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Entry version 115 (12 Aug 2020)
Sequence version 1 (01 Mar 2001)
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Protein

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Gene

rlmD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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

Catalyzes the formation of 5-methyl-uridine at position 1939 (m5U1939) in 23S rRNA.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi91Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi97Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi100Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi179Iron-sulfur (4Fe-4S)UniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei283S-adenosyl-L-methionineUniRule annotation1
Binding sitei312S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei317S-adenosyl-L-methionineUniRule annotation1
Binding sitei333S-adenosyl-L-methionineUniRule annotation1
Binding sitei360S-adenosyl-L-methionineUniRule annotation1
Binding sitei381S-adenosyl-L-methionineUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> 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 sitei407NucleophileUniRule 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

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 functionMethyltransferase, Transferase
Biological processrRNA processing
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
PAER208964:G1FZ6-953-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%5Fand%5Ftaxonomy%5Fsection">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:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmDUniRule annotation (EC:2.1.1.190UniRule annotation)
Alternative name(s):
23S rRNA(m5U1939)-methyltransferaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:rlmDUniRule annotation
Synonyms:rumA
Ordered Locus Names:PA0933
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri208964 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000002438 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

Organism-specific databases

Pseudomonas genome database

More...
PseudoCAPi
PA0933

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001619071 – 45023S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST450

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q9I525

PRoteomics IDEntifications database

More...
PRIDEi
Q9I525

<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

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

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SMRi
Q9I525

Database of comparative protein structure models

More...
ModBasei
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%5Fand%5Fdomains%5Fsection">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>Domaini20 – 78TRAMUniRule annotationAdd BLAST59

<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

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_014689_8_2_6

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
Q9I525

KEGG Orthology (KO)

More...
KOi
K03215

Identification of Orthologs from Complete Genome Data

More...
OMAi
PAWGYRY

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q9I525

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_01010, 23SrRNA_methyltr_RlmD, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001566, 23S_rRNA_MeTrfase_RlmD
IPR030390, MeTrfase_TrmA_AS
IPR030391, MeTrfase_TrmA_CS
IPR012340, NA-bd_OB-fold
IPR029063, SAM-dependent_MTases
IPR002792, TRAM_dom
IPR010280, U5_MeTrfase_fam

The PANTHER Classification System

More...
PANTHERi
PTHR11061, PTHR11061, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF05958, tRNA_U5-meth_tr, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249, SSF50249, 1 hit
SSF53335, SSF53335, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51687, SAM_MT_RNA_M5U, 1 hit
PS50926, TRAM, 1 hit
PS01230, TRMA_1, 1 hit
PS01231, TRMA_2, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q9I525-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MARNKGGLRF QPSGGARGPA IPVGKKQRLT IERLAHDGRG IAHEAGMTWF
60 70 80 90 100
VSGGLPGEEL EARVLGARSK VVDARSERLF SSSDLRRREP CTVAGRCGGC
110 120 130 140 150
TLQHLEHGEQ LALKQRTLQE QLQRFAGIEP EEWAAPLVGP EFGYRRRARI
160 170 180 190 200
AVRWDARARR LDVGFRASAS QEIVAFDECL VLVPPLQTIA RALPALLQDF
210 220 230 240 250
RKPESIGHVE LFHGTASALL LRHTTALVDE DRQRLAAFCS AHQAQLWLQG
260 270 280 290 300
AEQPLPVEPA AELGYSLGDW QLTLAYRPGD FVQVNAPVNE SMIRQALDWL
310 320 330 340 350
APTADERVLD LFCGLGNFSL PLARRVARVV GVEGVAAMVE RAGANALANG
360 370 380 390 400
LGNAHFFQAD LSKALAEAPW AEQGFTAVLL DPPRDGAFEA VREMSSLGAR
410 420 430 440 450
RVVYVSCNPA TLARDAGEMA RQGYRLKRAG ILDMFPQTAH VEAMALFEAG
Length:450
Mass (Da):49,071
Last modified:March 1, 2001 - 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:i22FEB0A4C4A4F6A9
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
AE004091 Genomic DNA Translation: AAG04322.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B83530

NCBI Reference Sequences

More...
RefSeqi
NP_249624.1, NC_002516.2
WP_003102417.1, NZ_QZGE01000007.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAG04322; AAG04322; PA0933

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
881477

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
pae:PA0933

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|208964.12.peg.968

<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
AE004091 Genomic DNA Translation: AAG04322.1
PIRiB83530
RefSeqiNP_249624.1, NC_002516.2
WP_003102417.1, NZ_QZGE01000007.1

3D structure databases

SMRiQ9I525
ModBaseiSearch...

Proteomic databases

PaxDbiQ9I525
PRIDEiQ9I525

Genome annotation databases

EnsemblBacteriaiAAG04322; AAG04322; PA0933
GeneIDi881477
KEGGipae:PA0933
PATRICifig|208964.12.peg.968

Organism-specific databases

PseudoCAPiPA0933

Phylogenomic databases

HOGENOMiCLU_014689_8_2_6
InParanoidiQ9I525
KOiK03215
OMAiPAWGYRY
PhylomeDBiQ9I525

Enzyme and pathway databases

BioCyciPAER208964:G1FZ6-953-MONOMER

Family and domain databases

HAMAPiMF_01010, 23SrRNA_methyltr_RlmD, 1 hit
InterProiView protein in InterPro
IPR001566, 23S_rRNA_MeTrfase_RlmD
IPR030390, MeTrfase_TrmA_AS
IPR030391, MeTrfase_TrmA_CS
IPR012340, NA-bd_OB-fold
IPR029063, SAM-dependent_MTases
IPR002792, TRAM_dom
IPR010280, U5_MeTrfase_fam
PANTHERiPTHR11061, PTHR11061, 1 hit
PfamiView protein in Pfam
PF05958, tRNA_U5-meth_tr, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
SSF53335, SSF53335, 1 hit
PROSITEiView protein in PROSITE
PS51687, SAM_MT_RNA_M5U, 1 hit
PS50926, TRAM, 1 hit
PS01230, TRMA_1, 1 hit
PS01231, TRMA_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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 nameiRLMD_PSEAE
<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: Q9I525
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 3, 2002
Last sequence update: March 1, 2001
Last modified: August 12, 2020
This is version 115 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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