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 2523358094 1310 DQSFDGWDVRNSDLNIEVGEISfspvgcVQLGKMFDT------MRPILRTPMPHIRDYNTRELMLALEKRNRNVPSMNGV 1383
Cdd:cd23251      8 DSDFDGYTVATSDINLNVEDCT------LDPSKSVKVwqekegLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094 1384 VDIEVSSSEMLDSLLEECFDPALLRfhlAEPItISSNSVGEWLSGQPLSVR-PMIVPDFALHCLALNEYNFSIKRKPKPN 1462
Cdd:cd23251     82 VNEFETIERVIKKAKDVFFDEDLID---RSPL-STRESFLRWWDKQSTTARaQLLADDRVLDEIDVCTYNFMIKNDVKPK 157

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2523358094 1463 LTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23251    158 LDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSAL 198

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094  250 YVCRSGMKTAEMFVRYFSTREYESAVSIG-GPGGEVQYLTNKGI-RVFGITktdlidfspsVKHHLFTQLIGD----TYD 323
Cdd:pfam01728    1 YRSRAAYKLLEIDEKFGLLKPGKTVLDLGaAPGGWSQVALQRGAgKVVGVD----------LGPMQLWKPRNDpgvtFIQ 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094  324 GDITKEcnvvAFRDSIRNCYSSGVCFFGGDVATSeSDSNHNFPALAKLV----AWEIvlCTTVLKNGGDAYFKVLDllSD 399
Cdd:pfam01728   71 GDIRDP----ETLDLLEELLGRKVDLVLSDGSPF-ISGNKVLDHLRSLDlvkaALEV--ALELLRKGGNFVCKVFQ--GE 141

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 2523358094  400 QMPHNIEFLNNSFDSVEIVKLETSRAASTELHLICRGF 437
Cdd:pfam01728  142 DFSELLYLLKLGFEKVGVFKPPASRPESSEEYLVCLGF 179

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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 2523358094 1310 DQSFDGWDVRNSDLNIEVGEISfspvgcVQLGKMFDT------MRPILRTPMPHIRDYNTRELMLALEKRNRNVPSMNGV 1383
Cdd:cd23251      8 DSDFDGYTVATSDINLNVEDCT------LDPSKSVKVwqekegLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094 1384 VDIEVSSSEMLDSLLEECFDPALLRfhlAEPItISSNSVGEWLSGQPLSVR-PMIVPDFALHCLALNEYNFSIKRKPKPN 1462
Cdd:cd23251     82 VNEFETIERVIKKAKDVFFDEDLID---RSPL-STRESFLRWWDKQSTTARaQLLADDRVLDEIDVCTYNFMIKNDVKPK 157

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2523358094 1463 LTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23251    158 LDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSAL 198

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 2523358094 1347 MRPILRTPMPHIRDYNTRELMLALEKRNRNVPSMNGVVDIEVSSSEMLDSLLEECFDPALLRFHlaEPITISSNSVGEWL 1426
Cdd:pfam00978   29 LVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVAERFKKSFLDKEKLDKL--DPIINTTENVSRWL 106

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2523358094 1427 SGQPLSVRPMIVPDF--ALHCLALNEYNFSIKRKPKPNLTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:pfam00978  107 DKQSGKKAAQLKLDDlvPLHEVDLDRYKHMIKSDVKPKLDLSPQSERPALQTITYHDKGVTAYFSPIFRELFERLLYVL 185

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094  884 DTLFIDEAlmshpGQIFYAIALSGATEVK---LLGDVLQI-PYVNRTPAYTTK--------YHRLADFVPII-DTLYISY 950
Cdd:COG1112    557 DLVIIDEA-----SQATLAEALGALARAKrvvLVGDPKQLpPVVFGEEAEEVAeegldeslLDRLLARLPERgVMLREHY 631

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094  951 RCPTDVAA---------RLDSHYAELNNN--------------GCGMKSVKFSTNTC---KVVRLSNENF---------- 994
Cdd:COG1112    632 RMHPEIIAfsnrlfydgKLVPLPSPKARRladpdsplvfidvdGVYERRGGSRTNPEeaeAVVELVRELLedgpdgesig 711

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094  995 ---PHDKNVQYLTFTQNEKKKLELLHLRVSTIHEFQGKEAKVIrVV-----RLNPFPQEELFL-----RFNyalVALTRH 1061
Cdd:COG1112    712 vitPYRAQVALIRELLREALGDGLEPVFVGTVDRFQGDERDVI-IFslvysNDEDVPRNFGFLnggprRLN---VAVSRA 787

                   ....
gi 2523358094 1062 TEQL 1065
Cdd:COG1112    788 RRKL 791

C-terminal helicase domain of Upf1-like family helicases; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2523358094 1018 LRVSTIHEFQGKEAKVI--RVVRLNPFPQEELFL----RFNyalVALTR 1060
Cdd:cd18808    111 VEVGTVDNFQGREKDVIilSLVRSNESGGSIGFLsdprRLN---VALTR 156

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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 2523358094 1310 DQSFDGWDVRNSDLNIEVGEISfspvgcVQLGKMFDT------MRPILRTPMPHIRDYNTRELMLALEKRNRNVPSMNGV 1383
Cdd:cd23251      8 DSDFDGYTVATSDINLNVEDCT------LDPSKSVKVwqekegLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGA 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2523358094 1384 VDIEVSSSEMLDSLLEECFDPALLRfhlAEPItISSNSVGEWLSGQPLSVR-PMIVPDFALHCLALNEYNFSIKRKPKPN 1462
Cdd:cd23251     82 VNEFETIERVIKKAKDVFFDEDLID---RSPL-STRESFLRWWDKQSTTARaQLLADDRVLDEIDVCTYNFMIKNDVKPK 157

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 2523358094 1463 LTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23251    158 LDLSPQSEYAALQTVVYPDKIVNALFGPIFKEINERILSAL 198

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2523358094 1449 NEYNFSIKRKPKPNLTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23254      1 NVYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVL 55

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. 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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2523358094 1449 NEYNFSIKRKPKPNLTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23208      1 DKYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCL 55

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
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2523358094 1449 NEYNFSIKRKPKPNLTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRVTSSL 1503
Cdd:cd23253      1 TSFKLMVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEVFDRIKYCL 55

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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 2523358094 1438 VPDFALHCLA-LNEYNFSIKRKPKPNLTVDATASYLALQTIVYHEKSINAMFCSIFREIKKRV 1499
Cdd:cd23256     21 VNDPVVLALTsLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPIFRQFKTRL 83

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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 2523358094 1347 MRPILRTPMPHIRDYNTRELMLALEKRNRNVPSMNGVVDIevsssemlDSLLEECFDpallRFhlaepitISSnsvgewl 1426
Cdd:cd23252     26 LEPVLNTGSGSKRVGTQREALLAIKKRNANVPELGDSVDL--------DRVSNAVAN----RF-------LTT------- 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2523358094 1427 sgqplsvrpMIVPDfalhclALNEYNFSIKRKPKPnlTVDATasyLALQ-----TIVYHEKSINAMFCSIF 1492
Cdd:cd23252     80 ---------VIDVD------RLDKYMHMIKSDLKP--VEDDS---LHVErpvpaTITYHKKGIVMQFSPLF 130

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. 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
                   ....*....|....*....|..
gi 2523358094 1477 IVYHEKSINAMFCSIFREIKKR 1498
Cdd:cd23255     61 IVWQRKGICAIFSPIFNEAKKR 82