Conserved Protein Domain Family
Medioniviridae_RdRp
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cd23188: Medioniviridae_RdRp 
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses
This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Medioniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The Medioniviridae subgenera includes Turrinivirus and Balbicanovirus. The structure of Medioniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. 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.
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Statistics
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PSSM-Id: 438038
Aligned: 3 rows
Threshold Bit Score: 247.299
Created: 24-Jun-2020
Updated: 17-Oct-2022
Structure
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Aligned Rows:
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  next features
Feature 1: catalytic residues [active site], 4 residue positions
Conserved feature residue pattern:D [GS] D DClick to see conserved feature residue pattern help
Evidence:
  • Comment:contains the classic divalent-cation-binding residue D618 in the motif A of SARS-CoV-2 structure, which is conserved in most viral polymerases
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                                                                         
APG77323     3047 SAGQPYVKVGDSdvvrg-vlgddRDTMIKHRCHSHHQTLVTANAKLAVGGKFKCRPISGINvlESDVGRTLFTAILEAIK 3125
YP_009333345 3047 SAGQPYVKVGDSdvvrg-vlgddRDTMIKHRCHSHHQTLVTANAKLAVGGKFKCRPISGINvlESDVGRTLFTAILEAIK 3125
QGQ56578     3949 SSGYPNRLVGNAktwrtaltdaeRDVVVNHRKHAHHQTVIYGHEKFAITEKVKSRPISGISvtESDAGRALFSPWLESIK 4028 Botrylloides ...

Feature 1                                                           #                             
APG77323     3126 HCcyENMIVIGWskftGFDRLFRNFlnsr----------ldhiDYRLSGKDFPQWDRSVESNMQLLTNFLIFCSYDWalc 3195
YP_009333345 3126 HCcyENMIVIGWskftGFDRLFRNFlnsr----------ldhiDYRLSGKDFPQWDRSVESNMQLLTNFLIFCSYDWalc 3195
QGQ56578     4029 AYhkKGKMVIGFnkahIHDILADLFhqidpskstqapitwadkEYDLIAIDFPKWDRGLAPERTMESNISIAEMYDWegh 4108 Botrylloides ...

Feature 1                                                                                         
APG77323     3196 refcslqeaLHLFCTEFT-NTVYSYFICDnLVMRKSGGVCSGNSKTAPGNSIMHAIWEYAAIiehlhYYRGEDPELIELR 3274
YP_009333345 3196 refcslqeaLHLFCTEFT-NTVYSYFICDnLVMRKSGGVCSGNSKTAPGNSIMHAIWEYAAIiehlhYYRGEDPELIELR 3274
QGQ56578     4109 tp--eerdgIYKMCMSEYlNTTPSITVLDqRVYHKSGGICSGSSKTANGNSYSHLFLDAAGKfdtvcYYTGKNRDLLELR 4186 Botrylloides ...

Feature 1                                              ###                                        
APG77323     3275 QFFMLYEshslsalrehdhlldtnllrlqshHLLRVLSDDGMVLHDKELLfdyssLFPYFYLYSNYHFTNDKhysCAPLH 3354
YP_009333345 3275 QFFMLYEshslsalrehdhlldtnllrlqshHLLRVLSDDGMVLHDKELLfdyssLFPYFYLYSNYHFTNDKhysCAPLH 3354
QGQ56578     4187 NIVMIFEtvplmriegrhelanracdilekyMNIKVLSDDGFSLVHRELTpsvplILKHYYLYSNYVFPREKwdvTKPSL 4266 Botrylloides ...

Feature 1                                                                                         
APG77323     3355 GPHEFCSAEAIIVDDKyYLCPEPGRHLGALFYSSRTTRFDinvRIALLSSYILEGIPLLFntllpyheRILPLILLDYIK 3434
YP_009333345 3355 GPHEFCSAEAIIVDDKyYLCPEPGRHLGALFYSSRTTRFDinvRIALLSSYILEGIPLLFntllpyheRILPLILLDYIK 3434
QGQ56578     4267 GPHEFCSSHFIVIDGRyFMVPRFDRILGSSLLTSKSRRFDptqRIAILSSLALEVVTLMFdtskplrqRGLFLYILRHMH 4346 Botrylloides ...

Feature 1            
APG77323     3435 KLS 3437
YP_009333345 3435 KLS 3437
QGQ56578     4347 DYY 4349 Botrylloides leachii nidovirus

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