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UniProtKB - Q9RX88 (RL25_DEIRA)

Entry version 134 (08 May 2019)
Sequence version 2 (15 Mar 2004)
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Protein

50S ribosomal protein L25

Gene

rplY

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
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>-Experimental evidence at protein leveli <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

This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit. This protein has three domains. The N-terminal one is bound on the solvent face, the middle domain fills the space between the 5S rRNA and the L11 arm contacting the 23S rRNA while the C-terminal domain is on the edge of the intersubunit interface and contacts the A site. The protein conformation changes upon binding of a tRNA mimic to the A site, although the mimic does not interact directly with CTC itself, consistent with CTCs presumed role in moderating A site binding.

<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

  • 5S rRNA binding Source: GO_Central
  • structural constituent of ribosome Source: InterPro
  • tRNA binding Source: UniProtKB-KW
View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

<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 functionRibonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding

<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:
50S ribosomal protein L25
Alternative name(s):
General stress protein CTC
<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:rplY
Synonyms:ctc
Ordered Locus Names:DR_0427
<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>OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
<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 identifieri243230 [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 lineageiBacteria › Deinococcus-Thermus › Deinococci › Deinococcales › Deinococcaceae › Deinococcus ›
<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
  • UP000002524 <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 I

<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

View the complete GO annotation on QuickGO ...

<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_00001815431 – 23750S ribosomal protein L25Add BLAST237

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Part of the 50S ribosomal subunit. Contacts proteins L11 and L16, the A site tRNA, and the 5S and 23S rRNAs.6 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		243230.DR_0427

<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

Secondary structure

1237
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJMX-ray3.60T1-237[»]
1NJPX-ray3.50T1-237[»]
1NKWX-ray3.10T1-237[»]
1NWXX-ray3.50T1-237[»]
1NWYX-ray3.30T1-237[»]
1SM1X-ray3.42T1-237[»]
1XBPX-ray3.50T1-237[»]
2ZJPX-ray3.70S1-237[»]
2ZJQX-ray3.30S1-237[»]
2ZJRX-ray2.91S1-237[»]
3CF5X-ray3.30S1-237[»]
3DLLX-ray3.50S1-237[»]
3PIOX-ray3.25S1-237[»]
3PIPX-ray3.45S1-237[»]
4IO9X-ray3.20S1-237[»]
4IOAX-ray3.20S1-237[»]
4IOCX-ray3.60S1-237[»]
4U67X-ray3.65S1-237[»]
4V49X-ray8.70T1-173[»]
4V4AX-ray9.50T1-173[»]
4V4GX-ray11.50W1-173[»]
4V4PX-ray5.50V1-237[»]
4V4RX-ray5.90Z1-237[»]
4V4SX-ray6.76Z1-237[»]
4V4TX-ray6.46Z1-237[»]
4WFNX-ray3.54S1-237[»]
5DM6X-ray2.90S1-175[»]
5DM7X-ray3.00S1-175[»]
5JVGX-ray3.43S1-237[»]
5JVHX-ray3.58S1-237[»]

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

More...SMRi		Q9RX88

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		Q9RX88

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 104N-terminal domainAdd BLAST104
Regioni105 – 189Middle domainAdd BLAST85
Regioni190 – 237C-terminal domainAdd BLAST48

<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 bacterial ribosomal protein bL25 family. CTC subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4107UH2 Bacteria
COG1825 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000214906

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q9RX88

KEGG Orthology (KO)

More...KOi		K02897

Identification of Orthologs from Complete Genome Data

More...OMAi		NIIHVDF

Database of Orthologous Groups

More...OrthoDBi		1673077at2

Family and domain databases

Conserved Domains Database

More...CDDi		cd00495 Ribosomal_L25_TL5_CTC, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		2.170.120.20, 1 hit
2.40.240.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01334 Ribosomal_L25_CTC, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR020056 Rbsml_L25/Gln-tRNA_synth_N
IPR029751 Ribosomal_L25
IPR011035 Ribosomal_L25/Gln-tRNA_synth
IPR020057 Ribosomal_L25_b-dom
IPR037121 Ribosomal_L25_C
IPR001021 Ribosomal_L25_long

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01386 Ribosomal_L25p, 1 hit
PF14693 Ribosomal_TL5_C, 1 hit

ProDom; a protein domain database

More...ProDomi		View protein in ProDom or Entries sharing at least one domain
PD012503 Ribosomal_L25, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF50715 SSF50715, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00731 bL25_bact_ctc, 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.

