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 1885452971   1 YDLRMPASLILAAFKCMINIAEECGDYHPSEIFIMKGIATEIAFACVSYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMR 80
Cdd:cd23195    87 YDKRMSAQLILAAFKILIDIAAKSGGYSEEDLKIMRGIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIVNSLYMR 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  81 SAYYHLWPAElgPIEDFRRNASVMTYGDDVSGSIRKGHDWFNHISYAQFLAERDMVFTMPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23195   167 YAYYSLYPEK--EVPPFRDVVALMTYGDDNIMSVSPGYPWFNHTSIAEFLAKIGIKYTMADKEAESVPFIHISEADFLKR 244

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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 1885452971   1 YDLRMPASLILAAFKCMINIAEECGDYHPSEIFIMKGIATEIAFACVSYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMR 80
Cdd:cd23195    87 YDKRMSAQLILAAFKILIDIAAKSGGYSEEDLKIMRGIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIVNSLYMR 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  81 SAYYHLWPAElgPIEDFRRNASVMTYGDDVSGSIRKGHDWFNHISYAQFLAERDMVFTMPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23195   167 YAYYSLYPEK--EVPPFRDVVALMTYGDDNIMSVSPGYPWFNHTSIAEFLAKIGIKYTMADKEAESVPFIHISEADFLKR 244

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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 1885452971   1 YDLRMPASLILAAFKCMINIAEECGDYHPSEIFIMKGIATEIAFACVSYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMR 80
Cdd:cd23195    87 YDKRMSAQLILAAFKILIDIAAKSGGYSEEDLKIMRGIATDIAYPLVDFNGDLIQFFGSNPSGHPLTVIINSIVNSLYMR 166

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  81 SAYYHLWPAElgPIEDFRRNASVMTYGDDVSGSIRKGHDWFNHISYAQFLAERDMVFTMPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23195   167 YAYYSLYPEK--EVPPFRDVVALMTYGDDNIMSVSPGYPWFNHTSIAEFLAKIGIKYTMADKEAESVPFIHISEADFLKR 244

RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. 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 1885452971  10 ILAAFKCMINiaEECGDyHPSEIFIMKGIATEIAFACVSYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMRSAYYHLWP- 88
Cdd:cd23194   102 ILWAILDIIN--EWYDD-GEENALIRRVLWEDIVNSVHICGGYVYQWTHSQPSGNPLTAIINSIYNSIIMRYVYLLLTKe 178

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1885452971  89 AELGPIEDFRRNASVMTYGDD----VSGSIRkghDWFNHISYAQFLAERDMVFTMPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23194   179 AGLMTMSDFNKHVSMVSYGDDnvinVSDEVS---EWFNQLTITEAMAEIGMTYTDETKTGEIVPYRSLEEVSFLKR 251

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1885452971  50 NGDV-IIHRGsNPSGQNLTVYINCIVNSLLMRSAYYHLWPAELGPIEDFRRNASVMTYGDD 109
Cdd:cd23172   138 TGEVtRVTKG-NPSGQISTTMDNCMVNTFLTAFEFAYVYGPKTGTLKELWDNYDTIVYGDD 197

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. 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 1885452971   7 ASLILAAFKCMINIAEECGDYHPSEIFIMKGIateiafaCVS---YNGDVIIHRGSNPSGQNLTVYINCIVNSLLMRSAY 83
Cdd:cd23193   146 ASLSSQLFEAAVEVLAECHGDPELVLRYLEPI-------INSkhvVGDERYTVEGGMPSGCPCTSILNSICNNLVVRYAL 218

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  84 YHLWPAElgpIEDFRrnasVMTYGDDVSGSIRKGHDWFnhiSYAQFLAErdmVFTM---PDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23193   219 LETGKFD---PDEYY----ILAYGDDVLVSTDEPIDPS---DLAEFYKK---YFGMtvtPADKSSDFPESSPIEDVFLKR 285

Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971   5 MPASLILAAFKCMiniAEECG--DYHPSEIFIMKG-IATEIAFacvsYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMRS 81
Cdd:pfam00680 240 VPPWLIRFAFEIL---RELLGfpSNVKEWRAILELlIYTPIAL----PNGTVFKKTGGLPSGSPFTSIINSIVNYLLILY 312

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  82 AYYHLWPAELGPIEDFRRNASVMTYGDD--VSGSIRK---GHDWFNHisyaqfLAERDMVFTMPDKTSEPTPymHDRDAD 156
Cdd:pfam00680 313 ALLKSLENDGPRVCNLDKYFDFFTYGDDslVAVSPDFdpvLDRLSPH------LKELGLTITPAKKTFPVSR--ELEEVS 384

                  ....
gi 1885452971 157 FLKR 160
Cdd:pfam00680 385 FLKR 388

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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 1885452971   5 MPASLILAAFKCMINIAEECGDYHPSEIFIMKGIATEIAFACVSYNGDVIIHRGSNPSGQNLTVYINCIVNSLLMRsayy 84
Cdd:cd23197    99 IPKECVAKAFHIIVDYYRKWHCLTVEIENALKTLFLDTADAELLVYGDVFKVNNGVLAGHPMTSVVNSVVNLILMN---- 174

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1885452971  85 HLWPAELG-PIEDFRRNASVMTYGDDVSGSI-RKGHDWFNHISYAQFLAERDMVFT--MPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23197   175 YMWIKITRrRASEFFKLTYIIVMGDDVVISLpKQLTEEFDCRKICAEFAKYDIKVTdsEKNLTGEPKPYDSFDKFEFLSR 254

RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Dicipivirus genus within the family Picornaviridae, order Picornavirales. The Dicipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Dicipivirus contains two species, Cadicivirus A and Cadicivirus B. A new dicipivirus has been found in hedgehogs. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. 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 1885452971  49 YNGDVIIHRGSNPSGQNLTVYINCIVNSLLMRSAYYHLWPaELGPIEDFrrnasVMTYGDDVsgSIRKGHDWFNHISYAQ 128
Cdd:cd23222   264 YDGNLYLIEGAMPSGCAGTSVFNCLINAMLCFSCFMDLEP-EMDPFEPL-----LIAYGDDI--LVSSDHDLFPSRVSEW 335

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1885452971 129 FLAERDMVFTMPDKTSEPTPYMHDRDADFLKR 160
Cdd:cd23222   336 MKANTTFKITPADKGEIFNDDSDVSDVRFLKR 367

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. 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 1885452971  61 PSGQNLTVYINCIVNSLLMRSAYYHLWPAELGPIEDFRRNASVMTYGDD----VSGSIRKGHDWFnhISYaqfLAERDMV 136
Cdd:cd23192   141 PSGMPFTSVINSLNHWLLFSAAVLKAYELVGIYTGNVFDEADFFTYGDDgvyaMPPATASVMDEI--IEN---LKSYGLK 215

                          90       100
                  ....*....|....*....|....
gi 1885452971 137 FTMPDKTSEPTPYMhDRDADFLKR 160
Cdd:cd23192   216 PTAADKTENPDIPP-LQGPVFLKR 238