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Conserved domains on  [gi|209868644|gb|ACI90857|]
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NS5B, partial [Hepatitis C virus subtype 3a]

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 ...
1-174 1.94e-137

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: 393.44  E-value: 1.94e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644   1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETARHTPVNSWLGNIIMYAPTIWVRMVMMTHFFSILQSQE 80
Cdd:cd23202  345 YDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWVRMVLMTHFFSILLAQE 424
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644  81 VLDRPLDFEMYGATYSVTPLDLPAIIERLHGLSAFTLHSYSPVELNRVAGTLRKLGCPPLRAWRHRARAVRAKLIAQGGK 160
Cdd:cd23202  425 QLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLGVPPLRAWRHRARAVRAKLIAQGGK 504
                        170
                 ....*....|....
gi 209868644 161 AKICGLYLFNWAVR 174
Cdd:cd23202  505 AAICGKYLFNWAVK 518
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
1-174 1.94e-137

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: 393.44  E-value: 1.94e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644   1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETARHTPVNSWLGNIIMYAPTIWVRMVMMTHFFSILQSQE 80
Cdd:cd23202  345 YDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWVRMVLMTHFFSILLAQE 424
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644  81 VLDRPLDFEMYGATYSVTPLDLPAIIERLHGLSAFTLHSYSPVELNRVAGTLRKLGCPPLRAWRHRARAVRAKLIAQGGK 160
Cdd:cd23202  425 QLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLGVPPLRAWRHRARAVRAKLIAQGGK 504
                        170
                 ....*....|....
gi 209868644 161 AKICGLYLFNWAVR 174
Cdd:cd23202  505 AAICGKYLFNWAVK 518
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
1-157 1.50e-55

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: 182.43  E-value: 1.50e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644    1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETArhTPVNSWLGNIIMYAPTIWVRMVMMTHFFSILQSQE 80
Cdd:pfam00998 340 YELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASWETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNG 417
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 209868644   81 VLDRPLDFEMYGATYSVtpldlpaIIERLHGLSAFTLHSYSPVELNRVAGTLrKLGCPPLRAWRHRARAVRAKLIAQ 157
Cdd:pfam00998 418 GLEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
 
Name Accession Description Interval E-value
Hepacivirus_RdRp cd23202
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
1-174 1.94e-137

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: 393.44  E-value: 1.94e-137
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644   1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETARHTPVNSWLGNIIMYAPTIWVRMVMMTHFFSILQSQE 80
Cdd:cd23202  345 YDLELITSCSSNVSVAHDATGKRYYYLTRDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWVRMVLMTHFFSILLAQE 424
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644  81 VLDRPLDFEMYGATYSVTPLDLPAIIERLHGLSAFTLHSYSPVELNRVAGTLRKLGCPPLRAWRHRARAVRAKLIAQGGK 160
Cdd:cd23202  425 QLEKALDFEMYGNTYSIPPLDLPAIIQRLHGLSAFSLHGYSPRELNRVAAALRKLGVPPLRAWRHRARAVRAKLIAQGGK 504
                        170
                 ....*....|....
gi 209868644 161 AKICGLYLFNWAVR 174
Cdd:cd23202  505 AAICGKYLFNWAVK 518
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
1-157 1.50e-55

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: 182.43  E-value: 1.50e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644    1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETArhTPVNSWLGNIIMYAPTIWVRMVMMTHFFSILQSQE 80
Cdd:pfam00998 340 YELELIEFCQSNPVFDGGKYGMVRNPLTSDSKDPLSRASWETA--TPAKSWLGAIGECGLSLWGGVPVLQHFYSCLLRNG 417
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 209868644   81 VLDRPLDFEMYGATYSVtpldlpaIIERLHGLSAFTLHSYSPVELNRVAGTLrKLGCPPLRAWRHRARAVRAKLIAQ 157
Cdd:pfam00998 418 GLEKAVSFEMYGKVYSD-------SGFRLHGLGAGSRHSYEPTEEARVSFWL-AFGITPDEQWALEAYYDRLKLLRQ 486
ps-ssRNAv_Flaviviridae_RdRp cd23178
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
1-61 1.66e-24

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: 96.82  E-value: 1.66e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 209868644   1 YDLELITSCSSNVSVARDDKGKRYYYLTRDATTPLARAAWETARHTPVNSWLGNIIMYAPT 61
Cdd:cd23178  224 YDLELIESCSHTVSEVRMKDGRRLYYLTRDPTTPLARAAWETGRHEPINSWLGYIIMYALT 284
Pegivirus_RdRp cd23203
RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of ...
2-140 1.07e-09

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: 56.50  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 209868644   2 DLELITSCSSNVSVARDDKGKRYYyLTRDATTPLARAAWETArhTPVNSWLGNIIMYaPT--IwVRMVMMTHFFS-ILQS 78
Cdd:cd23203  339 SLDTAESCSAYLAECNAGGGRHYF-LSTDMRRPLARASSEYG--DPVASALGYILLY-PWhpI-TRYVLLPHLLTlAFRG 413
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 209868644  79 QEVLDRPLDFEMYGATYSVtPLD-LPAIIERLHGLSAFTLHSYSPVELNRVAGTLRKLGCPPL 140
Cdd:cd23203  414 GGTPDDLVTCQVHGNSYKF-PLKlLPRILVGLHGPDCLRVTADSTKTLMEAGKALQAFGMRGL 475
 
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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