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 89213756   1 EISAALLGLPCAEDYRALRAGSYCTLRELGTTETGCERTSGEPATLLHNTTVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 80
Cdd:cd23260 102 EISASLLGLPSAEDYRALRAGSYCLLRDLASTETGCERTSGEPATLLHNTLVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 181

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89213756  81 PEGARSAALKWTPAEVGLFGFHIPVKHVSTPTPSFCGHVGTAAGLFHDVMHQAIKVLCRRFDPDVLEEQQVALLDR 156
Cdd:cd23260 182 PEGARRAALRWTPAELGLFGFHIPVKHVATATPSFCGHVGSAAGLFHDVLHLAIKLLCRRFDPDVLEEQQVAMLDR 257

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Matonaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Matonaviridae, order Hepelivirales. Members of the family Matonaviridae have a (+)ssRNA genome enclosed by an icosahedral capsid. Matonaviridae has a single genus, Rubivirus, which contains three species: Rubivirus rubella (commonly called rubella virus), Rubivirus ruteetense (commonly called ruhugu virus), and Rubivirus strelense (commonly called rustrela virus). Rubella virus (RuV) is the etiologic agent of the disease rubella (also called German measles). RuV is transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome (severe congenital birth defects, miscarriage, and stillbirth) when infection occurs during the first trimester of pregnancy. In vitro studies with cell lines showed that RuV has an apoptotic effect on certain cell types; there is evidence for a p53-dependent mechanism. 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 89213756   1 EISAALLGLPCAEDYRALRAGSYCTLRELGTTETGCERTSGEPATLLHNTTVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 80
Cdd:cd23260 102 EISASLLGLPSAEDYRALRAGSYCLLRDLASTETGCERTSGEPATLLHNTLVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 181

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89213756  81 PEGARSAALKWTPAEVGLFGFHIPVKHVSTPTPSFCGHVGTAAGLFHDVMHQAIKVLCRRFDPDVLEEQQVALLDR 156
Cdd:cd23260 182 PEGARRAALRWTPAELGLFGFHIPVKHVATATPSFCGHVGSAAGLFHDVLHLAIKLLCRRFDPDVLEEQQVAMLDR 257

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Matonaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Matonaviridae, order Hepelivirales. Members of the family Matonaviridae have a (+)ssRNA genome enclosed by an icosahedral capsid. Matonaviridae has a single genus, Rubivirus, which contains three species: Rubivirus rubella (commonly called rubella virus), Rubivirus ruteetense (commonly called ruhugu virus), and Rubivirus strelense (commonly called rustrela virus). Rubella virus (RuV) is the etiologic agent of the disease rubella (also called German measles). RuV is transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome (severe congenital birth defects, miscarriage, and stillbirth) when infection occurs during the first trimester of pregnancy. In vitro studies with cell lines showed that RuV has an apoptotic effect on certain cell types; there is evidence for a p53-dependent mechanism. 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 89213756   1 EISAALLGLPCAEDYRALRAGSYCTLRELGTTETGCERTSGEPATLLHNTTVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 80
Cdd:cd23260 102 EISASLLGLPSAEDYRALRAGSYCLLRDLASTETGCERTSGEPATLLHNTLVAMCMAMRMVPKGVRWAGIFQGDDMVIFL 181

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 89213756  81 PEGARSAALKWTPAEVGLFGFHIPVKHVSTPTPSFCGHVGTAAGLFHDVMHQAIKVLCRRFDPDVLEEQQVALLDR 156
Cdd:cd23260 182 PEGARRAALRWTPAELGLFGFHIPVKHVATATPSFCGHVGSAAGLFHDVLHLAIKLLCRRFDPDVLEEQQVAMLDR 257

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89213756    22 SYCTLRELG-TTETGCERTSGEPATLLHNTTVAMCMAMRMVPKGVRWAGIFQGDDMVIFLPEGARSAALKWTpaevGLFG 100
Cdd:pfam00978 257 SYIKDRKNGvGFSVDYQRKSGDANTYLGNTLVTMAMLASVYDLEKIDCAAFSGDDSLIFSPKPIEDPASRFA----TLFN 332

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89213756   101 FHipVKHVSTPTPSFCG----HVGTAAGLFHDvmhqAIKVL------CRRFDPDVLEEQQVALLDRLRG-----VYAALP 165
Cdd:pfam00978 333 ME--AKVFDPSVPYFCSkfllEVDGGAFFVPD----PLKLLqklgkkKIPDDEQHLDEIFTSLCDLTKSfnddcVVLELL 406

                         170       180
                  ....*....|....*....|..
gi 89213756   166 DTVAANAAYYDYSAERVLAIVR 187
Cdd:pfam00978 407 DLAVARYYKYAPEGYAALCALH 428

RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89213756   9 LPCAEDYRALRAGSYCTLRELGTTetgceRTSGEPATLLHNT--TVAMCMAMRMVPKGVrwAGIFQGDDMVIFLPEGARS 86
Cdd:cd23249 184 LDLIEAYLEMKASITSHLGPLAIM-----RFSGEVWTYLFNTlgNMAYTAAKYEVPPPV--PRVYGGDDKSINSRITVRP 256

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 89213756  87 AALKWtpaevgLFGFHIPVKHVSTPTPSFCGHVGTAAGLFHD 128
Cdd:cd23249 257 GWSQL------VGQFNLVEKPVVTYEPTFCGWRITPGGIVKD 292

RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 89213756  14 DYRALRAGSYCTLrelgTTETGCERTSGEPATLLHNTTVAMCMAMrMVPKGVRWAGI-FQGDDMVIF----LPEGARSAA 88
Cdd:cd23253 128 EYFSCRATSDSGV----SLELGAQRRTGSPNTWLGNTLVTLGILS-SSYDLDDIDLLlVSGDDSLIFskkpLPNKANEIN 202

                        90       100
                ....*....|....*....|....*....
gi 89213756  89 LKwtpaevglFGFHipVKHVSTPTPSFCG 117
Cdd:cd23253 203 LD--------FGFE--AKFIENSVPYFCS 221