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Conserved domains on  [gi|1132350693|ref|YP_009337262|]
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hypothetical protein 2 [Wenling tombus-like virus 5]

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 ...
29-248 2.59e-101

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 cd23174:

Pssm-ID: 477363  Cd Length: 229  Bit Score: 299.78  E-value: 2.59e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  29 GLSPSDAVMKVFIKTETSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARSPYLVKGLTPTERARKLAPFRR-GAVIET 107
Cdd:cd23174     8 EPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTEyERFLEI 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 108 DFSRFDMTVSADIITTVERMAFRQAYPKGLFPLFDEALHLLTSMVGIGTLGATYTVEGTRASGDAHTSIANGIINRFVIW 187
Cdd:cd23174    88 DFSRFDMTLMKDLLRIVELRFLLDPYTQRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGFLNAFIIW 167
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1132350693 188 ACLRHLP-CPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFTLGFRLKCVVPNPMGSATFCGR 248
Cdd:cd23174   168 LCLRKLPtNSWQSAHEGDDGIIGLRANVVNQVEYNLKFLSCLGFRAKIRVVSELSQATFCGR 229
 
Name Accession Description Interval E-value
ps-ssRNAv_CBPV-like_RdRp cd23174
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ...
29-248 2.59e-101

catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024  Cd Length: 229  Bit Score: 299.78  E-value: 2.59e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  29 GLSPSDAVMKVFIKTETSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARSPYLVKGLTPTERARKLAPFRR-GAVIET 107
Cdd:cd23174     8 EPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTEyERFLEI 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 108 DFSRFDMTVSADIITTVERMAFRQAYPKGLFPLFDEALHLLTSMVGIGTLGATYTVEGTRASGDAHTSIANGIINRFVIW 187
Cdd:cd23174    88 DFSRFDMTLMKDLLRIVELRFLLDPYTQRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGFLNAFIIW 167
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1132350693 188 ACLRHLP-CPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFTLGFRLKCVVPNPMGSATFCGR 248
Cdd:cd23174   168 LCLRKLPtNSWQSAHEGDDGIIGLRANVVNQVEYNLKFLSCLGFRAKIRVVSELSQATFCGR 229
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
34-246 1.14e-13

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 72.27  E-value: 1.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAAR-------SPYLVKGLTPTERARKLA----P 98
Cdd:pfam00998 119 DAILKTFVKAEkiniTAKPDPAPRVIQPRPPRYNVEPGRYLRPCEKMIYKaidkafgGPTVLKGYTPEQRGEILLkkwdS 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFPLFDEALHLLTSM---VGIGTL--G-ATYTVEGTRASGDA 172
Cdd:pfam00998 199 FKKPVAIGLDASRFDQHVS------VEALRFEHSIYLAAFLGPEELIRLLTWQlynGGPMYAsdGqIKYGVRGCRMSGDM 272
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1132350693 173 HTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFT-LGFRlkCVVPNP---MGSATFC 246
Cdd:pfam00998 273 NTSLGNCLLMCLKVHAACKALGIDARLLNNGDDCVVICESADLDEVKEALTEAFArYGFT--MKVEEPvyeLELIEFC 348
 
Name Accession Description Interval E-value
ps-ssRNAv_CBPV-like_RdRp cd23174
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ...
29-248 2.59e-101

catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024  Cd Length: 229  Bit Score: 299.78  E-value: 2.59e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  29 GLSPSDAVMKVFIKTETSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARSPYLVKGLTPTERARKLAPFRR-GAVIET 107
Cdd:cd23174     8 EPRRKYALIKNFVKNETTAKFVDPRNISPRSDEFLVVVGPYISAIEHAAVHCPFLIKGLTPKKRCDKLSWLTEyERFLEI 87
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 108 DFSRFDMTVSADIITTVERMAFRQAYPKGLFPLFDEALHLLTSMVGIGTLGATYTVEGTRASGDAHTSIANGIINRFVIW 187
Cdd:cd23174    88 DFSRFDMTLMKDLLRIVELRFLLDPYTQRAHQLFIAFMLYTLTNVGVSRFGTHYKRDGTRCSGDPHTSIGNGFLNAFIIW 167
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1132350693 188 ACLRHLP-CPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFTLGFRLKCVVPNPMGSATFCGR 248
Cdd:cd23174   168 LCLRKLPtNSWQSAHEGDDGIIGLRANVVNQVEYNLKFLSCLGFRAKIRVVSELSQATFCGR 229
ps_ssRNAv_Tolivirales_RdRp cd23179
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
38-235 1.32e-35

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.


