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UniProtKB - P77268 (DDPD_ECOLI)

Entry version 150 (02 Dec 2020)
Sequence version 1 (01 Feb 1997)
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Protein

Probable D,D-dipeptide transport ATP-binding protein DdpD

Gene

ddpD

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

Annotation score:3 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 transcript 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

Part of the ABC transporter complex DdpABCDF, which is probably involved in D,D-dipeptide transport (PubMed:9097039). Probably responsible for energy coupling to the transport system.1 Publication

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 bindingi42 – 49ATPPROSITE-ProRule annotation8

<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

Biological processPeptide transport, Protein transport, Transport
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:YDDP-MONOMER

Protein family/group databases

Transport Classification Database

More...TCDBi		3.A.1.5.38, the atp-binding cassette (abc) 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:
Probable D,D-dipeptide transport ATP-binding protein DdpD
<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:ddpD1 Publication
Synonyms:yddP
Ordered Locus Names:b1484, JW1479
<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 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

GO - Cellular componenti

Complete GO annotation on QuickGO ...

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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000931651 – 328Probable D,D-dipeptide transport ATP-binding protein DdpDAdd BLAST328

Proteomic databases

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

More...PaxDbi		P77268

PRoteomics IDEntifications database

More...PRIDEi		P77268

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Induced by RpoS in stationary phase.1 Publication

<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

The complex is composed of two ATP-binding proteins (DdpD and DdpF), two transmembrane proteins (DdpB and DdpC) and a solute-binding protein (DdpA).

Curated

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4260962, 121 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-4321, Dipeptide ABC transporter complex

Database of interacting proteins

More...DIPi		DIP-11669N

Protein interaction database and analysis system

More...IntActi		P77268, 9 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1484

<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		P77268

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>Domaini6 – 257ABC transporterPROSITE-ProRule annotationAdd BLAST252

<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 ABC transporter superfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0444, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_000604_1_23_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P77268

Database for complete collections of gene phylogenies

More...PhylomeDBi		P77268

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR003593, AAA+_ATPase
IPR003439, ABC_transporter-like
IPR017871, ABC_transporter_CS
IPR013563, Oligopep_ABC_C
IPR027417, P-loop_NTPase

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00005, ABC_tran, 1 hit
PF08352, oligo_HPY, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00382, AAA, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF52540, SSF52540, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01727, oligo_HPY, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00211, ABC_TRANSPORTER_1, 1 hit
PS50893, ABC_TRANSPORTER_2, 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.

P77268-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTQPVLDIQQ LHLSFPGFNG DVHALNNVSL QINRGEIVGL VGESGSGKSV 
        60         70         80         90        100
TAMLIMRLLP TGSYCVHRGQ ISLLGEDVLN AREKQLRQWR GARVAMIFQE 
       110        120        130        140        150
PMTALNPTRR IGLQMMDVIR HHQPISRREA RAKAIDLLEE MQIPDAVEVM 
       160        170        180        190        200
SRYPFELSGG MRQRVMIALA FSCEPQLIIA DEPTTALDVT VQLQVLRLLK 
       210        220        230        240        250
HKARASGTAV LFISHDMAVV SQLCDSVYVM YAGSVIESGV TADVIHHPRH 
       260        270        280        290        300
PYTIGLLQCA PEHGVPRQLL PAIPGTVPNL THLPDGCAFR DRCYAAGAQC 
       310        320 
ENVPALTACG DNNQRCACWY PQQEVISV
Length:328
Mass (Da):36,100
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:i76EAFDCAEFED5E6C
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: AAC74557.1
AP009048 Genomic DNA Translation: BAA15139.1

Protein sequence database of the Protein Information Resource

More...PIRi		G64901

NCBI Reference Sequences

More...RefSeqi		NP_416001.1, NC_000913.3
WP_000193547.1, NZ_SSZK01000038.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74557; AAC74557; b1484
BAA15139; BAA15139; BAA15139

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946002

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1479
eco:b1484

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.783

<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: AAC74557.1
AP009048 Genomic DNA Translation: BAA15139.1
PIRiG64901
RefSeqiNP_416001.1, NC_000913.3
WP_000193547.1, NZ_SSZK01000038.1

3D structure databases

SMRiP77268
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4260962, 121 interactors
ComplexPortaliCPX-4321, Dipeptide ABC transporter complex
DIPiDIP-11669N
IntActiP77268, 9 interactors
STRINGi511145.b1484

Protein family/group databases

TCDBi3.A.1.5.38, the atp-binding cassette (abc) superfamily

Proteomic databases

PaxDbiP77268
PRIDEiP77268

Genome annotation databases

EnsemblBacteriaiAAC74557; AAC74557; b1484
BAA15139; BAA15139; BAA15139
GeneIDi946002
KEGGiecj:JW1479
eco:b1484
PATRICifig|1411691.4.peg.783

Organism-specific databases

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

More...EchoBASEi		EB3548

Phylogenomic databases

eggNOGiCOG0444, Bacteria
HOGENOMiCLU_000604_1_23_6
InParanoidiP77268
PhylomeDBiP77268

Enzyme and pathway databases

BioCyciEcoCyc:YDDP-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P77268

Family and domain databases

InterProiView protein in InterPro
IPR003593, AAA+_ATPase
IPR003439, ABC_transporter-like
IPR017871, ABC_transporter_CS
IPR013563, Oligopep_ABC_C
IPR027417, P-loop_NTPase
PfamiView protein in Pfam
PF00005, ABC_tran, 1 hit
PF08352, oligo_HPY, 1 hit
SMARTiView protein in SMART
SM00382, AAA, 1 hit
SUPFAMiSSF52540, SSF52540, 1 hit
TIGRFAMsiTIGR01727, oligo_HPY, 1 hit
PROSITEiView protein in PROSITE
PS00211, ABC_TRANSPORTER_1, 1 hit
PS50893, ABC_TRANSPORTER_2, 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 nameiDDPD_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: P77268
<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: December 2, 2020
This is version 150 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. SIMILARITY comments
    Index of protein domains and families
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