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UniProtKB - P08555 (DSDX_ECOLI)

Entry version 158 (18 Sep 2019)
Sequence version 2 (01 Nov 1995)
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Protein

D-serine transporter DsdX

Gene

dsdX

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 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

A D-serine-specific transporter, may function as a H+ symporter.By similarity

Caution

An ORF called dsdC was originally (PubMed:3275618) assigned to the wrong DNA strand and thought to be a D-serine deaminase activator, it was then resequenced by Ref. 2 and still thought to be "dsdC", but this time to function as a D-serine permease. It is PubMed:7592420 that showed that dsdC is another gene and that this sequence should be called dsdX. It should also be noted that the C-terminal part of dsdX (from 338 onward) was also sequenced (PubMed:3029015 and PubMed:1659648) and was thought to be a separate ORF (don't worry, we also had difficulties understanding what happened!).1 Publication

<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 processAmino-acid transport, Transport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:DSDX-MONOMER
ECOL316407:JW2362-MONOMER

Protein family/group databases

Transport Classification Database

More...TCDBi		2.A.8.1.5 the gluconate:h(+) symporter (gntp) 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:
D-serine transporter DsdX
<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:dsdX1 Publication
Synonyms:orf4451 Publication, yfdA, yfdD
Ordered Locus Names:b2365, JW2362
<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

Organism-specific databases

Escherichia coli strain K12 genome database

More...EcoGenei		EG10250 dsdX

<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 – 4CytoplasmicSequence analysis4
<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>Transmembranei5 – 25HelicalSequence analysisAdd BLAST21
Topological domaini26 – 28PeriplasmicSequence analysis3
Transmembranei29 – 49HelicalSequence analysisAdd BLAST21
Topological domaini50 – 56CytoplasmicSequence analysis7
Transmembranei57 – 77HelicalSequence analysisAdd BLAST21
Topological domaini78 – 105PeriplasmicSequence analysisAdd BLAST28
Transmembranei106 – 126HelicalSequence analysisAdd BLAST21
Topological domaini127 – 139CytoplasmicSequence analysisAdd BLAST13
Transmembranei140 – 160HelicalSequence analysisAdd BLAST21
Topological domaini161 – 177PeriplasmicSequence analysisAdd BLAST17
Transmembranei178 – 198HelicalSequence analysisAdd BLAST21
Topological domaini199 – 223CytoplasmicSequence analysisAdd BLAST25
Transmembranei224 – 244HelicalSequence analysisAdd BLAST21
Topological domaini245 – 257PeriplasmicSequence analysisAdd BLAST13
Transmembranei258 – 278HelicalSequence analysisAdd BLAST21
Topological domaini279 – 301CytoplasmicSequence analysisAdd BLAST23
Transmembranei302 – 322HelicalSequence analysisAdd BLAST21
Topological domaini323 – 342PeriplasmicSequence analysisAdd BLAST20
Transmembranei343 – 363HelicalSequence analysisAdd BLAST21
Transmembranei364 – 384HelicalSequence analysisAdd BLAST21
Transmembranei385 – 405HelicalSequence analysisAdd BLAST21
Topological domaini406 – 424CytoplasmicSequence analysisAdd BLAST19
Transmembranei425 – 445HelicalSequence analysisAdd BLAST21

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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000619371 – 445D-serine transporter DsdXAdd BLAST445

Proteomic databases

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

More...PaxDbi		P08555

PRoteomics IDEntifications database

More...PRIDEi		P08555

<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

By growth in D-serine, controlled by DsdC.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

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4260554, 2 interactors

Database of interacting proteins

More...DIPi		DIP-9481N

Protein interaction database and analysis system

More...IntActi		P08555, 1 interactor

STRING: functional protein association networks

More...STRINGi		511145.b2365

<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

Belongs to the GntP permease family.Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105C6Z Bacteria
COG2610 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000237115

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P08555

KEGG Orthology (KO)

More...KOi		K13629

Database for complete collections of gene phylogenies

More...PhylomeDBi		P08555

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR003474 Glcn_transporter

The PANTHER Classification System

More...PANTHERi		PTHR30354 PTHR30354, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02447 GntP_permease, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF002746 Gluconate_transporter, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00791 gntP, 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.

