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Entry version 159 (07 Oct 2020)
Sequence version 5 (10 Jul 2007)
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Protein

UPF0053 inner membrane protein YfjD

Gene

yfjD

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

<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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7356-MONOMER

Protein family/group databases

Transport Classification Database

More...
TCDBi
1.A.112.2.5, the cyclin m mg2+ exporter (cnnm) 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%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:
UPF0053 inner membrane protein YfjD
<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:yfjD
Synonyms:ypjE
Ordered Locus Names:b4461, JW5415
ORF Names:b2612/b2613
<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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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 – 3CytoplasmicSequence analysis3
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'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>Transmembranei4 – 24HelicalSequence analysisAdd BLAST21
Topological domaini25 – 64PeriplasmicSequence analysisAdd BLAST40
Transmembranei65 – 85HelicalSequence analysisAdd BLAST21
Topological domaini86 – 91CytoplasmicSequence analysis6
Transmembranei92 – 112HelicalSequence analysisAdd BLAST21
Topological domaini113 – 129PeriplasmicSequence analysisAdd BLAST17
Transmembranei130 – 150HelicalSequence analysisAdd BLAST21
Topological domaini151 – 428CytoplasmicSequence analysisAdd BLAST278

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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000883571 – 428UPF0053 inner membrane protein YfjDAdd BLAST428

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P37908

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

More...
PaxDbi
P37908

PRoteomics IDEntifications database

More...
PRIDEi
P37908

<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
4260620, 11 interactors
853486, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-12070N

Protein interaction database and analysis system

More...
IntActi
P37908, 2 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b4461

<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
P37908

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>Domaini2 – 192CNNM transmembranePROSITE-ProRule annotationAdd BLAST191
Domaini208 – 270CBS 1PROSITE-ProRule annotationAdd BLAST63
Domaini272 – 332CBS 2PROSITE-ProRule annotationAdd BLAST61

<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 UPF0053 family.Curated

Keywords - Domaini

CBS domain, Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG4536, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_015237_4_1_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P37908

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P37908

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.465.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR000644, CBS_dom
IPR002550, CNNM
IPR036318, FAD-bd_PCMH-like_sf
IPR016169, FAD-bd_PCMH_sub2
IPR005170, Transptr-assoc_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00571, CBS, 1 hit
PF03471, CorC_HlyC, 1 hit
PF01595, DUF21, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01091, CorC_HlyC, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF56176, SSF56176, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51371, CBS, 1 hit
PS51846, CNNM, 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.

P37908-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEHISTTTLI IILIIMVVIS AYFSGSETGM MTLNRYRLRH MAKQGNRSAK
60 70 80 90 100
RVEKLLRKPD RLISLVLIGN NLVNILASAL GTIVGMRLYG DAGVAIATGV
110 120 130 140 150
LTFVVLVFAE VLPKTIAALY PEKVAYPSSF LLAPLQILMM PLVWLLNAIT
160 170 180 190 200
RMLMRMMGIK TDIVVSGSLS KEELRTIVHE SRSQISRRNQ DMLLSVLDLE
210 220 230 240 250
KMTVDDIMVP RSEIIGIDIN DDWKSILRQL SHSPHGRIVL YRDSLDDAIS
260 270 280 290 300
MLRVREAWRL MSEKKEFTKE TMLRAADEIY FVPEGTPLST QLVKFQRNKK
310 320 330 340 350
KVGLVVNEYG DIQGLVTVED ILEEIVGDFT TSMSPTLAEE VTPQNDGSVI
360 370 380 390 400
IDGTANVREI NKAFNWHLPE DDARTVNGVI LEALEEIPVA GTRVRIGEYD
410 420
IDILDVQDNM IKQVKVFPVK PLRESVAE
Length:428
Mass (Da):48,044
Last modified:July 10, 2007 - v5
<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:i38456865EDBCB151
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 BAA16497 differs from that shown. Reason: Erroneous initiation.Curated
The sequence X07863 differs from that shown. Reason: Frameshift.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
U00096 Genomic DNA Translation: AAT48144.3
AP009048 Genomic DNA Translation: BAA16497.2 Different initiation.
X07863 Genomic DNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
WP_010723175.1, NZ_STEB01000040.1
YP_026171.3, NC_000913.3

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAT48144; AAT48144; b4461
BAA16497; BAA16497; BAA16497

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2847739
52077886

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW5415
eco:b4461

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.2710

<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: AAT48144.3
AP009048 Genomic DNA Translation: BAA16497.2 Different initiation.
X07863 Genomic DNA No translation available.
RefSeqiWP_010723175.1, NZ_STEB01000040.1
YP_026171.3, NC_000913.3

3D structure databases

SMRiP37908
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4260620, 11 interactors
853486, 1 interactor
DIPiDIP-12070N
IntActiP37908, 2 interactors
STRINGi511145.b4461

Protein family/group databases

TCDBi1.A.112.2.5, the cyclin m mg2+ exporter (cnnm) family

Proteomic databases

jPOSTiP37908
PaxDbiP37908
PRIDEiP37908

Genome annotation databases

EnsemblBacteriaiAAT48144; AAT48144; b4461
BAA16497; BAA16497; BAA16497
GeneIDi2847739
52077886
KEGGiecj:JW5415
eco:b4461
PATRICifig|511145.12.peg.2710

Organism-specific databases

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

More...
EchoBASEi
EB2336

Phylogenomic databases

eggNOGiCOG4536, Bacteria
HOGENOMiCLU_015237_4_1_6
InParanoidiP37908
PhylomeDBiP37908

Enzyme and pathway databases

BioCyciEcoCyc:G7356-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P37908

Family and domain databases

Gene3Di3.30.465.10, 1 hit
InterProiView protein in InterPro
IPR000644, CBS_dom
IPR002550, CNNM
IPR036318, FAD-bd_PCMH-like_sf
IPR016169, FAD-bd_PCMH_sub2
IPR005170, Transptr-assoc_dom
PfamiView protein in Pfam
PF00571, CBS, 1 hit
PF03471, CorC_HlyC, 1 hit
PF01595, DUF21, 1 hit
SMARTiView protein in SMART
SM01091, CorC_HlyC, 1 hit
SUPFAMiSSF56176, SSF56176, 1 hit
PROSITEiView protein in PROSITE
PS51371, CBS, 1 hit
PS51846, CNNM, 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 nameiYFJD_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: P37908
Secondary accession number(s): P76600
, P76601, P77009, Q6BF70
<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: October 1, 1994
Last sequence update: July 10, 2007
Last modified: October 7, 2020
This is version 159 of the entry and version 5 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. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  3. SIMILARITY comments
    Index of protein domains and families
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