Conserved Protein Domain Family
ps_ssRNAv_Tolivirales_RdRp

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cd23179: ps_ssRNAv_Tolivirales_RdRp 
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.
Statistics
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PSSM-Id: 438029
Aligned: 81 rows
Threshold Bit Score: 255.14
Created: 1-Jun-2020
Updated: 17-Oct-2022
Structure
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Aligned Rows:
 
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
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
NP_062897    443 SHLTTFVKAEKistsk--gdpaPRVIQPRNPRYNVeLGRYLRHMESKLmkAVDGVfg-----etTCIKGYTadeVGAIFR 515
YP_009345057 167 ARVSMFLKVEKvfaed-paekaPRAIQYRGPRFNLvLGRFILAYEEAFyrAFNHVnas----rcHTSKGLTpdaRAALLW 241 Xinzhou nematod...
QDH88963     109 WKLKLFIKVEKhyks---pvkePRTIQHRQERYTLeLARYLQPLEDAFisHYSALrynt--qevYTTKGLTnekKATAIS 183 Riboviria sp.
YP_009342294 170 KHASSFVKLQRfdpts-kehqvPRVVSFRQYTNAFsLGRYIRPLEHQFvnAPSFGrfk---gyrWLAKTRNltqRATDIS 245 Wenzhou tombus-...
QDH89942      44 AQVAAFVKAEKlany---kvhkPRIIMGRTPRYNLeLAAYLKPLEHALypAFRGWgrmfltrtrLIGKGLNgeeRASLLR 120 Riboviria sp.
QDH87260      18 GKLKPFLKAEKfnpql--kqakPRMIMARSPRFNLeLSRYLKPFEHELwgRLKTPkhwgvgksrVVAKGLNqyqRANLIV 95  Riboviria sp.
YP_009342296  92 ARLKYFLKFETynfde-kpnpsPRGINPRSDRYLVeLGRFLHSIEKRIykAIALVfg-----hpVIMKGYNqaqRGAILD 165 Wenzhou tombus-...
YP_009336773 128 SKIRAFIKFEKmlaketgkpkaPRMISPPSPRFLVrTGCYVKPAEHAIyeAIDHMfg-----fkVVTKGMNfgeIGRLFK 202 Hubei tombus-li...
QDH91075     135 AILKFFMKFEAynlhv-kgnpsPRGINPPSDEYLVeLGRYIKPIEKLIykALRELfg-----fiVVLKGFNqqqRGRIIS 208 Riboviria sp.
YP_009337093 130 SKIGFFVKTEAtqhl---krqvPRIISPRSYEFNYlLGRYTLAIEHPLfeALPSLfkg----vpVIAKGRTqqeKAQLIV 202 Changjiang tomb...
Feature 1                      #                                                                 
NP_062897    516 AKWdrfdkpVAIGLDASRFDQHCSVEALQYEHSFYRAMYpg--nKLLGKLLEWQLHNkgkGYVPDGtityrkeGCRMSGD 593
YP_009345057 242 ELWsknprpAALNVDASRFDAHVTVEMLLLESLYYESSFpn--cRLLRWLLRCQRRNr--GCGKFGtty-tlkGGRMSGD 316 Xinzhou nematod...
QDH88963     184 EHWdrv-gvWALCLDFSRFDCHVTLDALKATHAWYKAHYpg--dDYLSWLLSKQEETk--GKTALGtky-rrvGGRCSGD 257 Riboviria sp.
YP_009342294 246 LIWdmipnvCCVSIDASRFEAHVSKDMLSLEFETYSDAYrg--dARLVKMLKAMLATk--MHTKYGlkc-silGRRLSGD 320 Wenzhou tombus-...
QDH89942     121 RKLyanpgtVCFEVDCKSFESHVSVEQLIAEHETYTTLCr---dPRLRELLSWQREFs--GGFRSGvrf-rakGCRASGD 194 Riboviria sp.
