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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047390988   2 QCCNLEPEARKVISSLTERLYCGGPTLNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPDFLVCGDDL 81
Cdd:cd23202   228 QCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDL 307

                  ...
gi 1047390988  82 VVV 84
Cdd:cd23202   308 VVI 310

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047390988   2 QCCNLEPEARKVISSLTERLYCGGPTLNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPDFLVCGDDL 81
Cdd:cd23202   228 QCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDL 307

                  ...
gi 1047390988  82 VVV 84
Cdd:cd23202   308 VVI 310

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047390988   2 QCCNLEPEARKVISSLTERLYCGGPTLNSKGAQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGLRNPDFLVCGDDL 81
Cdd:cd23202   228 QCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAACRAAGLKDPTMLVCGDDL 307

                  ...
gi 1047390988  82 VVV 84
Cdd:cd23202   308 VVI 310

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

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047390988   2 QCCNLEPEarKVISSLTERLYCGGPTLNSKG-AQCGYRRCRASGVLPTSFGNTITCYIKATAAAKAAGlRNPDFLVCGDD 80
Cdd:pfam00998 229 LAAFLGPE--ELIRLLTWQLYNGGPMYASDGqIKYGVRGCRMSGDMNTSLGNCLLMCLKVHAACKALG-IDARLLNNGDD 305

                  ....
gi 1047390988  81 LVVV 84
Cdd:pfam00998 306 CVVI 309

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1047390988   5 NLEPEARKVISSLTERLYcggPTLNSKgaQCGYRRCRASGVLPTSFGNTITCYIK----ATAAAKAAGLRNPDFLVCGDD 80
Cdd:cd01699   129 DDELERRNLLRSLTNNSL---HIGFNE--VYKVRGGRPSGDPLTSIGNSIINCILvryaFRKLGGKSFFKNVRLLNYGDD 203

                  ...
gi 1047390988  81 LVV 83
Cdd:cd01699   204 CLL 206