tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
6-309
2.23e-103
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification
:
Pssm-ID: 439900 [Multi-domain] Cd Length: 288 Bit Score: 303.90 E-value: 2.23e-103
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
6-309
2.23e-103
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439900 [Multi-domain] Cd Length: 288 Bit Score: 303.90 E-value: 2.23e-103
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
3-242
1.67e-85
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Pssm-ID: 211339 [Multi-domain] Cd Length: 213 Bit Score: 255.83 E-value: 1.67e-85
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
2-241
1.33e-60
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129523 Cd Length: 209 Bit Score: 192.20 E-value: 1.33e-60
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
22-155
4.00e-54
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Pssm-ID: 426297 Cd Length: 148 Bit Score: 173.43 E-value: 4.00e-54
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal ...
6-309
2.23e-103
tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]; tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 439900 [Multi-domain] Cd Length: 288 Bit Score: 303.90 E-value: 2.23e-103
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial ...
3-242
1.67e-85
Pseudouridine synthase, Escherichia coli TruB like; This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Pssm-ID: 211339 [Multi-domain] Cd Length: 213 Bit Score: 255.83 E-value: 1.67e-85
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to ...
2-241
1.33e-60
tRNA pseudouridine(55) synthase; TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 129523 Cd Length: 209 Bit Score: 192.20 E-value: 1.33e-60
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved ...
22-155
4.00e-54
TruB family pseudouridylate synthase (N terminal domain); Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA.
Pssm-ID: 426297 Cd Length: 148 Bit Score: 173.43 E-value: 4.00e-54
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal ...
3-241
1.69e-51
Pseudouridine synthase, TruB family; This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dyskerin cause X-linked dyskeratosis congenitas.
Pssm-ID: 211323 [Multi-domain] Cd Length: 210 Bit Score: 168.87 E-value: 1.69e-51
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to ...
3-228
1.28e-34
Pseudouridine synthase homolog 4; This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Pssm-ID: 211344 [Multi-domain] Cd Length: 312 Bit Score: 127.94 E-value: 1.28e-34
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes ...
1-287
6.15e-19
rRNA pseudouridine synthase, putative; This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 273073 [Multi-domain] Cd Length: 322 Bit Score: 85.59 E-value: 6.15e-19
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal ...
6-242
4.34e-18
Pseudouridine synthase, human dyskerin like; This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl results in miniflies that suffer abnormalities.
Pssm-ID: 211338 Cd Length: 182 Bit Score: 80.38 E-value: 4.34e-18
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset ...
203-242
6.73e-03
tRNA pseudouridylate synthase B C-terminal domain; This C-terminal region is found on a subset of TruB_B protein family members pfam01509. It is found from bacteria and archaea to fungi, plants and human.
Pssm-ID: 465060 [Multi-domain] Cd Length: 65 Bit Score: 34.76 E-value: 6.73e-03
PUA RNA-binding domain of bacterial pseudouridine synthase TruB and similar proteins; The ...
255-308
8.37e-03
PUA RNA-binding domain of bacterial pseudouridine synthase TruB and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this bacterial subfamily of pseudouridine synthases, including TruB and similar proteins, are modules that assist in the binding and positioning (guide and/or substrate) of RNA to the pseudouridine synthase complex. Pseudouridine synthases are enzymes that are responsible for post-translational modifications of RNAs by specifically isomerizing uracil residues. The pseudouridine synthase TruB (also called tRNA pseudouridylate synthase B or Psi55 synthase) is responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of elongator tRNAs.
Pssm-ID: 409294 Cd Length: 60 Bit Score: 34.09 E-value: 8.37e-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.
Click on the triangle to view details about the feature, including a multiple sequence alignment
of your query sequence and the protein sequences used to curate the domain model,
where hash marks (#) above the aligned sequences show the location of the conserved feature residues.
The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
Click here to see more details.
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
(labeled illustration) or all hits
(labeled illustration).
Domains are color coded according to superfamilies
to which they have been assigned. Hits with scores that pass a domain-specific threshold
(specific hits) are drawn in bright colors.
Others (non-specific hits) and
superfamily placeholders are drawn in pastel colors.
if a domain or superfamily has been annotated with functional sites (conserved features),
they are mapped to the query sequence and indicated through sets of triangles
with the same color and shade of the domain or superfamily that provides the annotation. Mouse over the colored bars or triangles to see descriptions of the domains and features.
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)
mapped to the query sequence.
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
meet or exceed the RPS-BLAST threshold for statistical significance (default E-value cutoff of 0.01, or an E-value selected by user via the
advanced search options)
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
(CDART).
Modify your query to search against a different database and/or use advanced search options
