RNA-dependent RNA polymerase [Hubei narna-like virus 17]
Protein Classification
RNA-dependent RNA polymerase family protein( domain architecture ID 1750808)
RNA-dependent RNA polymerase (RdRp) family protein similar to the RdRp catalytic domain of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| ps-ssRNAv_RdRp-like super family | cl40470 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
327-532 | 3.69e-10 | ||||
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 cd23183: Pssm-ID: 477363 Cd Length: 223 Bit Score: 60.77 E-value: 3.69e-10
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| Name | Accession | Description | Interval | E-value | ||||
| ps-ssRNAv_Botourmiaviridae_RdRp | cd23183 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Botourmiaviridae of ... |
327-532 | 3.69e-10 | ||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Botourmiaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Botourmiaviridae, order Ourlivirales. The family includes six genera: Ourmiavirus, Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus. Family Botourmiaviridae genomes can be monopartite (Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus) (2-3 kb) or tripartate (Ourmiavirus). Members of genus Ourmiavirus infect plants and the other genera infect fungi. Members of the genera Botoulivirus, Magoulivirus and Scleroulivirus infect fungi from the genera Botrytis, Magnaporthe or Sclerotinia, respectively. Members of the genus Ourmiavirus infect plants: Ourmia melon virus infects melon, producing chlorotic spots and irregular ringspots, Epirus cherry virus produces rasp-leaf symptoms in cherry, and cassava virus C induces severe stunting and a yellow mosaic pattern in cassava. Ourmiavirus replication is dependent on the virus RdRp. Synthesis of the ourmiavirus coat protein from actively replicating RNA3 is necessary for both virion assembly and systemic infection of the host. The ourmiavirus movement protein determines symptoms and forms tubular structures involved in cell-to-cell movement and may undergo post-translational modification. Botoulivirus, magoulivirus and scleroulivirus replication is strictly dependent on the virus RNA-dependent RNA polymerase. 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: 438033 Cd Length: 223 Bit Score: 60.77 E-value: 3.69e-10
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| Name | Accession | Description | Interval | E-value | ||||
| ps-ssRNAv_Botourmiaviridae_RdRp | cd23183 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Botourmiaviridae of ... |
327-532 | 3.69e-10 | ||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Botourmiaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Botourmiaviridae, order Ourlivirales. The family includes six genera: Ourmiavirus, Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus. Family Botourmiaviridae genomes can be monopartite (Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus) (2-3 kb) or tripartate (Ourmiavirus). Members of genus Ourmiavirus infect plants and the other genera infect fungi. Members of the genera Botoulivirus, Magoulivirus and Scleroulivirus infect fungi from the genera Botrytis, Magnaporthe or Sclerotinia, respectively. Members of the genus Ourmiavirus infect plants: Ourmia melon virus infects melon, producing chlorotic spots and irregular ringspots, Epirus cherry virus produces rasp-leaf symptoms in cherry, and cassava virus C induces severe stunting and a yellow mosaic pattern in cassava. Ourmiavirus replication is dependent on the virus RdRp. Synthesis of the ourmiavirus coat protein from actively replicating RNA3 is necessary for both virion assembly and systemic infection of the host. The ourmiavirus movement protein determines symptoms and forms tubular structures involved in cell-to-cell movement and may undergo post-translational modification. Botoulivirus, magoulivirus and scleroulivirus replication is strictly dependent on the virus RNA-dependent RNA polymerase. 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: 438033 Cd Length: 223 Bit Score: 60.77 E-value: 3.69e-10
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| ps-ssRNAv_Narnaviridae_RdRp | cd23177 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Narnaviridae of ... |
310-531 | 2.09e-06 | ||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Narnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Narnaviridae, order Wolframvirales. Narnaviridae is a family of (+)ssRNA viruses which are the simplest of known RNA viruses, consisting of a single molecule of (+)ssRNA that may be as small as 2.3 kb and encoding only an RdRp to direct their own replication. They encode no protein capsid and no virus particles other than lipid vesicles are known to be associated with infection. The family Narnaviridae became the second virus family with members lacking a protein capsid, following the acceptance of the family Hypoviridae as the first such family. The two genera of the family, the genus Narnavirus and the genus Mitovirus, share basic genome organization properties. The single feature distinguishing the two genera is the site of translation of the RdRp, and presumably of replication: members of the genus Narnavirus are found in the cytosol (the cytoplasm exclusive of organelles) and the genus Mitovirus are confined to mitochondria. 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: 438027 Cd Length: 235 Bit Score: 49.91 E-value: 2.09e-06
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