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Conserved domains on  [gi|1827633748|dbj|BBJ21307|]
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RNA dependent RNA polymerase [Cryphonectria nitschkei chrysovirus 1]

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 ...
305-761 5.06e-61

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 pfam02123:

Pssm-ID: 477363  Cd Length: 465  Bit Score: 216.17  E-value: 5.06e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  305 YHVGEPHVFVCSLIAEWKGLMVRLPCARLVARW--FCVSYDKW---PNILKELHTLVRtsrflMNTEITEKERQALMYMD 379
Cdd:pfam02123   43 FWLGRFLSAVTPYNDYVAAILLYTIEAYAASKPggYRLRRAAWansSDFAKDLSDILK-----SLGLNASSPGPKLVEGN 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  380 LLVGRTSYVINEMNEVDKRGGDTYEsehlsydPNLQLFTREQYKKDFPRAVRKAYARmrytkqpRLNVNSFRQFYRRRKE 459
Cdd:pfam02123  118 PLLGRGVTNVDWEEEAKNRVDLAVV-------CRLVLLPMEELRAHIDAVLDELVVR-------RGLCDPIRLFVKNEPL 183
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  460 WLTKGslvYNHLPP-EARKTVVQALDSVNQsiidlearHNKQSLFEEMDLAELLKHVgdaSDFNTTKTmiKFETGrKDRT 538
Cdd:pfam02123  184 WCVNG---HPDHKLrEGRLRLLSSVSLVDQ--------LVRRMLFEPQNNNEIAWWG---SVPSKPSM--KLEHG-KSRA 246
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  539 LLPGTLIHFIVLTYVLELAERLSQVGSVRLNAmADEEFLWYDRKITT---GLFHVLYDWADFNEQHTASEMSAVIKELDL 615
Cdd:pfam02123  247 IYACDTRSYLAFEYLLAPVEKAWANKSVILNP-GEGDISGFDWSVQDwkrGGVSLMLDYDDFNSQHSTESMRAVFERLRR 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  616 AVqaPEDYHIFIHAISESMYNMSLHDRDGNRHKIWRG-LYSGWRGTTWINSVLNFCYIDVALTSFERiygyDPVVYidHG 694
Cdd:pfam02123  326 RL--PDEPAEAADWLVCSMDSMYQLSDGTLLAQRVPGtLKSGHRATTFINSVLNCAYAELAGAPWAD----VPTSI--HM 397
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1827633748  695 GDDVDAAVDSAASMPKFMAIMDDMMFNANAWKQLFS-TRSEFFRNTVTSSRAYASPTRALASFIAGDW 761
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 ...
305-761 5.06e-61

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: 216.17  E-value: 5.06e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  305 YHVGEPHVFVCSLIAEWKGLMVRLPCARLVARW--FCVSYDKW---PNILKELHTLVRtsrflMNTEITEKERQALMYMD 379
Cdd:pfam02123   43 FWLGRFLSAVTPYNDYVAAILLYTIEAYAASKPggYRLRRAAWansSDFAKDLSDILK-----SLGLNASSPGPKLVEGN 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  380 LLVGRTSYVINEMNEVDKRGGDTYEsehlsydPNLQLFTREQYKKDFPRAVRKAYARmrytkqpRLNVNSFRQFYRRRKE 459
Cdd:pfam02123  118 PLLGRGVTNVDWEEEAKNRVDLAVV-------CRLVLLPMEELRAHIDAVLDELVVR-------RGLCDPIRLFVKNEPL 183
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  460 WLTKGslvYNHLPP-EARKTVVQALDSVNQsiidlearHNKQSLFEEMDLAELLKHVgdaSDFNTTKTmiKFETGrKDRT 538
Cdd:pfam02123  184 WCVNG---HPDHKLrEGRLRLLSSVSLVDQ--------LVRRMLFEPQNNNEIAWWG---SVPSKPSM--KLEHG-KSRA 246
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  539 LLPGTLIHFIVLTYVLELAERLSQVGSVRLNAmADEEFLWYDRKITT---GLFHVLYDWADFNEQHTASEMSAVIKELDL 615
Cdd:pfam02123  247 IYACDTRSYLAFEYLLAPVEKAWANKSVILNP-GEGDISGFDWSVQDwkrGGVSLMLDYDDFNSQHSTESMRAVFERLRR 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  616 AVqaPEDYHIFIHAISESMYNMSLHDRDGNRHKIWRG-LYSGWRGTTWINSVLNFCYIDVALTSFERiygyDPVVYidHG 694
Cdd:pfam02123  326 RL--PDEPAEAADWLVCSMDSMYQLSDGTLLAQRVPGtLKSGHRATTFINSVLNCAYAELAGAPWAD----VPTSI--HM 397
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1827633748  695 GDDVDAAVDSAASMPKFMAIMDDMMFNANAWKQLFS-TRSEFFRNTVTSSRAYASPTRALASFIAGDW 761
Cdd:pfam02123  398 GDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGhTIAEFLRVAFCSHEVRGYLARAIASLVSGNW 465
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
593-711 1.21e-03

