NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|537366261|gb|AGU46444|]
View 

VP1, partial [enterovirus D120]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 92-240 1.62e-31

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: 118.18  E-value: 1.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261   92 PEEAIQTRTVINMHGTAECLVENFLGRAALV---CMQSIEYKNHTTSGANSQDNFFTWTINT--REFVQIRRKMELFTYL 166
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpdVQGERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537366261  167 RFDTEITIIPTlrlySSANvsyaglPNLTLQAMYVPTGAPKPKKQDsYEWQSSCNPSIFFKID-DPPARITIPFM 240
Cdd:pfam00073  81 RGGLEVTVQFN----GSKF------HQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYI 144
Pico_P2A super family cl03031
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 370-431 4.45e-30

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


The actual alignment was detected with superfamily member pfam00947:

Pssm-ID: 395757  Cd Length: 127  Bit Score: 112.86  E-value: 4.45e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537366261  370 NYHLATDEERERAVYVDWQSDILVTTVAAHGKHQIARCKCNTGVYYCRHKDRSYPVCFEGPG 431
Cdd:pfam00947   1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPT 62
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 92-240 1.62e-31

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: 118.18  E-value: 1.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261   92 PEEAIQTRTVINMHGTAECLVENFLGRAALV---CMQSIEYKNHTTSGANSQDNFFTWTINT--REFVQIRRKMELFTYL 166
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpdVQGERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537366261  167 RFDTEITIIPTlrlySSANvsyaglPNLTLQAMYVPTGAPKPKKQDsYEWQSSCNPSIFFKID-DPPARITIPFM 240
Cdd:pfam00073  81 RGGLEVTVQFN----GSKF------HQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYI 144
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 112-310 1.13e-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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 116.34  E-value: 1.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261 112 VENFLGRAALVCMQSIEYKNHTTSgansqdnFFTWTIN------TREFVQIRRKMELFTYLRFDTEITIIPTLRLYSSan 185
Cdd:cd00205    1 VESFADRPTTVGTNNWNSSASGTQ-------LFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHT-- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261 186 vsyaglpnLTLQAMYVPTGAPKPKKqDSYEWQSSCNPSIFFKI-DDPPARITIPFMRTPPHIKKIYDGFAgfekraadly 264
Cdd:cd00205   72 --------GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLgTNSSVTFVVPYVSPTPYRSTRYDGYG---------- 132

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 537366261 265 ginPANTMGNLCLRVVNSYQP---AQYTLTVRVYMKPKHIKAWAPRPPR 310
Cdd:cd00205  133 ---PLNSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 370-431 4.45e-30

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


Pssm-ID: 395757  Cd Length: 127  Bit Score: 112.86  E-value: 4.45e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537366261  370 NYHLATDEERERAVYVDWQSDILVTTVAAHGKHQIARCKCNTGVYYCRHKDRSYPVCFEGPG 431
Cdd:pfam00947   1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPT 62
 
Name Accession Description Interval E-value
Rhv pfam00073
picornavirus capsid protein; CAUTION: This alignment is very weak. It can not be generated by ...
 92-240 1.62e-31

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: 118.18  E-value: 1.62e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261   92 PEEAIQTRTVINMHGTAECLVENFLGRAALV---CMQSIEYKNHTTSGANSQDNFFTWTINT--REFVQIRRKMELFTYL 166
Cdd:pfam00073   1 TTQTPETRTVGYGKNPLELAVENFLGRDAPVqpdVQGERFYTLDSTDWTSLSKGFFWWKLPLalLSMGLLGRLLRYHTYY 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 537366261  167 RFDTEITIIPTlrlySSANvsyaglPNLTLQAMYVPTGAPKPKKQDsYEWQSSCNPSIFFKID-DPPARITIPFM 240
Cdd:pfam00073  81 RGGLEVTVQFN----GSKF------HQGKLLVAYVPPGAPPPGSRD-YLWQATLNPHQFWNLGlNSSARLSVPYI 144
rhv_like cd00205
Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA ...
 112-310 1.13e-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


Pssm-ID: 119412  Cd Length: 178  Bit Score: 116.34  E-value: 1.13e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261 112 VENFLGRAALVCMQSIEYKNHTTSgansqdnFFTWTIN------TREFVQIRRKMELFTYLRFDTEITIIPTLRLYSSan 185
Cdd:cd00205    1 VESFADRPTTVGTNNWNSSASGTQ-------LFQWKLSpalgflLLQNTPLGALLSYFTYWRGDLEVTVQFNGSKFHT-- 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 537366261 186 vsyaglpnLTLQAMYVPTGAPKPKKqDSYEWQSSCNPSIFFKI-DDPPARITIPFMRTPPHIKKIYDGFAgfekraadly 264
Cdd:cd00205   72 --------GRLLVAYVPPGAPAPTT-GDTRWQATLNPHVIWDLgTNSSVTFVVPYVSPTPYRSTRYDGYG---------- 132

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 537366261 265 ginPANTMGNLCLRVVNSYQP---AQYTLTVRVYMKPKHIKAWAPRPPR 310
Cdd:cd00205  133 ---PLNSFGTLVVRVLTPLTVpsgAPTTVDITVYVRAGDFELYGPRPPR 178
Pico_P2A pfam00947
Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the ...
 370-431 4.45e-30

Picornavirus core protein 2A; This protein is a protease, involved in cleavage of the polyprotein.


Pssm-ID: 395757  Cd Length: 127  Bit Score: 112.86  E-value: 4.45e-30
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 537366261  370 NYHLATDEERERAVYVDWQSDILVTTVAAHGKHQIARCKCNTGVYYCRHKDRSYPVCFEGPG 431
Cdd:pfam00947   1 NRHLATHEDWHNSVWVDYSRDLLVTRTTAHGCDTIARCNCTTGVYYCKSRNKYYPVTFTGPT 62
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH