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Conserved domains on  [gi|9630639|ref|NP_047197|]
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viral protein 1 [Infectious pancreatic necrosis virus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Birna_RdRp_palm super family cl04445
Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. ...
1-522 0e+00

Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.


The actual alignment was detected with superfamily member pfam04197:

Pssm-ID: 461223  Cd Length: 531  Bit Score: 1000.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639      1 MSDIFNSPQNKASILTALMKSTTGD-VEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPR 79
Cdd:pfam04197   1 MSDVFNSPQARSKISAALGKPTAGDdVEDLLIPKVWVPPEDPLASPQRAAKFLRENGYRILQPRAIPENEELETDQILPD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639     80 LRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLE--NDFPTGPETLRQVREAIATL 157
Cdd:pfam04197  81 LAWMVEGGVLKPTLSVPIGDTEYFPKYYPTHKPSHEKPNAFGPPDIALLKQMTYLLLQvtDNLKDEVTTLRQVRENIRDK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    158 QYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHED--PDLRWAPSWLINYTGDLSTDK 235
Cdd:pfam04197 161 QYGSGTYMGQLTRLVAMKEVATGRNPNKDPKKLGYTFESIAQLLEQTLPIGPPGEDDkwPPLTRVPSRLLNLTGDVDGEE 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    236 SYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGR-----AATSADPEAGVKKTITDFWYLSCGLLFPKGERYT 310
Cdd:pfam04197 241 DYLPHITLKSSSGLPYIGKTKGETIGEALAISDQFLRELSAllkqgAGTKASNKKKLLKMLSDYWYLSCGLLFPKAERYD 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    311 QVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQ-TPSLYGFSPFHGGMDRIMTIIRdsLDNDEDLVMIYADN 389
Cdd:pfam04197 321 KSTWCTKTRNIWSAPSPTHLLLSMISWPVMNNSKNNILNIEgCPSLYGFNPFRGGMDRIVTWIR--MAPDEPLALIYADN 398
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    390 IYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQ 469
Cdd:pfam04197 399 IYIVHDNTWYSIDLEKGEANCTPQHMQAAMYYLLTRGWTNDDGSPMFNQTWATFAMNIAPSLVVDSSCLIMNLQLKTYGQ 478
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 9630639    470 GSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELK 522
Cdd:pfam04197 479 GSGNAATFLNNHLLSTIVVDQWNLAGQPNPDSKEFMDLEDKTGINFKIEREID 531
Birna_VP1_thumb pfam20488
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687 1.40e-97

Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.


:

Pssm-ID: 466637  Cd Length: 167  Bit Score: 301.44  E-value: 1.40e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    523 NLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKP 602
Cdd:pfam20488   1 NLRETLVEAVETAPQDGYLADGSDLPPERPGPTVELDLLGWSATYSRQMEMFVPVLDKERLIASAAYPKGLENKALKRKP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    603 GAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPL--TNQTL 680
Cdd:pfam20488  81 GAEIAYKIVRYEALRLVGGWNYPLLETAAKHNSSAARKRLEVKGIPLDGFLDDWNNMSEFGGDFEGITISEKLevTNETL 160

                  ....*..
gi 9630639    681 VDINTPL 687
Cdd:pfam20488 161 VDLNTPL 167
Birna_RdRp_C super family cl48643
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. ...
689-790 2.73e-37

Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.


The actual alignment was detected with superfamily member pfam20489:

Pssm-ID: 466638  Cd Length: 103  Bit Score: 135.20  E-value: 2.73e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    689 SFDPKARPQTPRSPkkTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLR---DQALALKPASSSVDnWAEATEELa 765
Cdd:pfam20489   1 SKDPNVNPQTPRSP--GLKEVTTALKSGTYRNPKSAVGLLLDARTKSRVSTARavfDEALALKPASSSVD-WAERTEEL- 76
                          90       100
                  ....*....|....*....|....*....
gi 9630639    766 qqQQLLMKANNL----LKSSLTETREALE 790
Cdd:pfam20489  77 --QDLLMKANNLymreAKSALTETREALE 103
 
Name Accession Description Interval E-value
Birna_RdRp_palm pfam04197
Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. ...
1-522 0e+00

Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.


Pssm-ID: 461223  Cd Length: 531  Bit Score: 1000.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639      1 MSDIFNSPQNKASILTALMKSTTGD-VEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPR 79
Cdd:pfam04197   1 MSDVFNSPQARSKISAALGKPTAGDdVEDLLIPKVWVPPEDPLASPQRAAKFLRENGYRILQPRAIPENEELETDQILPD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639     80 LRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLE--NDFPTGPETLRQVREAIATL 157
Cdd:pfam04197  81 LAWMVEGGVLKPTLSVPIGDTEYFPKYYPTHKPSHEKPNAFGPPDIALLKQMTYLLLQvtDNLKDEVTTLRQVRENIRDK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    158 QYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHED--PDLRWAPSWLINYTGDLSTDK 235
Cdd:pfam04197 161 QYGSGTYMGQLTRLVAMKEVATGRNPNKDPKKLGYTFESIAQLLEQTLPIGPPGEDDkwPPLTRVPSRLLNLTGDVDGEE 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    236 SYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGR-----AATSADPEAGVKKTITDFWYLSCGLLFPKGERYT 310
Cdd:pfam04197 241 DYLPHITLKSSSGLPYIGKTKGETIGEALAISDQFLRELSAllkqgAGTKASNKKKLLKMLSDYWYLSCGLLFPKAERYD 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    311 QVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQ-TPSLYGFSPFHGGMDRIMTIIRdsLDNDEDLVMIYADN 389
Cdd:pfam04197 321 KSTWCTKTRNIWSAPSPTHLLLSMISWPVMNNSKNNILNIEgCPSLYGFNPFRGGMDRIVTWIR--MAPDEPLALIYADN 398
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    390 IYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQ 469
Cdd:pfam04197 399 IYIVHDNTWYSIDLEKGEANCTPQHMQAAMYYLLTRGWTNDDGSPMFNQTWATFAMNIAPSLVVDSSCLIMNLQLKTYGQ 478
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 9630639    470 GSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELK 522
Cdd:pfam04197 479 GSGNAATFLNNHLLSTIVVDQWNLAGQPNPDSKEFMDLEDKTGINFKIEREID 531
Birna_VP1_thumb pfam20488
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687 1.40e-97

Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.


Pssm-ID: 466637  Cd Length: 167  Bit Score: 301.44  E-value: 1.40e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    523 NLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKP 602
Cdd:pfam20488   1 NLRETLVEAVETAPQDGYLADGSDLPPERPGPTVELDLLGWSATYSRQMEMFVPVLDKERLIASAAYPKGLENKALKRKP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    603 GAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPL--TNQTL 680
Cdd:pfam20488  81 GAEIAYKIVRYEALRLVGGWNYPLLETAAKHNSSAARKRLEVKGIPLDGFLDDWNNMSEFGGDFEGITISEKLevTNETL 160

                  ....*..
gi 9630639    681 VDINTPL 687
Cdd:pfam20488 161 VDLNTPL 167
Birna_RdRp_C pfam20489
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. ...
689-790 2.73e-37

Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.


Pssm-ID: 466638  Cd Length: 103  Bit Score: 135.20  E-value: 2.73e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    689 SFDPKARPQTPRSPkkTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLR---DQALALKPASSSVDnWAEATEELa 765
Cdd:pfam20489   1 SKDPNVNPQTPRSP--GLKEVTTALKSGTYRNPKSAVGLLLDARTKSRVSTARavfDEALALKPASSSVD-WAERTEEL- 76
                          90       100
                  ....*....|....*....|....*....
gi 9630639    766 qqQQLLMKANNL----LKSSLTETREALE 790
Cdd:pfam20489  77 --QDLLMKANNLymreAKSALTETREALE 103
 
Name Accession Description Interval E-value
Birna_RdRp_palm pfam04197
Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. ...
1-522 0e+00

Birnavirus RNA dependent RNA polymerase (VP1), palm domain; Birnaviruses are dsRNA viruses. This entry corresponds to the "palm" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence.


Pssm-ID: 461223  Cd Length: 531  Bit Score: 1000.26  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639      1 MSDIFNSPQNKASILTALMKSTTGD-VEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPR 79
Cdd:pfam04197   1 MSDVFNSPQARSKISAALGKPTAGDdVEDLLIPKVWVPPEDPLASPQRAAKFLRENGYRILQPRAIPENEELETDQILPD 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639     80 LRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLE--NDFPTGPETLRQVREAIATL 157
Cdd:pfam04197  81 LAWMVEGGVLKPTLSVPIGDTEYFPKYYPTHKPSHEKPNAFGPPDIALLKQMTYLLLQvtDNLKDEVTTLRQVRENIRDK 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    158 QYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHED--PDLRWAPSWLINYTGDLSTDK 235
Cdd:pfam04197 161 QYGSGTYMGQLTRLVAMKEVATGRNPNKDPKKLGYTFESIAQLLEQTLPIGPPGEDDkwPPLTRVPSRLLNLTGDVDGEE 240
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    236 SYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGR-----AATSADPEAGVKKTITDFWYLSCGLLFPKGERYT 310
Cdd:pfam04197 241 DYLPHITLKSSSGLPYIGKTKGETIGEALAISDQFLRELSAllkqgAGTKASNKKKLLKMLSDYWYLSCGLLFPKAERYD 320
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    311 QVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQ-TPSLYGFSPFHGGMDRIMTIIRdsLDNDEDLVMIYADN 389
Cdd:pfam04197 321 KSTWCTKTRNIWSAPSPTHLLLSMISWPVMNNSKNNILNIEgCPSLYGFNPFRGGMDRIVTWIR--MAPDEPLALIYADN 398
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    390 IYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQ 469
Cdd:pfam04197 399 IYIVHDNTWYSIDLEKGEANCTPQHMQAAMYYLLTRGWTNDDGSPMFNQTWATFAMNIAPSLVVDSSCLIMNLQLKTYGQ 478
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|...
gi 9630639    470 GSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELK 522
Cdd:pfam04197 479 GSGNAATFLNNHLLSTIVVDQWNLAGQPNPDSKEFMDLEDKTGINFKIEREID 531
Birna_VP1_thumb pfam20488
Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. ...
523-687 1.40e-97

Birnavirus RNA dependent RNA polymerase (VP1), thumb domain; Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses.


Pssm-ID: 466637  Cd Length: 167  Bit Score: 301.44  E-value: 1.40e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    523 NLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKP 602
Cdd:pfam20488   1 NLRETLVEAVETAPQDGYLADGSDLPPERPGPTVELDLLGWSATYSRQMEMFVPVLDKERLIASAAYPKGLENKALKRKP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    603 GAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPL--TNQTL 680
Cdd:pfam20488  81 GAEIAYKIVRYEALRLVGGWNYPLLETAAKHNSSAARKRLEVKGIPLDGFLDDWNNMSEFGGDFEGITISEKLevTNETL 160

                  ....*..
gi 9630639    681 VDINTPL 687
Cdd:pfam20488 161 VDLNTPL 167
Birna_RdRp_C pfam20489
Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. ...
689-790 2.73e-37

Birnavirus RNA dependent RNA polymerase (VP1), C-terminal; Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic "palm" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming.


Pssm-ID: 466638  Cd Length: 103  Bit Score: 135.20  E-value: 2.73e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    689 SFDPKARPQTPRSPkkTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLR---DQALALKPASSSVDnWAEATEELa 765
Cdd:pfam20489   1 SKDPNVNPQTPRSP--GLKEVTTALKSGTYRNPKSAVGLLLDARTKSRVSTARavfDEALALKPASSSVD-WAERTEEL- 76
                          90       100
                  ....*....|....*....|....*....
gi 9630639    766 qqQQLLMKANNL----LKSSLTETREALE 790
Cdd:pfam20489  77 --QDLLMKANNLymreAKSALTETREALE 103
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
181-368 7.17e-03

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 39.70  E-value: 7.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    181 RNPNKTPKTVGYTNEQLAKLLEQTLpintpkheDPDLRWAPSWLINYTGDLStdKSYLPHVTIKSSAGLPYI--GKTKGD 258
Cdd:pfam00680  46 KLPGPADERDKLLNRSAAKMVLSEL--------RGVPKKANSTLIVYRAIDG--VEQIDPLNWDTSAGYPYVglGGKKGD 115
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9630639    259 TTA------EALVLADSFIRDlGRAATSADPEAGVKKTitdfwylscgllFPKGERYTQVDWDK-KTRNIWSAPYPTHLL 331
Cdd:pfam00680 116 LIEhlkdgtEARELAERLAAD-WEVLQNGTPLKLVYQT------------CLKDELRPLEKVEKgKTRLVWGEPVEYLLL 182
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 9630639    332 LSMVSTPVMNESKLNitNTQTPSLYGFSPFHGGMDRI 368
Cdd:pfam00680 183 ERAFFDPFNQAFMLN--NGFHPIQVGINPFDRGWPRL 217
 
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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