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Protein

Probable tRNA pseudouridine synthase B

Gene

truB

Organism
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
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-55 in the psi GC loop of 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 sitei82NucleophileUniRule 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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
TKOD69014:G1G2A-1514-MONOMER

<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 BUniRule annotation (EC:5.4.99.25UniRule annotation)
Alternative name(s):
tRNA pseudouridine(55) synthaseUniRule annotation
Short name:
Psi55 synthaseUniRule annotation
tRNA pseudouridylate synthaseUniRule annotation
tRNA-uridine isomeraseUniRule 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:truBUniRule annotation
Ordered Locus Names:TK1509
<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>OrganismiThermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1))
<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 identifieri69014 [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 lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaeThermococcus
<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
  • UP000000536 <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 provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<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_00001219701 – 338Probable tRNA pseudouridine synthase BAdd BLAST338

<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
69014.TK1509

<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
Q5JJE8

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

More...
SMRi
Q5JJE8

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>Domaini250 – 325PUAUniRule annotationAdd BLAST76

<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 TruB family. Type 2 subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG00987 Archaea
COG0130 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000231224

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q5JJE8

KEGG Orthology (KO)

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KOi
K11131

Identification of Orthologs from Complete Genome Data

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OMAi
IYQRPPL

Database of Orthologous Groups

More...
OrthoDBi
POG093Z08NS

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01081 TruB_arch, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012960 Dyskerin-like
IPR020103 PsdUridine_synth_cat_dom_sf
IPR002501 PsdUridine_synth_N
IPR002478 PUA
IPR015947 PUA-like_sf
IPR004802 tRNA_PsdUridine_synth_B_fam
IPR026326 TruB_arch
IPR032819 TruB_C
IPR004521 Uncharacterised_CHP00451

The PANTHER Classification System

More...
PANTHERi
PTHR23127 PTHR23127, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF08068 DKCLD, 1 hit
PF01472 PUA, 1 hit
PF16198 TruB_C_2, 1 hit
PF01509 TruB_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01136 DKCLD, 1 hit
SM00359 PUA, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF55120 SSF55120, 1 hit
SSF88697 SSF88697, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00425 CBF5, 1 hit
TIGR00451 unchar_dom_2, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50890 PUA, 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.

Q5JJE8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MARDEVRRIL PADIKREVVV KDEKAETNPK WGFPPEKRPI EMHIQFGIIN
60 70 80 90 100
LDKPPGPTSH EVVAWVKRIL NLNKAGHGGT LDPKVSGVLP VALERATRVV
110 120 130 140 150
QALLPAGKEY VALMHLHGDV PEDKILAVMR EFQGEIIQRP PLRSAVKRRL
160 170 180 190 200
RTRKVYYIDV LEIEGRDVLF RVGVEAGTYI RSLIHHIGLA LGVGAHMAEL
210 220 230 240 250
RRTRSGPFKE DETLVTLHDL VDYYHFWKED GVEEYFRKAI QPMEKAVEHL
260 270 280 290 300
PKVWIRDSAV AAVTHGADLA VPGVVKLHKG IKKGDLVAIM TLKDELVALG
310 320 330
KAMMTTGEML QKSKGIAVDV DKVFMPRDWY PKLWKEKE
Length:338
Mass (Da):38,215
Last modified:February 15, 2005 - 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:i96230D6C1D75EC23
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AP006878 Genomic DNA Translation: BAD85698.1

NCBI Reference Sequences

More...
RefSeqi
WP_011250460.1, NC_006624.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
BAD85698; BAD85698; TK1509

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
3235127

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
tko:TK1509

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|69014.16.peg.1469

<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
AP006878 Genomic DNA Translation: BAD85698.1
RefSeqiWP_011250460.1, NC_006624.1

3D structure databases

ProteinModelPortaliQ5JJE8
SMRiQ5JJE8
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi69014.TK1509

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD85698; BAD85698; TK1509
GeneIDi3235127
KEGGitko:TK1509
PATRICifig|69014.16.peg.1469

Phylogenomic databases

eggNOGiarCOG00987 Archaea
COG0130 LUCA
HOGENOMiHOG000231224
InParanoidiQ5JJE8
KOiK11131
OMAiIYQRPPL
OrthoDBiPOG093Z08NS

Enzyme and pathway databases

BioCyciTKOD69014:G1G2A-1514-MONOMER

Family and domain databases

HAMAPiMF_01081 TruB_arch, 1 hit
InterProiView protein in InterPro
IPR012960 Dyskerin-like
IPR020103 PsdUridine_synth_cat_dom_sf
IPR002501 PsdUridine_synth_N
IPR002478 PUA
IPR015947 PUA-like_sf
IPR004802 tRNA_PsdUridine_synth_B_fam
IPR026326 TruB_arch
IPR032819 TruB_C
IPR004521 Uncharacterised_CHP00451
PANTHERiPTHR23127 PTHR23127, 1 hit
PfamiView protein in Pfam
PF08068 DKCLD, 1 hit
PF01472 PUA, 1 hit
PF16198 TruB_C_2, 1 hit
PF01509 TruB_N, 1 hit
SMARTiView protein in SMART
SM01136 DKCLD, 1 hit
SM00359 PUA, 1 hit
SUPFAMiSSF55120 SSF55120, 1 hit
SSF88697 SSF88697, 1 hit
TIGRFAMsiTIGR00425 CBF5, 1 hit
TIGR00451 unchar_dom_2, 1 hit
PROSITEiView protein in PROSITE
PS50890 PUA, 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 nameiTRUB_THEKO
<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: Q5JJE8
<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: April 26, 2005
Last sequence update: February 15, 2005
Last modified: December 5, 2018
This is version 87 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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