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 685438330   1 CFDSTVTERDIRTENDIYQACQLDPVARKAVSSLTERLYVGGPMVNSKGQSCGYRRCRASGVLPTSMGNTMTCYLKAQAA 80
Cdd:cd23202  210 CFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAA 289

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 685438330  81 CRAANIKDCDMLVCGDDLVVICESAGVQEDTASLRAF 117
Cdd:cd23202  290 CRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAF 326

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 685438330   1 CFDSTVTERDIRTENDIYQACQLDPVARKAVSSLTERLYVGGPMVNSKGQSCGYRRCRASGVLPTSMGNTMTCYLKAQAA 80
Cdd:cd23202  210 CFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAA 289

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 685438330  81 CRAANIKDCDMLVCGDDLVVICESAGVQEDTASLRAF 117
Cdd:cd23202  290 CRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAF 326

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 685438330   1 CFDSTVTERDIRTENDIYQACQLDPVARKAVSSLTERLYVGGPMVNSKGQSCGYRRCRASGVLPTSMGNTMTCYLKAQAA 80
Cdd:cd23202  210 CFDSTVTERDIRTEESIYQCCDLDPEARKAIRSLTERLYVGGPMTNSKGQSCGYRRCRASGVFTTSSGNTLTCYLKASAA 289

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 685438330  81 CRAANIKDCDMLVCGDDLVVICESAGVQEDTASLRAF 117
Cdd:cd23202  290 CRAAGLKDPTMLVCGDDLVVIAESAGVEEDAAALRAF 326

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 685438330    1 CFDSTVTERDIRTENDIYQACQLDPVarKAVSSLTERLYVGGPMVNSKGQ-SCGYRRCRASGVLPTSMGNTMTCYLKAQA 79
Cdd:pfam00998 211 RFDQHVSVEALRFEHSIYLAAFLGPE--ELIRLLTWQLYNGGPMYASDGQiKYGVRGCRMSGDMNTSLGNCLLMCLKVHA 288

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 685438330   80 ACRAANIkDCDMLVCGDDLVVICESAGVQEDTASL-RAF 117
Cdd:pfam00998 289 ACKALGI-DARLLNNGDDCVVICESADLDEVKEALtEAF 326

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 685438330   1 CFDSTVTERDIRTENDIYQACQLDP---VARKAVSSLTERLYvggPMVNskGQSCGYRRCRASGVLPTSMGNTMTCYLKA 77
Cdd:cd01699  105 RFDSSLSPQLLEAEHSIYNALYDDDdelERRNLLRSLTNNSL---HIGF--NEVYKVRGGRPSGDPLTSIGNSIINCILV 179

                         90       100       110
                 ....*....|....*....|....*....|..
gi 685438330  78 QAACRAA----NIKDCDMLVCGDDLVVICESA 105
Cdd:cd01699  180 RYAFRKLggksFFKNVRLLNYGDDCLLSVEKA 211

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 685438330  57 CRASGVLPTSMGNTMTCYLKAQAACRAANI-----KDCDMLVCGDDLVVICE 103
Cdd:cd23167   22 GQPSGSPNTSADNSLINLLLARLALRKACGraeflNSVGILVYGDDSLVSVP 73

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 685438330   2 FDSTVTERDIRTENDIYQACQLDPVARKAVSSLTE---RLYVGGPMVNSKgqscgYRRCRASGVLPTSMGNTMTCYLKAQ 78
Cdd:cd23233  120 FDQHVSEQALKWEHSIYNGIFGDPELAELLEWQLDnkiKLFVEDKMLRFK-----VKGHRMSGDINTSMGNKLIMCGMMH 194

                         90       100
                 ....*....|....*....|....*
gi 685438330  79 AACRAANIKdCDMLVCGDDLVVICE 103
Cdd:cd23233  195 AYFKELGVE-AELCNNGDDCVIICE 218

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 685438330   2 FDSTVTERDIRTENDIYQAcqLDPvARKAVSSLTE-RLYVGGPMVNSKGqSCGYRR--CRASGVLPTSMGNTMTCYLKAQ 78
Cdd:cd23236  210 FDQHCSVEALQFEHSFYRA--MYP-GNKLLSKLLEwQLHNKGKGYVPDG-TITYRKegCRMSGDINTSLGNYLLMCAMVY 285

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 685438330  79 AACRAANIKDCDMLVCGDDLVVICESAGVQEDTASL 114
Cdd:cd23236  286 GYMRHLGINEFSLANCGDDCVLIVERRNLKQVQGTL 321