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 270303814   1 SYGFQYSPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEARKAITSLNERLYCGGPMFNS 80
Cdd:cd23202  177 AYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNS 256

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270303814  81 RNQSCGYRRCRASGVLTTSLGNTLTCYLKAQAACRAAKLKDYDMLVCGDDLVVISESAGVTEDASALRAFTDAM 154
Cdd:cd23202  257 KGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAM 330

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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 270303814   1 SYGFQYSPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEARKAITSLNERLYCGGPMFNS 80
Cdd:cd23202  177 AYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNS 256

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270303814  81 RNQSCGYRRCRASGVLTTSLGNTLTCYLKAQAACRAAKLKDYDMLVCGDDLVVISESAGVTEDASALRAFTDAM 154
Cdd:cd23202  257 KGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAM 330

RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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 270303814   1 SYGFQYSPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEARKAITSLNERLYCGGPMFNS 80
Cdd:cd23202  177 AYGFQYSPAQRVEFLLKMWRSKKTPMGFSYDTRCFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNS 256

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270303814  81 RNQSCGYRRCRASGVLTTSLGNTLTCYLKAQAACRAAKLKDYDMLVCGDDLVVISESAGVTEDASALRAFTDAM 154
Cdd:cd23202  257 KGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAFTEAM 330

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 270303814    1 SYGFQYSPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEarKAITSLNERLYCGGPMFNS 80
Cdd:pfam00998 178 TVLKGYTPEQRGEILLKKWDSFKKPVAIGLDASRFDQHVSVEALRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYAS 255

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270303814   81 RNQ-SCGYRRCRASGVLTTSLGNTLTCYLKAQAACRAAKlKDYDMLVCGDDLVVISESAGVTEDASAL-RAFTD 152
Cdd:pfam00998 256 DGQiKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDDCVVICESADLDEVKEALtEAFAR 328

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270303814   2 YGFQYSPKQR-VERLLQMWRAKrTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEARKAITSLNERLYCGGPMFNs 80
Cdd:cd01699   73 IAVGINPYSRdWTILANKLRSF-SPVAIALDYSRFDSSLSPQLLEAEHSIYNALYDDDDELERRNLLRSLTNNSLHIGF- 150

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 270303814  81 rNQSCGYRRCRASGVLTTSLGNTLTCYLKAQAACRAAK----LKDYDMLVCGDDLVVISESAGVTEDASALRAF 150
Cdd:cd01699  151 -NEVYKVRGGRPSGDPLTSIGNSIINCILVRYAFRKLGgksfFKNVRLLNYGDDCLLSVEKADDKFNLETLAEW 223

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
                 ....*....|....*....|....*....|....*....|....*....|..
gi 270303814  90 CRASGVLTTSLGNTLTCYLKAQAACRAAK-----LKDYDMLVCGDDLVVISE 136
Cdd:cd23167   22 GQPSGSPNTSADNSLINLLLARLALRKACgraefLNSVGILVYGDDSLVSVP 73

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 270303814  17 QMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIY-QCCQLDPEARKAIT-SLNERLYCggpmfNSRNQSCGYRR--CRA 92
Cdd:cd23242  185 DAWDSFVSPVAIGFDMKRFDQHVSRDALEWEHSVYlDAFCNDPYLAELLSwQLENKGVG-----YASDGSIKYKVdgCRM 259

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 270303814  93 SGVLTTSLGNTLTCYLKAQAACRAAKLKdYDMLVCGDDLVVISES 137
Cdd:cd23242  260 SGDMNTAMGNCLLACAITWDFFKGRGIK-ARLLNNGDDCVVITEK 303

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270303814   6 YSPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCC-QLDPEARKAitsLNERLYCGGPMFNSrNQS 84
Cdd:cd23239  184 YTVEEVAQHISSAWDQFQIPVAIGFDMSRFDQHVSVPALQFEHSCYLACfPGDRHLAQL---LSWQLKNFGVGFAS-NGM 259

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 270303814  85 CGYRR--CRASGVLTTSLGNTLTCYLKAQAACRAAKLKdydMLVCGDDLVVISES 137
Cdd:cd23239  260 IRYKKegCRMSGDMNTALGNCLLACLITKHLMKGVNCR---LINNGDDCVLICER 311

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 270303814  10 QRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEESIYQCCQLDPEArkaitslneRLYCGGPMFNSRNQSCGYRR 89
Cdd:cd23205   67 QRANLLQRMWHLYERPVSISFDLSRWDMHVQVPLLKRVLEIYSQHVTCPLL---------LDMCQNLLKNVCYTNKGIRY 137

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 270303814  90 C----RASGVLTTSLGNtltCYLKAQAA--CRAAKLKDydmlvcGDDLVVISESAGVTEDASALRAFTDAM 154
Cdd:cd23205  138 HvdggIMSGDMTTGLGN---CIAVLVIVmsFRLSILDD------GDDHVIICEKSHTWICERVLPLWWTAM 199

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 270303814   7 SPKQRVERLLQMWRAKRTPMGFSYDTRCFDSTVTERDIRTEE----SIYQCCQLDPEARKAITSLNERLYCGGPMFNSRN 82
Cdd:cd23244  183 NADQAGMEMKAMWDSFDDPVGIGMDASRFDQHISKEALEFEHkmwlSMFPGSDRKELARLLGMQIHNRGLARCPDGEIRY 262

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 270303814  83 QSCGyrrCRASGVLTTSLGNtltCYLKAQAA---CRAAKLKDYDMLVCGDDLVVISES 137
Cdd:cd23244  263 TVEG---CRMSGDMNTSSGN---CYIMCATVhnwCSRLGVKHFRLANNGDDCMLVVER 314