hypothetical protein 2 [Hubei sobemo-like virus 9]
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 ... |
1-298 | 8.34e-26 | ||||||
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 cd23180: Pssm-ID: 477363 Cd Length: 447 Bit Score: 106.97 E-value: 8.34e-26
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| Name | Accession | Description | Interval | E-value | ||||||
| ps-ssRNAv_Solemoviridae_RdRp | cd23180 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of ... |
1-298 | 8.34e-26 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Solemoviridae, order Sobelivirales. Plant viruses in the family Solemoviridae have stable icosahedral particles assembled on T=3 symmetry and a relatively small (4-4.6 kb) monopartite (+)ssRNA genome with 4-5 open reading frames (ORFs). The natural host range is relatively narrow for each virus. Viral transmission occurs via mechanical wounding, by vegetative propagation or abiotically through soil; insects (beetles, aphids, thrips, hoppers, mirid bugs, moths) can also be vectors. Viruses infecting legumes or plants from the family Chenopodiaceae may be seed-transmissible. Members of the family are classified into four genera: Sobemovirus, Polemovirus, Polerovirus, Enamovirus. The viral polyprotein contains domains of the membrane anchor, a serine protease, a genome-linked viral protein (VPg) and C-terminal protein(s) or an RdRp, expressed by means of ribosomal frameshifting. 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: 438030 Cd Length: 447 Bit Score: 106.97 E-value: 8.34e-26
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| RdRP_4 | pfam02123 | Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ... |
44-266 | 2.95e-07 | ||||||
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Pssm-ID: 280316 Cd Length: 465 Bit Score: 51.69 E-value: 2.95e-07
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| Name | Accession | Description | Interval | E-value | ||||||
| ps-ssRNAv_Solemoviridae_RdRp | cd23180 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of ... |
1-298 | 8.34e-26 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Solemoviridae, order Sobelivirales. Plant viruses in the family Solemoviridae have stable icosahedral particles assembled on T=3 symmetry and a relatively small (4-4.6 kb) monopartite (+)ssRNA genome with 4-5 open reading frames (ORFs). The natural host range is relatively narrow for each virus. Viral transmission occurs via mechanical wounding, by vegetative propagation or abiotically through soil; insects (beetles, aphids, thrips, hoppers, mirid bugs, moths) can also be vectors. Viruses infecting legumes or plants from the family Chenopodiaceae may be seed-transmissible. Members of the family are classified into four genera: Sobemovirus, Polemovirus, Polerovirus, Enamovirus. The viral polyprotein contains domains of the membrane anchor, a serine protease, a genome-linked viral protein (VPg) and C-terminal protein(s) or an RdRp, expressed by means of ribosomal frameshifting. 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: 438030 Cd Length: 447 Bit Score: 106.97 E-value: 8.34e-26
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| ps-ssRNAv_Barnaviridae_RdRp | cd23184 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Barnaviridae of ... |
55-281 | 1.35e-19 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Barnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Barnaviridae, order Sobelivirales, and related viruses. Barnaviridae is a family of non-enveloped, (+)ssRNA viruses. Cultivated mushrooms serve as natural hosts. The family has one genus, Barnavirus, which contains one species: Mushroom bacilliform virus (MBV) which infects the common cultivated button mushroom (Agaricus bisporus), and Bacilliform particles, which are morphologically similar to MBV, have been observed in the field mushroom Agaricus campestris. MBV viral transmission is horizontal via mycelium and possibly basidiospores. Distribution of MBV coincides with that of the commercial cultivation of Agaricus bisporus; the virus has been reported to occur in most major mushroom-growing countries. MBV is capable of autonomous replication, but commonly occurs as a double infection with a double-stranded RNA (dsRNA) virus (LaFrance isometric virus, LFIV) in mushrooms afflicted with La France disease. MBV is not required in pathogenesis involving LFIV, but it remains to be determined if it is a second, minor causal agent of LaFrance disease. MBV ssRNA and LFIV dsRNA do not share sequence homology. 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: 438034 Cd Length: 261 Bit Score: 86.81 E-value: 1.35e-19
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
60-281 | 3.66e-10 | ||||||
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: 59.99 E-value: 3.66e-10
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| RdRP_4 | pfam02123 | Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ... |
44-266 | 2.95e-07 | ||||||
Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Pssm-ID: 280316 Cd Length: 465 Bit Score: 51.69 E-value: 2.95e-07
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
1-242 | 1.04e-06 | ||||||
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: 50.10 E-value: 1.04e-06
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| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
60-262 | 1.91e-05 | ||||||
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: 45.66 E-value: 1.91e-05
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| Sapelovirus_RdRp | cd23218 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of ... |
59-242 | 3.94e-05 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Sapelovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Viruses in Sapelovirus are non-enveloped, with icosahedral, spherical, and round geometries, and T=pseudo3 symmetry. Sapelovirus, formerly known as porcine enterovirus (PEV)-8, is known to infect pigs asymptomatically but can cause reproductive failure and severe neurologic, enteric, or respiratory signs. Sapelovirus infections have been reported worldwide in pigs. The genus Sapelovirus contains three species, with a unique genome organization: Sapelovirus A, also known as porcine sapelovirus (PSV); Sapelovirus B as simian sapelovirus; and Avian sapelovirus represented by duck picornavirus. 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: 438068 Cd Length: 366 Bit Score: 44.89 E-value: 3.94e-05
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| Kunsagivirus_RdRp | cd23219 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of ... |
1-251 | 1.16e-04 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Kunsagivirus genus within the family Picornaviridae, order Picornavirales. The Kunsagivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Kunsagivirus is a new picornavirus genus containing a three species. Viral RNA of kunsagivirus A1 was detected in feces of an apparently healthy European roller (Coracias garrulus), of kunsagivirus B1 (bat kunsagivirus) in feces of the fruit bat Eidolon helvum, and of kunsagivirus C1 (bakunsavirus) in wild baboons (Papio cynocephalus). 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: 438069 Cd Length: 346 Bit Score: 43.70 E-value: 1.16e-04
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| Mischivirus_RdRp | cd23227 | RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded ... |
1-95 | 2.45e-03 | ||||||
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: 39.54 E-value: 2.45e-03
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| Avisivirus_RdRp | cd23231 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of ... |
60-265 | 5.04e-03 | ||||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Avisivirus genus within the family Picornaviridae, order Picornavirales. The Avisivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Avisivirus is a picornavirus genus containing three species Avisivirus A, Avisivirus B and Avisivirus C. The name Avisivirus is derived from Avihepato sister-clade. Turkeys serve as natural hosts. 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: 438081 Cd Length: 362 Bit Score: 38.33 E-value: 5.04e-03
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