yedD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

yedD

Gene Synonym(s)

ECK1927, b1928, JW1913[1], JW1913

Product Desc.

conserved protein[2]; putative lipoprotein[3]

Novel verified lipoprotein, function unknown[4]

Product Synonyms(s)

predicted protein[1], B1928[2][1], YedD[2][1] , ECK1927, JW1913, b1928

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yedD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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First 15 aa are a type II signal peptide.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

yedD

Mnemonic

Systematic nomenclature

Synonyms

ECK1927, b1928, JW1913[1], JW1913

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

43.23 minutes 

MG1655: 2006114..2005701
<gbrowseImage> name=NC_000913:2005701..2006114 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1898184..1898597
<gbrowseImage> name=NC_012759:1898184..1898597 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2010227..2009814
<gbrowseImage> name=NC_007779:2009814..2010227 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2097122..2096709
<gbrowseImage> name=NC_010473:2096709..2097122 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔyedD (Keio:JW1913)

deletion

deletion

PMID:16738554

Shigen
CGSC9591[5]

yedD::Tn5KAN-I-SceI (FB20535)

Insertion at nt 162 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20535

contains pKD46

ΔyedD774::kan

PMID:16738554

CGSC:104462


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1913

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAAAACTCGCAATTGCAGG

Primer 2:CCtGGCAGTGGCGTCGGTAACGG

4B9

Kohara Phage

Genobase

PMID:3038334

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[5]

est. P1 cotransduction: 58% [6]

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[5]

est. P1 cotransduction: 29% [6]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11659

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11659

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001602

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949082

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1611

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006416

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

YedD

Synonyms

predicted protein[1], B1928[2][1], YedD[2][1] , ECK1927, JW1913, b1928

Product description

conserved protein[2]; putative lipoprotein[3]

Novel verified lipoprotein, function unknown[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0031225

anchored to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9901

C

Seeded from EcoCyc (v14.0)

complete

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

iscS

PMID:19402753

MALDI(Z-score):32.372661

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

Outer membrane

PMID:15174130

EchoLocation:yedD


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc

MKKLAIAGAL LLLAGCAEVE NYNNVVKTPA PDWLAGYWQT KGPQRALVSP EAIGSLIVTK
EGDTLDCRQW QRVIAVPGKL TLMSDDLTNV TVKRELYEVE RDGNTIEYDG MTMERVDRPT
AECAAALDKA PLPTPLP
Length

137

Mol. Wt

14.982 kDa

pI

4.7 (calculated)

Extinction coefficient

22,460 - 22,835 (calc based on 4 Y, 3 W, and 3 C residues)


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

motif

1-15

UniProt Manual:Signal Peptides

UniProt:P31063


<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=yedD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129875

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949082

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006416

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31063

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11659

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11659

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949082

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001602

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1611

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

5007

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1276

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2889

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

yedD

Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2006094..2006134 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1928 (EcoliWiki Page)

NCBI GEO profiles for yedD

microarray

GenExpDB:b1928 (EcoliWiki Page)

Summary of data for yedD from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

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Notes

Accessions Related to yedD Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11659

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1611

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1928

EcoGene

EcoGene:EG11659

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001602

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006416

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Shigella flexneri

YEDD

From SHIGELLACYC

E. coli O157

YEDD

From ECOO157CYC

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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