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Conserved domains on  [gi|1571812004|ref|YP_009551557|]
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RNA dependent RNA polymerase [Diatom colony associated dsRNA virus 4 genome type A]

Protein Classification

RNA-dependent RNA polymerase family protein; pol protein pepsin-like aspartate protease and reverse transcriptase( domain architecture ID 10489330)

RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2; pol protein pepsin-like aspartate protease and reverse transcriptase; the retropepsin-like (A2 family) peptidase is an aspartic protease that hydrolyzes the peptide bonds of substrates

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
86-537 1.10e-82

Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.


:

Pssm-ID: 280316  Cd Length: 465  Bit Score: 271.64  E-value: 1.10e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004  86 FPLKLHPGAATKVNVffrdVWADAKRHFSKPAAYLSRHpELLVGLFNDQASAWV-------IWFCLTWEEDPRVAVSVLN 158
Cdd:pfam02123  15 FPLKSWPAAGEKANA----IARSLQSYLPTLAFWLGRF-LSAVTPYNDYVAAILlytieayAASKPGGYRLRRAAWANSS 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 159 ecqnmDYLKELSDTVKALGITRTKLGCLCTELKTMACRGAKSFDPDEEVRCRVDKKAfrAEKSCKITGEQIRPYVRQVLR 238
Cdd:pfam02123  90 -----DFAKDLSDILKSLGLNASSPGPKLVEGNPLLGRGVTNVDWEEEAKNRVDLAV--VCRLVLLPMEELRAHIDAVLD 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 239 EEMAKNPEWAGVKEYWQRRWLYTRSGAHARRVEDIKLGGRLDLP--DRPTRREFAEAVSENMVAkGEPGCHAGQSSKLEN 316
Cdd:pfam02123 163 ELVVRRGLCDPIRLFVKNEPLWCVNGHPDHKLREGRLRLLSSVSlvDQLVRRMLFEPQNNNEIA-WWGSVPSKPSMKLEH 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 317 GSTRAIYAGDSINYFTFDYLLRPIEAVWRNRSCLLDPGARQPSELYGALAASAD--VSLMVDFEDYNSQHEKSAMKVVIE 394
Cdd:pfam02123 242 GKSRAIYACDTRSYLAFEYLLAPVEKAWANKSVILNPGEGDISGFDWSVQDWKRggVSLMLDYDDFNSQHSTESMRAVFE 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 395 EACAG---APEEILEWALASIDNEVVYwvsaDGTTKMAVTV-GSLFSGHRATTFINTVLNSAYIRYVCGTLTLPMKSYHA 470
Cdd:pfam02123 322 RLRRRlpdEPAEAADWLVCSMDSMYQL----SDGTLLAQRVpGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHM 397
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1571812004 471 GDDVYLS-GTADQVEHVMKSVLASSVRVNRSKQGCGKLVGEFLRTAFTRECARGYMARSVSSLVSGNW 537
Cdd:pfam02123 398 GDDVLEGlRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGNW 465
 
Name Accession Description Interval E-value
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
86-537 1.10e-82

Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.


