zraR: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

zraR

Gene Synonym(s)

ECK3996, b4004, JW3968, hydG[1], hydG

Product Desc.

ZraR transcriptional activator[2][3]

Two component response regulator for zraP; responsive to Zn(2+) and Pb(2+); autoregulated; regulation of Hyd-3 activity is probably due to crosstalk of overexpressed protein[4]

Product Synonyms(s)

fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator [1], sigma54 interaction protein [1], B4004 [2][1], HydG [2][1], transcriptional regulatory protein HydG-Pasp [2][1], phospho-HydG [2][1], modified transcriptional regulatory protein HydG[2][1], phosphorylated transcriptional regulatory protein HydG [2][1], ZraR-phosphate [2][1], positive DNA-binding transcriptional regulator for zraP expression, response regulator in two-component reguatory system with ZraS [2][1] , ECK3996, hydG, JW3968, b4004

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): zraSR[2], hydHG

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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The N-terminal sequencing of overexpressed protein showed that the fMet is not clipped (Leonhartsberger et al. 2001. However, natural RBS was not used, so it is not included in the Verified set, although this is almost certainly the correct in vivo start site.[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

zraR

Mnemonic

Zn resistance-associated

Synonyms

ECK3996, b4004, JW3968, hydG[1], hydG

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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

90.55 minutes, 90.55 minutes 

MG1655: 4201343..4202668
<gbrowseImage> name=NC_000913:4201343..4202668 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4182905..4184230
<gbrowseImage> name=NC_012967:4182905..4184230 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4091023..4092348
<gbrowseImage> name=NC_012759:4091023..4092348 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3433361..3432036
<gbrowseImage> name=NC_007779:3432036..3433361 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4301039..4302364
<gbrowseImage> name=NC_010473:4301039..4302364 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

ΔzraR (Keio:JW3968)

deletion

deletion

PMID:16738554

Shigen
CGSC10854[5]

ΔhydG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔhydG::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

ΔhydG::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938

ΔhydG::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938

ΔzraR775::kan

PMID:16738554

CGSC:106114


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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

JW3968

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGCACGATAATATCGATAT

Primer 2:CCACGCGACAGTTTTGCCAATAG

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[5]

est. P1 cotransduction: 79% [6]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[5]

est. P1 cotransduction: 19% [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:EG10482

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10482

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000475

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948505

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0477

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013093

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

ZraR

Synonyms

fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator [1], sigma54 interaction protein [1], B4004 [2][1], HydG [2][1], transcriptional regulatory protein HydG-Pasp [2][1], phospho-HydG [2][1], modified transcriptional regulatory protein HydG[2][1], phosphorylated transcriptional regulatory protein HydG [2][1], ZraR-phosphate [2][1], positive DNA-binding transcriptional regulator for zraP expression, response regulator in two-component reguatory system with ZraS [2][1] , ECK3996, hydG, JW3968, b4004

Product description

ZraR transcriptional activator[2][3]

Two component response regulator for zraP; responsive to Zn(2+) and Pb(2+); autoregulated; regulation of Hyd-3 activity is probably due to crosstalk of overexpressed protein[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:0000156

two-component response regulator activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

F

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

P

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0902

P

Seeded from EcoCyc (v14.0)

complete

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: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:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002197

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020441

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

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:IPR002078

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:IPR002197

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:IPR020441

P

Seeded from EcoCyc (v14.0)

complete

GO:0008134

transcription factor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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

GO:0003677

DNA binding

PMID:11243806

IDA: Inferred from Direct Assay

F

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

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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

MTHDNIDILV VDDDISHCTI LQALLRGWGY NVALANSGRQ ALEQVREQVF DLVLCDVRMA
EMDGIATLKE IKALNPAIPV LIMTAYSSVE TAVEALKTGA LDYLIKPLDF DNLQATLEKA
LAHTHSIDAE TPAVTASQFG MVGKSPAMQH LLSEIALVAP SEATVLIHGD SGTGKELVAR
AIHASSARSE KPLVTLNCAA LNESLLESEL FGHEKGAFTG ADKRREGRFV EADGGTLFLD
EIGDISPMMQ VRLLRAIQER EVQRVGSNQI ISVDVRLIAA THRDLAAEVN AGRFRQDLYY
RLNVVAIEVP SLRQRREDIP LLAGHFLQRF AERNRKAVKG FTPQAMDLLI HYDWPGNIRE
LENAVERAVV LLTGEYISER ELPLAIASTP IPLGQSQDIQ PLVEVEKEVI LAALEKTGGN
KTEAARQLGI TRKTLLAKLS R
Length

441

Mol. Wt

48.395 kDa

pI

5.4 (calculated)

Extinction coefficient

21,430 - 21,805 (calc based on 7 Y, 2 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

Domain

401..441

PF02954 Bacterial regulatory protein, Fis family

PMID:19920124

Domain

8..118

PF00072 Response regulator receiver domain

PMID:19920124

Domain

141..308

PF00158 Sigma-54 interaction domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=zraR 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:16131834

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948505

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013093

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P14375

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10482

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10482

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948505

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000475

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0477

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

98

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

30

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

50

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)

zraSR

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_000913:4201323..4201363 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:b4004 (EcoliWiki Page)

NCBI GEO profiles for zraR

microarray

GenExpDB:b4004 (EcoliWiki Page)

Summary of data for zraR 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 zraR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10482

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0477

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4004

EcoGene

EcoGene:EG10482

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000475

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013093

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

Arabidopsis thaliana

  • AT1G19050 (score: 1.000; bootstrap: 100%)
  • AT1G74890 (score: 0.581)
  • AT5G24470 (score: 0.061)
  • AT5G02810 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q4GZL0 (score: 1.000; bootstrap: 100%)
  • Q9FRY8 (score: 0.455)
  • Q6YVX7 (score: 0.448)
  • Q4GZK9 (score: 0.448)
  • Q7XRI1 (score: 0.361)
  • Q6H468 (score: 0.164)
  • Q9FRZ0 (score: 0.159)
  • Q9FXQ7 (score: 0.157)
  • Q7XKF6 (score: 0.157)
  • Q4GZK6 (score: 0.152)
  • Q942A1 (score: 0.152)
  • Q4GZK7 (score: 0.152)
  • Q9FRZ1 (score: 0.147)
  • Q6K9T0 (score: 0.144)
  • Q4GZK8 (score: 0.144)
  • Q4GZK2 (score: 0.137)
  • Q9FRY9 (score: 0.134)
  • Q9S7U8 (score: 0.134)
  • Q7XQA6 (score: 0.134)
  • Q4JF20 (score: 0.134)
  • Q4GZK5 (score: 0.134)
  • Q8H5N4 (score: 0.122)
  • Q4GZK4 (score: 0.122)
  • Q9ZQW0 (score: 0.117)
  • Q8GVV6 (score: 0.092)
  • Q4GZK3 (score: 0.092)
  • Q8GVV1 (score: 0.055)
  • Q6YZK8 (score: 0.055)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000041194 (score: 1.000; bootstrap: 78%)

From Inparanoid:20070104

Shigella flexneri

HYDG

From SHIGELLACYC

E. coli O157

HYDG

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)

PF02954 Bacterial regulatory protein, Fis family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:52172

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR24423:SF440

Pfam (EcoliWiki Page)

PF00072 Response regulator receiver domain

Pfam (EcoliWiki Page)

PF00158 Sigma-54 interaction domain

EcoCyc

EcoCyc:EG10482

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10482

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000475

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0477

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013093

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 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 2.15 2.16 2.17 2.18 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 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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