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Conserved domains on  [gi|2235495225|gb|UQB76108|]
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RNA-dependent RNA polymerase [Flumine sobemo-like virus 21]

Protein Classification

RNA-dependent RNA polymerase family protein( domain architecture ID 1750808)

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

EC:  2.7.7.48
Gene Ontology:  GO:0097747
PubMed:  29439438

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ps-ssRNAv_RdRp-like super family cl40470
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 1-150 2.99e-54

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


The actual alignment was detected with superfamily member cd23180:

Pssm-ID: 477363  Cd Length: 447  Bit Score: 181.70  E-value: 2.99e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   1 MRNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIGAPWAIAMGDDCLEGEVPQAIEKYAELGH 80
Cdd:cd23180   293 AINRFYCFMNSVFQLSNGTLIAQELPGLMKSGSYCTSSTNSRIRCLMAELIGAPWCIAMGDDSVEGYVEGALEKYEELGH 372

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2235495225  81 VCKSYEVVDPKQG-----FEFCSHRF-CGAAWPVDPSKMVFSCLDkSGNEMERIvaLESELHNHPQCREIMAIVRQ 150
Cdd:cd23180   373 TCKEYEPCDVDSDgeleeVNFCSHLIsRGKFWLTSWPKTLYRFLS-SPSPEFED--LEAELGSSPAWPRILRYLRH 445
 
Name Accession Description Interval E-value
ps-ssRNAv_Solemoviridae_RdRp cd23180
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of ...
 1-150 2.99e-54

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Solemoviridae, order Sobelivirales. Plant viruses in the family Solemoviridae have stable icosahedral particles assembled on T=3 symmetry and a relatively small (4-4.6 kb) monopartite (+)ssRNA genome with 4-5 open reading frames (ORFs). The natural host range is relatively narrow for each virus. Viral transmission occurs via mechanical wounding, by vegetative propagation or abiotically through soil; insects (beetles, aphids, thrips, hoppers, mirid bugs, moths) can also be vectors. Viruses infecting legumes or plants from the family Chenopodiaceae may be seed-transmissible. Members of the family are classified into four genera: Sobemovirus, Polemovirus, Polerovirus, Enamovirus. The viral polyprotein contains domains of the membrane anchor, a serine protease, a genome-linked viral protein (VPg) and C-terminal protein(s) or an RdRp, expressed by means of ribosomal frameshifting. 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: 438030  Cd Length: 447  Bit Score: 181.70  E-value: 2.99e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   1 MRNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIGAPWAIAMGDDCLEGEVPQAIEKYAELGH 80
Cdd:cd23180   293 AINRFYCFMNSVFQLSNGTLIAQELPGLMKSGSYCTSSTNSRIRCLMAELIGAPWCIAMGDDSVEGYVEGALEKYEELGH 372

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2235495225  81 VCKSYEVVDPKQG-----FEFCSHRF-CGAAWPVDPSKMVFSCLDkSGNEMERIvaLESELHNHPQCREIMAIVRQ 150
Cdd:cd23180   373 TCKEYEPCDVDSDgeleeVNFCSHLIsRGKFWLTSWPKTLYRFLS-SPSPEFED--LEAELGSSPAWPRILRYLRH 445
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
 2-103 3.52e-16

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: 77.89  E-value: 3.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   2 RNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIGAPWA-----IAMGDDCLEGEV-----PQA 71
Cdd:pfam02123 335 ADWLVCSMDSMYQLSDGTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWAdvptsIHMGDDVLEGLRtpadaTSL 414

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2235495225  72 IEKYAELGHVCKSYEVVDPKQGFEF-----CSHRFCG 103
Cdd:pfam02123 415 LDKYARLGFKVNPSKQSVGHTIAEFlrvafCSHEVRG 451
 
Name Accession Description Interval E-value
ps-ssRNAv_Solemoviridae_RdRp cd23180
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of ...
 1-150 2.99e-54

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Solemoviridae, order Sobelivirales. Plant viruses in the family Solemoviridae have stable icosahedral particles assembled on T=3 symmetry and a relatively small (4-4.6 kb) monopartite (+)ssRNA genome with 4-5 open reading frames (ORFs). The natural host range is relatively narrow for each virus. Viral transmission occurs via mechanical wounding, by vegetative propagation or abiotically through soil; insects (beetles, aphids, thrips, hoppers, mirid bugs, moths) can also be vectors. Viruses infecting legumes or plants from the family Chenopodiaceae may be seed-transmissible. Members of the family are classified into four genera: Sobemovirus, Polemovirus, Polerovirus, Enamovirus. The viral polyprotein contains domains of the membrane anchor, a serine protease, a genome-linked viral protein (VPg) and C-terminal protein(s) or an RdRp, expressed by means of ribosomal frameshifting. 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: 438030  Cd Length: 447  Bit Score: 181.70  E-value: 2.99e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   1 MRNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIGAPWAIAMGDDCLEGEVPQAIEKYAELGH 80
Cdd:cd23180   293 AINRFYCFMNSVFQLSNGTLIAQELPGLMKSGSYCTSSTNSRIRCLMAELIGAPWCIAMGDDSVEGYVEGALEKYEELGH 372

