fdoG: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

fdoG

Gene Synonym(s)

ECK3887, b3894, JW3865[1], JW3865

Product Desc.

formate dehydrogenase-O, α subunit[2][3];

Component of formate dehydrogenase-O[2][3]

Formate dehydrogenase-O, selenopeptide, aerobic[4]

Product Synonyms(s)

formate dehydrogenase-O, large subunit[1], B3894[2][1], FdoG[2][1] , ECK3887, JW3865, b3894

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): fdoGHI-fdhE[2]

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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Also known as FDH-Z. Verified Tat substrate: FdoG has a predicted Tat-only (Class I) 33 aa signal peptide (Tullman-Ercek, 2007). Binds TrxA (Kumar, 2004). HT_Cmplx13_Mem: FdoG+FdoH. The UGA stop codon 196 is translated as selenocysteine in vivo and indicated as a "U" in the protein sequence.[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

fdoG

Mnemonic

Formate dehydrogenase-O

Synonyms

ECK3887, b3894, JW3865[1], JW3865

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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

87.95 minutes 

MG1655: 4083845..4080795
<gbrowseImage> name=NC_000913:4080795..4083845 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4063969..4060919
<gbrowseImage> name=NC_012967:4060919..4063969 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3970464..3973514
<gbrowseImage> name=NC_012759:3970464..3973514 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3550859..3553909
<gbrowseImage> name=NC_007779:3550859..3553909 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4183542..4180492
<gbrowseImage> name=NC_010473:4180492..4183542 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

Strain DH10B

N307T

Nonsynonomous mutation

PMID:18245285

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔfdoG (Keio:JW3865)

deletion

deletion

PMID:16738554

Shigen
CGSC10790[5]

ΔfdoG757::kan

PMID:16738554

CGSC:100806


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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

JW3865

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGGTCAGCAGAAGGCAGTT

Primer 2:CCaACCTTTTCCACATTCACAAG

7G8

Kohara Phage

Genobase

PMID:3038334

6H5

Kohara Phage

Genobase

PMID:3038334

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[5]

est. P1 cotransduction: 56% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 4% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG11858

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11858

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001789

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948394

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1804

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012710

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

FdoG

Synonyms

formate dehydrogenase-O, large subunit[1], B3894[2][1], FdoG[2][1] , ECK3887, JW3865, b3894

Product description

formate dehydrogenase-O, α subunit[2][3];

Component of formate dehydrogenase-O[2][3]

Formate dehydrogenase-O, selenopeptide, aerobic[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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

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:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006443

C

Seeded from EcoCyc (v14.0)

complete

GO:0008430

selenium binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0711

F

Seeded from EcoCyc (v14.0)

complete

GO:0008863

formate dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006443

F

Seeded from EcoCyc (v14.0)

complete

GO:0008863

formate dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.2.1.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006655

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006655

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006656

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006657

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006963

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0030151

molybdenum ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006657

F

Seeded from EcoCyc (v14.0)

complete

GO:0030151

molybdenum ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0500

F

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0574

C

Seeded from EcoCyc (v14.0)

complete

GO:0042597

periplasmic space

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0200

C

Seeded from EcoCyc (v14.0)

complete

GO:0045333

cellular respiration

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006443

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0411

F

Seeded from EcoCyc (v14.0)

complete

GO:0051539

4 iron, 4 sulfur cluster binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0004

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006443

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

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 formate dehydrogenase-O

could be indirect

Protein

nadE

PMID:16606699

Experiment(s):EBI-1146913

Protein

polA

PMID:16606699

Experiment(s):EBI-1146913

Protein

ileS

PMID:16606699

Experiment(s):EBI-1146913

Protein

cyaA

PMID:16606699

Experiment(s):EBI-1146913
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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

