGVESQRNTNnGATRAHEAVIATNSAKFTPKLGSVQFSTWStGDFLGNQPWR 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 395 FTPVGVGVDtdEEFQQWVLPRYSGQVTHNMNLAPAVAPNFPGEQLLFFRSQLPSSGGTSSGTLDCLVPQEWVQHFYQESA 474
Cdd:pfam08435  80 FTPVGIAGD--DWFPQWTIPDYGGSLTLNTNLAPAVAPPGPGEQLLFFRSYIPGAGGVNPGAIDCLLPQEWVQHFYQEQA 157
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2133186835 475 PAQTQVALVRYVNPDTGRVLFEAKLHKLGFITIAKNGDSPITVPPNGYFRFESWVNPFYTLAPMGTG 541
Cdd:pfam08435 158 PSQSDVALLRYVNPDTGRNLFEAKLYPEGFITVNSSGSGPQVLPTNGYFRFVSWVSRFYQLAPVGTG 224
Calici_coat pfam00915
Calicivirus coat protein;
8-274 1.70e-73

Calicivirus coat protein;


Pssm-ID: 459994  Cd Length: 291  Bit Score: 235.56  E-value: 1.70e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835   8 AAPSSDGAAG---LVPEIN-NEAMALEPVAGAAIAAPLTGQQNIID-PWIMNNFVQAPGGEFTVSPrnsPGEVLLNLELG 82
Cdd:pfam00915  13 ATSESDGASGtgiLVPEVGaSVPLAMAPVSGSSATAATAGQGKSVDqEWITNFSYHTSQNWSTIEP---QGKVLFDQSLG 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  83 PEINPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNfpIDNLSAAQITMCPHVIVDVRQLEPINLPMPDVR 162
Cdd:pfam00915  90 PHLNPFLLHLSQMYNGWSGGMRVRFMVAGSGVFGGKLAASVIPPG--VEPITSASMLQFPHVLFDARQLEPVIFTIPDLR 167
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835 163 NNFFHYNQGSDSRLRLIAMLYTPLRANNSGDDVFTVSCRVLTRPSPDFSFNFLVPP--TVESKTKP-FTLPILTISEMSN 239
Cdd:pfam00915 168 NTLFHNMDRNTDTTRLVIMVYNPLINPGGTGDSSVCAVTVETRPSPDFNFLLLKPPgsTVEHGSRPsDTIPNLSLSWLGN 247
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 2133186835 240 sRFPVPIDSLHTSPTdnvIVQCQNGRVTLDGELMG 274
Cdd:pfam00915 248 -RWWSPISGFGISPQ---VFQFQNRHFDLDGRTVG 278
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
86-219 3.46e-16

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: 76.67  E-value: 3.46e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  86 NPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNFPI--DNLSAAQITMCPHVIVDVRQLEPINLPMPDVRN 163
Cdd:cd00205    41 NTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAptTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSP 120
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2133186835 164 NFFHYNQGSDSRL-----RLIAMLYTPLRANNSGDDvfTVSCRVLTRPSpDFSFNFLVPPT 219
Cdd:cd00205   121 TPYRSTRYDGYGPlnsfgTLVVRVLTPLTVPSGAPT--TVDITVYVRAG-DFELYGPRPPR 178
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
69-169 8.37e-07

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: 49.23  E-value: 8.37e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2133186835  69 RNSPGEVLLNLELGPEINPYLAHLSRMYNGYAGGFEVQVVLAGNAFTAGKVIFAAIPPNFPIDN--LSAAQITMCPHVIV 146
Cdd:pfam00073  50 SLSKGFFWWKLPLALLSMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGsrDYLWQATLNPHQFW 129
                          90       100
                  ....*....|....*....|....*...
gi 2133186835 147 DVRQLEPINLPMP-----DVRNNFFHYN 169
Cdd:pfam00073 130 NLGLNSSARLSVPyisiaHYYSTFYDGN 157
 
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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