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Protein

Probable ABC transporter permease protein YphD

Gene

yphD

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>
-Protein inferred from homologyi <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

Probably part of the binding-protein-dependent transport system YphDEF. Probably responsible for the translocation of the substrate across the membrane.

<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

<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 processTransport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:YPHD-MONOMER

Protein family/group databases

Transport Classification Database

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TCDBi
3.A.1.2.27 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_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:
Probable ABC transporter permease protein YphD
<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:yphD
Ordered Locus Names:b2546, JW2530
<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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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
EG13465 yphD

<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 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>Transmembranei28 – 48HelicalSequence analysisAdd BLAST21
Transmembranei63 – 83HelicalSequence analysisAdd BLAST21
Transmembranei84 – 104HelicalSequence analysisAdd BLAST21
Transmembranei105 – 125HelicalSequence analysisAdd BLAST21
Transmembranei131 – 151HelicalSequence analysisAdd BLAST21
Transmembranei172 – 192HelicalSequence analysisAdd BLAST21
Transmembranei222 – 242HelicalSequence analysisAdd BLAST21
Transmembranei251 – 271HelicalSequence analysisAdd BLAST21
Transmembranei278 – 298HelicalSequence analysisAdd BLAST21
Transmembranei303 – 323HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

  • integral component of membrane Source: GO_Central
  • integral component of plasma membrane Source: EcoCyc
  • plasma membrane Source: EcoCyc

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_00000602641 – 332Probable ABC transporter permease protein YphDAdd BLAST332

Proteomic databases

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

More...
PaxDbi
P77315

PRoteomics IDEntifications database

More...
PRIDEi
P77315

<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)

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BioGridi
4261317, 8 interactors

STRING: functional protein association networks

More...
STRINGi
316385.ECDH10B_2713

<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

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P77315

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P77315

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105CNN Bacteria
COG1172 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000212232

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P77315

KEGG Orthology (KO)

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KOi
K02057

Database for complete collections of gene phylogenies

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PhylomeDBi
P77315

Family and domain databases

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR001851 ABC_transp_permease

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02653 BPD_transp_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_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<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.

P77315-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSASSLPLPQ GKSVSLKQFV SRHINEIGLL VVIAILYLVF SLNAPGFISL
60 70 80 90 100
NNQMNVLRDA ATIGIAAWAM TLIIISGEID VSVGPMVAFV SVCLAFLLQF
110 120 130 140 150
EVPLAVACLL VLLLGALMGT LAGVLRGVFN VPSFVATLGL WSALRGMGLF
160 170 180 190 200
MTNALPVPID ENEVLDWLGG QFLGVPVSAL IMIVLFALFV FISRKTAFGR
210 220 230 240 250
SVFAVGGNAT AAQLCGINVR RVRILIFTLS GLLAAVTGIL LAARLGSGNA
260 270 280 290 300
GAANGLEFDV IAAVVVGGTA LSGGRGSLFG TLLGVLVITL IGNGLVLLGI
310 320 330
NSFFQQVVRG VIIVVAVLAN ILLTQRSSKA KR
Length:332
Mass (Da):34,483
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:i226C21E6C6C2F719
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75599.1
AP009048 Genomic DNA Translation: BAA16448.1

Protein sequence database of the Protein Information Resource

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PIRi
A65032

NCBI Reference Sequences

More...
RefSeqi
NP_417041.1, NC_000913.3
WP_001276670.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75599; AAC75599; b2546
BAA16448; BAA16448; BAA16448

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
949063

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2530
eco:b2546

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.4188

<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: AAC75599.1
AP009048 Genomic DNA Translation: BAA16448.1
PIRiA65032
RefSeqiNP_417041.1, NC_000913.3
WP_001276670.1, NZ_LN832404.1

3D structure databases

ProteinModelPortaliP77315
SMRiP77315
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261317, 8 interactors
STRINGi316385.ECDH10B_2713

Protein family/group databases

TCDBi3.A.1.2.27 the atp-binding cassette (abc) superfamily

Proteomic databases

PaxDbiP77315
PRIDEiP77315

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75599; AAC75599; b2546
BAA16448; BAA16448; BAA16448
GeneIDi949063
KEGGiecj:JW2530
eco:b2546
PATRICifig|1411691.4.peg.4188

Organism-specific databases

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

More...
EchoBASEi
EB3238
EcoGeneiEG13465 yphD

Phylogenomic databases

eggNOGiENOG4105CNN Bacteria
COG1172 LUCA
HOGENOMiHOG000212232
InParanoidiP77315
KOiK02057
PhylomeDBiP77315

Enzyme and pathway databases

BioCyciEcoCyc:YPHD-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P77315

Family and domain databases

InterProiView protein in InterPro
IPR001851 ABC_transp_permease
PfamiView protein in Pfam
PF02653 BPD_transp_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiYPHD_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: P77315
<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: July 15, 1998
Last sequence update: February 1, 1997
Last modified: November 7, 2018
This is version 129 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

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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