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Conserved domains on  [gi|4704678|gb|AAD28207|]
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capsid protein VP1, partial [Enterovirus A71]

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 ...
 20-167 9.44e-32

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 pfam00073:

Pssm-ID: 417456  Cd Length: 170  Bit Score: 112.79  E-value: 9.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     20 DESMIETRCVLNSHSTAETTLDSFFSRAGLVGE-------IDLPL-EGTTNPNGYANWDIDITG--YAQMRRKVELFTYM 89
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPdvqgerfYTLDStDWTSLSKGFFWWKLPLALlsMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     90 RFDAEFTFVACtptGEVVPQL-LQYMFVPPGAPKPDSREsLAWQTATNPSVFVKL-SDPPAQVSVPFMSPASAYQWFYDG 167
Cdd:pfam00073  81 RGGLEVTVQFN---GSKFHQGkLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLgLNSSARLSVPYISIAHYYSTFYDG 156
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 20-167 9.44e-32

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: 112.79  E-value: 9.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     20 DESMIETRCVLNSHSTAETTLDSFFSRAGLVGE-------IDLPL-EGTTNPNGYANWDIDITG--YAQMRRKVELFTYM 89
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPdvqgerfYTLDStDWTSLSKGFFWWKLPLALlsMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     90 RFDAEFTFVACtptGEVVPQL-LQYMFVPPGAPKPDSREsLAWQTATNPSVFVKL-SDPPAQVSVPFMSPASAYQWFYDG 167
Cdd:pfam00073  81 RGGLEVTVQFN---GSKFHQGkLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLgLNSSARLSVPYISIAHYYSTFYDG 156
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 40-198 3.48e-27

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: 101.32  E-value: 3.48e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678   40 LDSFFSRAGLVGeiDLPLEGTTNPNGYANWDIDITGY------AQMRRKVELFTYMRFDAEFTFVACTPTGevVPQLLQY 113
Cdd:cd00205   1 VESFADRPTTVG--TNNWNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNGSKF--HTGRLLV 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678  114 MFVPPGAPKPDSRESLaWQTATNPSVFVKLS-DPPAQVSVPFMSPASAYQWFYDGYptfgehkqekdleygaCPNNMMGT 192
Cdd:cd00205  77 AYVPPGAPAPTTGDTR-WQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGY----------------GPLNSFGT 139


                ....*.
gi 4704678  193 FSVRTV 198
Cdd:cd00205 140 LVVRVL 145
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 20-167 9.44e-32

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: 112.79  E-value: 9.44e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     20 DESMIETRCVLNSHSTAETTLDSFFSRAGLVGE-------IDLPL-EGTTNPNGYANWDIDITG--YAQMRRKVELFTYM 89
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVQPdvqgerfYTLDStDWTSLSKGFFWWKLPLALlsMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678     90 RFDAEFTFVACtptGEVVPQL-LQYMFVPPGAPKPDSREsLAWQTATNPSVFVKL-SDPPAQVSVPFMSPASAYQWFYDG 167
Cdd:pfam00073  81 RGGLEVTVQFN---GSKFHQGkLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLgLNSSARLSVPYISIAHYYSTFYDG 156
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 40-198 3.48e-27

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: 101.32  E-value: 3.48e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678   40 LDSFFSRAGLVGeiDLPLEGTTNPNGYANWDIDITGY------AQMRRKVELFTYMRFDAEFTFVACTPTGevVPQLLQY 113
Cdd:cd00205   1 VESFADRPTTVG--TNNWNSSASGTQLFQWKLSPALGflllqnTPLGALLSYFTYWRGDLEVTVQFNGSKF--HTGRLLV 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4704678  114 MFVPPGAPKPDSRESLaWQTATNPSVFVKLS-DPPAQVSVPFMSPASAYQWFYDGYptfgehkqekdleygaCPNNMMGT 192
Cdd:cd00205  77 AYVPPGAPAPTTGDTR-WQATLNPHVIWDLGtNSSVTFVVPYVSPTPYRSTRYDGY----------------GPLNSFGT 139


                ....*.
gi 4704678  193 FSVRTV 198
Cdd:cd00205 140 LVVRVL 145
 
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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