Pssm-ID: 280316  Cd Length: 465  Bit Score: 271.64  E-value: 1.10e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004  86 FPLKLHPGAATKVNVffrdVWADAKRHFSKPAAYLSRHpELLVGLFNDQASAWV-------IWFCLTWEEDPRVAVSVLN 158
Cdd:pfam02123  15 FPLKSWPAAGEKANA----IARSLQSYLPTLAFWLGRF-LSAVTPYNDYVAAILlytieayAASKPGGYRLRRAAWANSS 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 159 ecqnmDYLKELSDTVKALGITRTKLGCLCTELKTMACRGAKSFDPDEEVRCRVDKKAfrAEKSCKITGEQIRPYVRQVLR 238
Cdd:pfam02123  90 -----DFAKDLSDILKSLGLNASSPGPKLVEGNPLLGRGVTNVDWEEEAKNRVDLAV--VCRLVLLPMEELRAHIDAVLD 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 239 EEMAKNPEWAGVKEYWQRRWLYTRSGAHARRVEDIKLGGRLDLP--DRPTRREFAEAVSENMVAkGEPGCHAGQSSKLEN 316
Cdd:pfam02123 163 ELVVRRGLCDPIRLFVKNEPLWCVNGHPDHKLREGRLRLLSSVSlvDQLVRRMLFEPQNNNEIA-WWGSVPSKPSMKLEH 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 317 GSTRAIYAGDSINYFTFDYLLRPIEAVWRNRSCLLDPGARQPSELYGALAASAD--VSLMVDFEDYNSQHEKSAMKVVIE 394
Cdd:pfam02123 242 GKSRAIYACDTRSYLAFEYLLAPVEKAWANKSVILNPGEGDISGFDWSVQDWKRggVSLMLDYDDFNSQHSTESMRAVFE 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 395 EACAG---APEEILEWALASIDNEVVYwvsaDGTTKMAVTV-GSLFSGHRATTFINTVLNSAYIRYVCGTLTLPMKSYHA 470
Cdd:pfam02123 322 RLRRRlpdEPAEAADWLVCSMDSMYQL----SDGTLLAQRVpGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHM 397
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1571812004 471 GDDVYLS-GTADQVEHVMKSVLASSVRVNRSKQGCGKLVGEFLRTAFTRECARGYMARSVSSLVSGNW 537
Cdd:pfam02123 398 GDDVLEGlRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGNW 465
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
335-477 5.40e-05

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 45.74  E-value: 5.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 335 YLLRPIEAVWRNRSCL-----LDPGARQPSELYGALAASADVSLMVDFEDYNSQHEKSAMKVVIE--EACAGAPEEILEW 407
Cdd:cd01699    56 YLGPFEAKLMKNRGGLpiavgINPYSRDWTILANKLRSFSPVAIALDYSRFDSSLSPQLLEAEHSiyNALYDDDDELERR 135
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1571812004 408 ALAsidNEVVYWVSADGTTKMAVTVGSLFSGHRATTFINTVLNSAYIRYVCGTLTLPMKSYHA-----GDDVYLS 477
Cdd:cd01699   136 NLL---RSLTNNSLHIGFNEVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVrllnyGDDCLLS 207
 
Name Accession Description Interval E-value
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
86-537 1.10e-82

Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus.


Pssm-ID: 280316  Cd Length: 465  Bit Score: 271.64  E-value: 1.10e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004  86 FPLKLHPGAATKVNVffrdVWADAKRHFSKPAAYLSRHpELLVGLFNDQASAWV-------IWFCLTWEEDPRVAVSVLN 158
Cdd:pfam02123  15 FPLKSWPAAGEKANA----IARSLQSYLPTLAFWLGRF-LSAVTPYNDYVAAILlytieayAASKPGGYRLRRAAWANSS 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 159 ecqnmDYLKELSDTVKALGITRTKLGCLCTELKTMACRGAKSFDPDEEVRCRVDKKAfrAEKSCKITGEQIRPYVRQVLR 238
Cdd:pfam02123  90 -----DFAKDLSDILKSLGLNASSPGPKLVEGNPLLGRGVTNVDWEEEAKNRVDLAV--VCRLVLLPMEELRAHIDAVLD 162
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 239 EEMAKNPEWAGVKEYWQRRWLYTRSGAHARRVEDIKLGGRLDLP--DRPTRREFAEAVSENMVAkGEPGCHAGQSSKLEN 316
Cdd:pfam02123 163 ELVVRRGLCDPIRLFVKNEPLWCVNGHPDHKLREGRLRLLSSVSlvDQLVRRMLFEPQNNNEIA-WWGSVPSKPSMKLEH 241
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 317 GSTRAIYAGDSINYFTFDYLLRPIEAVWRNRSCLLDPGARQPSELYGALAASAD--VSLMVDFEDYNSQHEKSAMKVVIE 394
Cdd:pfam02123 242 GKSRAIYACDTRSYLAFEYLLAPVEKAWANKSVILNPGEGDISGFDWSVQDWKRggVSLMLDYDDFNSQHSTESMRAVFE 321
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 395 EACAG---APEEILEWALASIDNEVVYwvsaDGTTKMAVTV-GSLFSGHRATTFINTVLNSAYIRYVCGTLTLPMKSYHA 470
Cdd:pfam02123 322 RLRRRlpdEPAEAADWLVCSMDSMYQL----SDGTLLAQRVpGTLKSGHRATTFINSVLNCAYAELAGAPWADVPTSIHM 397
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1571812004 471 GDDVYLS-GTADQVEHVMKSVLASSVRVNRSKQGCGKLVGEFLRTAFTRECARGYMARSVSSLVSGNW 537
Cdd:pfam02123 398 GDDVLEGlRTPADATSLLDKYARLGFKVNPSKQSVGHTIAEFLRVAFCSHEVRGYLARAIASLVSGNW 465
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
335-477 5.40e-05