Pssm-ID: 438029  Cd Length: 227  Bit Score: 130.33  E-value: 1.32e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  38 KVFIKTE---TSPKGTDPRNISPRQPQFLAVLGPHVASLEKA--------AARSPYLVKGLTPTERA----RKLAPFRRG 102
Cdd:cd23179     4 KAFLKAEkynPLAKNKKPRMIQPRSPRYNLELARYLKPIEHAlygaldagRGGTRVVAKGLNPRQRAnlirRKWDEFDDP 83
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 103 AVIETDFSRFDMTVSADIITtVERMAFRQAYPKglFPLFDEALHLLTSMVGIGTLGATYTVEGTRASGDAHTSIANGIIN 182
Cdd:cd23179    84 VVFSLDASRFDAHVSVELLR-LEHSVYLACYPG--DPELRKLLKWQLVNKGRTSNGVKYKTRGGRMSGDMNTGLGNCLIM 160
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1132350693 183 RFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFTLGFRLKCV 235
Cdd:cd23179   161 LAMVYAVLRELGIKYDLLVDGDDALVFVEREDLERLLEEFAEFFLEGGGEETV 213
Tombusviridae_RdRp cd23206
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
34-234 1.36e-27

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. 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: 438056  Cd Length: 231  Bit Score: 108.74  E-value: 1.36e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAAR-------SPYLVKGLTPTERARKLAP---- 98
Cdd:cd23206     1 DARVKTFVKAEkinlTKKPDPAPRVIQPRSPRYNVELGRYLKPLEHRLYKaidrvfgSPTVMKGYNAEERGRILREkwds 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSADIItTVERMAFRQAYPkglfplFDEALHLLTSM------VGIGTLGA-TYTVEGTRASGD 171
Cdd:cd23206    81 FRDPVAVGLDASRFDQHVSVDAL-KWEHSVYLRIFP------DDKELSRLLRWqlhnkgVARCKDGKvKYKVKGGRMSGD 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1132350693 172 AHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFT-LGFRLKC 234
Cdd:cd23206   154 MNTSLGNCLIMCAMVYAYLEELGIKAELANNGDDCVLIMERSDLLRFLDGLEEWFLrFGFTMVV 217
ps-ssRNAv_Nodaviridae_RdRp cd23173
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
38-249 4.11e-26

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023  Cd Length: 236  Bit Score: 104.90  E-value: 4.11e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  38 KVFIKTETSPKGTDPRNISPRQPQFLAVLGPHVASL-EKAAARSPYLVKGLTPTERARKLAPFRRGA--VIETDFSRFDM 114
Cdd:cd23173    16 KAFIKREAYAKPKDPRNISTVDPEHTLKLSRYTYAFkEEVLKNQPWYAPGKTPKEIAERVQEIASSSdgVIETDYSRFDG 95
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 115 TVSADIITTVERMAFRQAYpkglFPLFDEALHLLTSMV----GIGTLGATYTVEGTRASGDAHTSIANGIINRFVIWACL 190
Cdd:cd23173    96 TISEWLRRNVEFAAYLRWF----HPEYRAELLKLLDAEincpARTKTGVKYDPGVSRLSGSPTTTDGNTIINAFVSYCAL 171
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1132350693 191 RHL-PCPWYSFHE-----GDDGV-IFIDKPHAAQAVEClqfaftLGFRLKCVVPNPMGSATFCGRY 249
Cdd:cd23173   172 RETgYSPEEAFALlglyyGDDGLsDNLPAEALEKVAKD------LGLKLKIEVVRPGQPVTFLGRV 231
RNA_dep_RNAP cd01699
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
29-248 7.12e-19

RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.


