frdB: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

frdB

Gene Synonym(s)

ECK4149, b4153, JW4114[1], JW4114

Product Desc.

fumarate reductase iron-sulfur protein[2][3];

Component of fumarate reductase[2][3]

Fumarate reductase iron-sulfur protein subunit[4]

Product Synonyms(s)

fumarate reductase (anaerobic), Fe-S subunit[1], B4153[2][1], FrdB[2][1] , ECK4149, JW4114, b4153

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): frdABCD[2], OP00030, frd

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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HT_Cmplx15_Mem: FrdA+FrdB.[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

frdB

Mnemonic

Fumarate reductase

Synonyms

ECK4149, b4153, JW4114[1], JW4114

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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

94.36 minutes, 94.36 minutes 

MG1655: 4378540..4377806
<gbrowseImage> name=NC_000913:4377806..4378540 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4359228..4358494
<gbrowseImage> name=NC_012967:4358494..4359228 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4316541..4317275
<gbrowseImage> name=NC_012759:4316541..4317275 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4385197..4384463
<gbrowseImage> name=NC_007779:4384463..4385197 source=W3110 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

Coding Start (SO:0000323)

MG1655

4377809

Edman degradation

PMID:6751816


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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

Strain DH10B

D51N

Nonsynonomous mutation

PMID:18245285

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔfrdB (Keio:JW4114)

deletion

deletion

PMID:16738554

Shigen
CGSC10963[5]

frdBC58S

C58S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC78S

C78S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC63S

C63S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

frdBC66S

C66S

Affects center 1 (2Fe-2S)

seeded from UniProt:P0AC47

ΔfrdB780::kan

PMID:16738554

CGSC:100994


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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

JW4114

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCTGAGATGAAAAACCTGAA

Primer 2:CCGCGTGGTTTCAGGGTCGCGAT

1D4

Kohara Phage

Genobase

PMID:3038334

3H6

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[5]

est. P1 cotransduction: 46% [6]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[5]

est. P1 cotransduction: 11% [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:EG10331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10331

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000325

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948666

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0327

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013602

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

FrdB

Synonyms

fumarate reductase (anaerobic), Fe-S subunit[1], B4153[2][1], FrdB[2][1] , ECK4149, JW4114, b4153

Product description

fumarate reductase iron-sulfur protein[2][3];

Component of fumarate reductase[2][3]

Fumarate reductase iron-sulfur protein subunit[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:0000104

succinate dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.3.99.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0001539

ciliary or flagellar motility

PMID:18337747

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:10373108

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004489

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0816

P

Seeded from EcoCyc (v14.0)

complete

GO:0006113

fermentation

PMID:14109218

IMP: Inferred from Mutant Phenotype

P

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:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001041

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006058

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017900

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

PMID:8499449

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009061

anaerobic respiration

PMID:14109218

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0009296

flagellum assembly

PMID:18337747

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004489

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009051

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012285

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0051537

2 iron, 2 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0001

F

Seeded from EcoCyc (v14.0)

complete

GO:0051537

2 iron, 2 sulfur cluster binding

PMID:10373108

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0051538

3 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0003

F

Seeded from EcoCyc (v14.0)

complete

GO:0051538

3 iron, 4 sulfur cluster binding

PMID:10373108

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

PMID:10373108

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004489

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009051

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

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 fumarate reductase

could be indirect


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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

PMID:8419359, PMID:6751816

EchoLocation:frdB


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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 

MAEMKNLKIE VVRYNPEVDT APHSAFYEVP YDATTSLLDA LGYIKDNLAP DLSYRWSCRM
AICGSCGMMV NNVPKLACKT FLRDYTDGMK VEALANFPIE RDLVVDMTHF IESLEAIKPY
IIGNSRTADQ GTNIQTPAQM AKYHQFSGCI NCGLCYAACP QFGLNPEFIG PAAITLAHRY
NEDSRDHGKK ERMAQLNSQN GVWSCTFVGY CSEVCPKHVD PAAAIQQGKV ESSKDFLIAT LKPR
Length

244

Mol. Wt

27.122 kDa

pI

6.5 (calculated)

Extinction coefficient

27,390 - 28,765 (calc based on 11 Y, 2 W, and 11 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

Initiator Methionine

1

Removed

UniProt:P0AC47


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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=frdB taxon=12017 </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:16131978

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948666

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013602

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AC47

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10331

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948666

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000325

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0327

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

404

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

144

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

318

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)

frdABCD

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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_000913:4378520..4378560 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
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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:b4153 (EcoliWiki Page)

NCBI GEO profiles for frdB

microarray

GenExpDB:b4153 (EcoliWiki Page)

Summary of data for frdB 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
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Notes

Accessions Related to frdB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10331

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0327

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4153

EcoGene

EcoGene:EG10331

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000325

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013602

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

FRDB

From SHIGELLACYC

E. coli O157

FRDB

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:46548

Superfamily (EcoliWiki Page)

SUPERFAMILY:54292

EcoCyc

EcoCyc:EG10331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10331

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000325

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0327

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013602

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 1.8 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 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).

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