QDH87260      96 RKFrgvadcVCVEVDGAQFEAHITDTVLKMEHSVYMAKFr---dPVLQKMLNIQLKLk--GTTRHGikf-erpGSRASGD 169 Riboviria sp.
YP_009342296 166 KLMsevddpVAIPADASRFEQSIDIPHLEVEHKWYLEFFrgedrKHLAFLLDLQKHNkgsAHASDGdlkfsidGKRMSGD 245 Wenzhou tombus-...
YP_009336773 203 SHWdalddpVAFDVDVEKMDRSTSSEMLAWTHKLIHACYrgddlDDIREMLKQQLSVrttVKCDDGnikytvdGTLTSGQ 282 Hubei tombus-li...
QDH91075     209 DYWkefddpIGIAADASKFEQSVSAECIEVERLVYSAYYs---dNVVSKLMGWQKFYrgkGSTTDGylsfkigGVRASGM 285 Riboviria sp.
YP_009337093 203 EKLkp--gwVCVGLDASRFDQSIGETLLRMEHSVYTKLFpg--dRLLPALLKQQLNNvgrALCRDGcvkarigAMRCSGD 278 Changjiang tomb...
Feature 1                                             ###                                        
NP_062897    594 INTSLGNYLLMCaMVHGYMrhlg-----ineFSLAnCGDDCVLIVErr--nLKQIQRTLPEYFLNlgytm-kveqpVFQL 665
YP_009345057 317 VNTALGNTLIQMtVLSFLAgr---------sFDLVvEGDDAVIFGDvd--dITRLEAVITSKALAvgfql--kvskALYL 383 Xinzhou nematod...
QDH88963     258 IDTSLGNTLINItLLRTITd-----------ALIIaEGDDSIIIGTpe--qVLRAKAALDSVSSRfgfkl--egeiAYSL 322 Riboviria sp.
YP_009342294 321 MCTSLGNALLMCgMLNFISedl------nidFKIYdDGDDCLLFMNkn--lLPRLEEMRNCFKRLgfdvr--vdkiAYCL 390 Wenzhou tombus-...
QDH89942     195 FNTGLGNTLIMCcLVLASAkri------gsrFDFLaDGDNAVIFVPcd--sLHLWLRELSQCFLSmghea-eigevQSEI 265 Riboviria sp.
QDH87260     170 VNTGLGNSIIMTtAMDATMrylrrlagnnfqYDMLvDGDNAILFIPrd--yLALVEARFKSVCTAisgqeaviekpAYCV 247 Riboviria sp.
YP_009342296 246 KNTSSGNCIISAsLWYEFAkekg----wltlTRFFcDGDDAVMIIPrk--yLKEFQQDYLVFCSKrgfrm-kldkvACIL 318 Wenzhou tombus-...
YP_009336773 283 MNTSLVGVSMVSsIMYTLFkerl-----dvpYRFVdAGDDCTVILDkr--nADRFLCEVRKIFGEvgfai-tigppSVEL 354 Hubei tombus-li...
QDH91075     286 PNTALGNCLLSClMAHTIFrila-----ikrYRFVcDGDDVHFIMErr--dSERFRDYARTYYQRlgfrm-kmehtVDVL 357 Riboviria sp.
YP_009337093 279 QNTSLGNCLISClLAALFFreh------gidGDVLnDGDDLLMFVPenqlaELSVLPEWYLQWGLrmkv----eppARVP 348 Changjiang tomb...
Feature 1               
NP_062897    666 EEVEFCQ 672
YP_009345057 384 EQLEYCS 390 Xinzhou nematode virus 7
QDH88963     323 EEIDYCS 329 Riboviria sp.
YP_009342294 391 EEIVFCQ 397 Wenzhou tombus-like virus 10
QDH89942     266 EGVVFGQ 272 Riboviria sp.
QDH87260     248 EHVTFGQ 254 Riboviria sp.
YP_009342296 319 EQIDFCQ 325 Wenzhou tombus-like virus 7
YP_009336773 355 EQIEFCQ 361 Hubei tombus-like virus 10
QDH91075     358 EHIDFCQ 364 Riboviria sp.
YP_009337093 349 EQVEFCQ 355 Changjiang tombus-like virus 16

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