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fdnI:On One Page

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Standard Name

fdnI

Gene Synonym(s)

ECK1470, b1476, JW1472[1]

Product Desc.

formate dehydrogenase N, γ subunit[2][3];

Component of trimer complex of formate dehydrogenase-N α, β and γ subunits[2][3]; formate dehydrogenase-N[2][3]

Formate dehydrogenase-N, cytochrome subunit, anaerobic[4]

Product Synonyms(s)

formate dehydrogenase-N, cytochrome B556 (gamma) subunit, nitrate-inducible[1], B1476[2][1], FdnI[2][1]

Function from GO

Molecular Function

Biological Process

Cellular Component

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): fdnGHI[2], OP00216

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(fdnI)    Textpresso(fdnI)

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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

fdnI

Mnemonic

Formate dehydrogenase-N

Synonyms

ECK1470, b1476, JW1472[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

33.39 minutes 

MG1655: 1549362..1550015
gbrowse_img.php?coord=1549362..1550015&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 1525488..1526141
gbrowse_img.php?coord=1525488..1526141&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 1553052..1553705
gbrowse_img.php?coord=1553052..1553705&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 1639957..1640610
gbrowse_img.php?coord=1639957..1640610&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 1441421..1442074
gbrowse_img.php?coord=1441421..1442074&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔfdnI (Keio:JW1472)

deletion

deletion

PMID:16738554

Shigen
CGSC9281[5]

ΔfdnI769::kan

PMID:16738554

CGSC:100804


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW1472

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTAAGTCGAAAATGATTGT

Primer 2:CCTATCCCTTCTTCACTCTCTTT

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 62% [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11229

EchoBASE (EcoliWiki Page)

EchoBASE:EB1211

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1476

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C1907

EcoGene (EcoliWiki Page)

EcoGene:EG11229

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:FDNI

CGSC (EcoliWiki Page)

CGSC:32168

ASAP (EcoliWikiPage)

ASAP:ABE-0004921


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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

FdnI

Synonyms

formate dehydrogenase-N, cytochrome B556 (gamma) subunit, nitrate-inducible[1], B1476[2][1], FdnI[2][1]

Product description

formate dehydrogenase N, γ subunit[2][3];

Component of trimer complex of formate dehydrogenase-N α, β and γ subunits[2][3]; formate dehydrogenase-N[2][3]

Formate dehydrogenase-N, cytochrome subunit, anaerobic[4]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0045333

cellular respiration

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006471

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0009326

formate dehydrogenase complex

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006471

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0008863

formate dehydrogenase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006471

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc [8]

complete

GO:0005506

iron ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc [8]

complete

GO:0008863

formate dehydrogenase activity

PMID:11752799

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0009055

electron carrier activity

PMID:1099094

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [8]

complete

GO:0009061

anaerobic respiration

PMID:1099093

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [8]

complete

GO:0009326

formate dehydrogenase complex

PMID:11752799

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0016021

integral to membrane

PMID:6755185

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0017004

cytochrome complex assembly

PMID:1099093

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [8]

complete

GO:0045333

cellular respiration

PMID:5996

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0009053

electron donor activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc [8]

complete

GO:0016020

membrane

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR016174
SP_KW:KW-0472

C

Seeded from EcoCyc [8]

complete

GO:0022900

electron transport chain

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc [8]

complete

GO:0022904

respiratory electron transport chain

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016174

P

Seeded from EcoCyc [8]

complete

GO:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [8]

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 TypePartnerNotesReferencesEvidence

Protein

Subunits of trimer complex of formate dehydrogenase-N α, β and γ subunits

could be indirect

Protein

Subunits of formate dehydrogenase-N

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.

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

C-terminus localized in the cytoplasm with 4 predicted transmembrane domains

Daley et al. (2005) [9]

plasma membrane

From EcoCyc[3]


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MSKSKMIVRT KFIDRACHWT VVICFFLVAL SGISFFFPTL QWLTQTFGTP QMGRILHPFF
GIAIFVALMF MFVRFVHHNI PDKKDIPWLL NIVEVLKGNE HKVADVGKYN AGQKMMFWSI
MSMIFVLLVT GVIIWRPYFA QYFPMQVVRY SLLIHAAAGI ILIHAILIHM YMAFWVKGSI
KGMIEGKVSR RWAKKHHPRW YREIEKAEAK KESEEGI
Length

217

Mol. Wt

25.368 kDa

pI

10.3 (calculated)

Extinction coefficient

52,940 - 53,190 (calc based on 6 Y, 8 W, and 2 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.

TypeResiduesDescriptionNotesReferences
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tmhmm.php?gene=fdnI&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:FDNI-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P0AEK7

UniProt (EcoliWiki Page)

UniProt:P0AEK7

RefSeq (EcoliWiki Page)

RefSeq:NP_415993


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

fdnGHI

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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=1549342..1549382&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

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

TypeReferenceNotes

microarray

GEO Profiles:b1476 (EcoliWiki Page)

NCBI GEO profiles for fdnI

microarray

GenExpDB:b1476 (EcoliWiki Page)

Summary of data for fdnI 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to fdnI Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11229

EchoBASE (EcoliWiki Page)

EchoBASE:EB1211

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1476

EcoGene (EcoliWiki Page)

EcoGene:EG11229


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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.

OrganismHomologs (Statistics)Comments

Xenopus tropicalis

  • ENSXETP00000000542 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

FDNI

From SHIGELLACYC

E. coli O157

FDNI

From ECOO157CYC

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Notes

Links

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References

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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 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 3.4 3.5 3.6 3.7 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 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. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 8.8 8.9 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page

Categories

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