Pssm-ID: 238843 [Multi-domain]  Cd Length: 278  Bit Score: 85.80  E-value: 7.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  29 GLSPSDAVMKVFIKTETSPKG----TDPRNISPRQPQFL----AVLGPHVASLEKAAARSPYLVkGLTP-----TERARK 95
Cdd:cd01699    12 PLIRPDLVFTTFLKDELRPLEkveaGKTRLIQPRPLDYNialrMYLGPFEAKLMKNRGGLPIAV-GINPysrdwTILANK 90
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  96 LAPFRRgAVIETDFSRFDMTVSADIITTVERMaFRQAYPkglFPLFDEALHLLTSMVGIGT---LGATYTVEGTRASGDA 172
Cdd:cd01699    91 LRSFSP-VAIALDYSRFDSSLSPQLLEAEHSI-YNALYD---DDDELERRNLLRSLTNNSLhigFNEVYKVRGGRPSGDP 165
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 173 HTSIANGIINRFVIWACLRHLpcPWYSFHE-------GDDGVIFIDKPHAAQAVECL-QFAFTLGFRLKCVVPN-----P 239
Cdd:cd01699   166 LTSIGNSIINCILVRYAFRKL--GGKSFFKnvrllnyGDDCLLSVEKADDKFNLETLaEWLKEYGLTMTDEDKVespfrP 243

                  ....*....
gi 1132350693 240 MGSATFCGR 248
Cdd:cd01699   244 LEEVEFLKR 252
Calvusvirinae_RdRp cd23234
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
4-237 6.32e-17

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084  Cd Length: 471  Bit Score: 82.09  E-value: 6.32e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   4 DQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLE----K 75
Cdd:cd23234    84 EQVVESYTGSQRTRYQQAMESLLERPLTRRDARVSTFIKAEkinfTAKPDPAPRVIQPRDPRFNVVFAKYIKPLEpllyK 163
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  76 AAAR---SPYLVKGLTPTER----ARKLAPFRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLF--PLFDEALH 146
Cdd:cd23234   164 ALGKlykYPCVAKGFNAVETgeiiAKKWKMFRDPVCVGLDASRFDQHVS------VEALRFTHSVYKRFIksREFNKLLQ 237
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 147 LLTSMVGIGTLG---ATYTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQ 223
Cdd:cd23234   238 WMYTNRGLGTAKdgfVKYKVKGCRMSGDMDTALGNCVLMVLMTRHLCKSLSIPHELMDNGDDCIVIFDKEHLSKFNAAVK 317
                         250
                  ....*....|....*
gi 1132350693 224 FAFT-LGFRLKCVVP 237
Cdd:cd23234   318 PYFAdLGFTMKVEAP 332
Tombusvirus-like_RdRp cd23236
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
3-237 1.24e-15

RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt 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: 438086 [Multi-domain]  Cd Length: 474  Bit Score: 78.13  E-value: 1.24e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   3 FDQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTE---TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAAR 79
Cdd:cd23236    87 YDGFLSYYSGAKLRTYTRAVESLHITPVSERDSHLTTFVKAEkisTSKGDPAPRVIQPRNPRYNVELGRYLRHMESKLMK 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  80 S-------PYLVKGLTPTERAR----KLAPFRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFP---LFDEAL 145
Cdd:cd23236   167 AvdgvfgeTTCIKGYTADEVGAifrdKWDRFDKPVAIGLDASRFDQHCS------VEALQFEHSFYRAMYPgnkLLSKLL 240
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 146 HLLTSMVGIGTL---GATYTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHE-GDDGVIFIDKPHAAQAVEC 221
Cdd:cd23236   241 EWQLHNKGKGYVpdgTITYRKEGCRMSGDINTSLGNYLLMCAMVYGYMRHLGINEFSLANcGDDCVLIVERRNLKQVQGT 320
                         250
                  ....*....|....*..
gi 1132350693 222 L-QFAFTLGFRLKCVVP 237
Cdd:cd23236   321 LpEYFLNLGYTMKVEPP 337
RdRP_3 pfam00998
Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase ...
34-246 1.14e-13

Viral RNA dependent RNA polymerase; This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses.


