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Conserved domains on  [gi|1942028]
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Chain 3, HUMAN RHINOVIRUS 3 COAT PROTEIN

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 ...
43-225 1.58e-35

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: 124.05  E-value: 1.58e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028   43 LLEIIQVGTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--YIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 120
Cdd:cd00205   1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028  121 ALSSAKIILAYTPPGTRGP---EDKKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYLTS 194
Cdd:cd00205  68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147
                       170       180       190
                ....*....|....*....|....*....|.
gi 1942028  195 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 225
Cdd:cd00205 148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
43-225 1.58e-35

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: 124.05  E-value: 1.58e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028   43 LLEIIQVGTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--YIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 120
Cdd:cd00205   1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028  121 ALSSAKIILAYTPPGTRGP---EDKKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYLTS 194
Cdd:cd00205  68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147
                       170       180       190
                ....*....|....*....|....*....|.
gi 1942028  195 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 225
Cdd:cd00205 148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
28-191 3.88e-35

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: 122.81  E-value: 3.88e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028     28 YEPTPRIHIPGKVRNLLEIIQVGTLIPMNNTGTN-DNVTNYLIPLHA-DRQNEQIFGTKLyiGDGVFKTTLLGEIAQYYT 105
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDvQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028    106 HWSGSLRISLMYTGPALSSAKIILAYTPPGTRGPEDK---KEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT---DPD 179
Cdd:pfam00073  79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158
                         170
                  ....*....|..
gi 1942028    180 TYTSAGYLSCWY 191
Cdd:pfam00073 159 TLVVAGWVPLNY 170
 
Name Accession Description Interval E-value
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
43-225 1.58e-35

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: 124.05  E-value: 1.58e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028   43 LLEIIQVGTLIPMNNTGTNDNvtnyliplhadrqNEQIFGTKL--YIGDGVFKTTLLGEIAQYYTHWSGSLRISLMYTGP 120
Cdd:cd00205   1 VESFADRPTTVGTNNWNSSAS-------------GTQLFQWKLspALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGS 67
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028  121 ALSSAKIILAYTPPGTRGP---EDKKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYTD---PDTYTSAGYLSCWYLTS 194
Cdd:cd00205  68 KFHTGRLLVAYVPPGAPAPttgDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRydgYGPLNSFGTLVVRVLTP 147
                       170       180       190
                ....*....|....*....|....*....|.
gi 1942028  195 LILPPQTSGQVYLLSFISACpDFKLRLMKDT 225
Cdd:cd00205 148 LTVPSGAPTTVDITVYVRAG-DFELYGPRPP 177
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
28-191 3.88e-35

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: 122.81  E-value: 3.88e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028     28 YEPTPRIHIPGKVRNLLEIIQVGTLIPMNNTGTN-DNVTNYLIPLHA-DRQNEQIFGTKLyiGDGVFKTTLLGEIAQYYT 105
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPDvQGERFYTLDSTDwTSLSKGFFWWKL--PLALLSMGLLGRLLRYHT 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028    106 HWSGSLRISLMYTGPALSSAKIILAYTPPGTRGPEDK---KEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT---DPD 179
Cdd:pfam00073  79 YYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGSRdylWQATLNPHQFWNLGLNSSARLSVPYISIAHYYSTfydGNW 158
                         170
                  ....*....|..
gi 1942028    180 TYTSAGYLSCWY 191
Cdd:pfam00073 159 TLVVAGWVPLNY 170
Calici_coat pfam00915
Calicivirus coat protein;
97-223 1.22e-06

Calicivirus coat protein;


Pssm-ID: 366366  Cd Length: 290  Bit Score: 48.35  E-value: 1.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1942028     97 LGEIAQYYTHWSGSLRISLMYTGPALSSAKIILAYTPPGTRgPEDKKEAMLGTHVVWDIGLQSTIVMTIPWTSGVQFRYT 176
Cdd:pfam00915  95 LAHLSQMYAGWSGGMDVRFIVAGSGVFGGKLAAAVIPPGVE-PIPSLSMLQFPHVLFDARQLEPVIFTIPDLRPTLYHPM 173
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1942028    177 DPDTYTSAgyLSCWYLTSLILPPQTSGQVYLLSFISACP--DFKLRLMK 223
Cdd:pfam00915 174 DDPTDTTT--LVIMVYNNLINPGGGSSSSACQVTVETRPsaDFEFVLLK 220
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.20
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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