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Protein

UPF0250 protein YbeD

Gene

ybeD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Enzyme and pathway databases

BioCyciEcoCyc:EG11592-MONOMER.
ECOL316407:JW0626-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
UPF0250 protein YbeD
Gene namesi
Name:ybeD
Ordered Locus Names:b0631, JW0626
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11592. ybeD.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8787UPF0250 protein YbeDPRO_0000209296Add
BLAST

Proteomic databases

EPDiP0A8J4.
PaxDbiP0A8J4.
PRIDEiP0A8J4.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
tufAP0CE472EBI-370708,EBI-301077

Protein-protein interaction databases

BioGridi4260679. 231 interactions.
DIPiDIP-31839N.
IntActiP0A8J4. 9 interactions.
MINTiMINT-1273776.
STRINGi511145.b0631.

Structurei

Secondary structure

1
87
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Beta strandi15 – 228Combined sources
Helixi27 – 3812Combined sources
Beta strandi39 – 413Combined sources
Beta strandi45 – 484Combined sources
Beta strandi53 – 6210Combined sources
Helixi67 – 7711Combined sources
Beta strandi80 – 823Combined sources
Beta strandi84 – 863Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RWUNMR-A1-87[»]
ProteinModelPortaliP0A8J4.
SMRiP0A8J4. Positions 1-87.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A8J4.

Family & Domainsi

Sequence similaritiesi

Belongs to the UPF0250 family.Curated

Phylogenomic databases

eggNOGiENOG4108Z43. Bacteria.
COG2921. LUCA.
HOGENOMiHOG000265101.
InParanoidiP0A8J4.
KOiK09158.
OMAiKVMGLAK.
OrthoDBiEOG6BGP43.
PhylomeDBiP0A8J4.

Family and domain databases

Gene3Di3.30.70.1460. 1 hit.
HAMAPiMF_00659. UPF0250.
InterProiIPR007454. UPF0250.
IPR027471. YbeD-like.
[Graphical view]
PfamiPF04359. DUF493. 1 hit.
[Graphical view]
SUPFAMiSSF117991. SSF117991. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A8J4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTKLNELLE FPTPFTYKVM GQALPELVDQ VVEVVQRHAP GDYTPTVKPS
60 70 80
SKGNYHSVSI TINATHIEQV ETLYEELGKI DIVRMVL
Length:87
Mass (Da):9,827
Last modified:June 7, 2005 - v1
Checksum:i13B14D3B2A6E1F95
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07636 Genomic DNA. Translation: AAA66341.1.
U82598 Genomic DNA. Translation: AAB40831.1.
U00096 Genomic DNA. Translation: AAC73732.1.
AP009048 Genomic DNA. Translation: BAA35274.1.
PIRiE64797.
RefSeqiNP_415164.1. NC_000913.3.
WP_000850550.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73732; AAC73732; b0631.
BAA35274; BAA35274; BAA35274.
GeneIDi945220.
KEGGiecj:JW0626.
eco:b0631.
PATRICi32116443. VBIEscCol129921_0661.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L07636 Genomic DNA. Translation: AAA66341.1.
U82598 Genomic DNA. Translation: AAB40831.1.
U00096 Genomic DNA. Translation: AAC73732.1.
AP009048 Genomic DNA. Translation: BAA35274.1.
PIRiE64797.
RefSeqiNP_415164.1. NC_000913.3.
WP_000850550.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1RWUNMR-A1-87[»]
ProteinModelPortaliP0A8J4.
SMRiP0A8J4. Positions 1-87.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260679. 231 interactions.
DIPiDIP-31839N.
IntActiP0A8J4. 9 interactions.
MINTiMINT-1273776.
STRINGi511145.b0631.

Proteomic databases

EPDiP0A8J4.
PaxDbiP0A8J4.
PRIDEiP0A8J4.

Protocols and materials databases

DNASUi945220.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73732; AAC73732; b0631.
BAA35274; BAA35274; BAA35274.
GeneIDi945220.
KEGGiecj:JW0626.
eco:b0631.
PATRICi32116443. VBIEscCol129921_0661.

Organism-specific databases

EchoBASEiEB1550.
EcoGeneiEG11592. ybeD.

Phylogenomic databases

eggNOGiENOG4108Z43. Bacteria.
COG2921. LUCA.
HOGENOMiHOG000265101.
InParanoidiP0A8J4.
KOiK09158.
OMAiKVMGLAK.
OrthoDBiEOG6BGP43.
PhylomeDBiP0A8J4.

Enzyme and pathway databases

BioCyciEcoCyc:EG11592-MONOMER.
ECOL316407:JW0626-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A8J4.
PROiP0A8J4.

Family and domain databases

Gene3Di3.30.70.1460. 1 hit.
HAMAPiMF_00659. UPF0250.
InterProiIPR007454. UPF0250.
IPR027471. YbeD-like.
[Graphical view]
PfamiPF04359. DUF493. 1 hit.
[Graphical view]
SUPFAMiSSF117991. SSF117991. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Lipoic acid metabolism in Escherichia coli: sequencing and functional characterization of the lipA and lipB genes."
    Reed K.E., Cronan J.E. Jr.
    J. Bacteriol. 175:1325-1336(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  6. "Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains."
    Kozlov G., Elias D., Semesi A., Yee A., Cygler M., Gehring K.
    J. Bacteriol. 186:8083-8088(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR.

Entry informationi

Entry nameiYBED_ECOLI
AccessioniPrimary (citable) accession number: P0A8J4
Secondary accession number(s): P30977
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: June 7, 2005
Last modified: March 16, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.