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Entry version 40 (07 Apr 2021)
Sequence version 1 (29 May 2013)
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Protein

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

Gene

rumA

Organism
Escherichia coli MP021561.2
Status
Unreviewed-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

Caution

The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data.Imported

<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 bindingi81Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi87Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi90Iron-sulfur (4Fe-4S)UniRule annotation1
Metal bindingi162Iron-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 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 sitei342S-adenosyl-L-methionineUniRule annotation1
Binding sitei363S-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 sitei389PROSITE-ProRule annotation1
Active sitei389NucleophileUniRule 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 functionMethyltransferaseUniRule annotationARBA annotation, Transferase
Biological processrRNA processingUniRule annotationARBA annotation
Ligand4Fe-4SUniRule annotationARBA annotation, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionineUniRule annotationARBA annotation

<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:rumAImported
Synonyms:rlmDUniRule annotation
ORF Names:ECMP0215612_3605Imported
<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>OrganismiEscherichia coli MP021561.2Imported
<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 identifieri1116136 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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
  • UP000012254 <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: Unassembled WGS sequence

<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

More...
SMRi
M9H2P9

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>Domaini10 – 68TRAMInterPro 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

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
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
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.

M9H2P9-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAQFYSAKRR TTTRQIITVS VNDLDSFGQG VARHNGKTLF IPGLLPQENA
60 70 80 90 100
EVTVTEDKKQ YARAKVVRRL SDSPERETPR CPHFGVCGGC QQQHASVDLQ
110 120 130 140 150
QRSKSAALAR LMKHDVSEVI ADVPWGYRRR ARLSLNYLPK TQQLQMGFRK
160 170 180 190 200
AGSSDIVDVK QCPILAPQLE ALLPKVRACL GSLQAMRHLG HVELVQATSG
210 220 230 240 250
TLMILRHTAP LSSADREKLE RFSHSEGLDL YLAPDSEILE TVSGEMPWYD
260 270 280 290 300
SNGLRLTFSP RDFIQVNAGV NQKMVARALE WLDVQPEDRV LDLFCGMGNF
310 320 330 340 350
TLPLATQAAS VVGVEGVPAL VEKGQQNARL NGLQNVTFYH ENLEEDVTKQ
360 370 380 390 400
PWAKNGFDKV LLDPARAGAA GVMQQIIKLE PIRIVYVSCN PATLARDSEA
410 420 430
LLKAGYTIAR LAMLDMFPHT GHLESMVLFS RVK
Length:433
Mass (Da):48,052
Last modified:May 29, 2013 - 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:iA46C07B0BD18EAAC
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
AQEV01000014 Genomic DNA Translation: EMX29336.1

NCBI Reference Sequences

More...
RefSeqi
WP_000046812.1, NZ_AQEV01000014.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
EMX29336; EMX29336; ECMP0215612_3605

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
57730411

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1116136.3.peg.3550

<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
AQEV01000014 Genomic DNA Translation: EMX29336.1
RefSeqiWP_000046812.1, NZ_AQEV01000014.1

3D structure databases

SMRiM9H2P9
ModBaseiSearch...

Genome annotation databases

EnsemblBacteriaiEMX29336; EMX29336; ECMP0215612_3605
GeneIDi57730411
PATRICifig|1116136.3.peg.3550

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
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
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 nameiM9H2P9_ECOLX
<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: M9H2P9
<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/TrEMBL: May 29, 2013
Last sequence update: May 29, 2013
Last modified: April 7, 2021
This is version 40 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 statusiUnreviewed (UniProtKB/TrEMBL)
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