catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
307-778
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae 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 Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084 Cd Length: 471 Bit Score: 994.25 E-value: 0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
307-778
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae 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 Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084 Cd Length: 471 Bit Score: 994.25 E-value: 0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of ...
307-778
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae 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 Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. 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: 438084 Cd Length: 471 Bit Score: 994.25 E-value: 0e+00
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense ...
330-773
2.30e-145
RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle 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: 438090 Cd Length: 451 Bit Score: 436.20 E-value: 2.30e-145
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of ...
421-650
1.15e-139
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. 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: 438056 Cd Length: 231 Bit Score: 412.66 E-value: 1.15e-139
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense ...
322-775
2.56e-138
RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic 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: 438092 Cd Length: 476 Bit Score: 418.76 E-value: 2.56e-138
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense ...
314-772
3.52e-136
RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name "Pelarspovirus" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. 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: 438091 [Multi-domain] Cd Length: 497 Bit Score: 414.14 E-value: 3.52e-136
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense ...
316-769
4.52e-136
RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus 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: 438089 [Multi-domain] Cd Length: 470 Bit Score: 412.60 E-value: 4.52e-136
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of ...
352-773
9.64e-124
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. 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: 438087 Cd Length: 439 Bit Score: 379.76 E-value: 9.64e-124
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded ...
322-785
3.61e-117
RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. 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: 438093 Cd Length: 488 Bit Score: 364.54 E-value: 3.61e-117
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of ...
295-775
2.75e-114
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Panicovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Viruses in Panicovirus are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. Their host range is restricted to monocotyledonous plants. There are 3 species in this genus: Cocksfoot mild mosaic virus, Panicum mosaic virus, and Thin paspalum asymptomatic virus. The virus typically forms a systemic mosaic. 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: 438088 [Multi-domain] Cd Length: 692 Bit Score: 363.45 E-value: 2.75e-114
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense ...
315-770
1.97e-110
RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily; This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. 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: 438094 Cd Length: 500 Bit Score: 347.27 E-value: 1.97e-110
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded ...
332-773
8.02e-106
RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps; This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt 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: 438086 [Multi-domain] Cd Length: 474 Bit Score: 334.29 E-value: 8.02e-106
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of ...
422-650
3.67e-100
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: 310.22 E-value: 3.67e-100
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of ...
395-775
8.39e-94
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. 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: 438083 Cd Length: 407 Bit Score: 300.12 E-value: 8.39e-94
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae ...
346-769
4.85e-90
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: 292.60 E-value: 4.85e-90
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ...
405-676
3.85e-70
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: 232.56 E-value: 3.85e-70
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae ...
422-676
4.96e-41
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal 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: 438055 Cd Length: 268 Bit Score: 151.71 E-value: 4.96e-41
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: 77.13 E-value: 9.82e-16
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ...
491-660
1.46e-08
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. 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: 438028 Cd Length: 284 Bit Score: 56.76 E-value: 1.46e-08
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of ...
406-646
1.50e-05
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: 47.12 E-value: 1.50e-05
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
507-611
1.84e-04
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: 40.40 E-value: 1.84e-04
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae ...
567-650
4.13e-04
RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. 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: 438052 Cd Length: 518 Bit Score: 43.68 E-value: 4.13e-04
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...
503-659
7.88e-03
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: 39.12 E-value: 7.88e-03
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
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(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
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