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Conserved domains on  [gi|1836406038|gb|QJI52187|]
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MAG: hypothetical protein 2 [Dicistroviridae sp.]

Protein Classification

capsid protein( domain architecture ID 10831599)

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 pfam08762
CRPV capsid protein like; This is a family of capsid proteins found in positive stranded ssRNA ...
 589-796 9.32e-83

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: 262.48  E-value: 9.32e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 589 SFTSSALTVGEKVTSLRQILKRFHLIYSNLTTTSKNNNLYRINSFKTPKPIAAQATMVNIDLYSYYSYIFAYYRGSFRFK 668
Cdd:pfam08762   1 TPNASLLISGEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAPRPIIAQEAKEGIDYFSIYSYLYAFYRGGMRYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 669 IAPFENKVYAARIrlipengatEANAGPVQEDNTVIDETRTAADVYMPRNLEGTFEFQVPHYSRYPLLPNTAGSIPVIGv 748
Cdd:pfam08762  81 IFPEKNNSAEVSV---------YSFSSLVDFYRTTDSPTSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNS- 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1836406038 749 QDLIQRNLVSVNILTEAETTKALFYRAVGDDFSFCGLLGPPFVTRCTN 796
Cdd:pfam08762 151 SDVLYKGLNNLDIATSPPGTNAYFARAAGDDFTFGWLIGTPPLIGAAQ 198
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 347-535 4.68e-34

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: 128.67  E-value: 4.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 347 VAHIARTPCFVKRFQWTANGKaGAVLYATPITPSIFSIAIDSTrvapsHLAYISSPFTMWRGGINFHFKFVKTKFHSGRV 426
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSAS-GTQLFQWKLSPALGFLLLQNT-----PLGALLSYFTYWRGDLEVTVQFNGSKFHTGRL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 427 RILFVPGDYSSDDKLPDDADPNASYSSVVDLRSDTDVTFNVPFVSVQPWKLSSADVTSPLkdyqHSVGRLYVLILNELRA 506
Cdd:cd00205    75 LVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPL----NSFGTLVVRVLTPLTV 150

                         170       180
                  ....*....|....*....|....*....
gi 1836406038 507 TATVSDTISCLVEVSgASDFELSMPRQPK 535
Cdd:cd00205   151 PSGAPTTVDITVYVR-AGDFELYGPRPPR 178
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 45-227 1.05e-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: 110.18  E-value: 1.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038  45 IIDFLQRPINIQNVEWSLSDNAGKTlmaVDLPLDP-----IINNSMYKAKCERFYGFRADVELKLQVNAQPFQAGRLLLV 119
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQL---FQWKLSPalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 120 YIPGYKYIGEdrqkyyddrtnvDDASLVPLTGSPRVDLDLSTCTEATMCVPYYSP----YLFSDLTNGVGHIGRFKVVVY 195
Cdd:cd00205    78 YVPPGAPAPT------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPtpyrSTRYDGYGPLNSFGTLVVRVL 145

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1836406038 196 SPLIDNA-ASGIVDCTLWINFKNIKIKYPTAMP 227
Cdd:cd00205   146 TPLTVPSgAPTTVDITVYVRAGDFELYGPRPPR 178
Dicistro_VP4 super family cl13011
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 240-291 2.62e-03

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: 36.81  E-value: 2.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1836406038 240 QDSAGAGVISSAAASVSSVLSPLQDVPLVSNYARPALWVSNTIRDVAKHFGW 291
Cdd:pfam11492   2 TDETGEGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 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 ...
 589-796 9.32e-83

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: 262.48  E-value: 9.32e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 589 SFTSSALTVGEKVTSLRQILKRFHLIYSNLTTTSKNNNLYRINSFKTPKPIAAQATMVNIDLYSYYSYIFAYYRGSFRFK 668
Cdd:pfam08762   1 TPNASLLISGEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAPRPIIAQEAKEGIDYFSIYSYLYAFYRGGMRYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 669 IAPFENKVYAARIrlipengatEANAGPVQEDNTVIDETRTAADVYMPRNLEGTFEFQVPHYSRYPLLPNTAGSIPVIGv 748
Cdd:pfam08762  81 IFPEKNNSAEVSV---------YSFSSLVDFYRTTDSPTSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNS- 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1836406038 749 QDLIQRNLVSVNILTEAETTKALFYRAVGDDFSFCGLLGPPFVTRCTN 796
Cdd:pfam08762 151 SDVLYKGLNNLDIATSPPGTNAYFARAAGDDFTFGWLIGTPPLIGAAQ 198
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 347-535 4.68e-34