Q9RX88-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MELTAKPRTP KQKLDESMIA AVAYNKENNV SFALDRKAFD RAFRQQSTTG 
        60         70         80         90        100
LFDITVEGGE TFPALVKAVQ MDKRKRAPIH VDFYMVTYGE PVEVSVPVHT 
       110        120        130        140        150
TGRSQGEVQG GLVDIVVHNL QIVAPGPRRI PQELVVDVTK MNIGDHITAG 
       160        170        180        190        200
DIKLPEGCTL AADPELTVVS VLPPRLTAEE LEAEVQAAQV AGLVAAGELS 
       210        220        230 
EEAAEAVLEG DASLEEVKAE ASEDNAGTDS EDNSDAQ
Length:237
Mass (Da):25,390
Last modified:March 15, 2004 - v2
<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:i1B67F7DD4D385C21
GO

<p>This subsection of the ‘Sequence’ section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAF10004 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
AE000513 Genomic DNA Translation: AAF10004.1 Different initiation.

Protein sequence database of the Protein Information Resource

More...PIRi		A75521

NCBI Reference Sequences

More...RefSeqi		NP_294150.1, NC_001263.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAF10004; AAF10004; DR_0427

Database of genes from NCBI RefSeq genomes

More...GeneIDi		1798774

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		dra:DR_0427

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|243230.17.peg.601

<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
AE000513 Genomic DNA Translation: AAF10004.1 Different initiation.
PIRiA75521
RefSeqiNP_294150.1, NC_001263.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NJMX-ray3.60T1-237[»]
1NJPX-ray3.50T1-237[»]
1NKWX-ray3.10T1-237[»]
1NWXX-ray3.50T1-237[»]
1NWYX-ray3.30T1-237[»]
1SM1X-ray3.42T1-237[»]
1XBPX-ray3.50T1-237[»]
2ZJPX-ray3.70S1-237[»]
2ZJQX-ray3.30S1-237[»]
2ZJRX-ray2.91S1-237[»]
3CF5X-ray3.30S1-237[»]
3DLLX-ray3.50S1-237[»]
3PIOX-ray3.25S1-237[»]
3PIPX-ray3.45S1-237[»]
4IO9X-ray3.20S1-237[»]
4IOAX-ray3.20S1-237[»]
4IOCX-ray3.60S1-237[»]
4U67X-ray3.65S1-237[»]
4V49X-ray8.70T1-173[»]
4V4AX-ray9.50T1-173[»]
4V4GX-ray11.50W1-173[»]
4V4PX-ray5.50V1-237[»]
4V4RX-ray5.90Z1-237[»]
4V4SX-ray6.76Z1-237[»]
4V4TX-ray6.46Z1-237[»]
4WFNX-ray3.54S1-237[»]
5DM6X-ray2.90S1-175[»]
5DM7X-ray3.00S1-175[»]
5JVGX-ray3.43S1-237[»]
5JVHX-ray3.58S1-237[»]
SMRiQ9RX88
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0427

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF10004; AAF10004; DR_0427
GeneIDi1798774
KEGGidra:DR_0427
PATRICifig|243230.17.peg.601

Phylogenomic databases

eggNOGiENOG4107UH2 Bacteria
COG1825 LUCA
HOGENOMiHOG000214906
InParanoidiQ9RX88
KOiK02897
OMAiNIIHVDF
OrthoDBi1673077at2

Miscellaneous databases

EvolutionaryTraceiQ9RX88

Family and domain databases

CDDicd00495 Ribosomal_L25_TL5_CTC, 1 hit
Gene3Di2.170.120.20, 1 hit
2.40.240.10, 1 hit
HAMAPiMF_01334 Ribosomal_L25_CTC, 1 hit
InterProiView protein in InterPro
IPR020056 Rbsml_L25/Gln-tRNA_synth_N
IPR029751 Ribosomal_L25
IPR011035 Ribosomal_L25/Gln-tRNA_synth
IPR020057 Ribosomal_L25_b-dom
IPR037121 Ribosomal_L25_C
IPR001021 Ribosomal_L25_long
PfamiView protein in Pfam
PF01386 Ribosomal_L25p, 1 hit
PF14693 Ribosomal_TL5_C, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD012503 Ribosomal_L25, 1 hit
SUPFAMiSSF50715 SSF50715, 1 hit
TIGRFAMsiTIGR00731 bL25_bact_ctc, 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 nameiRL25_DEIRA
<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: Q9RX88
<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: March 15, 2004
Last sequence update: March 15, 2004
Last modified: May 8, 2019
This is version 134 of the entry and version 2 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
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