Pssm-ID: 395794 [Multi-domain]  Cd Length: 486  Bit Score: 72.27  E-value: 1.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAAR-------SPYLVKGLTPTERARKLA----P 98
Cdd:pfam00998 119 DAILKTFVKAEkiniTAKPDPAPRVIQPRPPRYNVEPGRYLRPCEKMIYKaidkafgGPTVLKGYTPEQRGEILLkkwdS 198
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFPLFDEALHLLTSM---VGIGTL--G-ATYTVEGTRASGDA 172
Cdd:pfam00998 199 FKKPVAIGLDASRFDQHVS------VEALRFEHSIYLAAFLGPEELIRLLTWQlynGGPMYAsdGqIKYGVRGCRMSGDM 272
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1132350693 173 HTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFT-LGFRlkCVVPNP---MGSATFC 246
Cdd:pfam00998 273 NTSLGNCLLMCLKVHAACKALGIDARLLNNGDDCVVICESADLDEVKEALTEAFArYGFT--MKVEEPvyeLELIEFC 348
Pelarspovirus_RdRp cd23241
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
34-367 7.51e-13

RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. 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: 438091 [Multi-domain]  Cd Length: 497  Bit Score: 69.77  E-value: 7.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE--TSPKGTDP--RNISPRQPQFLAVLGPHVASLEKAAARS-------PYLVKGLTPTERAR----KLAP 98
Cdd:cd23241   118 DSYLKTFVKCEklNFSKKPDPapRVIQPRDPRYNVELGRYLKPFEHHCYRAldklwggPTVMKGYTVQEMGNiirdKWNK 197
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSADIITtVERMAFRQAYPKglfplfDEALHLLTSMvGIGTLGATYT--------VEGTRASG 170
Cdd:cd23241   198 YQKPAAIGFDMSRFDQHVSVDALK-FEHKIYRRCFSN------DGNLARLLGH-QIENRGVAYAkdgwlkykVEGKRMSG 269
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 171 DAHTSIANgiinrfVIWAC------LRHLPCPWYSFHEGDDGVIFIDKPHaAQAVECLQFAFTLGFRLKCVVPNP---MG 241
Cdd:cd23241   270 DVNTALGN------CILACcitkelMGGIGIKCSLINNGDDCVLIGESRD-CRAVEDILTEGWLRFGFTCIAEKPvteLE 342
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 242 SATFCGRYTCLdCGREHCdVIRTlTKFHISHRPGSA---QSLVLAKAYSYA------STDSHTPIVGPLCAALIHH-LQP 311
Cdd:cd23241   343 KIEFCQMQPVL-VGDGYK-MVRN-PRISLSKDAHSTtpfETVKLAREWAYSvglgglSLTSGIPVVQEFYQCLLRNgKKP 419
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1132350693 312 lvnirTLRRRLNHL---SWYERERAERGiGHTDfsVSPCCRASVAETASIDPVLQAAVE 367
Cdd:cd23241   420 -----TKEKKMRHFygdYYWKWVKQHRG-KYTP--VTEESRHSFHLAFGISPDQQLAME 470
Alphacarmovirus_RdRp cd23239
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
30-239 2.52e-12

RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus 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: 438089 [Multi-domain]  Cd Length: 470  Bit Score: 68.24  E-value: 2.52e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  30 LSPSDAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARS-------PYLVKGLTPTERARKLA- 97
Cdd:cd23239   116 LDRKDAHLKTFIKAEkfcvSLKPDPAPRVIQPRSPRYNVELGRYLKKFEHHAYRAldkiwggPTVMKGYTVEEVAQHISs 195
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  98 ---PFRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFPlFDEALHLLTSM------VGIGTLGAT-YTVEGTR 167
Cdd:cd23239   196 awdQFQIPVAIGFDMSRFDQHVS------VPALQFEHSCYLACFP-GDRHLAQLLSWqlknfgVGFASNGMIrYKKEGCR 268
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1132350693 168 ASGDAHTSIANGIInrfviwACL--RHL--PCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAFtLGFRLKCVVPNP 239
Cdd:cd23239   269 MSGDMNTALGNCLL------ACLitKHLmkGVNCRLINNGDDCVLICERKDLGFVVSNLTTGW-RRFGFTCIAEEP 337
Alphanecrovirus_RdRp cd23237
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
4-237 5.15e-12

