dfp: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

dfp

Gene Synonym(s)

ECK3629, b3639, JW5642, dnaS, coaBC[1], coaBC

Product Desc.

EG10004[2][3]

Coenzyme A biosynthesis, bifunctional enzyme; phosphopantothenoylcysteine decarboxylase (N) and phosphopantothenoylcysteine synthase (C)[4]

Product Synonyms(s)

fused 4'-phosphopantothenoylcysteine decarboxylase[1], phosphopantothenoylcysteine synthetase, FMN-binding[1], B3639[2][1], DnaS[2][1], Dfp[2][1] , coaBC, ECK3629, JW5642, b3639

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s):

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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Dfp was originally identified as a flavoprotein affecting DNA synthesis and pantothenate metabolism. The N-terminal domain catalyzes the decarboxylation of (R)-4'-phospho-N-pantothenoylcysteine to 4'-phosphopantetheine.[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

dfp

Mnemonic

DNA synthesis FlavoProtein

Synonyms

ECK3629, b3639, JW5642, dnaS, coaBC[1], coaBC

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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

82.13 minutes, 82.13 minutes 

MG1655: 3810754..3811974
<gbrowseImage> name=NC_000913:3810754..3811974 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3751086..3752306
<gbrowseImage> name=NC_012967:3751086..3752306 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3699080..3700300
<gbrowseImage> name=NC_012759:3699080..3700300 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3827684..3826464
<gbrowseImage> name=NC_007779:3826464..3827684 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3908331..3909551
<gbrowseImage> name=NC_010473:3908331..3909551 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

3810757

Edman degradation

PMID:10922366


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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

coaBCP89A

P89A

Binds FMN, but more loosely than wild-type

seeded from UniProt:P0ABQ0

coaBCP89D

P89D

No FMN binding

seeded from UniProt:P0ABQ0

coaBCT91V

T91V

Binds FMN

seeded from UniProt:P0ABQ0

coaBCN125D,Q

N125D,Q

Loss of activity

seeded from UniProt:P0ABQ0

coaBCM128L

M128L

Severely reduced activity

seeded from UniProt:P0ABQ0

coaBCD203N

D203N

Loss of dimerization

seeded from UniProt:P0ABQ0

coaBCN210D

N210D

Loss of activity, reaction intermediate detectable

seeded from UniProt:P0ABQ0

coaBCG14S

G14S

No FMN binding

seeded from UniProt:P0ABQ0

coaBCG15A

G15A

Less than 5% of wild-type activity

seeded from UniProt:P0ABQ0

coaBCI16L

I16L

Severely reduced activity

seeded from UniProt:P0ABQ0

coaBCK289Q

K289Q

Loss of activity

seeded from UniProt:P0ABQ0

coaBCK291Q

K291Q

Reduced activity

seeded from UniProt:P0ABQ0

coaBCK292Q

K292Q

Small effect on activity

seeded from UniProt:P0ABQ0

coaBCK215Q

K215Q

No effect

seeded from UniProt:P0ABQ0

coaBCA275V

A275V

Loss of dimerization

seeded from UniProt:P0ABQ0

coaBCN210H,K

N210H,K

Loss of activity, reaction intermediate not detectable

seeded from UniProt:P0ABQ0

coaBCS212A

S212A

Small effect on activity

seeded from UniProt:P0ABQ0

coaBCC158A,S

C158A,S

Loss of activity

seeded from UniProt:P0ABQ0

coaBCT194V

T194V

Loss of dimerization

seeded from UniProt:P0ABQ0

coaBCT198V

T198V

Loss of dimerization

seeded from UniProt:P0ABQ0

coaBCM124L

M124L

No effect

seeded from UniProt:P0ABQ0

coaBCA17G,S

A17G,S

Almost wild-type activity

seeded from UniProt:P0ABQ0

coaBCY19F

Y19F

Almost wild-type activity

seeded from UniProt:P0ABQ0

coaBCY19L

Y19L

Reduced activity

seeded from UniProt:P0ABQ0

coaBCK20N,Q

K20N,Q

Reduced activity

seeded from UniProt:P0ABQ0

coaBCK20R

K20R

Almost wild-type activity

seeded from UniProt:P0ABQ0

coaBCF46L

F46L

Reduced activity

seeded from UniProt:P0ABQ0

coaBCH75N

H75N

Loss of activity

seeded from UniProt:P0ABQ0

coaBCA17D

A17D

Less than 5% of wild-type activity

seeded from UniProt:P0ABQ0

coaBCG11D

G11D

In Dfp-707; temperature-sensitive, impairs folding

seeded from UniProt:P0ABQ0

coaBCI16V

I16V

Slightly reduced activity

seeded from UniProt:P0ABQ0

dfp::Tn5KAN-I-SceI (FB21356)

Insertion at nt 1182 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21356

contains pKD46

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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

