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Conserved domains on  [gi|2239984648|gb|UQS94387|]
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MAG: structural polyprotein [Corattcep virus 1]

Protein Classification

capsid protein( domain architecture ID 10716150)

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
CRPV_capsid super family cl07393
CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA ...
 561-729 9.38e-28

CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV). It forms an all beta sheet structure.


The actual alignment was detected with superfamily member pfam08762:

Pssm-ID: 370104  Cd Length: 198  Bit Score: 111.09  E-value: 9.38e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 561 GEVIDNLRYLTRASRYIKTVTIPDGGAIGLSLYDQIQT-------------DYVGFISQMYRYARGGMNYKLFAV-GSSV 626
Cdd:pfam08762  10 GEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAprpiiaqeakegiDYFSIYSYLYAFYRGGMRYKIFPEkNNSA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 627 NPLLGLRSRLTFNRGLT----ERTPTHITYPAINPVHEISIPFYSKYKRIPVINVVGGSTNTTNLGQPLIPSVrIELMNT 702
Cdd:pfam08762  90 EVSVYSFSSLVDFYRTTdsptSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNSSDVLYKGLNNLD-IATSPP 168

                         170       180
                  ....*....|....*....|....*..
gi 2239984648 703 GEAMQldVYRATKDDFSFGVLVGPPMF 729
Cdd:pfam08762 169 GTNAY--FARAAGDDFTFGWLIGTPPL 193
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 346-509 1.27e-20

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: 89.76  E-value: 1.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 346 RSGTWDLNTQIGDSITTLLVA-PVSDdtldANGFRYYSTSAVDFVASLFGMWRGTMCYRICVVKTAYHTGRLEICFVPNQ 424
Cdd:cd00205     7 RPTTVGTNNWNSSASGTQLFQwKLSP----ALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 425 FSRVTMD---QDTTNTYRYILDITNEAEVVIKIPFFSDAYMLPV----GDRFSSLGILQIRSISALVAPSAVNGNVDILV 497
Cdd:cd00205    83 APAPTTGdtrWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTrydgYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITV 162

                         170
                  ....*....|..
gi 2239984648 498 WKWMEDPVFAVP 509
Cdd:cd00205   163 YVRAGDFELYGP 174
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 23-177 8.75e-19

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: 84.37  E-value: 8.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  23 QQNPIFRFSLPFDLIKLGGKD----QKIARFEYLKADVVIKLMLNANNMTSGRFWLCYAPIDALVSTGNQlinrHRAGIT 98
Cdd:cd00205    21 SGTQLFQWKLSPALGFLLLQNtplgALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGD----TRWQAT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  99 AYPGVEIDININNAVELVVPYVYWAEAMSIT-SADPIQGSMATLYLFALTPLRSSNNYP--ITIQVWGWFDNITLVGPTT 175
Cdd:cd00205    97 LNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRyDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFELYGPRP 176


                  ..
gi 2239984648 176 LN 177
Cdd:cd00205   177 PR 178
Dicistro_VP4 super family cl13011
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 233-279 8.35e-12

Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome.


The actual alignment was detected with superfamily member pfam11492:

Pssm-ID: 288362  Cd Length: 53  Bit Score: 60.69  E-value: 8.35e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2239984648 233 PGPVQQIASTVSTVASAVSGIPIIGEIAGTVGWISDMVGGVASIFGW 279
Cdd:pfam11492   7 EGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 53
 
Name Accession Description Interval E-value
CRPV_capsid pfam08762
CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA ...
 561-729 9.38e-28

CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV). It forms an all beta sheet structure.


Pssm-ID: 370104  Cd Length: 198  Bit Score: 111.09  E-value: 9.38e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 561 GEVIDNLRYLTRASRYIKTVTIPDGGAIGLSLYDQIQT-------------DYVGFISQMYRYARGGMNYKLFAV-GSSV 626
Cdd:pfam08762  10 GEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAprpiiaqeakegiDYFSIYSYLYAFYRGGMRYKIFPEkNNSA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 627 NPLLGLRSRLTFNRGLT----ERTPTHITYPAINPVHEISIPFYSKYKRIPVINVVGGSTNTTNLGQPLIPSVrIELMNT 702
Cdd:pfam08762  90 EVSVYSFSSLVDFYRTTdsptSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNSSDVLYKGLNNLD-IATSPP 168

                         170       180
                  ....*....|....*....|....*..
gi 2239984648 703 GEAMQldVYRATKDDFSFGVLVGPPMF 729
Cdd:pfam08762 169 GTNAY--FARAAGDDFTFGWLIGTPPL 193
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 346-509 1.27e-20

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: 89.76  E-value: 1.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 346 RSGTWDLNTQIGDSITTLLVA-PVSDdtldANGFRYYSTSAVDFVASLFGMWRGTMCYRICVVKTAYHTGRLEICFVPNQ 424
Cdd:cd00205     7 RPTTVGTNNWNSSASGTQLFQwKLSP----ALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 425 FSRVTMD---QDTTNTYRYILDITNEAEVVIKIPFFSDAYMLPV----GDRFSSLGILQIRSISALVAPSAVNGNVDILV 497
Cdd:cd00205    83 APAPTTGdtrWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTrydgYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITV 162

                         170
                  ....*....|..
gi 2239984648 498 WKWMEDPVFAVP 509
Cdd:cd00205   163 YVRAGDFELYGP 174
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 23-177 8.75e-19

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: 84.37  E-value: 8.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  23 QQNPIFRFSLPFDLIKLGGKD----QKIARFEYLKADVVIKLMLNANNMTSGRFWLCYAPIDALVSTGNQlinrHRAGIT 98
Cdd:cd00205    21 SGTQLFQWKLSPALGFLLLQNtplgALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGD----TRWQAT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  99 AYPGVEIDININNAVELVVPYVYWAEAMSIT-SADPIQGSMATLYLFALTPLRSSNNYP--ITIQVWGWFDNITLVGPTT 175
Cdd:cd00205    97 LNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRyDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFELYGPRP 176


                  ..
gi 2239984648 176 LN 177
Cdd:cd00205   177 PR 178
Dicistro_VP4 pfam11492
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 233-279 8.35e-12

Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome.


