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Protein

Probable tRNA pseudouridine synthase D

Gene

truD

Organism
Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Protein inferred from homologyi <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Could be responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei97NucleophileUniRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • pseudouridine synthase activity Source: GO_Central
  • RNA binding Source: InterPro
  • tRNA pseudouridine synthase activity Source: UniProtKB-EC

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionIsomerase
Biological processtRNA processing

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Probable tRNA pseudouridine synthase DUniRule annotation (EC:5.4.99.27UniRule annotation)
Alternative name(s):
tRNA pseudouridine(13) synthaseUniRule annotation
tRNA pseudouridylate synthase DUniRule annotation
tRNA-uridine isomerase DUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:truDUniRule annotation
Ordered Locus Names:PAE3134
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiPyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri178306 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermoproteaceaePyrobaculum
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002439 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001525501 – 413Probable tRNA pseudouridine synthase DAdd BLAST413

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q8ZTR2

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
178306.PAE3134

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
Q8ZTR2

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
Q8ZTR2

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini167 – 370TRUDUniRule annotationAdd BLAST204

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the pseudouridine synthase TruD family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
arCOG04252 Archaea
COG0585 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000224849

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q8ZTR2

KEGG Orthology (KO)

More...
KOi
K06176

Identification of Orthologs from Complete Genome Data

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OMAi
LRYERAM

Database of Orthologous Groups

More...
OrthoDBi
POG093Z087N

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01082 TruD, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR020103 PsdUridine_synth_cat_dom_sf
IPR001656 PsdUridine_synth_TruD
IPR020119 PsdUridine_synth_TruD_CS
IPR011760 PsdUridine_synth_TruD_insert

The PANTHER Classification System

More...
PANTHERi
PTHR13326 PTHR13326, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01142 TruD, 1 hit

PIRSF; a whole-protein classification database

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PIRSFi
PIRSF037016 Pseudouridin_synth_euk_prd, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF55120 SSF55120, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00094 tRNA_TruD_broad, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50984 TRUD, 1 hit
PS01268 UPF0024, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q8ZTR2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLEAPSFDKM LGMFYYATDT CPSGGVIKRS PEDFVVEEVL LDGTVIATSG
60 70 80 90 100
VELRPRVGNW TWIHVVKRNV DTIKLVLRLA RALGLSHRDV SVGGLKDTKA
110 120 130 140 150
VTSQIISVRG PVANLPQLPG VQFLGMWSMD KPITPSQIYG NRFTIILRDV
160 170 180 190 200
ERISCAEGAL EALKKTAAPN YYGYQRFGTI RPVTHLLGKA LLKKDPHLFF
210 220 230 240 250
EVMFCKIFSR ESEVAKRARE AACKGDYAKA LELFPKKFVE ERVFLKRLAG
260 270 280 290 300
GYDMWNAIMA IPPQILRVYI EAAQSYIFNR FLSIRMEIGP IDRPVEGDLV
310 320 330 340 350
EINRQIAYYA EGLGGEVVLP VVGAGVRMPR GKVGEALLRV LREEGLDPSA
360 370 380 390 400
FLKMPRGLRV YGTYRRVRLE PAGFEYKIMG NDVFMQFTLP RGSYATVLLR
410
EVVKPAEPHK HGF
Length:413
Mass (Da):46,357
Last modified:March 1, 2002 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC533FDF84538791A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AE009441 Genomic DNA Translation: AAL64697.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAL64697; AAL64697; PAE3134

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pai:PAE3134

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|178306.9.peg.2356

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009441 Genomic DNA Translation: AAL64697.1

3D structure databases

ProteinModelPortaliQ8ZTR2
SMRiQ8ZTR2
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi178306.PAE3134

Proteomic databases

PRIDEiQ8ZTR2

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL64697; AAL64697; PAE3134
KEGGipai:PAE3134
PATRICifig|178306.9.peg.2356

Phylogenomic databases

eggNOGiarCOG04252 Archaea
COG0585 LUCA
HOGENOMiHOG000224849
InParanoidiQ8ZTR2
KOiK06176
OMAiLRYERAM
OrthoDBiPOG093Z087N

Family and domain databases

HAMAPiMF_01082 TruD, 1 hit
InterProiView protein in InterPro
IPR020103 PsdUridine_synth_cat_dom_sf
IPR001656 PsdUridine_synth_TruD
IPR020119 PsdUridine_synth_TruD_CS
IPR011760 PsdUridine_synth_TruD_insert
PANTHERiPTHR13326 PTHR13326, 1 hit
PfamiView protein in Pfam
PF01142 TruD, 1 hit
PIRSFiPIRSF037016 Pseudouridin_synth_euk_prd, 1 hit
SUPFAMiSSF55120 SSF55120, 1 hit
TIGRFAMsiTIGR00094 tRNA_TruD_broad, 1 hit
PROSITEiView protein in PROSITE
PS50984 TRUD, 1 hit
PS01268 UPF0024, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiTRUD_PYRAE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q8ZTR2
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2003
Last sequence update: March 1, 2002
Last modified: December 5, 2018
This is version 90 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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