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UniProtKB - P75828 (YBJD_ECOLI)

Entry version 126 (07 Oct 2020)
Sequence version 1 (01 Feb 1997)
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Protein

Uncharacterized protein YbjD

Gene

ybjD

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 predictedi <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

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi29 – 36ATPSequence analysis8

<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 ...

GO - Biological processi

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

LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G6459-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:
Uncharacterized protein YbjD
<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:ybjD
Ordered Locus Names:b0876, JW0860
<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 (strain K12)
<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 identifieri83333 [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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • 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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001687361 – 552Uncharacterized protein YbjDAdd BLAST552

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P75828

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

More...PaxDbi		P75828

PRoteomics IDEntifications database

More...PRIDEi		P75828

<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		4260001, 56 interactors

Database of interacting proteins

More...DIPi		DIP-11446N

Protein interaction database and analysis system

More...IntActi		P75828, 6 interactors

STRING: functional protein association networks

More...STRINGi		511145.b0876

<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		P75828

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>Domaini379 – 469ToprimPROSITE-ProRule annotationAdd BLAST91

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG3593, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_034845_0_0_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P75828

KEGG Orthology (KO)

More...KOi		K07459

Family and domain databases

Conserved Domains Database

More...CDDi		cd01026, TOPRIM_OLD, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR022602, DUF2813
IPR027417, P-loop_NTPase
IPR006171, TOPRIM_domain
IPR034139, TOPRIM_OLD

Pfam protein domain database

More...Pfami		View protein in Pfam
PF11398, DUF2813, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52540, SSF52540, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50880, TOPRIM, 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.

P75828-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MILERVEIVG FRGINRLSLM LEQNNVLIGE NAWGKSSLLD ALTLLLSPES 
        60         70         80         90        100
DLYHFERDDF WFPPGDINGR EHHLHIILTF RESLPGRHRV RRYRPLEACW 
       110        120        130        140        150
TPCTDGYHRI FYRLEGESAE DGSVMTLRSF LDKDGHPIDV EDINDQARHL 
       160        170        180        190        200
VRLMPVLRLR DARFMRRIRN GTVPNVPNVE VTARQLDFLA RELSSHPQNL 
       210        220        230        240        250
SDGQIRQGLS AMVQLLEHYF SEQGAGQARY RLMRRRASNE QRSWRYLDII 
       260        270        280        290        300
NRMIDRPGGR SYRVILLGLF ATLLQAKGTL RLDKDARPLL LIEDPETRLH 
       310        320        330        340        350
PIMLSVAWHL LNLLPLQRIA TTNSGELLSL TPVEHVCRLV RESSRVAAWR 
       360        370        380        390        400
LGPSGLSTED SRRISFHIRF NRPSSLFARC WLLVEGETET WVINELARQC 
       410        420        430        440        450
GHHFDAEGIK VIEFAQSGLK PLVKFARRMG IEWHVLVDGD EAGKKYAATV 
       460        470        480        490        500
RSLLNNDREA EREHLTALPA LDMEHFMYRQ GFSDVFHRMA QIPENVPMNL 
       510        520        530        540        550
RKIISKAIHR SSKPDLAIEV AMEAGRRGVD SVPTLLKKMF SRVLWLARGR 

AD
Length:552
Mass (Da):63,589
Last modified:February 1, 1997 - 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:i969D8AB605C923A0
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
U00096 Genomic DNA Translation: AAC73963.1
AP009048 Genomic DNA Translation: BAA35594.1

Protein sequence database of the Protein Information Resource

More...PIRi		D64826

NCBI Reference Sequences

More...RefSeqi		NP_415397.1, NC_000913.3
WP_000599802.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73963; AAC73963; b0876
BAA35594; BAA35594; BAA35594

Database of genes from NCBI RefSeq genomes

More...GeneIDi		945498

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0860
eco:b0876

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.905

<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
U00096 Genomic DNA Translation: AAC73963.1
AP009048 Genomic DNA Translation: BAA35594.1
PIRiD64826
RefSeqiNP_415397.1, NC_000913.3
WP_000599802.1, NZ_LN832404.1

3D structure databases

SMRiP75828
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4260001, 56 interactors
DIPiDIP-11446N
IntActiP75828, 6 interactors
STRINGi511145.b0876

Proteomic databases

jPOSTiP75828
PaxDbiP75828
PRIDEiP75828

Genome annotation databases

EnsemblBacteriaiAAC73963; AAC73963; b0876
BAA35594; BAA35594; BAA35594
GeneIDi945498
KEGGiecj:JW0860
eco:b0876
PATRICifig|511145.12.peg.905

Organism-specific databases

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

More...EchoBASEi		EB3199

Phylogenomic databases

eggNOGiCOG3593, Bacteria
HOGENOMiCLU_034845_0_0_6
InParanoidiP75828
KOiK07459

Enzyme and pathway databases

BioCyciEcoCyc:G6459-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P75828

Family and domain databases

CDDicd01026, TOPRIM_OLD, 1 hit
InterProiView protein in InterPro
IPR022602, DUF2813
IPR027417, P-loop_NTPase
IPR006171, TOPRIM_domain
IPR034139, TOPRIM_OLD
PfamiView protein in Pfam
PF11398, DUF2813, 1 hit
SUPFAMiSSF52540, SSF52540, 1 hit
PROSITEiView protein in PROSITE
PS50880, TOPRIM, 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 nameiYBJD_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: P75828
<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: July 15, 1998
Last sequence update: February 1, 1997
Last modified: October 7, 2020
This is version 126 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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