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UniProtKB - P76103 (YDCO_ECOLI)

Entry version 127 (13 Nov 2019)
Sequence version 2 (27 Mar 2002)
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Protein

Inner membrane protein YdcO

Gene

ydcO

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

<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 ...

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:B1433-MONOMER
ECOL316407:JW5229-MONOMER

Protein family/group databases

Transport Classification Database

More...TCDBi		2.A.46.1.9 the benzoate:h+ symporter (bene) family

<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:
Inner membrane protein YdcO
<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:ydcO
Ordered Locus Names:b1433, JW5229
<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 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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the subcellular compartment where each non-membrane region of a membrane-spanning protein is found.<p><a href='/help/topo_dom' target='_top'>More...</a></p>Topological domaini1 – 9CytoplasmicSequence analysis9
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular_location_section">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei10 – 30HelicalSequence analysisAdd BLAST21
Topological domaini31 – 42PeriplasmicSequence analysisAdd BLAST12
Transmembranei43 – 63HelicalSequence analysisAdd BLAST21
Topological domaini64 – 93CytoplasmicSequence analysisAdd BLAST30
Transmembranei94 – 114HelicalSequence analysisAdd BLAST21
Topological domaini115 – 123PeriplasmicSequence analysis9
Transmembranei124 – 144HelicalSequence analysisAdd BLAST21
Topological domaini145 – 167CytoplasmicSequence analysisAdd BLAST23
Transmembranei168 – 188HelicalSequence analysisAdd BLAST21
Topological domaini189 – 200PeriplasmicSequence analysisAdd BLAST12
Transmembranei201 – 221HelicalSequence analysisAdd BLAST21
Topological domaini222 – 246CytoplasmicSequence analysisAdd BLAST25
Transmembranei247 – 267HelicalSequence analysisAdd BLAST21
Topological domaini268 – 287PeriplasmicSequence analysisAdd BLAST20
Transmembranei288 – 308HelicalSequence analysisAdd BLAST21
Topological domaini309 – 311CytoplasmicSequence analysis3
Transmembranei312 – 332HelicalSequence analysisAdd BLAST21
Topological domaini333 – 361PeriplasmicSequence analysisAdd BLAST29
Transmembranei362 – 382HelicalSequence analysisAdd BLAST21
Topological domaini383 – 391CytoplasmicSequence analysis9

GO - Cellular componenti

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>Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

<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_00002013201 – 391Inner membrane protein YdcOAdd BLAST391

Proteomic databases

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

More...PaxDbi		P76103

PRoteomics IDEntifications database

More...PRIDEi		P76103

<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		4261752, 256 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1433

<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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105DKK Bacteria
COG3135 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000221975

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P76103

KEGG Orthology (KO)

More...KOi		K05782

Database for complete collections of gene phylogenies

More...PhylomeDBi		P76103

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR004711 Benzoate_Transporter

The PANTHER Classification System

More...PANTHERi		PTHR30199 PTHR30199, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF03594 BenE, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00843 benE, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00041 HTH_ARAC_FAMILY_1, 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.

P76103-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRLFSIPPPT LLAGFLAVLI GYASSAAIIW QAAIVAGATT AQISGWMTAL 
        60         70         80         90        100
GLAMGVSTLT LTLWYRVPVL TAWSTPGAAL LVTGLQGLTL NEAIGVFIVT 
       110        120        130        140        150
NALIVLCGIT GLFARLMRII PHSLAAAMLA GILLRFGLQA FASLDGQFTL 
       160        170        180        190        200
CGSMLLVWLA TKAVAPRYAV IAAMIIGIVI VIAQGDVVTT DVVFKPVLPT 
       210        220        230        240        250
YITPDFSFAH SLSVALPLFL VTMASQNAPG IAAMKAAGYS APVSPLIVFT 
       260        270        280        290        300
GLLALVFSPF GVYSVGIAAI TAAICQSPEA HPDKDQRWLA AAVAGIFYLL 
       310        320        330        340        350
AGLFGSAITG MMAALPVSWI QMLAGLALLS TIGGSLYQAL HNERERDAAV 
       360        370        380        390 
VAFLVTASGL TLVGIGSAFW GLIAGGVCYV VLNLIADRNR Y
Length:391
Mass (Da):40,583
Last modified:March 27, 2002 - 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:iECA73015E1B7D1A8
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: AAC74515.2
AP009048 Genomic DNA Translation: BAA15061.2

Protein sequence database of the Protein Information Resource

More...PIRi		D64895

NCBI Reference Sequences

More...RefSeqi		NP_415950.4, NC_000913.3

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74515; AAC74515; b1433
BAA15061; BAA15061; BAA15061

Database of genes from NCBI RefSeq genomes

More...GeneIDi		947247

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW5229
eco:b1433

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.836

<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: AAC74515.2
AP009048 Genomic DNA Translation: BAA15061.2
PIRiD64895
RefSeqiNP_415950.4, NC_000913.3

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

BioGridi4261752, 256 interactors
STRINGi511145.b1433

Protein family/group databases

TCDBi2.A.46.1.9 the benzoate:h+ symporter (bene) family

Proteomic databases

PaxDbiP76103
PRIDEiP76103

Genome annotation databases

EnsemblBacteriaiAAC74515; AAC74515; b1433
BAA15061; BAA15061; BAA15061
GeneIDi947247
KEGGiecj:JW5229
eco:b1433
PATRICifig|1411691.4.peg.836

Organism-specific databases

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

More...EchoBASEi		EB3521

Phylogenomic databases

eggNOGiENOG4105DKK Bacteria
COG3135 LUCA
HOGENOMiHOG000221975
InParanoidiP76103
KOiK05782
PhylomeDBiP76103

Enzyme and pathway databases

BioCyciEcoCyc:B1433-MONOMER
ECOL316407:JW5229-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P76103

Family and domain databases

InterProiView protein in InterPro
IPR004711 Benzoate_Transporter
PANTHERiPTHR30199 PTHR30199, 1 hit
PfamiView protein in Pfam
PF03594 BenE, 1 hit
TIGRFAMsiTIGR00843 benE, 1 hit
PROSITEiView protein in PROSITE
PS00041 HTH_ARAC_FAMILY_1, 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 nameiYDCO_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: P76103
Secondary accession number(s): P77540
<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: March 27, 2002
Last sequence update: March 27, 2002
Last modified: November 13, 2019
This is version 127 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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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