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UniProtKB - P0A8J4 (YBED_ECOLI)

Entry version 111 (18 Sep 2019)
Sequence version 1 (07 Jun 2005)
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Protein

UPF0250 protein YbeD

Gene

ybeD

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>-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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11592-MONOMER
ECOL316407:JW0626-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:
UPF0250 protein YbeD
<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:ybeD
Ordered Locus Names:b0631, JW0626
<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

Organism-specific databases

Escherichia coli strain K12 genome database

More...EcoGenei		EG11592 ybeD

<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

<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 - Cellular componenti

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_00002092961 – 87UPF0250 protein YbeDAdd BLAST87

Proteomic databases

Encyclopedia of Proteome Dynamics

More...EPDi		P0A8J4

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P0A8J4

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

More...PaxDbi		P0A8J4

PRoteomics IDEntifications database

More...PRIDEi		P0A8J4

<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%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

WithEntry#Exp.IntActNotes
tufAP0CE473EBI-370708,EBI-301077

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4260679, 235 interactors

Database of interacting proteins

More...DIPi		DIP-31839N

Protein interaction database and analysis system

More...IntActi		P0A8J4, 10 interactors

STRING: functional protein association networks

More...STRINGi		511145.b0631

<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

187
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...SMRi		P0A8J4

Database of comparative protein structure models

More...ModBasei		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P0A8J4

<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

<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 UPF0250 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4108Z43 Bacteria
COG2921 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000265101

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P0A8J4

KEGG Orthology (KO)

More...KOi		K09158

Database for complete collections of gene phylogenies

More...PhylomeDBi		P0A8J4

Family and domain databases

HAMAP database of protein families

More...HAMAPi		MF_00659 UPF0250, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR007454 UPF0250
IPR027471 YbeD-like_sf

The PANTHER Classification System

More...PANTHERi		PTHR38036 PTHR38036, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04359 DUF493, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF117991 SSF117991, 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.

P0A8J4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKTKLNELLE FPTPFTYKVM GQALPELVDQ VVEVVQRHAP GDYTPTVKPS 
        60         70         80 
SKGNYHSVSI TINATHIEQV ETLYEELGKI DIVRMVL
Length:87
Mass (Da):9,827
Last modified:June 7, 2005 - 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:i13B14D3B2A6E1F95
GO

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
L07636 Genomic DNA Translation: AAA66341.1
U82598 Genomic DNA Translation: AAB40831.1
U00096 Genomic DNA Translation: AAC73732.1
AP009048 Genomic DNA Translation: BAA35274.1

Protein sequence database of the Protein Information Resource

More...PIRi		E64797

NCBI Reference Sequences

More...RefSeqi		NP_415164.1, NC_000913.3
WP_000850550.1, NZ_STEB01000031.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73732; AAC73732; b0631
BAA35274; BAA35274; BAA35274

Database of genes from NCBI RefSeq genomes

More...GeneIDi		945220

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0626
eco:b0631

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.661

<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
L07636 Genomic DNA Translation: AAA66341.1
U82598 Genomic DNA Translation: AAB40831.1
U00096 Genomic DNA Translation: AAC73732.1
AP009048 Genomic DNA Translation: BAA35274.1
PIRiE64797
RefSeqiNP_415164.1, NC_000913.3
WP_000850550.1, NZ_STEB01000031.1

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
1RWUNMR-A1-87[»]
SMRiP0A8J4
ModBaseiSearch...

Protein-protein interaction databases

BioGridi4260679, 235 interactors
DIPiDIP-31839N
IntActiP0A8J4, 10 interactors
STRINGi511145.b0631

Proteomic databases

EPDiP0A8J4
jPOSTiP0A8J4
PaxDbiP0A8J4
PRIDEiP0A8J4

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		945220
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73732; AAC73732; b0631
BAA35274; BAA35274; BAA35274
GeneIDi945220
KEGGiecj:JW0626
eco:b0631
PATRICifig|511145.12.peg.661

Organism-specific databases

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

More...EchoBASEi		EB1550
EcoGeneiEG11592 ybeD

Phylogenomic databases

eggNOGiENOG4108Z43 Bacteria
COG2921 LUCA
HOGENOMiHOG000265101
InParanoidiP0A8J4
KOiK09158
PhylomeDBiP0A8J4

Enzyme and pathway databases

BioCyciEcoCyc:EG11592-MONOMER
ECOL316407:JW0626-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0A8J4

Protein Ontology

More...PROi		PR:P0A8J4

Family and domain databases

HAMAPiMF_00659 UPF0250, 1 hit
InterProiView protein in InterPro
IPR007454 UPF0250
IPR027471 YbeD-like_sf
PANTHERiPTHR38036 PTHR38036, 1 hit
PfamiView protein in Pfam
PF04359 DUF493, 1 hit
SUPFAMiSSF117991 SSF117991, 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 nameiYBED_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: P0A8J4
Secondary accession number(s): P30977
<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: June 7, 2005
Last sequence update: June 7, 2005
Last modified: September 18, 2019
This is version 111 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

<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>Keywords - Technical termi

3D-structure, Complete proteome, 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. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  4. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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