yadG:On One Page

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

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Standard Name

yadG

Gene Synonym(s)

ECK0126, b0127, JW0123[1], JW0123

Product Desc.

YadG[2][3];

Component of YadG/YadH ABC transporter[2][3]

Function unknown[4]

Product Synonyms(s)

predicted transporter subunit: ATP-binding component of ABC superfamily[1], B0127[2][1], YadG[2][1] , ECK0126, JW0123, b0127

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yadG[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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Notes

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AFMB Structural Genomics target No. 4 (http://afmb.cnrs-mrs.fr/article171.html)[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

yadG

Mnemonic

Systematic nomenclature

Synonyms

ECK0126, b0127, JW0123[1], JW0123

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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

3.08 minutes 

MG1655: 142779..143705
<gbrowseImage> name=NC_000913:142779..143705 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 145582..146508
<gbrowseImage> name=NC_012967:145582..146508 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 142778..143704
<gbrowseImage> name=NC_012759:142778..143704 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 142779..143705
<gbrowseImage> name=NC_007779:142779..143705 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 116883..117809
<gbrowseImage> name=NC_010473:116883..117809 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

yadG(del) (Keio:JW0123)

deletion

deletion

PMID:16738554

Shigen

CGSC8401[5]

yadG744(del)::kan

PMID:16738554

CGSC:103466


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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

JW0123

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCATTGCACTGGAACTTCA

Primer 2:CCTGCGCGATCTCCTTGTTTTTC

17C11

Kohara Phage

Genobase

PMID:3038334

11C5

Kohara Phage

Genobase

PMID:3038334

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 5% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 83% [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:EG12320

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12320

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944833

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002196

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2225

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000447

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

YadG

Synonyms

predicted transporter subunit: ATP-binding component of ABC superfamily[1], B0127[2][1], YadG[2][1] , ECK0126, JW0123, b0127

Product description

YadG[2][3];

Component of YadG/YadH ABC transporter[2][3]

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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

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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

Subunits of YadG/YadH ABC transporter

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1135675

Protein

glpD

PMID:16606699

Experiment(s):EBI-1135675

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.6

Protein

eno

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.6

Protein

ibpA

PMID:19402753

LCMS(ID Probability):99.4

Protein

argT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

ftnA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rluB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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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

cytoplasm

From EcoCyc[3]


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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 

MTIALELQQL KKTYPGGVQA LRGIDLQVEA GDFYALLGPN GAGKSTTIGI ISSLVNKTSG
RVSVFGYDLE KDVVNAKRQL GLVPQEFNFN PFETVQQIVV NQAGYYGVER KEAYIRSEKY
LKQLDLWGKR NERARMLSGG MKRRLMIARA LMHEPKLLIL DEPTAGVDIE LRRSMWGFLK
DLNDKGTTII LTTHYLEEAE MLCRNIGIIQ HGELVENTSM KALLAKLKSE TFILDLAPKS
PLPKLDGYQY RLVDTATLEV EVLREQGINS VFTQLSEQGI QVLSMRNKAN RLEELFVSLV
NEKQGDRA
Length

308

Mol. Wt

34.647 kDa

pI

8.7 (calculated)

Extinction coefficient

25,900 - 26,025 (calc based on 10 Y, 2 W, and 1 C residues)

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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

Domain

45..165

PF00005 ABC transporter

PMID:19920124

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<motif_map/>

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

Structures

<beststructure> gene=yadG 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:16128120

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944833

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000447

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P36879

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12320

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12320

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944833

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002196

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2225

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 MC4100

1.53E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

11.416+/-0.142

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.057775378

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

724

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

292

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

633

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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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)

yadG

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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_000913:142759..142799 source=MG1655 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
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0127 (EcoliWiki Page)

NCBI GEO profiles for yadG

microarray

GenExpDB:b0127 (EcoliWiki Page)

Summary of data for yadG from multiple microarray studies

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

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (142574..142812) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:C2[7]

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Notes

Accessions Related to yadG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12320

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2225

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0127

EcoGene

EcoGene:EG12320

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002196

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000447

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Arabidopsis thaliana

  • AT5G61730 (score: 1.000; bootstrap: 84%)
  • AT5G61690 (score: 0.800)
  • AT3G47730 (score: 0.744)
  • AT3G47780 (score: 0.088)
  • AT3G47740 (score: 0.083)
  • AT3G47790 (score: 0.080)
  • AT3G47770 (score: 0.077)
  • AT5G61700 (score: 0.076)
  • AT3G47750 (score: 0.076)
  • AT5G61740 (score: 0.070)
  • AT3G47760 (score: 0.068)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00026658 (score: 1.000; bootstrap: 97%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000013883 (score: 1.000; bootstrap: 95%)
  • ENSCINP00000011530 (score: 0.219)

From Inparanoid:20070104

Oryza gramene

  • Q6ZIW1 (score: 1.000; bootstrap: 89%)
  • Q6ZIV9 (score: 0.083)
  • Q69XA0 (score: 0.080)
  • Q6H8C3 (score: 0.056)

From Inparanoid:20070104

Shigella flexneri

YADG

From SHIGELLACYC

E. coli O157

YADG

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR24220:SF186

EcoCyc

EcoCyc:EG12320

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12320

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002196

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2225

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000447

Escherichia coli str. K-12 substr. MG1655

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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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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