replicase [Beihai barnacle virus 3]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| Viral_helicase1 super family | cl26263 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
666-910 | 3.13e-20 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. The actual alignment was detected with superfamily member pfam01443: Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 91.67 E-value: 3.13e-20
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| ps-ssRNAv_RdRp-like super family | cl40470 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
1187-1359 | 1.22e-12 | |||||||
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. The actual alignment was detected with superfamily member cd23209: Pssm-ID: 477363 [Multi-domain] Cd Length: 183 Bit Score: 68.67 E-value: 1.22e-12
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| RdRP_2 super family | cl03049 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1105-1506 | 1.36e-11 | |||||||
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 The actual alignment was detected with superfamily member pfam00978: Pssm-ID: 395779 Cd Length: 440 Bit Score: 69.21 E-value: 1.36e-11
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| Vmethyltransf super family | cl46422 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
139-345 | 1.38e-05 | |||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. The actual alignment was detected with superfamily member pfam01660: Pssm-ID: 480762 Cd Length: 308 Bit Score: 49.60 E-value: 1.38e-05
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| Name | Accession | Description | Interval | E-value | |||||||
| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
666-910 | 3.13e-20 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 91.67 E-value: 3.13e-20
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| ps-ssRNAv_Hepelivirales_RdRp | cd23209 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ... |
1187-1359 | 1.22e-12 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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. Pssm-ID: 438059 [Multi-domain] Cd Length: 183 Bit Score: 68.67 E-value: 1.22e-12
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1105-1506 | 1.36e-11 | |||||||
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 Pssm-ID: 395779 Cd Length: 440 Bit Score: 69.21 E-value: 1.36e-11
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
664-770 | 1.24e-07 | |||||||
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350695 [Multi-domain] Cd Length: 137 Bit Score: 52.82 E-value: 1.24e-07
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
139-345 | 1.38e-05 | |||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 49.60 E-value: 1.38e-05
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| Name | Accession | Description | Interval | E-value | |||||||
| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
666-910 | 3.13e-20 | |||||||
Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 91.67 E-value: 3.13e-20
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| ps-ssRNAv_Hepelivirales_RdRp | cd23209 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ... |
1187-1359 | 1.22e-12 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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. Pssm-ID: 438059 [Multi-domain] Cd Length: 183 Bit Score: 68.67 E-value: 1.22e-12
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| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1105-1506 | 1.36e-11 | |||||||
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 Pssm-ID: 395779 Cd Length: 440 Bit Score: 69.21 E-value: 1.36e-11
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| ps-ssRNAv_Alsuviricetes_RdRp | cd23182 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ... |
1187-1347 | 2.03e-10 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. 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. Pssm-ID: 438032 [Multi-domain] Cd Length: 187 Bit Score: 62.23 E-value: 2.03e-10
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| ps-ssRNAv_Martellivirales_RdRp | cd23208 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ... |
1174-1347 | 6.52e-10 | |||||||
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. Pssm-ID: 438058 [Multi-domain] Cd Length: 190 Bit Score: 60.84 E-value: 6.52e-10
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
664-770 | 1.24e-07 | |||||||
DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Pssm-ID: 350695 [Multi-domain] Cd Length: 137 Bit Score: 52.82 E-value: 1.24e-07
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| Mayoviridae_RdRp | cd23256 | RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ... |
1271-1348 | 1.56e-06 | |||||||
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. Pssm-ID: 438106 Cd Length: 329 Bit Score: 52.44 E-value: 1.56e-06
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| Benyviridae_RdRp | cd23257 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ... |
1175-1347 | 5.41e-06 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Benyviridae, order Hepelivirales. The Benyviridae is a family of plant viruses with rod-shaped virions. Their genomes are multipartite (+)ssRNAs with 5' m7G-cap and 3' poly(A) and there is post-translational cleavage of the viral replicase. Beet necrotic yellow vein virus belongs to the genus Benyvirus and is the cause of 'rhizomania' disease of sugar beet. This widespread soil-borne disease can severely reduce sugar beet growth and beet sucrose production. BNYVV RNA1 contains one open reading frame (ORF) encoding a replicase protein that harbors motifs for methyltransferase, helicase, papain-like protease, and RdRp. 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. Pssm-ID: 438107 [Multi-domain] Cd Length: 188 Bit Score: 49.15 E-value: 5.41e-06
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
139-345 | 1.38e-05 | |||||||
Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. Pssm-ID: 396298 Cd Length: 308 Bit Score: 49.60 E-value: 1.38e-05
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| ps-ssRNA_RdRp_Tymovirales | cd23207 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of ... |
1142-1347 | 1.01e-04 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). 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. Pssm-ID: 438057 [Multi-domain] Cd Length: 188 Bit Score: 45.47 E-value: 1.01e-04
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| Bromoviridae_RdRp | cd23252 | RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ... |
1271-1346 | 2.89e-04 | |||||||
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. Pssm-ID: 438102 Cd Length: 332 Bit Score: 45.30 E-value: 2.89e-04
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| Closteroviridae_RdRp | cd23253 | RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ... |
1264-1427 | 8.36e-04 | |||||||
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. Pssm-ID: 438103 Cd Length: 266 Bit Score: 43.70 E-value: 8.36e-04
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