RNA-directed RNA polymerase [Rotavirus B]
Protein Classification
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 ... |
148-739 | 6.00e-46 | |||||||||
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 pfam02123: Pssm-ID: 477363 Cd Length: 465 Bit Score: 172.64 E-value: 6.00e-46
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| DotY_NTD super family | cl45571 | N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of ... |
57-96 | 8.53e-03 | |||||||||
N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins,and DotY and DotZ. The DotLMNYZ hetero-pentamer and plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that utilizes a T4S system to inject effector proteins into human macrophages. This model corresponds to the N-terminal domain of DotY, which is responsible for interaction with DotZ. DotY and DotZ are integral parts of the T4CC and play significant roles in the translocation of effectors. They are unique to the Legionella genus. The actual alignment was detected with superfamily member cd22643: Pssm-ID: 439348 Cd Length: 72 Bit Score: 36.10 E-value: 8.53e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| RdRP_4 | pfam02123 | Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ... |
148-739 | 6.00e-46 | |||||||||
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: 172.64 E-value: 6.00e-46
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| seadorna_RNAP | TIGR04234 | seadornavirus RNA-directed RNA polymerase; Members of this protein family are the ... |
565-692 | 2.11e-03 | |||||||||
seadornavirus RNA-directed RNA polymerase; Members of this protein family are the seadornavirus VP1 protein, the RNA-directed RNA polymerase. Pssm-ID: 275072 Cd Length: 1144 Bit Score: 42.51 E-value: 2.11e-03
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| DotY_NTD | cd22643 | N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of ... |
57-96 | 8.53e-03 | |||||||||
N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins,and DotY and DotZ. The DotLMNYZ hetero-pentamer and plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that utilizes a T4S system to inject effector proteins into human macrophages. This model corresponds to the N-terminal domain of DotY, which is responsible for interaction with DotZ. DotY and DotZ are integral parts of the T4CC and play significant roles in the translocation of effectors. They are unique to the Legionella genus. Pssm-ID: 439348 Cd Length: 72 Bit Score: 36.10 E-value: 8.53e-03
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
642-694 | 9.49e-03 | |||||||||
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: 36.16 E-value: 9.49e-03
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| Name | Accession | Description | Interval | E-value | |||||||||
| RdRP_4 | pfam02123 | Viral RNA-directed RNA-polymerase; This family includes RNA-dependent RNA polymerase proteins ... |
148-739 | 6.00e-46 | |||||||||
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: 172.64 E-value: 6.00e-46
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| seadorna_RNAP | TIGR04234 | seadornavirus RNA-directed RNA polymerase; Members of this protein family are the ... |
565-692 | 2.11e-03 | |||||||||
seadornavirus RNA-directed RNA polymerase; Members of this protein family are the seadornavirus VP1 protein, the RNA-directed RNA polymerase. Pssm-ID: 275072 Cd Length: 1144 Bit Score: 42.51 E-value: 2.11e-03
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| DotY_NTD | cd22643 | N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of ... |
57-96 | 8.53e-03 | |||||||||
N-terminal domain of Legionella pneumophila DotY and similar proteins; DotY is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins,and DotY and DotZ. The DotLMNYZ hetero-pentamer and plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that utilizes a T4S system to inject effector proteins into human macrophages. This model corresponds to the N-terminal domain of DotY, which is responsible for interaction with DotZ. DotY and DotZ are integral parts of the T4CC and play significant roles in the translocation of effectors. They are unique to the Legionella genus. Pssm-ID: 439348 Cd Length: 72 Bit Score: 36.10 E-value: 8.53e-03
|
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
642-694 | 9.49e-03 | |||||||||
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: 36.16 E-value: 9.49e-03
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