RNA-dependent RNA polymerase [Macrobrachium rosenbergii nodavirus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Nodaviridae_RdRp | cd23173 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ... |
509-749 | 9.55e-112 | |||||
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: 345.65 E-value: 9.55e-112
|
|||||||||
| Noda_Vmethyltr super family | cl41194 | Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ... |
102-248 | 2.20e-46 | |||||
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping. The actual alignment was detected with superfamily member pfam19222: Pssm-ID: 408991 Cd Length: 148 Bit Score: 163.18 E-value: 2.20e-46
|
|||||||||
| Viral_RdRp_C | pfam17501 | Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase ... |
916-1016 | 2.52e-42 | |||||
Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase (Protein A) found in Alphanodaviruses such as Flock House Virus (FHV). FHV is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2. RNA1 encodes protein A, which is the catalytic subunit of the RNA-dependent RNA polymerase (RdRp) and functions as the sole viral replicase protein responsible for RNA replication. FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which is able to restore the nucleotide loss at the 3'-end initiation site of RNA template to rescue RNA synthesis initiation. It has also been reported that FHV protein A replicates viral RNA in concert with the mitochondrial outer membrane and other viral or cellular factors and mediates the formation of viral RNA replication complexes and small spherules by inducing membrane rearrangement.This domain is also found in B1 proteins which are encoded by the subgenomic RNA3 during FHV replication. The function of translated B1 protein is poorly defined, but may be important for maintenance of RNA replication. : Pssm-ID: 340216 [Multi-domain] Cd Length: 101 Bit Score: 149.80 E-value: 2.52e-42
|
|||||||||
| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Nodaviridae_RdRp | cd23173 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ... |
509-749 | 9.55e-112 | |||||
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: 345.65 E-value: 9.55e-112
|
|||||||||
| Noda_Vmethyltr | pfam19222 | Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ... |
102-248 | 2.20e-46 | |||||
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping. Pssm-ID: 408991 Cd Length: 148 Bit Score: 163.18 E-value: 2.20e-46
|
|||||||||
| Viral_RdRp_C | pfam17501 | Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase ... |
916-1016 | 2.52e-42 | |||||
Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase (Protein A) found in Alphanodaviruses such as Flock House Virus (FHV). FHV is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2. RNA1 encodes protein A, which is the catalytic subunit of the RNA-dependent RNA polymerase (RdRp) and functions as the sole viral replicase protein responsible for RNA replication. FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which is able to restore the nucleotide loss at the 3'-end initiation site of RNA template to rescue RNA synthesis initiation. It has also been reported that FHV protein A replicates viral RNA in concert with the mitochondrial outer membrane and other viral or cellular factors and mediates the formation of viral RNA replication complexes and small spherules by inducing membrane rearrangement.This domain is also found in B1 proteins which are encoded by the subgenomic RNA3 during FHV replication. The function of translated B1 protein is poorly defined, but may be important for maintenance of RNA replication. Pssm-ID: 340216 [Multi-domain] Cd Length: 101 Bit Score: 149.80 E-value: 2.52e-42
|
|||||||||
| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
597-745 | 7.14e-08 | |||||
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. Pssm-ID: 425815 Cd Length: 450 Bit Score: 56.26 E-value: 7.14e-08
|
|||||||||
| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Nodaviridae_RdRp | cd23173 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ... |
509-749 | 9.55e-112 | |||||
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: 345.65 E-value: 9.55e-112
|
|||||||||
| Noda_Vmethyltr | pfam19222 | Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is ... |
102-248 | 2.20e-46 | |||||
Nodavirus Vmethyltransferase; This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping. Pssm-ID: 408991 Cd Length: 148 Bit Score: 163.18 E-value: 2.20e-46
|
|||||||||
| Viral_RdRp_C | pfam17501 | Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase ... |
916-1016 | 2.52e-42 | |||||
Viral RNA-directed RNA polymerase; This is the C-terminal of RNA-directed RNA polymerase (Protein A) found in Alphanodaviruses such as Flock House Virus (FHV). FHV is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2. RNA1 encodes protein A, which is the catalytic subunit of the RNA-dependent RNA polymerase (RdRp) and functions as the sole viral replicase protein responsible for RNA replication. FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which is able to restore the nucleotide loss at the 3'-end initiation site of RNA template to rescue RNA synthesis initiation. It has also been reported that FHV protein A replicates viral RNA in concert with the mitochondrial outer membrane and other viral or cellular factors and mediates the formation of viral RNA replication complexes and small spherules by inducing membrane rearrangement.This domain is also found in B1 proteins which are encoded by the subgenomic RNA3 during FHV replication. The function of translated B1 protein is poorly defined, but may be important for maintenance of RNA replication. Pssm-ID: 340216 [Multi-domain] Cd Length: 101 Bit Score: 149.80 E-value: 2.52e-42
|
|||||||||
| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
598-748 | 4.44e-13 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members 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 picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. 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: 438019 Cd Length: 309 Bit Score: 71.47 E-value: 4.44e-13
|
|||||||||
| ps-ssRNAv_CBPV-like_RdRp | cd23174 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) ... |
522-743 | 5.91e-12 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. 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: 438024 Cd Length: 229 Bit Score: 66.35 E-value: 5.91e-12
|
|||||||||
| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
525-769 | 2.57e-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: 56.52 E-value: 2.57e-08
|
|||||||||
| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
597-745 | 7.14e-08 | |||||
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. Pssm-ID: 425815 Cd Length: 450 Bit Score: 56.26 E-value: 7.14e-08
|
|||||||||
| ps_ssRNAv_Tolivirales_RdRp | cd23179 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ... |
523-731 | 8.85e-06 | |||||
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: 8.85e-06
|
|||||||||
| Mischivirus_RdRp | cd23227 | RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ... |
599-723 | 1.82e-04 | |||||
RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. 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. Pssm-ID: 438077 Cd Length: 466 Bit Score: 45.32 E-value: 1.82e-04
|
|||||||||
| Cardiovirus_RdRp | cd23211 | RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded ... |
599-745 | 5.60e-03 | |||||
RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Cardiovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Vertebrates serve as natural hosts for the cardioviruses. There are currently six species in the genus: Cardiovirus A-F. Diseases associated with cardioviruses include: myocarditis, encephalitis, multiple sclerosis, and type 1 diabetes. Cardiovirus A is composed of only one serotype, encephalomycarditis virus (EMCV) which causes encephalomyocarditis and reproductive disease in pigs. Cardiovirus B comprises 15 genetic types, Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), thera virus (formerly named Theiler-like virus of rats), Saffold virus (SAFV) types 1 to 11, and genet fecal theilovirus (from Geneta geneta). Of these types, only VHEV and SAFV are thought to cause infection in humans. Thus far, Cardiovirus C has only been observed in the brown rat. 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: 438061 Cd Length: 460 Bit Score: 40.60 E-value: 5.60e-03
|
|||||||||
| Blast search parameters | ||||
|