P08555-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MHSQIWVVST LLISIVLIVL TIVKFKFHPF LALLLASFFV GTMMGMGPLD 
        60         70         80         90        100
MVNAIESGIG GTLGFLAAVI GLGTILGKMM EVSGAAERIG LTLQRCRWLS 
       110        120        130        140        150
VDVIMVLVGL ICGITLFVEV GVVLLIPLAF SIAKKTNTSL LKLAIPLCTA 
       160        170        180        190        200
LMAVHCVVPP HPAALYVANK LGADIGSVIV YGLLVGLMAS LIGGPLFLKF 
       210        220        230        240        250
LGQRLPFKPV PTEFADLKVR DEKTLPSLGA TLFTILLPIA LMLVKTIAEL 
       260        270        280        290        300
NMARESGLYI LVEFIGNPIT AMFIAVFVAY YVLGIRQHMS MGTMLTHTEN 
       310        320        330        340        350
GFGSIANILL IIGAGGAFNA ILKSSSLADT LAVILSNMHM HPILLAWLVA 
       360        370        380        390        400
LILHAAVGSA TVAMMGATAI VAPMLPLYPD ISPEIIAIAI GSGAIGCTIV 
       410        420        430        440 
TDSLFWLVKQ YCGATLNETF KYYTTATFIA SVVALAGTFL LSFII
Length:445
Mass (Da):47,163
Last modified:November 1, 1995 - 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:iF88D821090A3F79F
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
X91821 Genomic DNA Translation: CAA62932.1
X86379 Genomic DNA Translation: CAA60138.1
J01603 Genomic DNA Translation: AAA87974.1
U00096 Genomic DNA Translation: AAC75424.1
AP009048 Genomic DNA Translation: BAA16225.1
M19035 Genomic DNA No translation available.
X81461 Genomic DNA Translation: CAA57221.2

Protein sequence database of the Protein Information Resource

More...PIRi		S54140

NCBI Reference Sequences

More...RefSeqi		NP_416866.1, NC_000913.3
WP_000556048.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75424; AAC75424; b2365
BAA16225; BAA16225; BAA16225

Database of genes from NCBI RefSeq genomes

More...GeneIDi		949103

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW2362
eco:b2365

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.4364

<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
X91821 Genomic DNA Translation: CAA62932.1
X86379 Genomic DNA Translation: CAA60138.1
J01603 Genomic DNA Translation: AAA87974.1
U00096 Genomic DNA Translation: AAC75424.1
AP009048 Genomic DNA Translation: BAA16225.1
M19035 Genomic DNA No translation available.
X81461 Genomic DNA Translation: CAA57221.2
PIRiS54140
RefSeqiNP_416866.1, NC_000913.3
WP_000556048.1, NZ_LN832404.1

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

BioGridi4260554, 2 interactors
DIPiDIP-9481N
IntActiP08555, 1 interactor
STRINGi511145.b2365

Protein family/group databases

TCDBi2.A.8.1.5 the gluconate:h(+) symporter (gntp) family

Proteomic databases

PaxDbiP08555
PRIDEiP08555

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75424; AAC75424; b2365
BAA16225; BAA16225; BAA16225
GeneIDi949103
KEGGiecj:JW2362
eco:b2365
PATRICifig|1411691.4.peg.4364

Organism-specific databases

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

More...EchoBASEi		EB0246
EcoGeneiEG10250 dsdX

Phylogenomic databases

eggNOGiENOG4105C6Z Bacteria
COG2610 LUCA
HOGENOMiHOG000237115
InParanoidiP08555
KOiK13629
PhylomeDBiP08555

Enzyme and pathway databases

BioCyciEcoCyc:DSDX-MONOMER
ECOL316407:JW2362-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P08555

Family and domain databases

InterProiView protein in InterPro
IPR003474 Glcn_transporter
PANTHERiPTHR30354 PTHR30354, 1 hit
PfamiView protein in Pfam
PF02447 GntP_permease, 1 hit
PIRSFiPIRSF002746 Gluconate_transporter, 1 hit
TIGRFAMsiTIGR00791 gntP, 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 nameiDSDX_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: P08555
Secondary accession number(s): P11693
<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: August 1, 1988
Last sequence update: November 1, 1995
Last modified: September 18, 2019
This is version 158 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. SIMILARITY comments
    Index of protein domains and families
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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