fdnG: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

fdnG

Gene Synonym(s)

ECK1468, b1474, JW1470[1], JW1470

Product Desc.

formate dehydrogenase N, α 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, selenopeptide, anaerobic; periplasmic[4]

Product Synonyms(s)

formate dehydrogenase-N, alpha subunit, nitrate-inducible[1], B1474[2][1], FdnG[2][1] , ECK1468, JW1470, b1474

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

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

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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Verified Tat substrate: FdnG has a Tat-only (Class I) predicted 37 aa signal peptide (Tullman-Ercek, 2007). Bound FdnH is co-exported. HT_Cmplx12_Mem: FdnG+FdnH. 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

fdnG

Mnemonic

Formate dehydrogenase-N

Synonyms

ECK1468, b1474, JW1470[1], JW1470

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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

33.31 minutes 

MG1655: 1545425..1548472
<gbrowseImage> name=NC_000913:1545425..1548472 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1521551..1524598
<gbrowseImage> name=NC_012967:1521551..1524598 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1437484..1440531
<gbrowseImage> name=NC_012759:1437484..1440531 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1549115..1552162
<gbrowseImage> name=NC_007779:1549115..1552162 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1636020..1639067
<gbrowseImage> name=NC_010473:1636020..1639067 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

ΔfdnG (Keio:JW1470)

deletion

deletion

PMID:16738554

Shigen
CGSC9280[5]

ΔfdnG767::kan

PMID:16738554

CGSC:100802


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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

JW1470

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGACGTCAGTCGCAGACAATT

Primer 2:CCgGCCTTCTCGATGTTGACTAA

1G9

Kohara Phage

Genobase

PMID:3038334

9B8

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 72% [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.

Database Accession Notes

EcoCyc

EcoCyc:EG11227

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001205

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946035

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004917

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

FdnG

Synonyms

formate dehydrogenase-N, alpha subunit, nitrate-inducible[1], B1474[2][1], FdnG[2][1] , ECK1468, JW1470, b1474

Product description

formate dehydrogenase N, α 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, selenopeptide, anaerobic; periplasmic[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:0008430

selenium binding

PMID:1650339

IEP: Inferred from Expression Pattern

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:0009055

electron carrier activity

PMID:1099094

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0009061

anaerobic respiration

PMID:1099093

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0009326

formate dehydrogenase complex

PMID:11752799

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

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:0030151

molybdenum ion binding

PMID:11752799

IDA: Inferred from Direct Assay

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

PMID:5996

IDA: Inferred from Direct Assay

P

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

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

could be indirect

Protein

aceE

PMID:16606699

Experiment(s):EBI-1139936

Protein

dnaE

PMID:16606699

Experiment(s):EBI-1139936

Protein

aceE

PMID:15690043

Experiment(s):EBI-879752

Protein

fdhE

PMID:15690043

Experiment(s):EBI-879752, EBI-884342

Protein

tufA

PMID:15690043

Experiment(s):EBI-879752, EBI-884342

Protein

tufB

PMID:19402753

MALDI(Z-score):21.618440

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.

Compartment Description Evidence Reference/Source Notes

periplasm

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

MDVSRRQFFK ICAGGMAGTT VAALGFAPKQ ALAQARNYKL LRAKEIRNTC TYCSVGCGLL
MYSLGDGAKN AREAIYHIEG DPDHPVSRGA LCPKGAGLLD YVNSENRLRY PEYRAPGSDK
WQRISWEEAF SRIAKLMKAD RDANFIEKNE QGVTVNRWLS TGMLCASGAS NETGMLTQKF
ARSLGMLAVD NQARVUHGPT VASLAPTFGR GAMTNHWVDI KNANVVMVMG GNAAEAHPVG
FRWAMEAKNN NDATLIVVDP RFTRTASVAD IYAPIRSGTD ITFLSGVLRY LIENNKINAE
YVKHYTNASL LVRDDFAFED GLFSGYDAEK RQYDKSSWNY QLDENGYAKR DETLTHPRCV
WNLLKEHVSR YTPDVVENIC GTPKADFLKV CEVLASTSAP DRTTTFLYAL GWTQHTVGAQ
NIRTMAMIQL LLGNMGMAGG GVNALRGHSN IQGLTDLGLL STSLPGYLTL PSEKQVDLQS
YLEANTPKAT LADQVNYWSN YPKFFVSLMK SFYGDAAQKE NNWGYDWLPK WDQTYDVIKY
FNMMDEGKVT GYFCQGFNPV ASFPDKNKVV SCLSKLKYMV VIDPLVTETS TFWQNHGESN
DVDPASIQTE VFRLPSTCFA EEDGSIANSG RWLQWHWKGQ DAPGEARNDG EILAGIYHHL
RELYQSEGGK GVEPLMKMSW NYKQPHEPQS DEVAKENNGY ALEDLYDANG VLIAKKGQLL
SSFAHLRDDG TTASSCWIYT GSWTEQGNQM ANRDNSDPSG LGNTLGWAWA WPLNRRVLYN
RASADINGKP WDPKRMLIQW NGSKWTGNDI PDFGNAAPGT PTGPFIMQPE GMGRLFAINK
MAEGPFPEHY EPIETPLGTN PLHPNVVSNP VVRLYEQDAL RMGKKEQFPY VGTTYRLTEH
FHTWTKHALL NAIAQPEQFV EISETLAAAK GINNGDRVTV SSKRGFIRAV AVVTRRLKPL
NVNGQQVETV GIPIHWGFEG VARKGYIANT LTPNVGDANS QTPEYKAFLV NIEKA
Length

1,014

Mol. Wt

112.814 kDa

pI

3.5 (calculated)

Extinction coefficient

208,100 - 209,725 (calc based on 40 Y, 27 W, and 13 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

motif

1-33

UniProt Manual:Signal Peptides

UniProt:P24183

Domain

43..104

PF04879 Molybdopterin oxidoreductase Fe4S4 domain

PMID:19920124

Domain

107..593

PF00384 Molybdopterin oxidoreductase

PMID:19920124

Domain

890..1009

PF01568 Molydopterin dinucleotide binding domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=fdnG 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:16129433

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946035

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004917

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P24183

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11227

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11227

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946035

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001205

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1209

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

7.27E+01

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

Ecoli K-12

0.209+/-0.06

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.001148671

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

2

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

0

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

0a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

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)

fdnGHI

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_000913:1545405..1545445 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:b1474 (EcoliWiki Page)

NCBI GEO profiles for fdnG

microarray

GenExpDB:b1474 (EcoliWiki Page)

Summary of data for fdnG 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 (1545113..1545481) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ03; Well:F2[7]

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Notes

Accessions Related to fdnG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11227

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1209

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1474

EcoGene

EcoGene:EG11227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001205

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004917

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

Xenopus tropicalis

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

From Inparanoid:20070104

E. coli O157

FDNG

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)

PF04879 Molybdopterin oxidoreductase Fe4S4 domain

Pfam (EcoliWiki Page)

PF00384 Molybdopterin oxidoreductase

Pfam (EcoliWiki Page)

PF01568 Molydopterin dinucleotide binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50692

Superfamily (EcoliWiki Page)

SUPERFAMILY:53706

EcoCyc

EcoCyc:EG11227

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11227

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001205

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1209

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004917

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. 2.00 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 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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