catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Leviviridae of ...
64-510
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Leviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Leviviridae, order Levivirales. Leviviridae is a family of (+)ssRNA viruses which are highly antigenic and are abundantly present in sewage, waste water, animal and human feces. Within this family two genera can be distinguished, Levivirus and Allolevivirus. Members of the family Leviviridae that propagate in Escherichia coli infect by adsorption to the sides of F(ertility) pili. This event leads to cleavage of the A-protein and release of the RNA from the virion into the bacterium. The infecting RNA encodes a replicase, which assembles with three host proteins, ribosomal protein S1 and translation elongation factors EF-Tu and EF-Ts, to form the active RNA polymerase. Leviviruses not only infect enterobacteria, but also species of the genera Caulobacter, Pseudomonas, and Acinetobacter, and probably many other Gram-negative bacteria. 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: 438026 Cd Length: 396 Bit Score: 555.54 E-value: 0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Leviviridae of ...
64-510
0e+00
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Leviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Leviviridae, order Levivirales. Leviviridae is a family of (+)ssRNA viruses which are highly antigenic and are abundantly present in sewage, waste water, animal and human feces. Within this family two genera can be distinguished, Levivirus and Allolevivirus. Members of the family Leviviridae that propagate in Escherichia coli infect by adsorption to the sides of F(ertility) pili. This event leads to cleavage of the A-protein and release of the RNA from the virion into the bacterium. The infecting RNA encodes a replicase, which assembles with three host proteins, ribosomal protein S1 and translation elongation factors EF-Tu and EF-Ts, to form the active RNA polymerase. Leviviruses not only infect enterobacteria, but also species of the genera Caulobacter, Pseudomonas, and Acinetobacter, and probably many other Gram-negative bacteria. 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: 438026 Cd Length: 396 Bit Score: 555.54 E-value: 0e+00
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...
269-366
4.96e-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: 38.86 E-value: 4.96e-04
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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To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(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.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
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specific hits meet or exceed a domain-specific e-value threshold
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