2CKW,1KHW,4NRT,3UQS,1SH0,1KHV,3QID


Conserved Protein Domain Family
Caliciviridae_RdRp

?
cd23192: Caliciviridae_RdRp 
Click on image for an interactive view with Cn3D
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses
This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. 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.
Statistics
?
PSSM-Id: 438042
Aligned: 28 rows
Threshold Bit Score: 393.167
Created: 29-May-2020
Updated: 17-Oct-2022
Structure
?
Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
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

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                         
2CKW_A        160 NAYKLALKDELRPIEKNk-AGKRRLLWGCDaatTLIATAAFKAVATRLQVVtpmtPVAVGINmd-svQMQVMNDSLkg-g 236  Sapporo virus
4NRT_A        160 PVYTGALKDELVKTDKIygKIKKRLLWGSDlatMIRCARAFGGLMDELKAHcvtlPIRVGMNmn--eDGPIIFERHsryk 237  Norwalk-like ...
3UQS_A        159 PIYTAALKDELVKPDKIygKIKKRLLWGSDlgtMIRAARAFGPFCDALKETcifnPIRVGMSmn--eDGPFIFARHanfr 236  Murine norovi...
1SH0_A        159 PVYTGALKDELVKTDKIygKIKKRLLWGSDlatMIRCARAFGGLMDELKTHcvtlPIRVGMNmn--eDGPIIFERHsryr 236  Norwalk virus
3QID_A        159 PIYTAALKDELVKPDKIygKIKKRLLWGSDlgtMIRAARAFGPFCDALKETcifnPIRVGMSmn--eDGPFIFARHanfr 236  Murine norovi...
AFH89835      198 NAYALALEDELLPSHKVa-QSRKRLLWGTDagvTLIASMAWGPLLDMLKAAcptsPIAVGCNmd-stYVAASVAQVvg-k 274  Chicken calic...
YP_009028574 1375 HAYQLALKDELLPKRKIa-ESRKRLLWGTDvglTTLAAMVWGQLLDSLKSVviasPISVGCQmd-stFVATIVAQIqd-r 1451 Goose caliciv...
YP_009272568 1320 NRYTVALKDELRPVEKIa-EGKRRLIWGCDarnALVCSAALTPLANVLKGLvhvlPIQVGVDpasqrVVNSWASRLattp 1398 Bovine calici...
YP_529550    1301 HTYIVALKDELRPVEKVa-EGKRRLIWGADarvALIASAALTPVANALKTVtnllPIQVGVDpssanCVSSWVGRLqrhd 1379 Newbury agent 1
NP_663315    1301 HTYIVALKDELRPVEKVa-EGKRRLIWGADarvALIASAALSPIANALKTVtnllPVQVGVDpssasCVSAWVNRLnrhd 1379 Calicivirus s...
Feature 1              #                                                                          
2CKW_A        237 VLYCLDYSKWDSTQNPAVTAASLAILERfaephpIVSCAIEALSspAEGYVNdIKFVTrgGLPSGMPFTSVVNSINHMiY 316  Sapporo virus
4NRT_A        238 YHYDADYSRWDSTQQRAVLAAALEIMVKfssephLAQVVAEDLLspSVVDVGdFKISIneGLPSGVPCTSQWNSIAHWlL 317  Norwalk-like ...
3UQS_A        237 YHMDADYTRWDSTQQRAILKRAGDIMVRlspepdLARVVMDDLLapSLLDVGdYKIVVeeGLPSGCPCTTQLNSLAHWiL 316  Murine norovi...
1SH0_A        237 YHYDADYSRWDSTQQRAVLAAALEIMVKfssephLAQVVAEDLLspSVVDVGdFTISIneGLPSGVPCTSQWNSIAHWlL 316  Norwalk virus
3QID_A        237 YHMDADYTRWDSTQQRAILKRAGDIMVRlspepdLARVVMDDLLapSLLDVGdYKIVVeeGLPSGCPCTTQLNSLAHWiL 316  Murine norovi...
AFH89835      275 STLCLDYSKWDSTMHPAVICHAINLMCDlvtpspIVDSVRATLTsaPVGYFMdKKVVAlrGLPSGTPATSVVNSVCHLiY 354  Chicken calic...
YP_009028574 1452 HTLCLDYKKWDSTMHPEVINFAVDILCDlcpdtpYRECLRSTLHmhPVGYFMdKKLTAlrGLPSGMPATSVINSLCHCiY 1531 Goose caliciv...
YP_009272568 1399 YVLELDYSKWDSTMSPALLRVAVEIMATscanarLARCVIDTLTapAEAWFEgIVLETsrGLPSGMPFTSQINSIIHWiL 1478 Bovine calici...
YP_529550    1380 HCLELDYSKWDSTMSPVIINIAIDILCNtcgsdsLRMAVAQTLKsrPTALVEgVSVPTksGLPSGMPFTSQINSIVHWiL 1459 Newbury agent 1
NP_663315    1380 HCLELDYSKWDSTMSPVLINIAIDILCNtcasdgLRVAVCQTLKtrPTALVEgVAVPTksGLPSGMPFTSQINSIVHWiL 1459 Calicivirus s...