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: 128.67  E-value: 4.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 347 VAHIARTPCFVKRFQWTANGKaGAVLYATPITPSIFSIAIDSTrvapsHLAYISSPFTMWRGGINFHFKFVKTKFHSGRV 426
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSAS-GTQLFQWKLSPALGFLLLQNT-----PLGALLSYFTYWRGDLEVTVQFNGSKFHTGRL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 427 RILFVPGDYSSDDKLPDDADPNASYSSVVDLRSDTDVTFNVPFVSVQPWKLSSADVTSPLkdyqHSVGRLYVLILNELRA 506
Cdd:cd00205    75 LVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPL----NSFGTLVVRVLTPLTV 150

                         170       180
                  ....*....|....*....|....*....
gi 1836406038 507 TATVSDTISCLVEVSgASDFELSMPRQPK 535
Cdd:cd00205   151 PSGAPTTVDITVYVR-AGDFELYGPRPPR 178
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 45-227 1.05e-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: 110.18  E-value: 1.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038  45 IIDFLQRPINIQNVEWSLSDNAGKTlmaVDLPLDP-----IINNSMYKAKCERFYGFRADVELKLQVNAQPFQAGRLLLV 119
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQL---FQWKLSPalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 120 YIPGYKYIGEdrqkyyddrtnvDDASLVPLTGSPRVDLDLSTCTEATMCVPYYSP----YLFSDLTNGVGHIGRFKVVVY 195
Cdd:cd00205    78 YVPPGAPAPT------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPtpyrSTRYDGYGPLNSFGTLVVRVL 145

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1836406038 196 SPLIDNA-ASGIVDCTLWINFKNIKIKYPTAMP 227
Cdd:cd00205   146 TPLTVPSgAPTTVDITVYVRAGDFELYGPRPPR 178
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 51-198 4.96e-08

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: 53.47  E-value: 4.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038  51 RPINIQNVEWSlSDNAGKTLMAVDLPLDpiiNNSMYKAKCERFYGFRADVELKLQVNAQPFQAGRLLLVYIPGYkyiged 130
Cdd:pfam00073  39 RFYTLDSTDWT-SLSKGFFWWKLPLALL---SMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPG------ 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1836406038 131 rQKYYDDRTNVDDASLvpltgSPRVDLDLSTCTEATMCVPYYSP----YLFSDltngvghiGRF--KVVVYSPL 198
Cdd:pfam00073 109 -APPPGSRDYLWQATL-----NPHQFWNLGLNSSARLSVPYISIahyySTFYD--------GNWtlVVAGWVPL 168
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 403-474 1.12e-06

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: 49.23  E-value: 1.12e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1836406038 403 FTMWRGGINFHFKFVKTKFHSGRVRILFVPGDYSSDDKlPDDADPNASYSSVV-DLRSDTDVTFNVPFVSVQP 474
Cdd:pfam00073  77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGS-RDYLWQATLNPHQFwNLGLNSSARLSVPYISIAH 148
Dicistro_VP4 pfam11492
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 240-291 2.62e-03

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: 36.81  E-value: 2.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1836406038 240 QDSAGAGVISSAAASVSSVLSPLQDVPLVSNYARPALWVSNTIRDVAKHFGW 291
Cdd:pfam11492   2 TDETGEGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 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 ...
 589-796 9.32e-83

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: 262.48  E-value: 9.32e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 589 SFTSSALTVGEKVTSLRQILKRFHLIYSNLTTTSKNNNLYRINSFKTPKPIAAQATMVNIDLYSYYSYIFAYYRGSFRFK 668
Cdd:pfam08762   1 TPNASLLISGEKFTSLRQLIKRFRFIKANLNGSRTPNTLDRNSLVTAPRPIIAQEAKEGIDYFSIYSYLYAFYRGGMRYK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 669 IAPFENKVYAARIrlipengatEANAGPVQEDNTVIDETRTAADVYMPRNLEGTFEFQVPHYSRYPLLPNTAGSIPVIGv 748
Cdd:pfam08762  81 IFPEKNNSAEVSV---------YSFSSLVDFYRTTDSPTSTGGSHYIYPNLNGVHEFQIPYYSQYRKLPATSTSFGSNS- 150