Periplasm

PMID:12923080

EchoLocation:fdoG

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 

MQVSRRQFFK ICAGGMAGTT AAALGFAPSV ALAETRQYKL LRTRETRNTC TYCSVGCGLL
MYSLGDGAKN AKASIFHIEG DPDHPVNRGA LCPKGAGLVD FIHSESRLKF PEYRAPGSDK
WQQISWEEAF DRIAKLMKED RDANYIAQNA EGVTVNRWLS TGMLCASASS NETGYLTQKF
SRALGMLAVD NQARVUHGPT VASLAPTFGR GAMTNHWVDI KNANLVVVMG GNAAEAHPVG
FRWAMEAKIH NGAKLIVIDP RFTRTAAVAD YYAPIRSGTD IAFLSGVLLY LLNNEKFNRE
YTEAYTNASL IVREDYGFED GLFTGYDAEK RKYDKSSWTY ELDENGFAKR DTTLQHPRCV
WNLLKQHVSR YTPDVVENIC GTPKDAFLKV CEYIAETSAH DKTASFLYAL GWTQHSVGAQ
NIRTMAMIQL LLGNMGMAGG GVNALRGHSN IQGLTDLGLL SQSLPGYMTL PSEKQTDLQT
YLTANTPKPL LEGQVNYWGN YPKFFVSMMK AFFGDKATAE NSWGFDWLPK WDKGYDVLQY
FEMMKEGKVN GYICQGFNPV ASFPNKNKVI GCLSKLKFLV TIDPLNTETS NFWQNHGELN
EVDSSKIQTE VFRLPSTCFA EENGSIVNSG RWLQWHWKGA DAPGIALTDG EILSGIFLRL
RKMYAEQGGA NPDQVLNMTW NYAIPHEPSS EEVAMESNGK ALADITDPAT GAVIVKKGQQ
LSSFAQLRDD GTTSCGCWIF AGSWTPEGNQ MARRDNADPS GLGNTLGWAW AWPLNRRILY
NRASADPQGN PWDPKRQLLK WDGTKWTGWD IPDYSAAPPG SGVGPFIMQQ EGMGRLFALD
KMAEGPFPEH YEPFETPLGT NPLHPNVISN PAARIFKDDA EALGKADKFP YVGTTYRLTE
HFHYWTKHAL LNAILQPEQF VEIGESLANK LGIAQGDTVK VSSNRGYIKA KAVVTKRIRT
LKANGKDIDT IGIPIHWGYE GVAKKGFIAN TLTPFVGDAN TQTPEFKSFL VNVEKV
Length

1,015

Mol. Wt

112.401 kDa

pI

7.3 (calculated)

Extinction coefficient

206,150 - 207,900 (calc based on 35 Y, 28 W, and 14 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

motif

1-33

UniProt Manual:Signal Peptides

UniProt:P32176

Domain

43..104

PF04879 Molybdopterin oxidoreductase Fe4S4 domain

PMID:19920124

Domain

107..592

PF00384 Molybdopterin oxidoreductase

PMID:19920124

Domain

891..1010

PF01568 Molydopterin dinucleotide 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=fdoG 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:16131734

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948394

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012710

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P32176

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11858

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11858

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948394

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001789

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1804

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

6.72E+02

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

219

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

11

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

37

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)

fdoGHI-fdhE

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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_000913:4083825..4083865 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:b3894 (EcoliWiki Page)

NCBI GEO profiles for fdoG

microarray

GenExpDB:b3894 (EcoliWiki Page)

Summary of data for fdoG 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

GFP Fusion

Intergenic region (4083317..4083666) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:B9[7]

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Notes

Accessions Related to fdoG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11858

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1804

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3894

EcoGene

EcoGene:EG11858

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001789

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012710

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

Xenopus tropicalis

  • ENSXETP00000000544 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

FDOG

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)

PF04879 Molybdopterin oxidoreductase Fe4S4 domain

Pfam (EcoliWiki Page)

PF01568 Molydopterin dinucleotide binding domain

Pfam (EcoliWiki Page)

PF00384 Molybdopterin oxidoreductase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50692

Panther (EcoliWiki Page)

PTHR11615:SF38

Superfamily (EcoliWiki Page)

SUPERFAMILY:53706

EcoCyc

EcoCyc:EG11858

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11858

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001789

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1804

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012710

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 1.6 1.7 1.8 1.9 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 2.8 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 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).
  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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