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. 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: 438087  Cd Length: 439  Bit Score: 66.98  E-value: 5.15e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   4 DQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAAR 79
Cdd:cd23237    47 EQFLMNYSGRKLTIYREAVDSLSHQPLSLRDAKLKTFVKAEklnlSKKPDPAPRVIQPRSPRYNVCLGRYLRHYEHHAFK 126
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  80 S-------PYLVKGLTPTERAR----KLAPFRRGAVIETDFSRFDMTVSADIITTVERMAFRQaYPKglfplfDEALHLL 148
Cdd:cd23237   127 TiakcfgeITVFKGFTLEQQGEimrsKWKKYVNPVAVGLDASRFDQHVSVEALQYEHEFYLRD-YPN------DKQLKWL 199
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 149 --TSMVGIGTLGAT-----YTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVEC 221
Cdd:cd23237   200 lkQQLCNIGTAFASdgiikYKKEGCRMSGDMNTSLGNCILMCAMVYGLKEHLGINLSLANNGDDCVIVCEKADLKKLTSS 279
                         250
                  ....*....|....*..
gi 1132350693 222 LQFAFT-LGFRLKCVVP 237
Cdd:cd23237   280 IEPYFKqFGFKMEVEKP 296
Betacarmovirus_RdRp cd23240
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
34-239 3.61e-11

RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle 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: 438090  Cd Length: 451  Bit Score: 64.48  E-value: 3.61e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARS-------PYLVKGLTPTERARKLA----P 98
Cdd:cd23240   100 DAFLKTFVKAEkinfTAKPDPAPRVIQPRDPRYNIEVGKYLKPYEHHLYRAidvvwggPTVLKGYTVEELGNIMHnhwsQ 179
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLF--PLFDEAL--HLLTSMVGIGTLG-ATYTVEGTRASGDAH 173
Cdd:cd23240   180 FQKPCAVGFDMKRFDQHVS------VDALRFEHSVYNRSFcsPELARLLewQLLNSGVGHASDGfIRYKVDGCRMSGDVN 253
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1132350693 174 TSIANGIINRFVIWACLRHLPCPWysFHEGDDGVIFIDKPHAAQAVECLQFAFTLGFrlKCVVPNP 239
Cdd:cd23240   254 TALGNCLLACLITKYLLKGIRCRL--INNGDDCVLFFEAPDLAAVTERLAHWLDFGF--QCVVEEP 315
Aureusvirus_RdRp cd23243
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
1-212 7.18e-11

RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093  Cd Length: 488  Bit Score: 63.70  E-value: 7.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   1 MPFDQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLE-- 74
Cdd:cd23243    88 MTRSEFVASYSGSRRATYERARLSLDVLPCTRSDAYLKTFVKAEkiniTLKPDPAPRVIQPRDPRYNVEVGRYLKPLEpr 167
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  75 --KAAAR---SPYLVKGLTpTER-----ARKLAPFRRGAVIETDFSRFDMTVSADIIT---TVERMAFRQAYPKglfplf 141
Cdd:cd23243   168 lmKAIDKlwgEKTAIKGYT-VEKvgeilHEKSLRFREPVFVGLDASRFDQHCSRQALEwehSVYNAIFRDPYLA------ 240
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1132350693 142 dEALHLLTSMVGIGTLG---ATYTVEGTRASGDAHTSIANgiinrFVIWACLRHLPCPWYSFHE-----GDDGVIFIDK 212
Cdd:cd23243   241 -ELLTWQIDNVGTAYLKdgfVRYRVDGCRMSGDMNTSMGN-----YLIMSCLVYQFCKEVGLDAslancGDDCVLFLEK 313
Gammacarmovirus_RdRp cd23242
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
4-227 1.89e-09

RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic 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: 438092  Cd Length: 476  Bit Score: 58.99  E-value: 1.89e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   4 DQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTETSP--KGTDP--RNISPRQPQFLAVLGPHVASLEKAAAR 79
Cdd:cd23242    80 DRFVDFYHGRRRTIYEQAVKSLEGLAVQRKDAYLKTFVKAEKINitRKPDPapRVIQPRNVRYNVEVGRYLRRFEHHLYR 159
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  80 -------SPYLVKGLTpTERARKLA-----PFRRGAVIETDFSRFDMTVSADIITtVERMAFRQAYpkGLFPLFDEALHL 147
Cdd:cd23242   160 gideiwgGPTVIKGYT-VEQIGNIAedawdSFVSPVAIGFDMKRFDQHVSRDALE-WEHSVYLDAF--CNDPYLAELLSW 235
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 148 LTSMVGIGTLG---ATYTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAqAVEC--- 221
Cdd:cd23242   236 QLENKGVGYASdgsIKYKVDGCRMSGDMNTAMGNCLLACAITWDFFKGRGIKARLLNNGDDCVVITEKECAA-AVVAgmv 314