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. 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: 438060  Cd Length: 458  Bit Score: 42.63  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  593 DWADFNEQHTASEMSAVIKELdlaVQAPEDYHIFIHAISESMYNmSLHDRDGNRHKIWRGLYSGWRGTTWINSVLNFCYI 672
Cdd:cd23210    233 DYSAFDANHCSDAMNIMFEEV---FRTEFGFHPNAEWILKTLVN-TEHAYENKRITVEGGMPSGCSATSIINTILNNIYV 308
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1827633748  673 DVALTSFERIYGYDPVVYIDHGGDDV---DAAVDSAASMPKF 711
Cdd:cd23210    309 LYALRRHYEGVELDTYTMISYGDDIVvasDYDLDFEALKPHF 350
 
Name Accession Description Interval E-value
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
305-761 5.06e-61

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: 216.17  E-value: 5.06e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  305 YHVGEPHVFVCSLIAEWKGLMVRLPCARLVARW--FCVSYDKW---PNILKELHTLVRtsrflMNTEITEKERQALMYMD 379
Cdd:pfam02123   43 FWLGRFLSAVTPYNDYVAAILLYTIEAYAASKPggYRLRRAAWansSDFAKDLSDILK-----SLGLNASSPGPKLVEGN 117
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  380 LLVGRTSYVINEMNEVDKRGGDTYEsehlsydPNLQLFTREQYKKDFPRAVRKAYARmrytkqpRLNVNSFRQFYRRRKE 459
Cdd:pfam02123  118 PLLGRGVTNVDWEEEAKNRVDLAVV-------CRLVLLPMEELRAHIDAVLDELVVR-------RGLCDPIRLFVKNEPL 183
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  460 WLTKGslvYNHLPP-EARKTVVQALDSVNQsiidlearHNKQSLFEEMDLAELLKHVgdaSDFNTTKTmiKFETGrKDRT 538
Cdd:pfam02123  184 WCVNG---HPDHKLrEGRLRLLSSVSLVDQ--------LVRRMLFEPQNNNEIAWWG---SVPSKPSM--KLEHG-KSRA 246
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  539 LLPGTLIHFIVLTYVLELAERLSQVGSVRLNAmADEEFLWYDRKITT---GLFHVLYDWADFNEQHTASEMSAVIKELDL 615
Cdd:pfam02123  247 IYACDTRSYLAFEYLLAPVEKAWANKSVILNP-GEGDISGFDWSVQDwkrGGVSLMLDYDDFNSQHSTESMRAVFERLRR 325
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  616 AVqaPEDYHIFIHAISESMYNMSLHDRDGNRHKIWRG-LYSGWRGTTWINSVLNFCYIDVALTSFERiygyDPVVYidHG 694
Cdd:pfam02123  326 RL--PDEPAEAADWLVCSMDSMYQLSDGTLLAQRVPGtLKSGHRATTFINSVLNCAYAELAGAPWAD----VPTSI--HM 397
                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1827633748  695 GDDVDAAVDSAASMPKFMAIMDDMMFNANAWKQLFS-TRSEFFRNTVTSSRAYASPTRALASFIAGDW 761
Cdd:pfam02123  398 GDDVLEGLRTPADATSLLDKYARLGFKVNPSKQSVGhTIAEFLRVAFCSHEVRGYLARAIASLVSGNW 465
Aphthovirus_RdRp cd23210
RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded ...
593-711 1.21e-03

RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. 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: 438060  Cd Length: 458  Bit Score: 42.63  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1827633748  593 DWADFNEQHTASEMSAVIKELdlaVQAPEDYHIFIHAISESMYNmSLHDRDGNRHKIWRGLYSGWRGTTWINSVLNFCYI 672
Cdd:cd23210    233 DYSAFDANHCSDAMNIMFEEV---FRTEFGFHPNAEWILKTLVN-TEHAYENKRITVEGGMPSGCSATSIINTILNNIYV 308
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 1827633748  673 DVALTSFERIYGYDPVVYIDHGGDDV---DAAVDSAASMPKF 711
Cdd:cd23210    309 LYALRRHYEGVELDTYTMISYGDDIVvasDYDLDFEALKPHF 350
 
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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