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UniProtKB - P25907 (YDBD_ECOLI)

Entry version 122 (07 Oct 2020)
Sequence version 2 (01 Nov 1997)
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Protein

Uncharacterized protein YdbD

Gene

ydbD

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

Annotation score:1 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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11310-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 YdbD
<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:ydbD
Ordered Locus Names:b1407, JW5221
<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_00001689211 – 768Uncharacterized protein YdbDAdd BLAST768

Proteomic databases

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

More...PaxDbi		P25907

PRoteomics IDEntifications database

More...PRIDEi		P25907

<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		4263020, 10 interactors
850345, 2 interactors

Protein interaction database and analysis system

More...IntActi		P25907, 3 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1407

<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		P25907

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

<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

To E.coli YkiA.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG5033PQ4, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_027788_0_0_6

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR024497, DUF2773

Pfam protein domain database

More...Pfami		View protein in Pfam
PF10971, DUF2773, 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.

P25907-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLKARNCGWI RLLPLFMLSL PVQAELRCVA NAVDIESFFS AATAEDKQQV 
        60         70         80         90        100
EQAINSSVNL VPFGLSASNW KVHRGDLVVE GNIESNQKLI VLGNLTVKGN 
       110        120        130        140        150
ISTFSLSNPW VILGNVTATN IVADSPLLIT GSINASGLVF IDSYYDNPST 
       160        170        180        190        200
IKGSINARGI FINDIIAPVV ASSTNSEFMV RASDKHDTEN VKKALMIINP 
       210        220        230        240        250
DAYYWGLIND EDALKEIFKR SNIRMAGNVC NQMKKEALFR PKPSPELVQE 
       260        270        280        290        300
LQMLDEGKVA AFEGRDIATF DLAVMRTLPR LKGISANLRK QLINSNDEQT 
       310        320        330        340        350
IESMARYMPD NEILELTDQQ LGYQPVVLGL LDREPLSVEI MTRMSRLPDG 
       360        370        380        390        400
VGPLNLALRE NLPLDIVMTL AKRDWDMIIQ ELYKDAWLLP ESIIDGYIRS 
       410        420        430        440        450
DDSSIRQVGA GGQLTYNQAM QLANDSSNNV VTSLAFKLAE MKHHGQLLRM 
       460        470        480        490        500
TPQESDKVAG YLYQKFENDD DLIRVLFLAL PDNLQFNFVK RMEKKSPAYF 
       510        520        530        540        550
CCRDMQVIHS DAALQRLLTR FNDPEGWSNL AKNQYLSTSM KQKIWQRALS 
       560        570        580        590        600
HRKNNPKADS DAYETSADMI LSELISHGEV DDQMLLNATA LIRSDDWDFL 
       610        620        630        640        650
ESALISWDNL PAVVLKELQQ NTPRNDIWAK FFLRQENSSR AQVDEALRVY 
       660        670        680        690        700
YALDPDALAQ LDVLAKQPDR IWWSTLAKSN LTFFKFGALN NRHTPPAVLA 
       710        720        730        740        750
AEIDPEWWIV AMNNPRFPVD VLKARLKRDP LLALELVNPE LDLVRQLALN 
       760 
GKTRAIREQA MRKLDELY
Length:768
Mass (Da):86,716
Last modified:November 1, 1997 - v2
<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:iA4B01C15871D1DA2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti347L → Y in CAA44554 (PubMed:1665988).Curated1

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: AAC74489.2
AP009048 Genomic DNA Translation: BAA15022.2
X62680 Genomic DNA Translation: CAA44554.1

Protein sequence database of the Protein Information Resource

More...PIRi		B64892

NCBI Reference Sequences

More...RefSeqi		NP_415925.2, NC_000913.3
WP_000910026.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74489; AAC74489; b1407
BAA15022; BAA15022; BAA15022

Database of genes from NCBI RefSeq genomes

More...GeneIDi		945983

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW5221
eco:b1407

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.864

<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: AAC74489.2
AP009048 Genomic DNA Translation: BAA15022.2
X62680 Genomic DNA Translation: CAA44554.1
PIRiB64892
RefSeqiNP_415925.2, NC_000913.3
WP_000910026.1, NZ_LN832404.1

3D structure databases

SMRiP25907
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4263020, 10 interactors
850345, 2 interactors
IntActiP25907, 3 interactors
STRINGi511145.b1407

Proteomic databases

PaxDbiP25907
PRIDEiP25907

Genome annotation databases

EnsemblBacteriaiAAC74489; AAC74489; b1407
BAA15022; BAA15022; BAA15022
GeneIDi945983
KEGGiecj:JW5221
eco:b1407
PATRICifig|1411691.4.peg.864

Organism-specific databases

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

More...EchoBASEi		EB1286

Phylogenomic databases

eggNOGiENOG5033PQ4, Bacteria
HOGENOMiCLU_027788_0_0_6

Enzyme and pathway databases

BioCyciEcoCyc:EG11310-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25907

Family and domain databases

InterProiView protein in InterPro
IPR024497, DUF2773
PfamiView protein in Pfam
PF10971, DUF2773, 1 hit

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 nameiYDBD_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: P25907
Secondary accession number(s): P76089, P76860, P76862
<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: May 1, 1992
Last sequence update: November 1, 1997
Last modified: October 7, 2020
This is version 122 of the entry and version 2 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

Reference proteome
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