tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; tRNA(Glu) U13 pseudouridine synthase TruD is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440350 [Multi-domain] Cd Length: 349 Bit Score: 447.72 E-value: 1.57e-158
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called ...
1-343
2.48e-134
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272903 [Multi-domain] Cd Length: 387 Bit Score: 387.98 E-value: 2.48e-134
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial ...
18-338
6.41e-122
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Pssm-ID: 211340 [Multi-domain] Cd Length: 253 Bit Score: 351.13 E-value: 6.41e-122
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from ...
18-337
5.18e-62
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.
Pssm-ID: 426077 [Multi-domain] Cd Length: 414 Bit Score: 203.58 E-value: 5.18e-62
tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]; tRNA(Glu) U13 pseudouridine synthase TruD is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440350 [Multi-domain] Cd Length: 349 Bit Score: 447.72 E-value: 1.57e-158
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called ...
1-343
2.48e-134
tRNA pseudouridine synthase, TruD family; an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 272903 [Multi-domain] Cd Length: 387 Bit Score: 387.98 E-value: 2.48e-134
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial ...
18-338
6.41e-122
Pseudouridine synthase, similar to Escherichia coli TruD; This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Pssm-ID: 211340 [Multi-domain] Cd Length: 253 Bit Score: 351.13 E-value: 6.41e-122
Pseudouridine synthase, TruD family; This group consists of eukaryotic, bacterial and archeal ...
18-338
1.90e-73
Pseudouridine synthase, TruD family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Pssm-ID: 211326 [Multi-domain] Cd Length: 232 Bit Score: 227.09 E-value: 1.90e-73
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from ...
18-337
5.18e-62
tRNA pseudouridine synthase D (TruD); TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft.
Pssm-ID: 426077 [Multi-domain] Cd Length: 414 Bit Score: 203.58 E-value: 5.18e-62
Pseudouridine synthase, a subgroup of the TruD family; This group consists of several ...
18-338
1.05e-35
Pseudouridine synthase, a subgroup of the TruD family; This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Pssm-ID: 211342 [Multi-domain] Cd Length: 319 Bit Score: 132.06 E-value: 1.05e-35
Pseudouridine synthase, TruD family; This group consists of eukaryotic pseudouridine synthases ...
17-338
6.47e-30
Pseudouridine synthase, TruD family; This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Pssm-ID: 211341 [Multi-domain] Cd Length: 371 Bit Score: 117.33 E-value: 6.47e-30
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
50-92
4.72e-12
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Pssm-ID: 211324 [Multi-domain] Cd Length: 87 Bit Score: 61.04 E-value: 4.72e-12
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to ...
303-338
2.05e-04
Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Pssm-ID: 211324 [Multi-domain] Cd Length: 87 Bit Score: 39.47 E-value: 2.05e-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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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
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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.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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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,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
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
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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