ihfB: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

ihfB

Gene Synonym(s)

ECK0903, b0912, JW0895, himD[1], hip[1], himD, hip

Product Desc.

IhfB[2][3];

Component of IHF transcriptional dual regulator[2][3]

Integration Host Factor (IHF), beta subunit; host infection, mutant phage lambda; site-specific recombination; sequence-specific DNA-binding transcriptional activator[4]

Product Synonyms(s)

Integration host factor (IHF) beta subunit[5], B0912[2][5], IhfB[2][5], HimD[5], Hip[5], ECK0903, himD, hip, JW0895, b0912

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpsA-ihfB[2], rpsA-himD, ihfB[2], OP00241, himD

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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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

ihfB

Mnemonic

Integration, host factor

Synonyms

ECK0903, b0912, JW0895, himD[1], hip[1], himD, hip

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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

20.76 minutes 

MG1655: 963051..963335
<gbrowseImage> name=NC_000913:963051..963335 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 866019..866303
<gbrowseImage> name=NC_012759:866019..866303 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 964250..964534
<gbrowseImage> name=NC_007779:964250..964534 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1016979..1017263
<gbrowseImage> name=NC_010473:1016979..1017263 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

Coding Start (SO:0000323)

MG1655

963051

Edman degradation

PMID:9868784


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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

ΔihfB (Keio:JW0895)

deletion

deletion

PMID:16738554

Shigen
CGSC8917[6]

ihfBE44G,K,V

E44G,K,V

Altered DNA-binding specificity

seeded from UniProt:P0A6Y1

Δhip-1::cat

PMID:3159903

CGSC:90848

ΔihfB735::kan

PMID:16738554

CGSC:101538


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Notes

Genetic Interactions

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<protect>

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

JW0895

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCAAGTCAGAATTGATAGA

Primer 2:CCACCGTAAATATTGGCGCGATC

6D12

Kohara Phage

Genobase

PMID:3038334

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[6]

est. P1 cotransduction: 55% [7]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[6]

est. P1 cotransduction: 19% [7]

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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:EG10441

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10441

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000434

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945533

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0436

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003107

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

IhfB

Synonyms

Integration host factor (IHF) beta subunit[5], B0912[2][5], IhfB[2][5], HimD[5], Hip[5], ECK0903, himD, hip, JW0895, b0912

Product description

IhfB[2][3];

Component of IHF transcriptional dual regulator[2][3]

Integration Host Factor (IHF), beta subunit; host infection, mutant phage lambda; site-specific recombination; sequence-specific DNA-binding transcriptional activator[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:0003677

DNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00381

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000119

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005685

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010992

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020816

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0005694

chromosome

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005685

C

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00381

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005685

P

Seeded from EcoCyc (v14.0)

complete

GO:0006310

DNA recombination

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0233

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00381

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005685

P

Seeded from EcoCyc (v14.0)

complete

GO:0006417

regulation of translation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00381

P

Seeded from EcoCyc (v14.0)

complete

GO:0006417

regulation of translation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0810

P

Seeded from EcoCyc (v14.0)

complete

Contributes to

GO:0043565

sequence-specific DNA binding

PMID:10551881

IDA: Inferred from Direct Assay

F

with IhfA

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 IHF transcriptional dual regulator

could be indirect

Protein

rplW

PMID:15690043

Experiment(s):EBI-883484

Protein

rpmC

PMID:15690043

Experiment(s):EBI-883484

Protein

rpmG

PMID:15690043

Experiment(s):EBI-883484

Protein

rpoC

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsC

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsD

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsE

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsF

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsG

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsH

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsM

PMID:15690043

Experiment(s):EBI-883484

Protein

rpsS

PMID:15690043

Experiment(s):EBI-883484

Protein

uxuB

PMID:15690043

Experiment(s):EBI-883484

Protein

yhbY

PMID:15690043

Experiment(s):EBI-883484

Protein

yjgD

PMID:15690043

Experiment(s):EBI-883484

Protein

rplM

PMID:15690043

Experiment(s):EBI-883484

Protein

rplO

PMID:15690043

Experiment(s):EBI-883484

Protein

rplP

PMID:15690043

Experiment(s):EBI-883484

Protein

rplS

PMID:15690043

Experiment(s):EBI-883484

Protein

rplU

PMID:15690043

Experiment(s):EBI-883484

Protein

rplV

PMID:15690043

Experiment(s):EBI-883484

Protein

aroB

PMID:15690043

Experiment(s):EBI-883484

Protein

gltS

PMID:15690043

Experiment(s):EBI-883484

Protein

hupA

PMID:15690043

Experiment(s):EBI-883484

Protein

hupB

PMID:15690043

Experiment(s):EBI-883484, EBI-884415

Protein

nusA

PMID:15690043

Experiment(s):EBI-883484

Protein

rplA

PMID:15690043

Experiment(s):EBI-883484

Protein

rplB

PMID:15690043

Experiment(s):EBI-883484

Protein

rplC

PMID:15690043

Experiment(s):EBI-883484

Protein

rplD

PMID:15690043

Experiment(s):EBI-883484

Protein

rplE

PMID:15690043

Experiment(s):EBI-883484

Protein

ihfA

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.0

Protein

aroB

PMID:19402753

LCMS(ID Probability):99.0

Protein

uxuB

PMID:19402753

LCMS(ID Probability):99.0

Protein

gltS

PMID:19402753

LCMS(ID Probability):99.0

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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
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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 

MTKSELIERL ATQQSHIPAK TVEDAVKEML EHMASTLAQG ERIEIRGFGS FSLHYRAPRT
GRNPKTGDKV ELEGKYVPHF KPGKELRDRA NIYG
Length

94

Mol. Wt

10.65 kDa

pI

9.8 (calculated)

Extinction coefficient

4,470 (calc based on 3 Y, 0 W, and 0 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

1..91

PF00216 Bacterial DNA-binding protein

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=ihfB 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:16128879

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945533

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003107

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6Y1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10441

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10441

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945533

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000434

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0436

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

2.11E+03

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

E. coli K-12 MG1655

15238

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

12357

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

9391

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)

rpsA-ihfB

ihfB

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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_000913:963031..963071 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:b0912 (EcoliWiki Page)

NCBI GEO profiles for ihfB

microarray

GenExpDB:b0912 (EcoliWiki Page)

Summary of data for ihfB 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 ihfB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10441

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0436

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0912

EcoGene

EcoGene:EG10441

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000434

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003107

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

Xenopus tropicalis

  • ENSXETP00000007174 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

HIMD

From SHIGELLACYC

E. coli O157

HIMD

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)

PF00216 Bacterial DNA-binding protein

Superfamily (EcoliWiki Page)

SUPERFAMILY:47729

EcoCyc

EcoCyc:EG10441

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10441

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000434

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0436

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003107

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 Berlyn, MK (1998) Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62 814-984 PubMed
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 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 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 5.3 5.4 5.5 5.6 5.7 5.8 5.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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