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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029    1 DVFERISFCQTSPVLTSGGWVMCRHPRV-MAKDLTYI----GPKSALSlWLDAIGQCGSALCDGVPILSAFY--ASLHSG 73
Cdd:pfam00998 340 YELELIEFCQSNPVFDGGKYGMVRNPLTsDSKDPLSRasweTATPAKS-WLGAIGECGLSLWGGVPVLQHFYscLLRNGG 418

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 953520029   74 VTRERHRVRNSMLYSCGMTRLA--EGLTYRGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:pfam00998 419 LEKAVSFEMYGKVYSDSGFRLHglGAGSRHSYEPTEEARVSFWLAFGITPDEQWA 473

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029    1 DVFERISFCQTSPVLTSGGWVMCRHPRV-MAKDLTYI----GPKSALSlWLDAIGQCGSALCDGVPILSAFY--ASLHSG 73
Cdd:pfam00998 340 YELELIEFCQSNPVFDGGKYGMVRNPLTsDSKDPLSRasweTATPAKS-WLGAIGECGLSLWGGVPVLQHFYscLLRNGG 418

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 953520029   74 VTRERHRVRNSMLYSCGMTRLA--EGLTYRGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:pfam00998 419 LEKAVSFEMYGKVYSDSGFRLHglGAGSRHSYEPTEEARVSFWLAFGITPDEQWA 473

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029    1 DVFERISFCQTSPVLTSGGWVMCRHPRV-MAKDLTYI----GPKSALSlWLDAIGQCGSALCDGVPILSAFY--ASLHSG 73
Cdd:pfam00998 340 YELELIEFCQSNPVFDGGKYGMVRNPLTsDSKDPLSRasweTATPAKS-WLGAIGECGLSLWGGVPVLQHFYscLLRNGG 418

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 953520029   74 VTRERHRVRNSMLYSCGMTRLA--EGLTYRGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:pfam00998 419 LEKAVSFEMYGKVYSDSGFRLHglGAGSRHSYEPTEEARVSFWLAFGITPDEQWA 473

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   1 DVFERISFCQTSPVLTSGGWVMCRHPRVMAKDLTYIGPKSALSLWLDAIGQCGSALCDGVPILSAFYASLHSGVTRERhR 80
Cdd:cd23234  334 YTLERVEFCQTQPVFDGTKWRMVRHISSIAKDCCSVINWEQLPGWWRAIGECGLAVAGGIPIHNSFYRWLCRAGGSNG-K 412

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 953520029  81 VRNSMLYSCGMTRLAEGLTYRG--LSVDDASRLSFARAFGILPDDQLA 126
Cdd:cd23234  413 VEKHPLWKNEGLNWYRMGMDLSheVTVTDEARLSFAAAFGISPPMQVA 460

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   1 DVFERISFCQTSPVLTSGGWVMCRHPRV-MAKDLTYIGPKSAL---SLWLDAIGQCGSALCDGVPILSAFYASLHSGVTR 76
Cdd:cd23242  331 YILEHIEFCQMRPVYDGSKYTMVRNPLVsLSKDSYSVGPWNNIkhaAKWVNAVGQCGLSLTGGIPVLQSYYNMLIRNTPG 410

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 953520029  77 ERHRVRNSMLYSCGMTRLAEGLTYRGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:cd23242  411 GNSLILRDVSFASGFYELALLGNRKDGPVSEEARFSFYLAFGITPDAQRA 460

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   1 DVFERISFCQTSPVLTSGGWVMCRH-PRVMAKD---LTYIGPKSALSLWLDAIGQCGSALCDGVPILSAFYA--SLHSGV 74
Cdd:cd23244  342 DVLERLEFCQTRPVLVDGAYRMVRNlHQGMSKDlhsLHDLGSRKAAEAWVSAVGSGGRVMNDGVPVLKSFFKqfPLNSGP 421

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 953520029  75 ---TRERHRVRNSMLYSCGMTRlaeglTYRGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:cd23244  422 ktkSDMSIALQEDWKYKFNRTG-----CFQDLTPTPQSRYSFWLAFGVLPDEQIA 471

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   2 VFERISFCQTSPVLTSGGWVMCRHPRV-MAKDLTYIGPKSALSL---WLDAIGQCGSALCDGVPILSAFYASL-HSGVtr 76
Cdd:cd23241  340 ELEKIEFCQMQPVLVGDGYKMVRNPRIsLSKDAHSTTPFETVKLareWAYSVGLGGLSLTSGIPVVQEFYQCLlRNGK-- 417

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 953520029  77 eRHRVRNSMLYSCGMTRLAEGLTYRGL--SVDDASRLSFARAFGILPDDQLA 126
Cdd:cd23241  418 -KPTKEKKMRHFYGDYYWKWVKQHRGKytPVTEESRHSFHLAFGISPDQQLA 468

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   4 ERISFCQTSPVLTSGGWVMCRHPRVMAKD----LTYIGPKSALSlWLDAIGQCGSALCDGVPILSAFYASLH--SG---V 74
Cdd:cd23233  249 EKLEFCQSKPVCINGKYRMVRRPDSISKDshslLSMLNQEDVKS-FMSATAQCGLVLNSGVPILEAFHRCLYrsSGykkV 327

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 953520029  75 TRErhRVRNSMLYSCGmTRLAEGLTYRGLSVDDASRLSFARAFGILPDDQ 124
Cdd:cd23233  328 SEE--YIKNVISYGTD-ERLQGRRTRVEEPVTMENRLSYWESFGVDPQTQ 374

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 953520029   3 FERISFCQTSPVLTSGGWVMCRHPRV-MAKD---LTYIGPKSALSLWLDAIGQCGSALCDGVPILSAFYASLHSGVTRER 78
Cdd:cd23236  341 LEEVEFCQAHPVQFQGGWKMVRNVRTaMSKDvhcVNNIRDLATRRAWSNAQHHGGLALSAGIPVVEKFYSRFTLYDVPKK 420

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 953520029  79 HRvRNSMLYSCGMTRLAEGltyrGLSVDDASRLSFARAFGILPDDQLA 126
Cdd:cd23236  421 HQ-RIDTVTNVHKWRGSGG----SYVVTPESRASFWAAFGLTGDEQLA 463