JW5642

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCCTtGCCGGTAAAAAAAT

Primer 2:CCACGTCGATTTTTTTCATCATA

2A6

Kohara Phage

Genobase

PMID:3038334

4D2

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 55% [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:EG10004

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10004

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000004

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949047

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011896

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

Dfp

Synonyms

fused 4'-phosphopantothenoylcysteine decarboxylase[1], phosphopantothenoylcysteine synthetase, FMN-binding[1], B3639[2][1], DnaS[2][1], Dfp[2][1] , coaBC, ECK3629, JW5642, b3639

Product description

EG10004[2][3]

Coenzyme A biosynthesis, bifunctional enzyme; phosphopantothenoylcysteine decarboxylase (N) and phosphopantothenoylcysteine synthase (C)[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:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0004632

phosphopantothenate--cysteine ligase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005252

F

Seeded from EcoCyc (v14.0)

complete

GO:0004632

phosphopantothenate--cysteine ligase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.2.5

F

Seeded from EcoCyc (v14.0)

complete

GO:0004633

phosphopantothenoylcysteine decarboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005252

F

Seeded from EcoCyc (v14.0)

complete

GO:0004633

phosphopantothenoylcysteine decarboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.36

F

Seeded from EcoCyc (v14.0)

complete

GO:0010181

FMN binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005252

F

Seeded from EcoCyc (v14.0)

complete

GO:0015937

coenzyme A biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005252

P

Seeded from EcoCyc (v14.0)

complete

GO:0015941

pantothenate catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005252

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

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

rplA

PMID:15690043

Experiment(s):EBI-882623

Protein

rpoA

PMID:15690043

Experiment(s):EBI-890190

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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

MKARQQKYCD KIANFWCHPT GKIIMSLAGK KIVLGVSGGI AAYKTPELVR RLRDRGADVR
VAMTEAAKAF ITPLSLQAVS GYPVSDSLLD PAAEAAMGHI ELGKWADLVI LAPATADLIA
RVAAGMANDL VSTICLATPA PVAVLPAMNQ QMYRAAATQH NLEVLASRGL LIWGPDSGSQ
ACGDIGPGRM LDPLTIVDMA VAHFSPVNDL KHLNIMITAG PTREPLDPVR YISNHSSGKM
GFAIAAAAAR RGANVTLVSG PVSLPTPPFV KRVDVMTALE MEAAVNASVQ QQNIFIGCAA
VADYRAATVA PEKIKKQATQ GDELTIKMVK NPDIVAGVAA LKDHRPYVVG FAAETNNVEE
YARQKRIRKN LDLICANDVS QPTQGFNSDN NALHLFWQDG DKVLPLERKE LLGQLLLDEI
VTRYDEKNRR
Length

430

Mol. Wt

46.3 kDa

pI

8.5 (calculated)

Extinction coefficient

35,410 - 36,160 (calc based on 9 Y, 4 W, and 6 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

Initiator Methionine

1

Removed

UniProt:P0ABQ0

Domain

186..384

PF04127 DNA / pantothenate metabolism flavoprotein

PMID:19920124

Domain

6..123

PF02441 Flavoprotein

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=dfp 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:90111624

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949047

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011896

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABQ0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10004

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10004

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949047

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000004

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0004

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

Ecoli K-12

17.072+/-0.53

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.038934426

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

1126

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

285

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

512

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)
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_000913:3810734..3810774 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


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

Type Reference Notes

microarray

GEO Profiles:b3639 (EcoliWiki Page)

NCBI GEO profiles for dfp

microarray

GenExpDB:b3639 (EcoliWiki Page)

Summary of data for dfp 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

GFP Fusion

Intergenic region (3810104..3810321) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ09; Well:G5[7]

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Notes

Accessions Related to dfp Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10004

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0004

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3639

EcoGene

EcoGene:EG10004

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011896

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

Anopheles gambiae

  • ENSANGP00000028590 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT3G18030 (score: 1.000; bootstrap: 100%)
  • AT1G48605 (score: 0.815)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000018730 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00028937 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00009138 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000026569 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-1749 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-2689 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231515 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0050290 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA15754-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000034138 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000343190 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000024748 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000011433 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q69K55 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000012477 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000025289 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000137213 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000000814 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DFP

From SHIGELLACYC

E. coli O157

DFP

From ECOO157CYC


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)

PF04127 DNA / pantothenate metabolism flavoprotein

Pfam (EcoliWiki Page)

PF02441 Flavoprotein

Superfamily (EcoliWiki Page)

SUPERFAMILY:52507

Panther (EcoliWiki Page)

PTHR14359:SF6

Superfamily (EcoliWiki Page)

SUPERFAMILY:102645

EcoCyc

EcoCyc:EG10004

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10004

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000004

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0004

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011896

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. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 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 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 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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