                  ....*....
gi 1132350693 222 ---LQFAFT 227
Cdd:cd23242   315 rhwRRFGFQ 323
Carmotetraviridae_RdRp cd23205
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
35-227 2.22e-09

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal 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: 438055  Cd Length: 268  Bit Score: 57.72  E-value: 2.22e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  35 AVMKVFIKTETSP---KGTDPRNISPRQPQFLAVLGPHVASLEKA-------AARSPYLVKGLTPTERARKL----APFR 100
Cdd:cd23205     1 ATIKAFVKMEKLQillKHGDPRLIQSRGTVFHLLFSTMTKPLEHAlmhvsdpETNLPMVAKGRNLDQRANLLqrmwHLYE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 101 RGAVIETDFSRFDMTVSADIITTVERMaFRQAYPKglfPLFDEALHLLTSMVGIGTLGATYTVEGTRASGDAHTSIANGI 180
Cdd:cd23205    81 RPVSISFDLSRWDMHVQVPLLKRVLEI-YSQHVTC---PLLLDMCQNLLKNVCYTNKGIRYHVDGGIMSGDMTTGLGNCI 156
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*..
gi 1132350693 181 INRFVIWACLRHLPCpwysfhEGDDGVIFIDKPHAAQAVECLQFAFT 227
Cdd:cd23205   157 AVLVIVMSFRLSILD------DGDDHVIICEKSHTWICERVLPLWWT 197
Regressovirinae_RdRp cd23235
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
34-226 3.25e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. 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: 438085 [Multi-domain]  Cd Length: 472  Bit Score: 55.31  E-value: 3.25e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE---TSPKGTDPRNISPRQPQFLAVLGPHVASLEKAAARSPYLV-------KGLTPTERARKLA----PF 99
Cdd:cd23235    86 DSKVRAFIKVEkleCDKKDPVPRTIQPRSKRYNLCIGQYLRLNEKRMLDAIDAVfgektvlSGLDNKAQGRAIAkkwsKY 165
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 100 RRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFPlFDEALHLL---------TSMVGIGTLgATYTVEGTRASG 170
Cdd:cd23235   166 ESPIGIGLDASRFDQHCS------KDALKFEHSFYRECFP-DDKTLEDLldwqlenegSALMPTGEL-VKYRTKGCRMSG 237
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1132350693 171 DAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVECLQFAF 226
Cdd:cd23235   238 DINTGLGNKILMCSMVHAYLKEVGVNASLANNGDDCVLFCEKGDFNRINDSLREWF 293
Panicovirus_RdRp cd23238
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of ...
3-208 7.54e-08

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Panicovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Viruses in Panicovirus are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. Their host range is restricted to monocotyledonous plants. There are 3 species in this genus: Cocksfoot mild mosaic virus, Panicum mosaic virus, and Thin paspalum asymptomatic virus. The virus typically forms a systemic mosaic. 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: 438088 [Multi-domain]  Cd Length: 692  Bit Score: 54.52  E-value: 7.54e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693   3 FDQWVSRFNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGPHVASLE---- 74
Cdd:cd23238   274 DEKFLSYYTGPQLTTYSKAVISLSERPVAVQDSYLKTFIKAEklnlTLKPDPCPRVIQPRHPRYNVELGKYLKHIEhpiy 353
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  75 KAAAR---SPYLVKGLT----PTERARKLAPFRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLFPlFDEALHL 147
Cdd:cd23238   354 KAIDKlwgGKTIFKGMNveamGAEIHKKMCKFSRPCAIGFDASRFDQHVS------VEALRFEHSIYKSIHG-YPELLNL 426
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1132350693 148 LT--SMVGIGTLGAT-----YTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVI 208
Cdd:cd23238   427 LLkwQIHNQGTAHANdgffkYSVDGKRMSGDMNTSLGNCILASLISKDLVDSLGIDAQLVNNGDDNVL 494
Betanecrovirus_RdRp cd23244
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
34-233 2.06e-06

RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. 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: 438094  Cd Length: 500  Bit Score: 49.51  E-value: 2.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  34 DAVMKVFIKTE----TSPKGTDPRNISPRQPQFLAVLGP---HVASLEKAAARSPY----LVKGLTPTERARKLA----P 98
Cdd:cd23244   118 DAWLSTFVKAEklniTAKPDPAPRVIQPRDPRYNVEVGRflrHAEEHLFDAINRVFggrtIFKGLNADQAGMEMKamwdS 197
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  99 FRRGAVIETDFSRFDMTVSADIITTVERM---AFRQAYPKGLFPLFDEALH---LLTSMVGigtlGATYTVEGTRASGDA 172
Cdd:cd23244   198 FDDPVGIGMDASRFDQHISKEALEFEHKMwlsMFPGSDRKELARLLGMQIHnrgLARCPDG----EIRYTVEGCRMSGDM 273
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1132350693 173 HTSIANGIINRFVIWACLRHLPCPWYSF-HEGDDGVIFIDKPHAAQAVECL-QFAFTLGFRLK 233
Cdd:cd23244   274 NTSSGNCYIMCATVHNWCSRLGVKHFRLaNNGDDCMLVVERKDEARVRQGLiEYYRELGFTMK 336
RdRP_1 pfam00680
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ...
32-248 2.46e-06

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.


Pssm-ID: 425815  Cd Length: 450  Bit Score: 49.33  E-value: 2.46e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  32 PSDAVMKVFIKTETSPKG----TDPRNISPRQPQFLAVLG---PHVASLEKAAARSPYLVKGLTP-----TERARKLAPF 99
Cdd:pfam00680 145 PLKLVYQTCLKDELRPLEkvekGKTRLVWGEPVEYLLLERaffDPFNQAFMLNNGFHPIQVGINPfdrgwPRLLRRLARF 224
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 100 RRgAVIETDFSRFDMTVSADIIttveRMAFRQAYPKGLFP-LFDEALHLLTSMVG--IGTLGAT-YTVEGTRASGDAHTS 175
Cdd:pfam00680 225 GD-YVYELDYSGFDSSVPPWLI----RFAFEILRELLGFPsNVKEWRAILELLIYtpIALPNGTvFKKTGGLPSGSPFTS 299
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 176 IANGIINRFVIWACL------RHLPCP-----WYSFHEGDDGVIFIDK------PHAAQAVECLQFAFTlgfRLKCVVP- 237
Cdd:pfam00680 300 IINSIVNYLLILYALlkslenDGPRVCnldkyFDFFTYGDDSLVAVSPdfdpvlDRLSPHLKELGLTIT---PAKKTFPv 376
                         250
                  ....*....|..
gi 1132350693 238 -NPMGSATFCGR 248
Cdd:pfam00680 377 sRELEEVSFLKR 388
Luteovirus_RdRp cd23233
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
10-212 4.92e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. 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: 438083  Cd Length: 407  Bit Score: 48.19  E-value: 4.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  10 FNPSRQTQLREGLIQAQRQGLSPSDAVMKVFIKTETS--PKGTDPRNISPRQPQFLAVLGPHVASLEK-------AAARS 80
Cdd:cd23233     5 YSSGKRSQYFKAVLSLKRKPVEQKDANVTAFLKMEKHwmCKAIAPRLICPRSKRYNVELGRRLKFNEKkfmhaidSVFGS 84
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  81 PYLVKGLTPTER----ARKLAPFRRGAVIETDFSRFDMTVSadiittVERMAFRQAYPKGLF--PLFDEALHLLTS---M 151
Cdd:cd23233    85 PTVLSGYDNFKVgriiAKKWQKFANPVAIGVDASRFDQHVS------EQALKWEHSIYNGIFgdPELAELLEWQLDnkiK 158
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1132350693 152 VGIGTLGATYTVEGTRASGDAHTSIANGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDK 212
Cdd:cd23233   159 LFVEDKMLRFKVKGHRMSGDINTSMGNKLIMCGMMHAYFKELGVEAELCNNGDDCVIICER 219
RdRP_2 pfam00978
RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...
61-280 2.83e-05

