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Conserved domains on  [gi|1955675057|gb|QQO86659|]
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RNA-dependent RNA polymerase, partial [Astrovirus VA1]

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 ...
 1-129 4.98e-71

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 cd23172:

Pssm-ID: 477363  Cd Length: 243  Bit Score: 212.72  E-value: 4.98e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRgDLQTKENRDVYNWYCENIFRRYVMLPSGEVTIQDRGNPSGQISTTMDNNICNVFFQAFEFA 80
Cdd:cd23172    94 IPAELFRHIRKLRWSFLD-PEKTEENRKVYDWYVHNLLNRYVLLPTGEVTRVTKGNPSGQISTTMDNCMVNTFLTAFEFA 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1955675057  81 YLNTElDSDELKENWDKYDSLIYGDDRLTTTPILCDNYVDRVIKMYADV 129
Cdd:cd23172   173 YVYGP-KTGTLKELWDNYDTIVYGDDRLSGYPSLPDPYVERVVDMYKDV 220
 
Name Accession Description Interval E-value
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
 1-129 4.98e-71

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022  Cd Length: 243  Bit Score: 212.72  E-value: 4.98e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRgDLQTKENRDVYNWYCENIFRRYVMLPSGEVTIQDRGNPSGQISTTMDNNICNVFFQAFEFA 80
Cdd:cd23172    94 IPAELFRHIRKLRWSFLD-PEKTEENRKVYDWYVHNLLNRYVLLPTGEVTRVTKGNPSGQISTTMDNCMVNTFLTAFEFA 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1955675057  81 YLNTElDSDELKENWDKYDSLIYGDDRLTTTPILCDNYVDRVIKMYADV 129
Cdd:cd23172   173 YVYGP-KTGTLKELWDNYDTIVYGDDRLSGYPSLPDPYVERVVDMYKDV 220
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1-129 9.69e-15

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: 68.98  E-value: 9.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRGDlqtkENRDVYNWYCENIFRRYVMLPSGEVTIQDRGNPSGQISTTMDNNICNVFFQAFEFA 80
Cdd:pfam00680 240 VPPWLIRFAFEILRELLGFP----SNVKEWRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALL 315

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1955675057  81 YL--NTELDSDELKENWDKYdslIYGDDRLTTTPILCDNYVDRVIKMYADV 129
Cdd:pfam00680 316 KSleNDGPRVCNLDKYFDFF---TYGDDSLVAVSPDFDPVLDRLSPHLKEL 363
 
Name Accession Description Interval E-value
ps-ssRNAv_Astroviridae_RdRp cd23172
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ...
 1-129 4.98e-71

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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: 438022  Cd Length: 243  Bit Score: 212.72  E-value: 4.98e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRgDLQTKENRDVYNWYCENIFRRYVMLPSGEVTIQDRGNPSGQISTTMDNNICNVFFQAFEFA 80
Cdd:cd23172    94 IPAELFRHIRKLRWSFLD-PEKTEENRKVYDWYVHNLLNRYVLLPTGEVTRVTKGNPSGQISTTMDNCMVNTFLTAFEFA 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1955675057  81 YLNTElDSDELKENWDKYDSLIYGDDRLTTTPILCDNYVDRVIKMYADV 129
Cdd:cd23172   173 YVYGP-KTGTLKELWDNYDTIVYGDDRLSGYPSLPDPYVERVVDMYKDV 220
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
 1-129 9.69e-15

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: 68.98  E-value: 9.69e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRGDlqtkENRDVYNWYCENIFRRYVMLPSGEVTIQDRGNPSGQISTTMDNNICNVFFQAFEFA 80
Cdd:pfam00680 240 VPPWLIRFAFEILRELLGFP----SNVKEWRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALL 315

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1955675057  81 YL--NTELDSDELKENWDKYdslIYGDDRLTTTPILCDNYVDRVIKMYADV 129
Cdd:pfam00680 316 KSleNDGPRVCNLDKYFDFF---TYGDDSLVAVSPDFDPVLDRLSPHLKEL 363
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1-108 1.95e-07

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: 48.05  E-value: 1.95e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRGDLQTkENRDVYNWYCENifrryvMLPSGEVTI--QDRGNPSGQISTTMDNNICNVFfqAFE 78
Cdd:cd01699   110 LSPQLLEAEHSIYNALYDDDDEL-ERRNLLRSLTNN------SLHIGFNEVykVRGGRPSGDPLTSIGNSIINCI--LVR 180

                          90       100       110
                  ....*....|....*....|....*....|
gi 1955675057  79 FAYLntELDSDELKENWdkyDSLIYGDDRL 108
Cdd:cd01699   181 YAFR--KLGGKSFFKNV---RLLNYGDDCL 205
ps-ssRNAv_Potyviridae_RdRp cd23175
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ...
 54-108 7.71e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. 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: 438025  Cd Length: 236  Bit Score: 43.21  E-value: 7.71e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1955675057  54 RGNPSGQISTTMDNNICNVFfqAFEFAYLNTELDSDELKENWdKYdsLIYGDDRL 108
Cdd:cd23175   145 KGNNSGQPSTVVDNTLMVMI--AMYYALLKLGIDFEEIDERC-VF--FCNGDDLL 194
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 55-112 1.74e-05

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: 40.01  E-value: 1.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1955675057  55 GNPSGQISTTMDNNICNVFFQAFEFAYLNTEldsdelKENWDKYDSLIYGDDRLTTTP 112
Cdd:cd23167    22 GQPSGSPNTSADNSLINLLLARLALRKACGR------AEFLNSVGILVYGDDSLVSVP 73
ps-ssRNAv-Picornavirales cd23169
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
 1-106 3.56e-03

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: 35.65  E-value: 3.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1955675057   1 IPNEVFRAIKDFRFSCLRgDLQTKENRDVYNWYCENIFRRYVmLPSGEVTIQDRGNPSGQISTTMDNNICNV--FFQAFE 78
Cdd:cd23169    93 LPPDVMEAAFDIINDWYD-EYVDDEDERVRKVLFEELINTIH-LVGNLVYQVHGGNPSGNPLTTIINSIVNLlyIRYAWL 170

                          90       100
                  ....*....|....*....|....*....
gi 1955675057  79 FAYLNTELDSdelkenWDKYDSLI-YGDD 106
Cdd:cd23169   171 RITGLTSLSD------FKKNVRLVtYGDD 193
 
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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