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Conserved domains on  [gi|897796|emb|CAA24362|]
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unnamed protein product, partial [Foot-and-mouth disease 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 ...
 19-167 3.34e-30

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: 113.95  E-value: 3.34e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      19 AETTSAGESADPVTTTVENYGGETQIQRRQHTDVSFIMDRFVKVTPQNQINILDLMQIP--SHTLVGALLRASTYYFSDL 96
Cdd:pfam00073   5 PETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYYRGGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      97 EIAVKHEG--------DLTWVPNGAP-----EKALDNTTNPTAYHK---APLTRLALPYTAPHRVLATVYNGecRYNRNA 160
Cdd:pfam00073  85 EVTVQFNGskfhqgklLVAYVPPGAPppgsrDYLWQATLNPHQFWNlglNSSARLSVPYISIAHYYSTFYDG--NWTLVV 162


                  ....*..
gi 897796     161 VPNLRGD 167
Cdd:pfam00073 163 AGWVPLN 169
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 19-167 3.34e-30

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: 113.95  E-value: 3.34e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      19 AETTSAGESADPVTTTVENYGGETQIQRRQHTDVSFIMDRFVKVTPQNQINILDLMQIP--SHTLVGALLRASTYYFSDL 96
Cdd:pfam00073   5 PETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYYRGGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      97 EIAVKHEG--------DLTWVPNGAP-----EKALDNTTNPTAYHK---APLTRLALPYTAPHRVLATVYNGecRYNRNA 160
Cdd:pfam00073  85 EVTVQFNGskfhqgklLVAYVPPGAPppgsrDYLWQATLNPHQFWNlglNSSARLSVPYISIAHYYSTFYDG--NWTLVV 162


                  ....*..
gi 897796     161 VPNLRGD 167
Cdd:pfam00073 163 AGWVPLN 169
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 52-212 2.78e-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: 75.90  E-value: 2.78e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796    52 VSFIMDRFVKVTPQN--------QINILDLMQ-----IPSHTLVGALLRASTYYFSDLEIAVK------HEGDL--TWVP 110
Cdd:cd00205   1 VESFADRPTTVGTNNwnssasgtQLFQWKLSPalgflLLQNTPLGALLSYFTYWRGDLEVTVQfngskfHTGRLlvAYVP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796   111 NGAPEK-----ALDNTTNPTAYHKAPLT---RLALPYTAPHRVLATVYNGECRYNRNavpnlrGDLQVLAQKVARTLPTS 182
Cdd:cd00205  81 PGAPAPttgdtRWQATLNPHVIWDLGTNssvTFVVPYVSPTPYRSTRYDGYGPLNSF------GTLVVRVLTPLTVPSGA 154

                       170       180       190
                ....*....|....*....|....*....|
gi 897796   183 FNYGAIKATrvtellYRMKRAETYCPRPLL 212
Cdd:cd00205 155 PTTVDITVY------VRAGDFELYGPRPPR 178
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 19-167 3.34e-30

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: 113.95  E-value: 3.34e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      19 AETTSAGESADPVTTTVENYGGETQIQRRQHTDVSFIMDRFVKVTPQNQINILDLMQIP--SHTLVGALLRASTYYFSDL 96
Cdd:pfam00073   5 PETRTVGYGKNPLELAVENFLGRDAPVQPDVQGERFYTLDSTDWTSLSKGFFWWKLPLAllSMGLLGRLLRYHTYYRGGL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796      97 EIAVKHEG--------DLTWVPNGAP-----EKALDNTTNPTAYHK---APLTRLALPYTAPHRVLATVYNGecRYNRNA 160
Cdd:pfam00073  85 EVTVQFNGskfhqgklLVAYVPPGAPppgsrDYLWQATLNPHQFWNlglNSSARLSVPYISIAHYYSTFYDG--NWTLVV 162


                  ....*..
gi 897796     161 VPNLRGD 167
Cdd:pfam00073 163 AGWVPLN 169
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 52-212 2.78e-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: 75.90  E-value: 2.78e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796    52 VSFIMDRFVKVTPQN--------QINILDLMQ-----IPSHTLVGALLRASTYYFSDLEIAVK------HEGDL--TWVP 110
Cdd:cd00205   1 VESFADRPTTVGTNNwnssasgtQLFQWKLSPalgflLLQNTPLGALLSYFTYWRGDLEVTVQfngskfHTGRLlvAYVP 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 897796   111 NGAPEK-----ALDNTTNPTAYHKAPLT---RLALPYTAPHRVLATVYNGECRYNRNavpnlrGDLQVLAQKVARTLPTS 182
Cdd:cd00205  81 PGAPAPttgdtRWQATLNPHVIWDLGTNssvTFVVPYVSPTPYRSTRYDGYGPLNSF------GTLVVRVLTPLTVPSGA 154

                       170       180       190
                ....*....|....*....|....*....|
gi 897796   183 FNYGAIKATrvtellYRMKRAETYCPRPLL 212
Cdd:cd00205 155 PTTVDITVY------VRAGDFELYGPRPPR 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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