Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome ...
598-1336
0e+00
Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment.
The actual alignment was detected with superfamily member pfam04196:
Pssm-ID: 282102 Cd Length: 739 Bit Score: 704.23 E-value: 0e+00
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal ...
6-186
3.65e-88
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal endonuclease domain of sNSV polymerases is essential for viral cap-dependent transcription; it has endonuclease activity and belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
:
Pssm-ID: 411753 Cd Length: 182 Bit Score: 285.21 E-value: 3.65e-88
Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome ...
598-1336
0e+00
Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment.
Pssm-ID: 282102 Cd Length: 739 Bit Score: 704.23 E-value: 0e+00
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal ...
6-186
3.65e-88
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal endonuclease domain of sNSV polymerases is essential for viral cap-dependent transcription; it has endonuclease activity and belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411753 Cd Length: 182 Bit Score: 285.21 E-value: 3.65e-88
RNA endonuclease, cap-snatching, arenavirus family; This model describes a shared signature ...
79-135
2.89e-16
RNA endonuclease, cap-snatching, arenavirus family; This model describes a shared signature region from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses. This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself.
Pssm-ID: 275049 Cd Length: 61 Bit Score: 74.92 E-value: 2.89e-16
Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome ...
598-1336
0e+00
Bunyavirus RNA dependent RNA polymerase; The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment.
Pssm-ID: 282102 Cd Length: 739 Bit Score: 704.23 E-value: 0e+00
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal ...
6-186
3.65e-88
Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases; The N-terminal endonuclease domain of sNSV polymerases is essential for viral cap-dependent transcription; it has endonuclease activity and belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.
Pssm-ID: 411753 Cd Length: 182 Bit Score: 285.21 E-value: 3.65e-88
RNA endonuclease, cap-snatching, arenavirus family; This model describes a shared signature ...
79-135
2.89e-16
RNA endonuclease, cap-snatching, arenavirus family; This model describes a shared signature region from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses. This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself.
Pssm-ID: 275049 Cd Length: 61 Bit Score: 74.92 E-value: 2.89e-16
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.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
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,
or click on the triangles, if present, that represent functional sites (conserved features)
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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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and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
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the domain superfamily to which the specific and non-specific hits belong
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