fdx: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

fdx

Gene Synonym(s)

ECK2522, b2525, JW2509[1], JW2509

Product Desc.

ferredoxin[2][3]

Ferredoxin, an iron-sulfur protein; involved in assembly of other Fe-S clusters[4]

Product Synonyms(s)

[2Fe-2S] ferredoxin [1], B2525 [2][1] , ECK2522, JW2509, b2525

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hscBA-fdx[2], hscA-fdx[2], hsc-fdx

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 fdx gene is cotranscribed with hscBA and is cold inducible.[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

fdx

Mnemonic

Ferredoxin

Synonyms

ECK2522, b2525, JW2509[1], JW2509

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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

57.22 minutes 

MG1655: 2655105..2654770
<gbrowseImage> name=NC_000913:2654770..2655105 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2577782..2577447
<gbrowseImage> name=NC_012967:2577447..2577782 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2540575..2540910
<gbrowseImage> name=NC_012759:2540575..2540910 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2655739..2655404
<gbrowseImage> name=NC_007779:2655404..2655739 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2746870..2746535
<gbrowseImage> name=NC_010473:2746535..2746870 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

2654773

Edman degradation

PMID:1317854
PMID:4375562


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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

Δfdx (Keio:JW2509)

deletion

deletion

PMID:16738554

Shigen
CGSC9997[5]

Δfdx-771::kan

PMID:16738554

CGSC:100812


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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

JW2509

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCAAAGATTGTTATTTTGCC

Primer 2:CCATGCTCACGCGCATGGTTGAT

7F8

Kohara Phage

Genobase

PMID:3038334

5E10

Kohara Phage

Genobase

PMID:3038334

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[5]

est. P1 cotransduction: 4% [6]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 75% [6]
Synonyms:zff-208::Tn10

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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:EG11328

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11328

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001299

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1304

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008311

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

Fdx

Synonyms

[2Fe-2S] ferredoxin [1], B2525 [2][1] , ECK2522, JW2509, b2525

Product description

ferredoxin[2][3]

Ferredoxin, an iron-sulfur protein; involved in assembly of other Fe-S clusters[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: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: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:IPR001055

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011536

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018298

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:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001041

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc (v14.0)

complete

GO:0051537

2 iron, 2 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001055

F

Seeded from EcoCyc (v14.0)

complete

GO:0051537

2 iron, 2 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011536

F

Seeded from EcoCyc (v14.0)

complete

GO:0051537

2 iron, 2 sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018298

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

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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

glpK

PMID:16606699

Experiment(s):EBI-1143120

Protein

iscS

PMID:16606699

Experiment(s):EBI-1143120

Protein

pepD

PMID:16606699

Experiment(s):EBI-1143120

Protein

tehB

PMID:16606699

Experiment(s):EBI-1143120

Protein

napC

PMID:16606699

Experiment(s):EBI-1143120

Protein

codA

PMID:16606699

Experiment(s):EBI-1143120

Protein

greB

PMID:16606699

Experiment(s):EBI-1143120

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1143120
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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 

MPKIVILPHQ DLCPDGAVLE ANSGETILDA ALRNGIEIEH ACEKSCACTT CHCIVREGFD
SLPESSEQED DMLDKAWGLE PESRLSCQAR VTDEDLVVEI PRYTINHARE H
Length

111

Mol. Wt

12.33 kDa

pI

4.4 (calculated)

Extinction coefficient

6,990 - 7,865 (calc based on 1 Y, 1 W, and 7 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:P0A9R4

Domain

11..92

PF00111 2Fe-2S iron-sulfur cluster binding domain

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=fdx 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:16130450

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947160

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008311

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9R4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11328

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11328

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947160

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001299

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1304

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

6027

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

1374

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

7392

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)

hscBA-fdx

hscA-fdx

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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_000913:2655085..2655125 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:b2525 (EcoliWiki Page)

NCBI GEO profiles for fdx

microarray

GenExpDB:b2525 (EcoliWiki Page)

Summary of data for fdx 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 fdx Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11328

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1304

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2525

EcoGene

EcoGene:EG11328

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001299

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008311

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

Anopheles gambiae

  • ENSANGP00000013242 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000014725 (score: 0.079)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000031287 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G05450 (score: 1.000; bootstrap: 100%)
  • AT4G21090 (score: 0.726)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000013630 (score: 1.000; bootstrap: 83%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00034438 (score: 1.000; bootstrap: 100%)
  • WBGene00042998 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00013532 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000020973 (score: 1.000; bootstrap: 100%)
  • ENSCAFP00000026369 (score: 0.103)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000014565 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0189319 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0011769 (score: 1.000; bootstrap: 100%)
  • FBgn0035529 (score: 0.059)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18029-PA (score: 1.000; bootstrap: 100%)
  • GA18016-PA (score: 0.606)
  • GA12105-PA (score: 0.073)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000007465 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000027649 (score: 0.585)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000260270 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000002810 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000006864 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000018154 (score: 0.058)

From Inparanoid:20070104

Mus musculus

  • MGI:1915415 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q7XIU2 (score: 1.000; bootstrap: 100%)
  • Q69LJ8 (score: 0.566)
  • Q7XIU1 (score: 0.455)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000028127 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000016263 (score: 0.057)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YPL252C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC22E120c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000160554 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00019614001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000046485 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000030454 (score: 0.102)
  • ENSXETP00000021528 (score: 0.090)

From Inparanoid:20070104

Shigella flexneri

FDX

From SHIGELLACYC

E. coli O157

FDX

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)

PF00111 2Fe-2S iron-sulfur cluster binding domain

Panther (EcoliWiki Page)

PTHR23426:SF8

Superfamily (EcoliWiki Page)

SUPERFAMILY:54292

EcoCyc

EcoCyc:EG11328

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11328

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001299

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1304

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008311

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 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 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 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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