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 45.74  E-value: 5.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 335 YLLRPIEAVWRNRSCL-----LDPGARQPSELYGALAASADVSLMVDFEDYNSQHEKSAMKVVIE--EACAGAPEEILEW 407
Cdd:cd01699    56 YLGPFEAKLMKNRGGLpiavgINPYSRDWTILANKLRSFSPVAIALDYSRFDSSLSPQLLEAEHSiyNALYDDDDELERR 135
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1571812004 408 ALAsidNEVVYWVSADGTTKMAVTVGSLFSGHRATTFINTVLNSAYIRYVCGTLTLPMKSYHA-----GDDVYLS 477
Cdd:cd01699   136 NLL---RSLTNNSLHIGFNEVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGGKSFFKNVrllnyGDDCLLS 207
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
312-457 5.25e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438019  Cd Length: 309  Bit Score: 42.97  E-value: 5.25e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 312 SKLENGSTRAIYAGDSinYFTFD---YLLRPIEAVWRNRSCL-----LDPGARQPSELYGALAASADVSLMVDFEDYNSQ 383
Cdd:cd23169    15 EKVKAGKTRLFSASPL--DYTIAfrkYFGDFIAAFQKNRIKLehavgINPDSVEWTRLYRRLLKKGPNIFAGDYSNFDGS 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 384 HEKSAMKvvieeacaGAPEEILEWALASID--NEVVYWVSAD---GTTKMA-----VTVGSLFSGHRATTFINTVLNSAY 453
Cdd:cd23169    93 LPPDVME--------AAFDIINDWYDEYVDdeDERVRKVLFEeliNTIHLVgnlvyQVHGGNPSGNPLTTIINSIVNLLY 164

                  ....
gi 1571812004 454 IRYV 457
Cdd:cd23169   165 IRYA 168
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
280-457 2.97e-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: 40.86  E-value: 2.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 280 DLPDRPTRREFAEAVSE--NMVAKGEPGCHAGQSS---------KLENGSTRAI-------------YAGDSINYFTFDY 335
Cdd:pfam00680 119 HLKDGTEARELAERLAAdwEVLQNGTPLKLVYQTClkdelrpleKVEKGKTRLVwgepveyllleraFFDPFNQAFMLNN 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 336 LLRPIEAVWrnrscllDPGARQPSELYGALAASADVSLMVDFEDYNSQHEKSAMKVVIE--EACAGAPEeILEWALASId 413
Cdd:pfam00680 199 GFHPIQVGI-------NPFDRGWPRLLRRLARFGDYVYELDYSGFDSSVPPWLIRFAFEilRELLGFPS-NVKEWRAIL- 269
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1571812004 414 NEVVYWVSADGTTKMAVTVGSLFSGHRATTFINTVLNSAYIRYV 457
Cdd:pfam00680 270 ELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYA 313
Mischivirus_RdRp cd23227
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ...
375-477 3.23e-03

RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.


Pssm-ID: 438077  Cd Length: 466  Bit Score: 40.70  E-value: 3.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1571812004 375 VDFEDYNSQHEKSAMKVVIEeaCAGAPEEILEWALASIDNEVVYWVSADGTTKMAVTvGSLFSGHRATTFINTVLNSAYI 454
Cdd:cd23227   237 IDYSNFDSTHGTGMFELLID--CFFTPENGFSPAVAPYLRSLAFSKHAWMDKRYKIE-GGLPSGCSATSVLNTVMNNIII 313
                          90       100
                  ....*....|....*....|...
gi 1571812004 455 RyvcGTLTLPMKSYHAGDDVYLS 477
Cdd:cd23227   314 R---ALLSLTYKNFHPEDVLVLA 333
 
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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