Pssm-ID: 288362  Cd Length: 53  Bit Score: 60.69  E-value: 8.35e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2239984648 233 PGPVQQIASTVSTVASAVSGIPIIGEIAGTVGWISDMVGGVASIFGW 279
Cdd:pfam11492   7 EGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 53
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 23-162 1.91e-04

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: 42.68  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  23 QQNPIFRFSLPFDLIKLGGKDQKIARFEYLKADVVIKLMLNANNMTSGRFWLCYAPIDALVSTgnqliNRHRAG-ITAYP 101
Cdd:pfam00073  51 LSKGFFWWKLPLALLSMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPG-----SRDYLWqATLNP 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2239984648 102 GVEIDININNAVELVVPYVywaeamSITSADpiqgSMAtlylfaltplrSSNNYPITIQVW 162
Cdd:pfam00073 126 HQFWNLGLNSSARLSVPYI------SIAHYY----STF-----------YDGNWTLVVAGW 165
 
Name Accession Description Interval E-value
CRPV_capsid pfam08762
CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA ...
 561-729 9.38e-28

CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV). It forms an all beta sheet structure.


Pssm-ID: 370104  Cd Length: 198  Bit Score: 111.09  E-value: 9.38e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 561 GEVIDNLRYLTRASRYIKTVTIPDGGAIGLSLYDQIQT-------------DYVGFISQMYRYARGGMNYKLFAV-GSSV 626
Cdd:pfam08762  10 GEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAprpiiaqeakegiDYFSIYSYLYAFYRGGMRYKIFPEkNNSA 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 627 NPLLGLRSRLTFNRGLT----ERTPTHITYPAINPVHEISIPFYSKYKRIPVINVVGGSTNTTNLGQPLIPSVrIELMNT 702
Cdd:pfam08762  90 EVSVYSFSSLVDFYRTTdsptSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNSSDVLYKGLNNLD-IATSPP 168

                         170       180
                  ....*....|....*....|....*..
gi 2239984648 703 GEAMQldVYRATKDDFSFGVLVGPPMF 729
Cdd:pfam08762 169 GTNAY--FARAAGDDFTFGWLIGTPPL 193
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 346-509 1.27e-20

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: 89.76  E-value: 1.27e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 346 RSGTWDLNTQIGDSITTLLVA-PVSDdtldANGFRYYSTSAVDFVASLFGMWRGTMCYRICVVKTAYHTGRLEICFVPNQ 424
Cdd:cd00205     7 RPTTVGTNNWNSSASGTQLFQwKLSP----ALGFLLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648 425 FSRVTMD---QDTTNTYRYILDITNEAEVVIKIPFFSDAYMLPV----GDRFSSLGILQIRSISALVAPSAVNGNVDILV 497
Cdd:cd00205    83 APAPTTGdtrWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTrydgYGPLNSFGTLVVRVLTPLTVPSGAPTTVDITV 162

                         170
                  ....*....|..
gi 2239984648 498 WKWMEDPVFAVP 509
Cdd:cd00205   163 YVRAGDFELYGP 174
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 23-177 8.75e-19

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: 84.37  E-value: 8.75e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  23 QQNPIFRFSLPFDLIKLGGKD----QKIARFEYLKADVVIKLMLNANNMTSGRFWLCYAPIDALVSTGNQlinrHRAGIT 98
Cdd:cd00205    21 SGTQLFQWKLSPALGFLLLQNtplgALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVAYVPPGAPAPTTGD----TRWQAT 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  99 AYPGVEIDININNAVELVVPYVYWAEAMSIT-SADPIQGSMATLYLFALTPLRSSNNYP--ITIQVWGWFDNITLVGPTT 175
Cdd:cd00205    97 LNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRyDGYGPLNSFGTLVVRVLTPLTVPSGAPttVDITVYVRAGDFELYGPRP 176


                  ..
gi 2239984648 176 LN 177
Cdd:cd00205   177 PR 178
Dicistro_VP4 pfam11492
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 233-279 8.35e-12

Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome.


Pssm-ID: 288362  Cd Length: 53  Bit Score: 60.69  E-value: 8.35e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2239984648 233 PGPVQQIASTVSTVASAVSGIPIIGEIAGTVGWISDMVGGVASIFGW 279
Cdd:pfam11492   7 EGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 53
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 23-162 1.91e-04

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: 42.68  E-value: 1.91e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2239984648  23 QQNPIFRFSLPFDLIKLGGKDQKIARFEYLKADVVIKLMLNANNMTSGRFWLCYAPIDALVSTgnqliNRHRAG-ITAYP 101
Cdd:pfam00073  51 LSKGFFWWKLPLALLSMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPG-----SRDYLWqATLNP 125

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2239984648 102 GVEIDININNAVELVVPYVywaeamSITSADpiqgSMAtlylfaltplrSSNNYPITIQVW 162
Cdd:pfam00073 126 HQFWNLGLNSSARLSVPYI------SIAHYY----STF-----------YDGNWTLVVAGW 165
 
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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