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Entry version 139 (13 Nov 2019)
Sequence version 1 (01 Oct 1994)
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Protein

Inner membrane protein YhjD

Gene

yhjD

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>
-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

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG12248-MONOMER
ECOL316407:JW3490-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
9.B.126.1.1 the putative lipid iv exporter (yhjd) 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:
Inner membrane protein YhjD
<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:yhjD
Ordered Locus Names:b3522, JW3490
<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 – 74CytoplasmicSequence analysisAdd BLAST74
<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>Transmembranei75 – 97HelicalSequence analysisAdd BLAST23
Topological domaini98 – 133PeriplasmicSequence analysisAdd BLAST36
Transmembranei134 – 156HelicalSequence analysisAdd BLAST23
Topological domaini157 – 185CytoplasmicSequence analysisAdd BLAST29
Transmembranei186 – 208HelicalSequence analysisAdd BLAST23
Topological domaini209 – 227PeriplasmicSequence analysisAdd BLAST19
Transmembranei228 – 250HelicalSequence analysisAdd BLAST23
Topological domaini251 – 261CytoplasmicSequence analysisAdd BLAST11
Transmembranei262 – 284HelicalSequence analysisAdd BLAST23
Topological domaini285 – 298PeriplasmicSequence analysisAdd BLAST14
Transmembranei299 – 321HelicalSequence analysisAdd BLAST23
Topological domaini322 – 337CytoplasmicSequence analysisAdd BLAST16

GO - Cellular componenti

<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>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_00001695701 – 337Inner membrane protein YhjDAdd BLAST337

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

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jPOSTi
P37642

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

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PaxDbi
P37642

PRoteomics IDEntifications database

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PRIDEi
P37642

<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
4262161, 590 interactors

Database of interacting proteins

More...
DIPi
DIP-12379N

Protein interaction database and analysis system

More...
IntActi
P37642, 2 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3522

<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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4107H3J Bacteria
COG1295 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000045666

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P37642

KEGG Orthology (KO)

More...
KOi
K07058

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P37642

Family and domain databases

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR005274 IM_pro_YhjD
IPR017039 Virul_fac_BrkB

The PANTHER Classification System

More...
PANTHERi
PTHR30213 PTHR30213, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF03631 Virul_fac_BrkB, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF035875 RNase_BN, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00766 TIGR00766, 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.

P37642-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTQENEIKRP IQDLEHEPIK PLDNSEKGSK VSQALETVTT TAEKVQRQPV
60 70 80 90 100
IAHLIRATER FNDRLGNQFG AAITYFSFLS MIPILMVSFA AGGFVLASHP
110 120 130 140 150
MLLQDIFDKI LQNISDPTLA ATLKNTINTA VQQRTTVGLV GLAVALYSGI
160 170 180 190 200
NWMGNLREAI RAQSRDVWER SPQDQEKFWV KYLRDFISLI GLLIALIVTL
210 220 230 240 250
SITSVAGSAQ QMIISALHLN SIEWLKPTWR LIGLAISIFA NYLLFFWIFW
260 270 280 290 300
RLPRHRPRKK ALIRGTFLAA IGFEVIKIVM TYTLPSLMKS PSGAAFGSVL
310 320 330
GLMAFFYFFA RLTLFCAAWI ATAEYKDDPR MPGKTQP
Length:337
Mass (Da):37,911
Last modified:October 1, 1994 - 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:iC41B2A224902E311
GO

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
U00039 Genomic DNA Translation: AAB18498.1
U00096 Genomic DNA Translation: AAC76547.1
AP009048 Genomic DNA Translation: BAE77772.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S47742

NCBI Reference Sequences

More...
RefSeqi
NP_417979.1, NC_000913.3
WP_000191237.1, NZ_SSZK01000039.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76547; AAC76547; b3522
BAE77772; BAE77772; BAE77772

Database of genes from NCBI RefSeq genomes

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GeneIDi
948033

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3490
eco:b3522

Pathosystems Resource Integration Center (PATRIC)

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PATRICi
fig|1411691.4.peg.3196

<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
U00039 Genomic DNA Translation: AAB18498.1
U00096 Genomic DNA Translation: AAC76547.1
AP009048 Genomic DNA Translation: BAE77772.1
PIRiS47742
RefSeqiNP_417979.1, NC_000913.3
WP_000191237.1, NZ_SSZK01000039.1

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

BioGridi4262161, 590 interactors
DIPiDIP-12379N
IntActiP37642, 2 interactors
STRINGi511145.b3522

Protein family/group databases

TCDBi9.B.126.1.1 the putative lipid iv exporter (yhjd) family

Proteomic databases

jPOSTiP37642
PaxDbiP37642
PRIDEiP37642

Genome annotation databases

EnsemblBacteriaiAAC76547; AAC76547; b3522
BAE77772; BAE77772; BAE77772
GeneIDi948033
KEGGiecj:JW3490
eco:b3522
PATRICifig|1411691.4.peg.3196

Organism-specific databases

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

More...
EchoBASEi
EB2159

Phylogenomic databases

eggNOGiENOG4107H3J Bacteria
COG1295 LUCA
HOGENOMiHOG000045666
InParanoidiP37642
KOiK07058
PhylomeDBiP37642

Enzyme and pathway databases

BioCyciEcoCyc:EG12248-MONOMER
ECOL316407:JW3490-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P37642

Family and domain databases

InterProiView protein in InterPro
IPR005274 IM_pro_YhjD
IPR017039 Virul_fac_BrkB
PANTHERiPTHR30213 PTHR30213, 1 hit
PfamiView protein in Pfam
PF03631 Virul_fac_BrkB, 1 hit
PIRSFiPIRSF035875 RNase_BN, 1 hit
TIGRFAMsiTIGR00766 TIGR00766, 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 nameiYHJD_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: P37642
Secondary accession number(s): Q2M7I4
<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: October 1, 1994
Last sequence update: October 1, 1994
Last modified: November 13, 2019
This is version 139 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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