MAG: polyprotein [XiangYun hepe-virga-like virus 3]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| RdRP_2 super family | cl03049 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1714-2153 | 6.53e-75 | |||||||
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: 257.18 E-value: 6.53e-75
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
7-292 | 1.04e-31 | |||||||
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: 127.41 E-value: 1.04e-31
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| Viral_helicase1 super family | cl26263 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
757-992 | 2.29e-24 | |||||||
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: 103.61 E-value: 2.29e-24
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| Name | Accession | Description | Interval | E-value | |||||||
| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1714-2153 | 6.53e-75 | |||||||
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: 257.18 E-value: 6.53e-75
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| Virgaviridae_RdRp | cd23251 | RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ... |
1704-2098 | 1.87e-74 | |||||||
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. Pssm-ID: 438101 Cd Length: 427 Bit Score: 255.62 E-value: 1.87e-74
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
7-292 | 1.04e-31 | |||||||
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: 127.41 E-value: 1.04e-31
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
757-992 | 2.29e-24 | |||||||
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: 103.61 E-value: 2.29e-24
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
757-858 | 1.53e-04 | |||||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 44.08 E-value: 1.53e-04
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
760-858 | 8.33e-03 | |||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 41.12 E-value: 8.33e-03
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| Name | Accession | Description | Interval | E-value | |||||||
| RdRP_2 | pfam00978 | RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ... |
1714-2153 | 6.53e-75 | |||||||
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: 257.18 E-value: 6.53e-75
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| Virgaviridae_RdRp | cd23251 | RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ... |
1704-2098 | 1.87e-74 | |||||||
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. Pssm-ID: 438101 Cd Length: 427 Bit Score: 255.62 E-value: 1.87e-74
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| Kitaviridae_RdRp | cd23254 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ... |
1846-2098 | 2.45e-56 | |||||||
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. Pssm-ID: 438104 Cd Length: 267 Bit Score: 197.37 E-value: 2.45e-56
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| Closteroviridae_RdRp | cd23253 | RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ... |
1847-2101 | 1.41e-53 | |||||||
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: 189.31 E-value: 1.41e-53
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| ps-ssRNAv_Martellivirales_RdRp | cd23208 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ... |
1845-2035 | 6.64e-39 | |||||||
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: 144.43 E-value: 6.64e-39
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| Vmethyltransf | pfam01660 | Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ... |
7-292 | 1.04e-31 | |||||||
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: 127.41 E-value: 1.04e-31
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| Mayoviridae_RdRp | cd23256 | RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ... |
1844-2141 | 3.05e-27 | |||||||
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: 114.84 E-value: 3.05e-27
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| Viral_helicase1 | pfam01443 | Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ... |
757-992 | 2.29e-24 | |||||||
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: 103.61 E-value: 2.29e-24
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| Bromoviridae_RdRp | cd23252 | RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ... |
1715-2097 | 7.33e-24 | |||||||
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: 105.00 E-value: 7.33e-24
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| ps-ssRNAv_Alsuviricetes_RdRp | cd23182 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ... |
1847-2035 | 1.01e-23 | |||||||
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: 100.75 E-value: 1.01e-23
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| Endornaviridae_RdRp | cd23255 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ... |
1839-2058 | 5.73e-19 | |||||||
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. Pssm-ID: 438105 Cd Length: 237 Bit Score: 88.36 E-value: 5.73e-19
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| Togaviridae_RdRp | cd23250 | RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ... |
1930-2166 | 4.92e-12 | |||||||
RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. 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: 438100 Cd Length: 458 Bit Score: 70.57 E-value: 4.92e-12
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| ps-ssRNAv_Hepelivirales_RdRp | cd23209 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ... |
1881-2035 | 1.62e-11 | |||||||
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: 65.20 E-value: 1.62e-11
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| Hepeviridae_RdRp | cd23259 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of ... |
1882-2032 | 8.18e-10 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped 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. Pssm-ID: 438109 Cd Length: 274 Bit Score: 62.07 E-value: 8.18e-10
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
1922-2085 | 1.60e-08 | |||||||
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. Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 58.06 E-value: 1.60e-08
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| ps-ssRNAv_Nodaviridae_RdRp | cd23173 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ... |
1929-2042 | 1.81e-06 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. 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: 438023 Cd Length: 236 Bit Score: 51.36 E-value: 1.81e-06
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| AAA_19 | pfam13245 | AAA domain; |
757-858 | 1.55e-05 | |||||||
AAA domain; Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 46.44 E-value: 1.55e-05
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| ps_ssRNAv_Tolivirales_RdRp | cd23179 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ... |
1930-2032 | 2.00e-05 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses; This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from "tombusvirus-like" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. 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: 438029 Cd Length: 227 Bit Score: 47.90 E-value: 2.00e-05
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| AAA_30 | pfam13604 | AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
757-858 | 8.49e-05 | |||||||
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 45.63 E-value: 8.49e-05
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| DEXSc_RecD-like | cd17933 | DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
757-858 | 1.53e-04 | |||||||
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 44.08 E-value: 1.53e-04
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| DEXXYc_viral_SF1-N | cd17937 | DEXXY-box helicase domain of viral superfamily 1 helicase; Superfamily 1 (SF1) helicases are ... |
754-858 | 7.21e-04 | |||||||
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: 41.65 E-value: 7.21e-04
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| Regressovirinae_RdRp | cd23235 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ... |
1933-2048 | 2.48e-03 | |||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. 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: 438085 [Multi-domain] Cd Length: 472 Bit Score: 42.60 E-value: 2.48e-03
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
1984-2035 | 5.39e-03 | |||||||
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. Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 37.70 E-value: 5.39e-03
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| RecD | COG0507 | ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
760-858 | 8.33e-03 | |||||||
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]; Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 41.12 E-value: 8.33e-03
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| Benyviridae_RdRp | cd23257 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of ... |
1884-2029 | 9.70e-03 | |||||||
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: 39.52 E-value: 9.70e-03
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