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Entry version 113 (07 Oct 2020)
Sequence version 1 (25 Oct 2005)
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Protein

Cytochrome bo(3) ubiquinol oxidase subunit 4

Gene

cyoD

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

Annotation score:5 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

Cytochrome bo3 ubiquinol terminal oxidase is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at high aeration. Has proton pump activity across the membrane in addition to electron transfer, pumping 2 protons/electron.3 Publications

<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

GO - Biological processi

<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 functionOxidoreductase
Biological processElectron transport, Transport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:CYOD-MONOMER
MetaCyc:CYOD-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
3.D.4.5.1, the proton-translocating cytochrome oxidase (cox) superfamily

<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:
Cytochrome bo(3) ubiquinol oxidase subunit 4
Alternative name(s):
Cytochrome o ubiquinol oxidase subunit 4
Short name:
Cytochrome o subunit 4
Oxidase bo(3) subunit 4
Ubiquinol oxidase chain D
Ubiquinol oxidase polypeptide IV
Ubiquinol oxidase subunit 4
<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:cyoD
Ordered Locus Names:b0429, JW0419
<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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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 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%5Flocation%5Fsection">'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 – 17CytoplasmicCuratedAdd BLAST17
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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>Transmembranei18 – 36HelicalCuratedAdd BLAST19
Topological domaini37 – 45PeriplasmicCurated9
Transmembranei46 – 64HelicalCuratedAdd BLAST19
Topological domaini65 – 80CytoplasmicCuratedAdd BLAST16
Transmembranei81 – 99HelicalCuratedAdd BLAST19
Topological domaini100 – 109PeriplasmicCurated10

GO - Cellular componenti

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Increased reduction of the ubiquinone pool (in aerobically grown minimal medium with glucose).2 Publications

<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_00001839101 – 109Cytochrome bo(3) ubiquinol oxidase subunit 4Add BLAST109

Proteomic databases

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

More...
PaxDbi
P0ABJ6

PRoteomics IDEntifications database

More...
PRIDEi
P0ABJ6

<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%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterooctamer of two A chains, two B chains, two C chains and two D chains.

2 Publications

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4260871, 223 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-2102, Cytochrome o ubiquinol oxidase complex

Database of interacting proteins

More...
DIPi
DIP-48238N

Protein interaction database and analysis system

More...
IntActi
P0ABJ6, 1 interactor

STRING: functional protein association networks

More...
STRINGi
511145.b0429

<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
P0ABJ6

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P0ABJ6

<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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG3125, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_140945_1_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P0ABJ6

KEGG Orthology (KO)

More...
KOi
K02300

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P0ABJ6

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR005171, Cyt_c_oxidase_su4_prok
IPR014210, Cyt_o_ubiqinol_oxidase_su4

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03626, COX4_pro, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02847, CyoD, 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.

P0ABJ6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSHSTDHSGA SHGSVKTYMT GFILSIILTV IPFWMVMTGA ASPAVILGTI
60 70 80 90 100
LAMAVVQVLV HLVCFLHMNT KSDEGWNMTA FVFTVLIIAI LVVGSIWIMW

NLNYNMMMH
Length:109
Mass (Da):12,029
Last modified:October 25, 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:iE2DBE23C893724BA
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 AAB40185 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
J05492 Genomic DNA Translation: AAA23634.1
U82664 Genomic DNA Translation: AAB40185.1 Different initiation.
U00096 Genomic DNA Translation: AAC73532.1
AP009048 Genomic DNA Translation: BAE76209.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D42226

NCBI Reference Sequences

More...
RefSeqi
NP_414963.1, NC_000913.3
WP_000019869.1, NZ_STEB01000007.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC73532; AAC73532; b0429
BAE76209; BAE76209; BAE76209

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
48723994
944918

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW0419
eco:b0429

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.1848

<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
J05492 Genomic DNA Translation: AAA23634.1
U82664 Genomic DNA Translation: AAB40185.1 Different initiation.
U00096 Genomic DNA Translation: AAC73532.1
AP009048 Genomic DNA Translation: BAE76209.1
PIRiD42226
RefSeqiNP_414963.1, NC_000913.3
WP_000019869.1, NZ_STEB01000007.1

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
1FFTX-ray3.50
SMRiP0ABJ6
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4260871, 223 interactors
ComplexPortaliCPX-2102, Cytochrome o ubiquinol oxidase complex
DIPiDIP-48238N
IntActiP0ABJ6, 1 interactor
STRINGi511145.b0429

Protein family/group databases

TCDBi3.D.4.5.1, the proton-translocating cytochrome oxidase (cox) superfamily

Proteomic databases

PaxDbiP0ABJ6
PRIDEiP0ABJ6

Genome annotation databases

EnsemblBacteriaiAAC73532; AAC73532; b0429
BAE76209; BAE76209; BAE76209
GeneIDi48723994
944918
KEGGiecj:JW0419
eco:b0429
PATRICifig|1411691.4.peg.1848

Organism-specific databases

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

More...
EchoBASEi
EB0178

Phylogenomic databases

eggNOGiCOG3125, Bacteria
HOGENOMiCLU_140945_1_0_6
InParanoidiP0ABJ6
KOiK02300
PhylomeDBiP0ABJ6

Enzyme and pathway databases

BioCyciEcoCyc:CYOD-MONOMER
MetaCyc:CYOD-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0ABJ6

Protein Ontology

More...
PROi
PR:P0ABJ6

Family and domain databases

InterProiView protein in InterPro
IPR005171, Cyt_c_oxidase_su4_prok
IPR014210, Cyt_o_ubiqinol_oxidase_su4
PfamiView protein in Pfam
PF03626, COX4_pro, 1 hit
TIGRFAMsiTIGR02847, CyoD, 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 nameiCYOD_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: P0ABJ6
Secondary accession number(s): P18403, P77116, Q2MBZ7
<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: October 25, 2005
Last sequence update: October 25, 2005
Last modified: October 7, 2020
This is version 113 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

3D-structure, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
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