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2235495225  81 VCKSYEVVDPKQG-----FEFCSHRF-CGAAWPVDPSKMVFSCLDkSGNEMERIvaLESELHNHPQCREIMAIVRQ 150
Cdd:cd23180   373 TCKEYEPCDVDSDgeleeVNFCSHLIsRGKFWLTSWPKTLYRFLS-SPSPEFED--LEAELGSSPAWPRILRYLRH 445
ps-ssRNAv_Barnaviridae_RdRp cd23184
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Barnaviridae of ...
 1-103 1.14e-24

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Barnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Barnaviridae, order Sobelivirales, and related viruses. Barnaviridae is a family of non-enveloped, (+)ssRNA viruses. Cultivated mushrooms serve as natural hosts. The family has one genus, Barnavirus, which contains one species: Mushroom bacilliform virus (MBV) which infects the common cultivated button mushroom (Agaricus bisporus), and Bacilliform particles, which are morphologically similar to MBV, have been observed in the field mushroom Agaricus campestris. MBV viral transmission is horizontal via mycelium and possibly basidiospores. Distribution of MBV coincides with that of the commercial cultivation of Agaricus bisporus; the virus has been reported to occur in most major mushroom-growing countries. MBV is capable of autonomous replication, but commonly occurs as a double infection with a double-stranded RNA (dsRNA) virus (LaFrance isometric virus, LFIV) in mushrooms afflicted with La France disease. MBV is not required in pathogenesis involving LFIV, but it remains to be determined if it is a second, minor causal agent of LaFrance disease. MBV ssRNA and LFIV dsRNA do not share sequence homology. 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: 438034  Cd Length: 261  Bit Score: 99.13  E-value: 1.14e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   1 MRNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAA---------KLIGAPWA--IAMGDDCLEGEVP 69
Cdd:cd23184   146 LRVHAYCVGHSVFVLPDGEMLEQTVPGGQLSGDYNTSSSNSRMRVCATlfarylagqPLLVFGLIpvKAMGDDSFELWFP 225

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2235495225  70 QAIEKYAELGHVCKSYEVVDPKQGFEFCSHRFCG 103
Cdd:cd23184   226 GLEEYLRSMGHTVKFVVQRPGLQGFEFCSQVFDG 259
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
 2-103 3.52e-16

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: 77.89  E-value: 3.52e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   2 RNRYKALALSVFVLPDGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIGAPWA-----IAMGDDCLEGEV-----PQA 71
Cdd:pfam02123 335 ADWLVCSMDSMYQLSDGTLLAQRVPGTLKSGHRATTFINSVLNCAYAELAGAPWAdvptsIHMGDDVLEGLRtpadaTSL 414

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2235495225  72 IEKYAELGHVCKSYEVVDPKQGFEF-----CSHRFCG 103
Cdd:pfam02123 415 LDKYARLGFKVNPSKQSVGHTIAEFlrvafCSHEVRG 451
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1-121 4.69e-04

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: 40.73  E-value: 4.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2235495225   1 MRNRYKALALSVFVLPDGTMYSQNRSGVqkSGSYNTGAGNS-----RMRVVAAKLIGAPWAIAM-----GDDCL------ 64
Cdd:cd01699   134 RRNLLRSLTNNSLHIGFNEVYKVRGGRP--SGDPLTSIGNSiinciLVRYAFRKLGGKSFFKNVrllnyGDDCLlsveka 211

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2235495225  65 EGEVPQ-AIEKY-AELGHVC----KSYEVVDPKQGFEFCSHRFCgaawpVDPSKMVFSCLDKS 121
Cdd:cd01699   212 DDKFNLeTLAEWlKEYGLTMtdedKVESPFRPLEEVEFLKRRFV-----LDEGGGWRAPLDPS 269
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 17-66 1.44e-03

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model.


Pssm-ID: 438017 [Multi-domain]  Cd Length: 73  Bit Score: 36.55  E-value: 1.44e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2235495225  17 DGTMYSQNRSGVQKSGSYNTGAGNSRMRVVAAKLIG-----------APWAIAMGDDCLEG 66
Cdd:cd23167    11 DSSISPDLLKAGQPSGSPNTSADNSLINLLLARLALrkacgraeflnSVGILVYGDDSLVS 71
 
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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