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1836406038 749 QDLIQRNLVSVNILTEAETTKALFYRAVGDDFSFCGLLGPPFVTRCTN 796
Cdd:pfam08762 151 SDVLYKGLNNLDIATSPPGTNAYFARAAGDDFTFGWLIGTPPLIGAAQ 198
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 347-535 4.68e-34

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: 128.67  E-value: 4.68e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 347 VAHIARTPCFVKRFQWTANGKaGAVLYATPITPSIFSIAIDSTrvapsHLAYISSPFTMWRGGINFHFKFVKTKFHSGRV 426
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSAS-GTQLFQWKLSPALGFLLLQNT-----PLGALLSYFTYWRGDLEVTVQFNGSKFHTGRL 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 427 RILFVPGDYSSDDKLPDDADPNASYSSVVDLRSDTDVTFNVPFVSVQPWKLSSADVTSPLkdyqHSVGRLYVLILNELRA 506
Cdd:cd00205    75 LVAYVPPGAPAPTTGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPTPYRSTRYDGYGPL----NSFGTLVVRVLTPLTV 150

                         170       180
                  ....*....|....*....|....*....
gi 1836406038 507 TATVSDTISCLVEVSgASDFELSMPRQPK 535
Cdd:cd00205   151 PSGAPTTVDITVYVR-AGDFELYGPRPPR 178
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 45-227 1.05e-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: 110.18  E-value: 1.05e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038  45 IIDFLQRPINIQNVEWSLSDNAGKTlmaVDLPLDP-----IINNSMYKAKCERFYGFRADVELKLQVNAQPFQAGRLLLV 119
Cdd:cd00205     1 VESFADRPTTVGTNNWNSSASGTQL---FQWKLSPalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHTGRLLVA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038 120 YIPGYKYIGEdrqkyyddrtnvDDASLVPLTGSPRVDLDLSTCTEATMCVPYYSP----YLFSDLTNGVGHIGRFKVVVY 195
Cdd:cd00205    78 YVPPGAPAPT------------TGDTRWQATLNPHVIWDLGTNSSVTFVVPYVSPtpyrSTRYDGYGPLNSFGTLVVRVL 145

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1836406038 196 SPLIDNA-ASGIVDCTLWINFKNIKIKYPTAMP 227
Cdd:cd00205   146 TPLTVPSgAPTTVDITVYVRAGDFELYGPRPPR 178
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 51-198 4.96e-08

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: 53.47  E-value: 4.96e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1836406038  51 RPINIQNVEWSlSDNAGKTLMAVDLPLDpiiNNSMYKAKCERFYGFRADVELKLQVNAQPFQAGRLLLVYIPGYkyiged 130
Cdd:pfam00073  39 RFYTLDSTDWT-SLSKGFFWWKLPLALL---SMGLLGRLLRYHTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPG------ 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1836406038 131 rQKYYDDRTNVDDASLvpltgSPRVDLDLSTCTEATMCVPYYSP----YLFSDltngvghiGRF--KVVVYSPL 198
Cdd:pfam00073 109 -APPPGSRDYLWQATL-----NPHQFWNLGLNSSARLSVPYISIahyySTFYD--------GNWtlVVAGWVPL 168
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 403-474 1.12e-06

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: 49.23  E-value: 1.12e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1836406038 403 FTMWRGGINFHFKFVKTKFHSGRVRILFVPGDYSSDDKlPDDADPNASYSSVV-DLRSDTDVTFNVPFVSVQP 474
Cdd:pfam00073  77 HTYYRGGLEVTVQFNGSKFHQGKLLVAYVPPGAPPPGS-RDYLWQATLNPHQFwNLGLNSSARLSVPYISIAH 148
Dicistro_VP4 pfam11492
Cricket paralysis virus, VP4; This is a family of minor capsid proteins, known as VP4, from ...
 240-291 2.62e-03

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: 36.81  E-value: 2.62e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1836406038 240 QDSAGAGVISSAAASVSSVLSPLQDVPLVSNYARPALWVSNTIRDVAKHFGW 291
Cdd:pfam11492   2 TDETGEGVISEPATTVARVAGRLSDIPVIGTYAKTTEWVAGKVGSIAKLFGY 53
 
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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