Feature 1                                      ###                                                
2CKW_A        317 VAAAIlqayeshnvpytgnvfqvETIHTYGDDCMYSVCpatasiFHTVLANLTSYGLKPTAADksda-------ikpTNT 389  Sapporo virus
4NRT_A        318 TLCALsevtnls----pdiiqanSLFSFYGDDEIVSTDik--ldPEKLTAKLKEYGLKPTRPDktegpl---visedLNG 388  Norwalk-like ...
3UQS_A        317 TLCAMvevtrvd----pdivmqeSEFSFYGDDEVVSTNle--ldMVKYTMALRRYGLLPTRADkeegpl---errqtLQG 387  Murine norovi...
1SH0_A        317 TLCALsevtnls----pdiiqanSLFSFYGDDEIVSTDik--ldPEKLTAKLKEYGLKPTRPDktegpl---visedLNG 387  Norwalk virus
3QID_A        317 TLCAMvevtrvd----pdivmqeSEFSFYGDDEVVSTNle--ldMVKYTMALRRYGLLPTRADkeegpl---errqtLQG 387  Murine norovi...
AFH89835      355 FTSAYwlaqdqvgmartpqplqeAFVRVYGDDCVYGFPprtatfVNEFVDSLRSLGLQPTAPDktqn-------fqlDQP 427  Chicken calic...
YP_009028574 1532 FTSALwlaedqagiartrdpltvNRIWTYGDDCIYAFHprcaaiMDSFIEALRQLGLTPTAADktqn-------flmDSD 1604 Goose caliciv...
YP_009272568 1479 WDAALteaarplq---ivdihssYPFLCYGDDGAYSIPralaksCDEIVERLKGFGLNPTAPDkgaviairsstitaHNG 1555 Bovine calici...
YP_529550    1460 WSATVrkcslplh---igsvnelAPFLTYGDDGLYTIPshltksIDEIISTLKGYGLSPTAPDkganveikrtsftyLSG 1536 Newbury agent 1
NP_663315    1460 WSATVrkcslpln---igsvnelAPFLTYGDDGLYTIPshltksIDEIVSTLKGYGLSPTAPDkgmnieikktsftyMSG 1536 Calicivirus s...
Feature 1                                                                                         
2CKW_A        390 PVFLKRTFTQTphGIRALLDITSITRQFYWLKanrtsdp----ssppafDRQARSAQLENALAYAsqHGPVMFDTVRQIA 465  Sapporo virus
4NRT_A        389 LTFLRRTVTRDpaGWFGKLEQSSILRQMYWTRgpnhed-----psetmiPHSQRPIQLMSLLGEAalHGPAFYSKISKLV 463  Norwalk-like ...
3UQS_A        388 ISFLRRAIVGDqfGWYGRLDRASIDRQLLWTKgpnhqn-----pfetlpGHAQRPSQLMALLGEAamHGEKYYRTVASRV 462  Murine norovi...
1SH0_A        388 LTFLRRTVTRDpaGWFGKLEQSSILRQMYWTRgpnhed-----psetmiPHSQRPIQLMSLLGEAalHGPAFYSKISKLV 462  Norwalk virus
3QID_A        388 ISFLRRAIVGDqfGWYGRLDRASIDRQLLWTKgpnhqn-----pfetlpGHAQRPSQLMALLGEAamHGEKYYRTVASRV 462  Murine norovi...
AFH89835      428 IQFLKRSIMPLgdLAVAPLELSSILQQAVWVKagvsgdh---tsaraasNLQARSVQIQEALYALalHGVDVYQEWLPLF 504  Chicken calic...
YP_009028574 1605 ITFLKRDIVPLnnLVVGRLDLHSILRQAVWVHgsmtmdh---tlpklpkDTSARTVQVQEALLALalHGQEIYNTWKHLF 1681 Goose caliciv...
YP_009272568 1556 PTFLKRKLTLTpgGVRALLDPTSIARQAVWVKtggrrdrwdtealpveiDHATRAIQLDNGLVEAayHDDDTWQNILRLY 1635 Bovine calici...
YP_529550    1537 PVFLKRRIVLTpgGHRALLDLTSLARQPVWVNgprrsvwn-heaqpieiDAETRTIQLQNVLIELawHQPQDFDHVLALV 1615 Newbury agent 1
NP_663315    1537 PVFLKRRIVLTpgGHRALLDLTSLARQPVWVNgprrsvwd-heaqpieiDSEVRTIQLQNVLIESawHQPQDFNQVAALV 1615 Calicivirus s...
Feature 1          
2CKW_A        466 I 466  Sapporo virus
4NRT_A        464 I 464  Norwalk-like virus
3UQS_A        463 S 463  Murine norovirus 1
1SH0_A        463 I 463  Norwalk virus
3QID_A        463 S 463  Murine norovirus 1
AFH89835      505 Q 505  Chicken calicivirus
YP_009028574 1682 H 1682 Goose calicivirus
YP_009272568 1636 T 1636 Bovine calicivirus strain Kirklareli
YP_529550    1616 V 1616 Newbury agent 1
NP_663315    1616 Y 1616 Calicivirus strain NB

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap