NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|408475274|gb|AFU72537|]
View 

protein 2a [Pelargonium zonate spot virus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
236-588 8.56e-159

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 cd23252:

Pssm-ID: 477363  Cd Length: 332  Bit Score: 460.93  E-value: 8.56e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 236 DVDFDNIRLRQSEVFCDRDLDRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSVDVERLSELVAKKFLSSYvc 315
Cdd:cd23252    3 SLDVDHCRLDQSDFNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTV-- 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 316 dlkpvvgvmekmrayhqkwgdkIDPmfllkeHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTA 395
Cdd:cd23252   81 ----------------------IDV------DRLDKYMHMIKSDLKPVEDDSLHVERPVPATITYHKKGIVMQFSPLFLA 132
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 396 LFDEFQKSLDERVVIPSGPISTIE-MDFDIRN--KYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYK 472
Cdd:cd23252  133 AFERLLRCLRSKIVIPSGKIHQLFmIDPSVLNasKHFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPFTKWWFDFHRR 212
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 473 SFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDT--RQFEKMLFAGDDSLAISSSPIVGC-SDYFVSLFNM 549
Cdd:cd23252  213 SYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLddPNFDFVVASGDDSLIGSVEPLPRDdEDLFTTLFNF 292
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|.
gi 408475274 550 EAKIMDPgVPYICSKFLVSDELG--RCFSAPDPIREFQRLG 588
Cdd:cd23252  293 EAKFPHN-QPFICSKFLLSDEFGdeNVFSVPDPLKLLQRLG 332
 
Name Accession Description Interval E-value
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
236-588 8.56e-159

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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: 438102  Cd Length: 332  Bit Score: 460.93  E-value: 8.56e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 236 DVDFDNIRLRQSEVFCDRDLDRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSVDVERLSELVAKKFLSSYvc 315
Cdd:cd23252    3 SLDVDHCRLDQSDFNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTV-- 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 316 dlkpvvgvmekmrayhqkwgdkIDPmfllkeHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTA 395
Cdd:cd23252   81 ----------------------IDV------DRLDKYMHMIKSDLKPVEDDSLHVERPVPATITYHKKGIVMQFSPLFLA 132
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 396 LFDEFQKSLDERVVIPSGPISTIE-MDFDIRN--KYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYK 472
Cdd:cd23252  133 AFERLLRCLRSKIVIPSGKIHQLFmIDPSVLNasKHFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPFTKWWFDFHRR 212
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 473 SFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDT--RQFEKMLFAGDDSLAISSSPIVGC-SDYFVSLFNM 549
Cdd:cd23252  213 SYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLddPNFDFVVASGDDSLIGSVEPLPRDdEDLFTTLFNF 292
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|.
gi 408475274 550 EAKIMDPgVPYICSKFLVSDELG--RCFSAPDPIREFQRLG 588
Cdd:cd23252  293 EAKFPHN-QPFICSKFLLSDEFGdeNVFSVPDPLKLLQRLG 332
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
236-660 3.93e-140

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses


Pssm-ID: 395779  Cd Length: 440  Bit Score: 417.04  E-value: 3.93e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  236 DVDFDNIRLRQSEVFC-DRDLDRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSVDVERLSELVAKKFLSSYV 314
Cdd:pfam00978   5 SLDLDDCRLDPSKSKPkPKDKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFKKSFL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  315 -----CDLKPVVGVMEKMRAYHQK------WGDKIDPMFLLKEHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGK 383
Cdd:pfam00978  85 dkeklDKLDPIINTTENVSRWLDKqsgkkaAQLKLDDLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTITYHDK 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  384 SICAGFSPWFTALFDEFQKSLDERVVIPSGPISTIEMDF--DIRNKYY-LEVDLSKFDKSQGLLHLEFQRKILCKIGLPT 460
Cdd:pfam00978 165 GVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHfeFLDASEDfLEIDFSKFDKSQGELHLLVQLEILKLLGLDP 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  461 HLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDTRQFEKMLFAGDDSLAISSSPIVGCS 540
Cdd:pfam00978 245 ELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPIEDPA 324
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  541 DYFVSLFNMEAKIMDPGVPYICSKFLVSDElGRCFSAPDPIREFQRLGKKKIsADNDDALFEQYVGFKDRMSHMRN-FSE 619
Cdd:pfam00978 325 SRFATLFNMEAKVFDPSVPYFCSKFLLEVD-GGAFFVPDPLKLLQKLGKKKI-PDDEQHLDEIFTSLCDLTKSFNDdCVV 402
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 408475274  620 YEIQQLKIFFNLKYKQSGEVIEDymgACMFYSDNFKNFKTL 660
Cdd:pfam00978 403 LELLDLAVARYYKYAPEGYAALC---ALHKALSSFTLFFSL 440
 
Name Accession Description Interval E-value
Bromoviridae_RdRp cd23252
RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...
236-588 8.56e-159

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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: 438102  Cd Length: 332  Bit Score: 460.93  E-value: 8.56e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 236 DVDFDNIRLRQSEVFCDRDLDRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSVDVERLSELVAKKFLSSYvc 315
Cdd:cd23252    3 SLDVDHCRLDQSDFNDWTKPDGYLEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDLDRVSNAVANRFLTTV-- 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 316 dlkpvvgvmekmrayhqkwgdkIDPmfllkeHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTA 395
Cdd:cd23252   81 ----------------------IDV------DRLDKYMHMIKSDLKPVEDDSLHVERPVPATITYHKKGIVMQFSPLFLA 132
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 396 LFDEFQKSLDERVVIPSGPISTIE-MDFDIRN--KYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYK 472
Cdd:cd23252  133 AFERLLRCLRSKIVIPSGKIHQLFmIDPSVLNasKHFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPFTKWWFDFHRR 212
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 473 SFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDT--RQFEKMLFAGDDSLAISSSPIVGC-SDYFVSLFNM 549
Cdd:cd23252  213 SYISDRRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLddPNFDFVVASGDDSLIGSVEPLPRDdEDLFTTLFNF 292
                        330       340       350       360
                 ....*....|....*....|....*....|....*....|.
gi 408475274 550 EAKIMDPgVPYICSKFLVSDELG--RCFSAPDPIREFQRLG 588
Cdd:cd23252  293 EAKFPHN-QPFICSKFLLSDEFGdeNVFSVPDPLKLLQRLG 332
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
236-660 3.93e-140

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses


Pssm-ID: 395779  Cd Length: 440  Bit Score: 417.04  E-value: 3.93e-140
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  236 DVDFDNIRLRQSEVFC-DRDLDRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSVDVERLSELVAKKFLSSYV 314
Cdd:pfam00978   5 SLDLDDCRLDPSKSKPkPKDKEPYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFKKSFL 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  315 -----CDLKPVVGVMEKMRAYHQK------WGDKIDPMFLLKEHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGK 383
Cdd:pfam00978  85 dkeklDKLDPIINTTENVSRWLDKqsgkkaAQLKLDDLVPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTITYHDK 164
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  384 SICAGFSPWFTALFDEFQKSLDERVVIPSGPISTIEMDF--DIRNKYY-LEVDLSKFDKSQGLLHLEFQRKILCKIGLPT 460
Cdd:pfam00978 165 GVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHfeFLDASEDfLEIDFSKFDKSQGELHLLVQLEILKLLGLDP 244
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  461 HLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDTRQFEKMLFAGDDSLAISSSPIVGCS 540
Cdd:pfam00978 245 ELADLWFKFHRQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPIEDPA 324
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274  541 DYFVSLFNMEAKIMDPGVPYICSKFLVSDElGRCFSAPDPIREFQRLGKKKIsADNDDALFEQYVGFKDRMSHMRN-FSE 619
Cdd:pfam00978 325 SRFATLFNMEAKVFDPSVPYFCSKFLLEVD-GGAFFVPDPLKLLQKLGKKKI-PDDEQHLDEIFTSLCDLTKSFNDdCVV 402
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 408475274  620 YEIQQLKIFFNLKYKQSGEVIEDymgACMFYSDNFKNFKTL 660
Cdd:pfam00978 403 LELLDLAVARYYKYAPEGYAALC---ALHKALSSFTLFFSL 440
Mayoviridae_RdRp cd23256
RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...
320-636 3.49e-63

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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: 438106  Cd Length: 329  Bit Score: 213.07  E-value: 3.49e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 320 VVGV-MEKMRAYHQKWGDKIDPMFLLKEHNLQRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTALFD 398
Cdd:cd23256    2 VVGSsADQIQLYQNKVGNKVNDPVVLALTSLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPIFRQFKT 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 399 EFQKSLDERVVIPSGPISTIEMDF-----DIRNKYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKS 473
Cdd:cd23256   82 RLLACKKSNLCIPLDHDHDISGWLtnrhlGSENGTFTEIDFSKFDKSQGELHQLIQDLILLRFGCDPEFVSLWSTAHRSS 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 474 FISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCY---DTRQFEKMLFAGDDSLAISSSPIVGCSDYFVSLFNME 550
Cdd:cd23256  162 SIKDQNVGISFKTDFQRRTGDAFTFLGNSLVTAVMLAYVLsfeDEKKIRYMLVGGDDSLICSYGPISVPLEPLSTIFNMS 241
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 551 AKIMDPGVPYICSKFLVSDElGRCFSAPDPIREFQRLGKKKISaDNDDALFEQYVGFKDrmsHMRNFSEYEI-QQLKIFF 629
Cdd:cd23256  242 CKLIQPSCPYFASRYIIRVG-DEILCVPDPYKLLVKMGRKDIP-DNEASLEEVRTGLAD---SAKPLFDDEVkQKLSILV 316

                 ....*..
gi 408475274 630 NLKYKQS 636
Cdd:cd23256  317 QIRYNKS 323
ps-ssRNAv_Martellivirales_RdRp cd23208
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...
350-533 3.98e-60

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. 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: 438058 [Multi-domain]  Cd Length: 190  Bit Score: 199.90  E-value: 3.98e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 350 QRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTALFDEFQKSLDERVVIPSGPISTIEM------DFD 423
Cdd:cd23208    1 DKYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLKKKVVIYTGMMTSAELndfisaLHL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 424 IRNKYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFGNTL 503
Cdd:cd23208   81 ESGYYVLEIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVLWEFAHTQSTTRDINNGISFETAYQRKSGDAFTYFGNTL 160
                        170       180       190
                 ....*....|....*....|....*....|
gi 408475274 504 VTMAMFSFCYDTRQFEKMLFAGDDSLAISS 533
Cdd:cd23208  161 VTMAALLDVLDLEKIVCIAFGGDDSLIFSK 190
Closteroviridae_RdRp cd23253
RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...
350-609 3.56e-56

RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. 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: 438103  Cd Length: 266  Bit Score: 192.00  E-value: 3.56e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 350 QRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTALFDEFQKSLDERVVIPSGpistieMDFD-----I 424
Cdd:cd23253    1 TSFKLMVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEVFDRIKYCLSDKIILYSG------MNLEelaslI 74
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 425 RNK--------YYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAF 496
Cdd:cd23253   75 RSKlgdpldeyKTVEIDFSKFDKSQGVLFKVYEELVYKFFGFSEELYDNWKCSEYFSCRATSDSGVSLELGAQRRTGSPN 154
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 497 TFFGNTLVTMAMFSFCYDTRQFEKMLFAGDDSLAISSSPIVGCSDYFVSLFNMEAKIMDPGVPYICSKFLVSDElGRCFS 576
Cdd:cd23253  155 TWLGNTLVTLGILSSSYDLDDIDLLLVSGDDSLIFSKKPLPNKANEINLDFGFEAKFIENSVPYFCSKFIIEDR-GKIKV 233
                        250       260       270
                 ....*....|....*....|....*....|...
gi 408475274 577 APDPIREFQRLGkKKISADNDDALFEQYVGFKD 609
Cdd:cd23253  234 VPDPVKLFEKLS-VPIRLEDETLLKERFTSFKD 265
Kitaviridae_RdRp cd23254
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...
350-588 8.02e-54

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104  Cd Length: 267  Bit Score: 185.81  E-value: 8.02e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 350 QRYEHMIKTDVKPTVAHSMHVERAIPATITFHGKSICAGFSPWFTALFDEFQKSLDERVVI-----PSGPISTIEMDFD- 423
Cdd:cd23254    1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIftdmsPEDFEELLNRRFPp 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 424 ---IRNKYYLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFG 500
Cdd:cd23254   81 evlSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELWFNAHVLTTLYDRTNKLKALVEYQRKSGDASTFFG 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 501 NTLVTMAMFSFCYDTRQFEKMLFAGDDSLAISSSPIVGC-SDYFVSLFNMEAKIMDPGVPYICSKFLVSDELGRCFSaPD 579
Cdd:cd23254  161 NTLFLMAVLADLFDLSDLELALFSGDDSLLFGRNLLDYDdSQHFALKFNLESKFLNYKYPYFCSKFLLPVGGRWYFV-PD 239

                 ....*....
gi 408475274 580 PIREFQRLG 588
Cdd:cd23254  240 PVKLLTKLG 248
Virgaviridae_RdRp cd23251
RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...
220-617 1.87e-42

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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: 438101  Cd Length: 427  Bit Score: 159.32  E-value: 1.87e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 220 YFDDtwhqYFVEGSKLDVDFDNIRL---RQSEVFCDRdldRYYQPELFAGASSRRIGTQKEALVAIRKRNADVPELADSV 296
Cdd:cd23251   10 DFDG----YTVATSDINLNVEDCTLdpsKSVKVWQEK---EGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGAV 82
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 297 DVERLSELVAKK----FLSSYVCDLKPvVGVMEKMrayhQKWGDK---------IDPMFLLKEHNLQRYEHMIKTDVKPT 363
Cdd:cd23251   83 NEFETIERVIKKakdvFFDEDLIDRSP-LSTRESF----LRWWDKqsttaraqlLADDRVLDEIDVCTYNFMIKNDVKPK 157
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 364 VAHSMHVERAIPATITFHGKSICAGFSPWFTALFDEFQKSLDERVVI-----PSGPISTIEmDFDIRNKY-YLEVDLSKF 437
Cdd:cd23251  158 LDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSALDPHVVFntrmtAEELNETVE-FLDPDEEYdALEIDFSKF 236
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 438 DKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDTRQ 517
Cdd:cd23251  237 DKSKTSLHIRAVIELYKLFGLDGMLAFLWEKSQCQTTVKDRQNGIKAYLLYQQKSGNCDTYGSNTWSAALALLSMLPLEK 316
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 518 FEKMLFAGDDSLAI--SSSPIVGCSDYFVSLFNMEAKIMDPGVPYICSKFLVSDElGRCFSAPDPIREFQRLGKKKISad 595
Cdd:cd23251  317 AIFMIFGGDDSLILfpKGLVIPDPCRRLASLWNFECKLFKFKYGYFCGKFLLKHG-DGYIFYPDPLKLITKLGRKDIK-- 393
                        410       420
                 ....*....|....*....|..
gi 408475274 596 NDDALFEQYVGFKDRMSHMRNF 617
Cdd:cd23251  394 DGEHLSEIFVSICDNYKSYRDY 415
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
357-529 5.87e-17

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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: 438059 [Multi-domain]  Cd Length: 183  Bit Score: 79.46  E-value: 5.87e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 357 KTDVKPTVAHSmHVERAIPAtitfHGKSICAGFSPWFTALFDEFQKSLDERVVIPSGPISTIEMD--FDIRNKYYLEVDL 434
Cdd:cd23209   12 KFTDCEPVAHG-KAGQGISA----WSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDkiNQAHSAVFIENDF 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 435 SKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCsfQRRTGDAFTFFGNTLVTMAMFSFCYD 514
Cdd:cd23209   87 TEFDSTQNLFSLLVELEILEACGMPPALAELYRALRAKWTLQAREGSLEGTC--KKTSGEPGTLLHNTIWNMAVMMHMVR 164
                        170
                 ....*....|....*
gi 408475274 515 TRQFEKMLFAGDDSL 529
Cdd:cd23209  165 GGVRKAAAFKGDDSV 179
ps-ssRNAv_Alsuviricetes_RdRp cd23182
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...
351-529 4.92e-16

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. 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: 438032 [Multi-domain]  Cd Length: 187  Bit Score: 76.87  E-value: 4.92e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 351 RYEHMIKTDVKPTVAHSMHVERAIpATITFHGKSICAGFSPWFTALFDEFQKSLDERVVIPSGPISTIEMDFDIRNKY-- 428
Cdd:cd23182    2 DIDFLIKTQQKVSPKTPFNTGKAG-QTIAAHSKSINFVLGPWIRYLEERLRDGSRTHRYSNGLMDEEEAMLSQWKINHvp 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 429 ---YLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPRAKVSFNCSFQRRTGDAFTFFGNTLVT 505
Cdd:cd23182   81 hatFVSNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNLFIELHGKRTLRAKVLGGSGELDGMRDSGAAWTYCRNTDYN 160
                        170       180
                 ....*....|....*....|....*
gi 408475274 506 MAMFSFCYdtRQFEKM-LFAGDDSL 529
Cdd:cd23182  161 LAVMLSLY--RLKVKPaAFSGDDSL 183
Endornaviridae_RdRp cd23255
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ...
378-536 1.13e-13

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. 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: 438105  Cd Length: 237  Bit Score: 71.03  E-value: 1.13e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 378 ITFHGKSICAGFSPWFTALFDEFQKSLDERVVIPSGpISTIEMDFDIR----NKYYLEVDLSKFDK--SQGLLHLEFQrk 451
Cdd:cd23255   61 IVWQRKGICAIFSPIFNEAKKRLKSLLKPKVVYADG-LTPDELSARLRlvknVKYFFEDDLSKQDRqtDKPIIDVEME-- 137
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 452 ILCKIGLPTHLANWW----CDFHYKSfisdprAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSFCYDT--RQFEKMLFAG 525
Cdd:cd23255  138 LYKLLGVDPNVIELWrevhENWRFKG------KGVRGVGDAMRLTGQATTALGNVITNLLVHSRLVKRngSNLKLMLVLG 211
                        170
                 ....*....|.
gi 408475274 526 DDSLAISSSPI 536
Cdd:cd23255  212 DDNLILTDTKI 222
Hepeviridae_RdRp cd23259
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ...
362-542 2.34e-07

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped virus. 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: 438109  Cd Length: 274  Bit Score: 52.83  E-value: 2.34e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 362 PTVAHSmHVERAIPAtitfHGKSICAGFSPWFTAL------------F--DEFQKSLDERVVIPSGPISTIEMDFdirnk 427
Cdd:cd23259   81 ETIAHG-KVGQGISA----WSKTFCALFGPWFRAIekaivallppniFygDAYEESVFSAAVAGAGSCRVFENDF----- 150
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 428 yylevdlSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDFHYKSFISDPraKVSFNCSFQRRTGDAFTFFGNTLVTMA 507
Cdd:cd23259  151 -------SEFDSTQNNFSLGLECEIMEECGMPQWLVRLYHLVRSAWVLQAP--KESLRGFWKKHSGEPGTLLWNTVWNMA 221
                        170       180       190
                 ....*....|....*....|....*....|....*
gi 408475274 508 MFSFCYDTRQFEKMLFAGDDSlaissspIVGCSDY 542
Cdd:cd23259  222 VIAHCYEFRDLAVAAFKGDDS-------VVLCSDY 249
Togaviridae_RdRp cd23250
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...
258-598 1.07e-04

RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. 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: 438100  Cd Length: 458  Bit Score: 45.15  E-value: 1.07e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 258 YYQPELFAGASSRRIGTQKEALVAIRKRNADVPELAD--SVDVERLSELVAKKFlssyVCD--------LKPVVGVMEKM 327
Cdd:cd23250   28 YHQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRElpTLDSAAFNVECFKKF----ACNneyweefkEKPIRLTTENV 103
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 328 RAYHQKW-GDKIDPMFLlKEHNLQ--------RYEHMIKTDVKPTVAhSMHVERAIPATItfhgksICAGfSPWFTALFD 398
Cdd:cd23250  104 TTYVTKLkGPKAAALFA-KTHNLVplqevpmdRFVMDMKRDVKVTPG-TKHTEERPKVQV------IQAA-DPLATAYLC 174
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 399 EFQKSLDER---VVIPSgpISTI-EM---DFD-IRNKYY------LEVDLSKFDKSQ-------GLLHLEfqrkilcKIG 457
Cdd:cd23250  175 GIHRELVRRlnaVLLPN--IHTLfDMsaeDFDaIIAEHFqpgdkvLETDIASFDKSQddamaltALMILE-------DLG 245
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 458 LPTHLANWW-CDFHYKSFISDPrAKVSFNCSFQRRTGDAFTFFGNTLVTMAMFSfcydtRQFEKML-------FAGDDSL 529
Cdd:cd23250  246 VDQELLDLIeAAFGEITSVHLP-TGTRFKFGAMMKSGMFLTLFVNTVLNIVIAS-----RVLRERLtnsrcaaFIGDDNI 319
                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 408475274 530 --AISSSPIVgcSDYFVSLFNMEAKIMD----PGVPYICSKFLVSDEL-GRCFSAPDPIREFQRLGKKKISADNDD 598
Cdd:cd23250  320 vhGVVSDKLM--ADRCATWLNMEVKIIDavigEKPPYFCGGFILYDSVtGTACRVADPLKRLFKLGKPLPADDEQD 393
Betaflexiviridae_RdRp cd23245
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Betaflexiviridae of ...
437-527 2.79e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Betaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Betaflexiviridae, order Tymovirales. Virions within the Betaflexiviridae family are flexuous filaments, usually 12#13 nm in diameter (range 10#15 nm) and from 600 to over 1000 nm in length, depending on the genus. They infect plants which share a distinct lineage of alphavirus-like replication proteins. There are 108 species in the family Betaflexiviridae, assigned to 13 genera in two subfamilies (Quinvirinae and Trivirinae). Diseases associated with this family include: mosaic and ringspot symptoms. 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: 438095  Cd Length: 318  Bit Score: 43.60  E-value: 2.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 437 FDKSQGLLHLEFQRKILCKIGLPTHLANwwcdfHYKsFIsdpraKVSFNC---SFQ--RRTGDAFTFFGNTLVTMAmFSF 511
Cdd:cd23245  145 FDASQDHYILAFEVELMKYLGLPEDLIE-----DYK-FL-----KTHLGCklgNFAimRFTGEFSTFLFNTLANML-FTF 212
                         90
                 ....*....|....*..
gi 408475274 512 C-YDTRQFEKMLFAGDD 527
Cdd:cd23245  213 LrYDINGDEPICFAGDD 229
Gammaflexiviridae_RdRp cd23249
RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ...
374-537 1.83e-03

RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438099  Cd Length: 354  Bit Score: 41.04  E-value: 1.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 374 IPATITFHGKSICAGFSPWFTALFDEFQKSLDErvvipsgpistiemdfdirnkyylevDLSKFDKSQGLLHLEFQRKIL 453
Cdd:cd23249  124 LPPHIYIHSGRTNEDFERFVAAHWDFTRESTEG--------------------------DYTAFDASQDADFLNFETLLM 177
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 454 CKIGLPTHLANWWCDfhyksfisdprAKVSFNC-----SFQRRTGDAFTFFGNTLVTMAMFSFCYDTRQFEKMLFAGDDS 528
Cdd:cd23249  178 RALGVPLDLIEAYLE-----------MKASITShlgplAIMRFSGEVWTYLFNTLGNMAYTAAKYEVPPPVPRVYGGDDK 246

                 ....*....
gi 408475274 529 LaISSSPIV 537
Cdd:cd23249  247 S-INSRITV 254
ps-ssRNA_RdRp_Tymovirales cd23207
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ...
429-530 2.30e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). 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: 438057 [Multi-domain]  Cd Length: 188  Bit Score: 39.69  E-value: 2.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 408475274 429 YLEVDLSKFDKSQGLLHLEFQRKILCKIGLPTHLANWWCDF--HYKSFISdprakvsfNCSFQRRTGDAFTFFGNTLVTM 506
Cdd:cd23207   90 STANDYTAFDQSQDGEFVVFEVLLMRHLHIPDDLIELYVDIktNAYSHLG--------PLSIMRLTGEPGTFDFNTDYNL 161
                         90       100
                 ....*....|....*....|....
gi 408475274 507 AMFSFCYDTRQFEKMLFAGDDSLA 530
Cdd:cd23207  162 ALTYAKYDLPPGTPICFSGDDSVA 185
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH