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Conserved domains on  [gi|1202234647|gb|ARX17271|]
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RNA-dependent RNA polymerase, partial [Hepacivirus hominis]

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 ...
 1-110 4.26e-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 cd23202:

Pssm-ID: 477363  Cd Length: 518  Bit Score: 220.11  E-value: 4.26e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEARKVISSLTERLYCGGPMFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPD 80
Cdd:cd23202   220 IRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPT 299

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  81 FLVCGDDLVVVAESDGVDEDRAALRAFTEA 110
Cdd:cd23202   300 MLVCGDDLVVIAESAGVEEDAAALRAFTEA 329
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-110 4.26e-71

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052  Cd Length: 518  Bit Score: 220.11  E-value: 4.26e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEARKVISSLTERLYCGGPMFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPD 80
Cdd:cd23202   220 IRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPT 299

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  81 FLVCGDDLVVVAESDGVDEDRAALRAFTEA 110
Cdd:cd23202   300 MLVCGDDLVVIAESAGVEEDAAALRAFTEA 329
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-108 7.07e-36

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 126.97  E-value: 7.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEarKVISSLTERLYCGGPMFNSKG-AQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGlRNP 79
Cdd:pfam00998 221 LRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDA 297

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  80 DFLVCGDDLVVVAESDGVDEDRAAL-RAFT 108
Cdd:pfam00998 298 RLLNNGDDCVVICESADLDEVKEALtEAFA 327
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
 1-110 4.26e-71

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052  Cd Length: 518  Bit Score: 220.11  E-value: 4.26e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEARKVISSLTERLYCGGPMFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPD 80
Cdd:cd23202   220 IRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPT 299

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  81 FLVCGDDLVVVAESDGVDEDRAALRAFTEA 110
Cdd:cd23202   300 MLVCGDDLVVIAESAGVEEDAAALRAFTEA 329
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
 1-110 1.61e-42

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028  Cd Length: 284  Bit Score: 140.34  E-value: 1.61e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLePEARKVISSLTERLYCGGPMFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPD 80
Cdd:cd23178   100 IQVEEEIYQACSL-KEARQAIVSITERLYVEGPMVNSDGQICGRRRCRASGVLTTSAGNT*TCYLK*LAACREAGIRLPT 178

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  81 FLVCGDDLVVVAESDGVDEDRAALRAFTEA 110
Cdd:cd23178   179 MLVCGDDCVVICESDGTQEDAALLAAFTEA 208
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
 1-108 7.07e-36

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 126.97  E-value: 7.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEarKVISSLTERLYCGGPMFNSKG-AQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGlRNP 79
Cdd:pfam00998 221 LRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDA 297

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  80 DFLVCGDDLVVVAESDGVDEDRAAL-RAFT 108
Cdd:pfam00998 298 RLLNNGDDCVVICESADLDEVKEALtEAFA 327
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
 1-107 7.56e-28

RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438053  Cd Length: 476  Bit Score: 105.04  E-value: 7.56e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCCNLEPEARKVISslteRLYCGGPMFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPD 80
Cdd:cd23203   223 VARETEIYAAASDDPELVRALG----KYYAEGPMVNPEGVPVGERRCRASGVLTTSSSNSITCYLKVKAACRKAGLKNPS 298

                          90       100       110
                  ....*....|....*....|....*....|
gi 1202234647  81 FLVCGDDLVVVAESDGVD---EDRAALRAF 107
Cdd:cd23203   299 FLIHGDDCLIICERPEEDpcdALKAALASY 328
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
 1-107 1.99e-09

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: 53.06  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIYQCC---NLEPEARKVISSLTERLYcggPMFNSKgaQCGYRRCRASGVLPTSFGNTITCYIK----ATAAAKA 73
Cdd:cd01699   115 LEAEHSIYNALyddDDELERRNLLRSLTNNSL---HIGFNE--VYKVRGGRPSGDPLTSIGNSIINCILvryaFRKLGGK 189

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1202234647  74 AGLRNPDFLVCGDDLVVVAESDGVDEDRAALRAF 107
Cdd:cd01699   190 SFFKNVRLLNYGDDCLLSVEKADDKFNLETLAEW 223
ps-ssRNAv_RdRp-like cd23167
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
 47-93 2.96e-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: 33.85  E-value: 2.96e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1202234647  47 CRASGVLPTSFGNT-----ITCYIKATAAAKAAGLRNPDFLVCGDDLVVVAE 93
Cdd:cd23167    22 GQPSGSPNTSADNSlinllLARLALRKACGRAEFLNSVGILVYGDDSLVSVP 73
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
 1-107 3.57e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029  Cd Length: 227  Bit Score: 35.19  E-value: 3.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1202234647   1 IRVEEEIY-QCCNLEPEARKVISsLTERLYCggpmFNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNp 79
Cdd:cd23179   102 LRLEHSVYlACYPGDPELRKLLK-WQLVNKG----RTSNGVKYKTRGGRMSGDMNTGLGNCLIMLAMVYAVLRELGIKY- 175

                          90       100
                  ....*....|....*....|....*...
gi 1202234647  80 DFLVCGDDLVVVAESDGVDEDRAALRAF 107
Cdd:cd23179   176 DLLVDGDDALVFVEREDLERLLEEFAEF 203
 
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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