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UniProtKB - P25531 (YICR_ECOLI)

Entry version 148 (13 Nov 2019)
Sequence version 3 (30 May 2000)
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Protein

UPF0758 protein YicR

Gene

yicR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:2 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

Caution

Was originally thought to be the site of the radC102 mutation, but it was subsequently shown that radC102 is an allele of RecG.1 Publication

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 bindingi171Zinc; catalyticPROSITE-ProRule annotation1
Metal bindingi173Zinc; catalyticPROSITE-ProRule annotation1
Metal bindingi184Zinc; catalyticPROSITE-ProRule 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

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 functionHydrolase, Metalloprotease, Protease
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11312-MONOMER
ECOL316407:JW5643-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:
UPF0758 protein YicR
<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:yicR
Ordered Locus Names:b3638, JW5643
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 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_00001906941 – 222UPF0758 protein YicRAdd BLAST222

Proteomic databases

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

More...PaxDbi		P25531

PRoteomics IDEntifications database

More...PRIDEi		P25531

<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

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4261656, 200 interactors

Database of interacting proteins

More...DIPi		DIP-10636N

Protein interaction database and analysis system

More...IntActi		P25531, 2 interactors

STRING: functional protein association networks

More...STRINGi		511145.b3638

<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		P25531

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>Domaini100 – 222MPNPROSITE-ProRule annotationAdd BLAST123

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a short (usually not more than 20 amino acids) conserved sequence motif of biological significance.<p><a href='/help/motif' target='_top'>More...</a></p>Motifi171 – 184JAMM motifPROSITE-ProRule annotationAdd BLAST14

<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 UPF0758 family. YicR subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105W5Q Bacteria
COG2003 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000273376

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P25531

KEGG Orthology (KO)

More...KOi		K03630

Database for complete collections of gene phylogenies

More...PhylomeDBi		P25531

Family and domain databases

Conserved Domains Database

More...CDDi		cd08071 MPN_DUF2466, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00018 UPF0758_YicR, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR037518 MPN
IPR025657 RadC_JAB
IPR010994 RuvA_2-like
IPR001405 UPF0758
IPR020891 UPF0758_CS
IPR022820 UPF0758_YicR

The PANTHER Classification System

More...PANTHERi		PTHR30471 PTHR30471, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04002 RadC, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47781 SSF47781, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00608 radc, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50249 MPN, 1 hit
PS01302 UPF0758, 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.

P25531-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKNNSQLLMP REKMLKFGIS ALTDVELLAL FLRTGTRGKD VLTLAKEMLE 
        60         70         80         90        100
NFGSLYGLLT SEYEQFSGVH GIGVAKFAQL KGIAELARRY YNVRMREESP 
       110        120        130        140        150
LLSPEMTREF LQSQLTGEER EIFMVIFLDS QHRVITHRRL FSGTLNHVEV 
       160        170        180        190        200
HPREIIREAI KINASALILA HNHPSGCAEP SKADKLITER IIKSCQFMDL 
       210        220 
RVLDHIVIGR GEYVSFAERG WI
Length:222
Mass (Da):25,343
Last modified:May 30, 2000 - v3
<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:i1E825DEB596D742A
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 AAA61991 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.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
L10328 Genomic DNA Translation: AAA61991.1 Different initiation.
U00096 Genomic DNA Translation: AAC76662.2
AP009048 Genomic DNA Translation: BAE77654.1
X63366 Genomic DNA Translation: CAA44966.1
X63367 Genomic DNA Translation: CAA44967.1

Protein sequence database of the Protein Information Resource

More...PIRi		H65164

NCBI Reference Sequences

More...RefSeqi		NP_418095.4, NC_000913.3
WP_001350561.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC76662; AAC76662; b3638
BAE77654; BAE77654; BAE77654

Database of genes from NCBI RefSeq genomes

More...GeneIDi		948968

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW5643
eco:b3638

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.3758

<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
L10328 Genomic DNA Translation: AAA61991.1 Different initiation.
U00096 Genomic DNA Translation: AAC76662.2
AP009048 Genomic DNA Translation: BAE77654.1
X63366 Genomic DNA Translation: CAA44966.1
X63367 Genomic DNA Translation: CAA44967.1
PIRiH65164
RefSeqiNP_418095.4, NC_000913.3
WP_001350561.1, NZ_LN832404.1

3D structure databases

SMRiP25531
ModBaseiSearch...

Protein-protein interaction databases

BioGridi4261656, 200 interactors
DIPiDIP-10636N
IntActiP25531, 2 interactors
STRINGi511145.b3638

Proteomic databases

PaxDbiP25531
PRIDEiP25531

Genome annotation databases

EnsemblBacteriaiAAC76662; AAC76662; b3638
BAE77654; BAE77654; BAE77654
GeneIDi948968
KEGGiecj:JW5643
eco:b3638
PATRICifig|511145.12.peg.3758

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1288

Phylogenomic databases

eggNOGiENOG4105W5Q Bacteria
COG2003 LUCA
HOGENOMiHOG000273376
InParanoidiP25531
KOiK03630
PhylomeDBiP25531

Enzyme and pathway databases

BioCyciEcoCyc:EG11312-MONOMER
ECOL316407:JW5643-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25531

Family and domain databases

CDDicd08071 MPN_DUF2466, 1 hit
HAMAPiMF_00018 UPF0758_YicR, 1 hit
InterProiView protein in InterPro
IPR037518 MPN
IPR025657 RadC_JAB
IPR010994 RuvA_2-like
IPR001405 UPF0758
IPR020891 UPF0758_CS
IPR022820 UPF0758_YicR
PANTHERiPTHR30471 PTHR30471, 1 hit
PfamiView protein in Pfam
PF04002 RadC, 1 hit
SUPFAMiSSF47781 SSF47781, 1 hit
TIGRFAMsiTIGR00608 radc, 1 hit
PROSITEiView protein in PROSITE
PS50249 MPN, 1 hit
PS01302 UPF0758, 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 nameiYICR_ECOLI
<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: P25531
Secondary accession number(s): Q2M7V2
<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: May 1, 1992
Last sequence update: May 30, 2000
Last modified: November 13, 2019
This is version 148 of the entry and version 3 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. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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