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Entry version 141 (13 Nov 2019)
Sequence version 2 (15 Dec 1998)
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Protein

Inner membrane amino-acid ABC transporter permease protein YhdY

Gene

yhdY

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

Probably part of the binding-protein-dependent transport system YdhWXYZ for an amino acid; 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

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

Biological processAmino-acid transport, Transport

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:YHDY-MONOMER
ECOL316407:JW5545-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
3.A.1.3.26 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:
Inner membrane amino-acid ABC transporter permease protein YhdY
<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:yhdY
Ordered Locus Names:b3270, JW5545
<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

<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 – 36CytoplasmicSequence analysisAdd BLAST36
<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>Transmembranei37 – 57HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini58 – 99PeriplasmicSequence analysisAdd BLAST42
Transmembranei100 – 120HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini121 – 125CytoplasmicSequence analysis5
Transmembranei126 – 146HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini147 – 162PeriplasmicSequence analysisAdd BLAST16
Transmembranei163 – 183HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini184 – 192CytoplasmicSequence analysis9
Transmembranei193 – 213HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini214 – 233PeriplasmicSequence analysisAdd BLAST20
Transmembranei234 – 254HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini255 – 291CytoplasmicSequence analysisAdd BLAST37
Transmembranei292 – 312HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini313 – 326PeriplasmicSequence analysisAdd BLAST14
Transmembranei327 – 347HelicalPROSITE-ProRule annotationAdd BLAST21
Topological domaini348 – 367CytoplasmicSequence analysisAdd BLAST20

GO - Cellular componenti

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_00000602541 – 367Inner membrane amino-acid ABC transporter permease protein YhdYAdd BLAST367

Proteomic databases

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

More...
PaxDbi
P45768

PRoteomics IDEntifications database

More...
PRIDEi
P45768

<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
4261009, 8 interactors
852076, 2 interactors

Database of interacting proteins

More...
DIPi
DIP-12306N

Protein interaction database and analysis system

More...
IntActi
P45768, 3 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3270

<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
P45768

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_and_domains_section">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>Domaini159 – 353ABC transmembrane type-1PROSITE-ProRule annotationAdd BLAST195

<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
ENOG4105DRP Bacteria
COG0765 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000125341

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P45768

KEGG Orthology (KO)

More...
KOi
K09971

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P45768

Family and domain databases

Conserved Domains Database

More...
CDDi
cd06261 TM_PBP2, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.3720.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR010065 AA_ABC_transptr_permease_3TM
IPR000515 MetI-like
IPR035906 MetI-like_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00528 BPD_transp_1, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF161098 SSF161098, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR01726 HEQRo_perm_3TM, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50928 ABC_TM1, 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.

P45768-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTKVLLSHPP RPASHNSSRA MVWVRKNLFS SWSNSLLTIG CIWLMWELIP
60 70 80 90 100
PLLNWAFLQA NWVGSTRADC TKAGACWVFI HERFGQFMYG LYPHDQRWRI
110 120 130 140 150
NLALLIGLVS IAPMFWKILP HRGRYIAAWA VIYPLIVWWL MYGGFFALER
160 170 180 190 200
VETRQWGGLT LTLIIASVGI AGALPWGILL ALGRRSHMPI VRILSVIFIE
210 220 230 240 250
FWRGVPLITV LFMSSVMLPL FMAEGTSIDK LIRALVGVIL FQSAYVAEVV
260 270 280 290 300
RGGLQALPKG QYEAAESLAL GYWKTQGLVI LPQALKLVIP GLVNTIIALF
310 320 330 340 350
KDTSLVIIIG LFDLFSSVQQ ATVDPAWLGM STEGYVFAAL IYWIFCFSMS
360
RYSQYLEKRF NTGRTPH
Length:367
Mass (Da):41,484
Last modified:December 15, 1998 - 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:iEC95E04BBC7418D1
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 AAA58074 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
U18997 Genomic DNA Translation: AAA58074.1 Different initiation.
U00096 Genomic DNA Translation: AAC76302.2
AP009048 Genomic DNA Translation: BAE77311.1

Protein sequence database of the Protein Information Resource

More...
PIRi
H65119

NCBI Reference Sequences

More...
RefSeqi
NP_417736.2, NC_000913.3
WP_001300681.1, NZ_SSZK01000072.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76302; AAC76302; b3270
BAE77311; BAE77311; BAE77311

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947764

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW5545
eco:b3270

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.3370

<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
U18997 Genomic DNA Translation: AAA58074.1 Different initiation.
U00096 Genomic DNA Translation: AAC76302.2
AP009048 Genomic DNA Translation: BAE77311.1
PIRiH65119
RefSeqiNP_417736.2, NC_000913.3
WP_001300681.1, NZ_SSZK01000072.1

3D structure databases

SMRiP45768
ModBaseiSearch...

Protein-protein interaction databases

BioGridi4261009, 8 interactors
852076, 2 interactors
DIPiDIP-12306N
IntActiP45768, 3 interactors
STRINGi511145.b3270

Protein family/group databases

TCDBi3.A.1.3.26 the atp-binding cassette (abc) superfamily

Proteomic databases

PaxDbiP45768
PRIDEiP45768

Genome annotation databases

EnsemblBacteriaiAAC76302; AAC76302; b3270
BAE77311; BAE77311; BAE77311
GeneIDi947764
KEGGiecj:JW5545
eco:b3270
PATRICifig|511145.12.peg.3370

Organism-specific databases

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

More...
EchoBASEi
EB2685

Phylogenomic databases

eggNOGiENOG4105DRP Bacteria
COG0765 LUCA
HOGENOMiHOG000125341
InParanoidiP45768
KOiK09971
PhylomeDBiP45768

Enzyme and pathway databases

BioCyciEcoCyc:YHDY-MONOMER
ECOL316407:JW5545-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P45768

Family and domain databases

CDDicd06261 TM_PBP2, 1 hit
Gene3Di1.10.3720.10, 1 hit
InterProiView protein in InterPro
IPR010065 AA_ABC_transptr_permease_3TM
IPR000515 MetI-like
IPR035906 MetI-like_sf
PfamiView protein in Pfam
PF00528 BPD_transp_1, 1 hit
SUPFAMiSSF161098 SSF161098, 1 hit
TIGRFAMsiTIGR01726 HEQRo_perm_3TM, 1 hit
PROSITEiView protein in PROSITE
PS50928 ABC_TM1, 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 nameiYHDY_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: P45768
Secondary accession number(s): Q2M8U5
<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: November 1, 1995
Last sequence update: December 15, 1998
Last modified: November 13, 2019
This is version 141 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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