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Conserved domains on  [gi|230271|pdb|1R09|1]
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Chain 1, HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT VP1)

Protein Classification

capsid protein( domain architecture ID 10442155)

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 pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 47-203 1.60e-46

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: 154.01  E-value: 1.60e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1         47 PSDSIETRTTYMHFNGSETDVECFLGRAACV--HVTEIQNKDATGIDNHREAKLFNDWKINLS--SLVQLRKKLELFTYV 122
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1        123 RFDSEYTILATASQpdsanySSNLVVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVG--DTSRFSVPYVGLASAYNCF 200
Cdd:pfam00073  81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                  ...
1R09_1        201 YDG 203
Cdd:pfam00073 154 YDG 156
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 47-203 1.60e-46

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: 154.01  E-value: 1.60e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1         47 PSDSIETRTTYMHFNGSETDVECFLGRAACV--HVTEIQNKDATGIDNHREAKLFNDWKINLS--SLVQLRKKLELFTYV 122
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1        123 RFDSEYTILATASQpdsanySSNLVVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVG--DTSRFSVPYVGLASAYNCF 200
Cdd:pfam00073  81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                  ...
1R09_1        201 YDG 203
Cdd:pfam00073 154 YDG 156
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 67-259 7.15e-39

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: 134.45  E-value: 7.15e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1       67 VECFLGRAACVHVTEIQNKDATgidnhreaKLFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPdsa 140
Cdd:cd00205   1 VESFADRPTTVGTNNWNSSASG--------TQLFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKF--- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1      141 nysSNLVVQAMYVPPGAPNPKEwDDYTWQSASNPSVFFKVGDTS--RFSVPYVGLASAYNCFYDGYShddaetqygitVL 218
Cdd:cd00205  70 ---HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
1R09_1      219 NHMGSMAFRIVNEHD---EHKTLVKIRVYHRAKHVEAWIPRAPR 259
Cdd:cd00205 135 NSFGTLVVRVLTPLTvpsGAPTTVDITVYVRAGDFELYGPRPPR 178
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 47-203 1.60e-46

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: 154.01  E-value: 1.60e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1         47 PSDSIETRTTYMHFNGSETDVECFLGRAACV--HVTEIQNKDATGIDNHREAKLFNDWKINLS--SLVQLRKKLELFTYV 122
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1        123 RFDSEYTILATASQpdsanySSNLVVQAMYVPPGAPNPKEWdDYTWQSASNPSVFFKVG--DTSRFSVPYVGLASAYNCF 200
Cdd:pfam00073  81 RGGLEVTVQFNGSK------FHQGKLLVAYVPPGAPPPGSR-DYLWQATLNPHQFWNLGlnSSARLSVPYISIAHYYSTF 153


                  ...
1R09_1        201 YDG 203
Cdd:pfam00073 154 YDG 156
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 67-259 7.15e-39

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: 134.45  E-value: 7.15e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1       67 VECFLGRAACVHVTEIQNKDATgidnhreaKLFNDWKINLS------SLVQLRKKLELFTYVRFDSEYTILATASQPdsa 140
Cdd:cd00205   1 VESFADRPTTVGTNNWNSSASG--------TQLFQWKLSPAlgflllQNTPLGALLSYFTYWRGDLEVTVQFNGSKF--- 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1R09_1      141 nysSNLVVQAMYVPPGAPNPKEwDDYTWQSASNPSVFFKVGDTS--RFSVPYVGLASAYNCFYDGYShddaetqygitVL 218
Cdd:cd00205  70 ---HTGRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLGTNSsvTFVVPYVSPTPYRSTRYDGYG-----------PL 134

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
1R09_1      219 NHMGSMAFRIVNEHD---EHKTLVKIRVYHRAKHVEAWIPRAPR 259
Cdd:cd00205 135 NSFGTLVVRVLTPLTvpsGAPTTVDITVYVRAGDFELYGPRPPR 178
 
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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