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Entry version 77 (08 May 2019)
Sequence version 1 (27 Jun 2006)
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Protein

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

Gene

rlmD

Organism
Methylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875)
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_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 <a href="http://www.uniprot.org/help/function_section">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 bindingi68Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi74Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi77Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi156Iron-sulfur (4Fe-4S)UniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei265S-adenosyl-L-methionineUniRule annotation1
Binding sitei294S-adenosyl-L-methionine; via carbonyl oxygenUniRule annotation1
Binding sitei299S-adenosyl-L-methionineUniRule annotation1
Binding sitei315S-adenosyl-L-methionineUniRule annotation1
Binding sitei343S-adenosyl-L-methionineUniRule annotation1
Binding sitei364S-adenosyl-L-methionineUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei399NucleophileUniRule 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

<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
MFLA265072:G1G69-1994-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:
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_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:rlmDUniRule annotation
Synonyms:rumA
Ordered Locus Names:Mfla_1851
<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>OrganismiMethylobacillus flagellatus (strain KT / ATCC 51484 / DSM 6875)
<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 identifieri265072 [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 lineageiBacteriaProteobacteriaBetaproteobacteriaNitrosomonadalesMethylophilaceaeMethylobacillus
<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
  • UP000002440 <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_00002820491 – 44523S rRNA (uracil(1939)-C(5))-methyltransferase RlmDAdd BLAST445

<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
265072.Mfla_1851

<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
Q1H069

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_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>Domaini1 – 55TRAMUniRule annotationAdd BLAST55

<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

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105BZT Bacteria
COG2265 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000029868

KEGG Orthology (KO)

More...
KOi
K03215

Identification of Orthologs from Complete Genome Data

More...
OMAi
FTQVNPH

Database of Orthologous Groups

More...
OrthoDBi
1421660at2

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
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
PF01938 TRAM, 1 hit
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
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_length">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_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.

Q1H069-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSTPIALVES LDQEGRGVAH VEGKTIFIDG ALPGEQVTYK VRRRKERYEV
60 70 80 90 100
ADVLDVLQAS HLRTQPGCEH FGVCGGCAIQ HLEFSGQVAA KQRMLESNLW
110 120 130 140 150
HIGKTRSERM LPPIYGPAWG YRHKARLRVR HVAKKGGVLV GFNEKSSSFV
160 170 180 190 200
ADMDSCRVLP PHVSNLIVPM KELVGQLSIR DRLPQIEVAV GELATVLVLR
210 220 230 240 250
ILEPLQPQDA APIKAFADRY GVEVWTQSKG PDTVQPFYPL QGPGLSYSLP
260 270 280 290 300
EFNLTYPFKP TEFTQVNPYI NRVMLRRAMQ LLQPQPGERI ADFFCGLGNF
310 320 330 340 350
TLPIARSGAS VFGMEGSAAL VARANESAAL NSLAGQVEFQ EADLFKMTPA
360 370 380 390 400
LLQSLGRFDK WLIDPPRDGA IELVKALPDI EDADADTSHV PQRIVYVSCN
410 420 430 440
PATLARDAGI LVHTKGYRLL ASGVINMFPH TSHVESIALF EKASP
Length:445
Mass (Da):49,009
Last modified:June 27, 2006 - 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:i69ABC8FF4E6C1C3E
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
CP000284 Genomic DNA Translation: ABE50118.1

NCBI Reference Sequences

More...
RefSeqi
WP_011480072.1, NC_007947.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABE50118; ABE50118; Mfla_1851

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mfa:Mfla_1851

<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
CP000284 Genomic DNA Translation: ABE50118.1
RefSeqiWP_011480072.1, NC_007947.1

3D structure databases

SMRiQ1H069
ModBaseiSearch...

Protein-protein interaction databases

STRINGi265072.Mfla_1851

Genome annotation databases

EnsemblBacteriaiABE50118; ABE50118; Mfla_1851
KEGGimfa:Mfla_1851

Phylogenomic databases

eggNOGiENOG4105BZT Bacteria
COG2265 LUCA
HOGENOMiHOG000029868
KOiK03215
OMAiFTQVNPH
OrthoDBi1421660at2

Enzyme and pathway databases

BioCyciMFLA265072:G1G69-1994-MONOMER

Family and domain databases

HAMAPiMF_01010 23SrRNA_methyltr_RlmD, 1 hit
InterProiView protein in InterPro
IPR001566 23S_rRNA_MeTrfase_RlmD
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
PF01938 TRAM, 1 hit
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
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_METFK
<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: Q1H069
<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 3, 2007
Last sequence update: June 27, 2006
Last modified: May 8, 2019
This is version 77 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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