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: 46.09  E-value: 2.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  61 QFLAVLGPHVaslekaaarspYLVKGLTPTERARKLAPF-RRGAVIETDFSRFDMtvSAD-IITTVERMAFRQAypkGLF 138
Cdd:pfam00978 180 RLLYVLKPKI-----------VFPTGMTSSLIAEHFEFLdASEDFLEIDFSKFDK--SQGeLHLLVQLEILKLL---GLD 243
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 139 PLF---DEALHlLTSMVGIGTLGATYTVEGTRASGDAHTSIANGIINRFVIWACLRhLPCPWYSFHEGDDGVIFIDKPha 215
Cdd:pfam00978 244 PELadlWFKFH-RQSYIKDRKNGVGFSVDYQRKSGDANTYLGNTLVTMAMLASVYD-LEKIDCAAFSGDDSLIFSPKP-- 319
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1132350693 216 aqaVECLQFAFTLGFRLKCVVPNPmGSATFCGRYTCLDcGREHC---DVIRTLTKFHISHRPGSAQSL 280
Cdd:pfam00978 320 ---IEDPASRFATLFNMEAKVFDP-SVPYFCSKFLLEV-DGGAFfvpDPLKLLQKLGKKKIPDDEQHL 382
ps-ssRNAv_Hepelivirales_RdRp cd23209
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...
40-211 1.68e-03

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: 39.01  E-value: 1.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693  40 FIKTETSPKGTDPRNISPRQPQFLAVLGPHVASLEK---AAARSPYLV-KGLTPTERARKLAPFRRGAVIETDFSRFDMT 115
Cdd:cd23209    13 FTDCEPVAHGKAGQGISAWSKELCFVFGPWFRALEKilrRALKPNVLYaNGHEAEPFVDKINQAHSAVFIENDFTEFDST 92
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 116 VsadiiTTVERMAFRQAYPKGLFPLFdeALHLLTSMVGIGTLGATY-TVEGT--RASGDAHTSIANGIINRFVIWACLRh 192
Cdd:cd23209    93 Q-----NLFSLLVELEILEACGMPPA--LAELYRALRAKWTLQAREgSLEGTckKTSGEPGTLLHNTIWNMAVMMHMVR- 164
                         170
                  ....*....|....*....
gi 1132350693 193 LPCPWYSFHEGDDGVIFID 211
Cdd:cd23209   165 GGVRKAAAFKGDDSVVCCS 183
ps-ssRNA_Picornaviridae cd23193
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ...
108-214 2.02e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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: 438043  Cd Length: 345  Bit Score: 39.84  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 108 DFSRFDMTVSADIIT-TVERMAFRQAYPKGLFPLFDealHLLTS--MVGigtlGATYTVEGTRASGDAHTSIANGIINRF 184
Cdd:cd23193   140 DYSGFDASLSSQLFEaAVEVLAECHGDPELVLRYLE---PIINSkhVVG----DERYTVEGGMPSGCPCTSILNSICNNL 212
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1132350693 185 VIWACLRHLPCPWYSFHE----GDDGVIFIDKPH 214
Cdd:cd23193   213 VVRYALLETGKFDPDEYYilayGDDVLVSTDEPI 246
RdRP_4 pfam02123
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ...
107-233 3.92e-03

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: 39.37  E-value: 3.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1132350693 107 TDFSRFDMTVSadiittveRMAFRQAYPKgLFPLFDEALH-----LLTSM----VGIGTLGATYTVEGTRASGDAHTSIA 177
Cdd:pfam02123 302 LDYDDFNSQHS--------TESMRAVFER-LRRRLPDEPAeaadwLVCSMdsmyQLSDGTLLAQRVPGTLKSGHRATTFI 372
                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1132350693 178 NGIINRFVIWACLRHLPCPWYSFHEGDDGVIFIDKPHAAQAVecLQFAFTLGFRLK 233
Cdd:pfam02123 373 NSVLNCAYAELAGAPWADVPTSIHMGDDVLEGLRTPADATSL--LDKYARLGFKVN 426
 
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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