ygfT: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

ygfT

Gene Synonym(s)

ECK2882, b2887, JW5469[1], JW5469

Product Desc.

fused predicted oxidoreductase, Fe-S subunit and nucleotide-binding subunit[2][3]

Putative oxidoreductase, Fe-S subunit, function unknown; aegA paralog[4]

Product Synonyms(s)

fused predicted oxidoreductase: Fe-S subunit[1], nucleotide-binding subunit[1], B2887[2][1], YgfT[2][1] , ECK2882, JW5469, b2887

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ygfS[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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AFMB Structural Genomics target No. 66 (http://afmb.cnrs-mrs.fr/article171.html).[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

ygfT

Mnemonic

Systematic nomenclature

Synonyms

ECK2882, b2887, JW5469[1], JW5469

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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

65.24 minutes 

MG1655: 3028953..3027034
<gbrowseImage> name=NC_000913:3027034..3028953 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2916685..2914766
<gbrowseImage> name=NC_012967:2914766..2916685 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2914182..2916101
<gbrowseImage> name=NC_012759:2914182..2916101 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3029587..3027668
<gbrowseImage> name=NC_007779:3027668..3029587 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3122823..3120904
<gbrowseImage> name=NC_010473:3120904..3122823 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

ΔygfT (Keio:JW5469)

deletion

deletion

PMID:16738554

Shigen
CGSC11411[5]

ΔygfT737::kan

PMID:16738554

CGSC:104976


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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

JW5469

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATAAGTTTATTGCTGCTGA

Primer 2:CCtGATGCCTTCGTATCAAACAG

5B4

Kohara Phage

Genobase

PMID:3038334

22H4

Kohara Phage

Genobase

PMID:3038334

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: 1% [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 5% [6]
Synonyms:zgd-210::Tn10, zgf-210::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:G7506

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004068

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949018

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2881

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009473

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

YgfT

Synonyms

fused predicted oxidoreductase: Fe-S subunit[1], nucleotide-binding subunit[1], B2887[2][1], YgfT[2][1] , ECK2882, JW5469, b2887

Product description

fused predicted oxidoreductase, Fe-S subunit and nucleotide-binding subunit[2][3]

Putative oxidoreductase, Fe-S subunit, function unknown; aegA paralog[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:0006537

glutamate biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006006

P

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001450

F

Seeded from EcoCyc (v14.0)

complete

GO:0009055

electron carrier activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017900

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001327

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012285

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:0016639

oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006006

F

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:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001327

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001450

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012285

F

Seeded from EcoCyc (v14.0)

complete

GO:0051536

iron-sulfur cluster binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017900

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:IPR001327

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

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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

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):11.431287

Protein

ruvA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.296594

Protein

mutT

PMID:19402753

MALDI(Z-score):27.385673

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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 

MKGMQMNKFI AAEAAECIGC HACEIACAVA HNQENWPLSH SDFRPRIHVV GKGQAANPVA
CHHCNNAPCV TACPVNALTF QSDSVQLDEQ KCIGCKRCAI ACPFGVVEMV DTIAQKCDLC
NQRSSGTQAC IEVCPTQALR LMDDKGLQQI KVARQRKTAA GKASSDAQPS RSAALLPVNS
RKGADKISAS ERKTHFGEIY CGLDPQQATY ESDRCVYCAE KANCNWHCPL HNAIPDYIRL
VQEGKIIEAA ELCHQTSSLP EICGRVCPQD RLCEGACTLK DHSGAVSIGN LERYITDTAL
AMGWRPDVSK VVPRSEKVAV IGAGPAGLGC ADILARAGVQ VDVFDRHPEI GGMLTFGIPP
FKLDKTVLSQ RREIFTAMGI DFHLNCEIGR DITFSDLTSE YDAVFIGVGT YGMMRADLPH
EDAPGVIQAL PFLTAHTRQL MGLPESEEYP LTDVEGKRVV VLGGGDTTMD CLRTSIRLNA
ASVTCAYRRD EVSMPGSRKE VVNAREEGVE FQFNVQPQYI ACDEDGRLTA VGLIRTAMGE
PGPDGRRRPR PVAGSEFELP ADVLIMAFGF QAHAMPWLQG SGIKLDKWGL IQTGDVGYLP
TQTHLKKVFA GGDAVHGADL VVTAMAAGRQ AARDMLTLFD TKAS
Length

644

Mol. Wt

69.663 kDa

pI

6.4 (calculated)

Extinction coefficient

43,890 - 47,765 (calc based on 11 Y, 5 W, and 31 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

Domain

80..103

PF00037 4Fe-4S binding domain

PMID:19920124

Domain

312..387

PF00070 Pyridine nucleotide-disulphide oxidoreductase

PMID:19920124

Domain

312..614

PF07992 Pyridine nucleotide-disulphide oxidoreductase

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=ygfT 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:90111509

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949018

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009473

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q46820

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7506

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13070

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949018

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004068

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2881

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

Ecoli K-12

0.572+/-0.055

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.001302762

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

0a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

1a

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

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

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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)

ygfS

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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_000913:3028933..3028973 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:b2887 (EcoliWiki Page)

NCBI GEO profiles for ygfT

microarray

GenExpDB:b2887 (EcoliWiki Page)

Summary of data for ygfT 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 ygfT Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7506

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2881

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2887

EcoGene

EcoGene:EG13070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004068

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009473

Escherichia coli str. K-12 substr. MG1655

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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

Oryza gramene

  • Q6I618 (score: 1.000; bootstrap: 100%)
  • Q9ZNX7 (score: 0.773)

From Inparanoid:20070104

E. coli O157

YGFT

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)

PF00070 Pyridine nucleotide-disulphide oxidoreductase

Pfam (EcoliWiki Page)

PF00037 4Fe-4S binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51971

Superfamily (EcoliWiki Page)

SUPERFAMILY:51971

Superfamily (EcoliWiki Page)

SUPERFAMILY:54862

Pfam (EcoliWiki Page)

PF07992 Pyridine nucleotide-disulphide oxidoreductase

EcoCyc

EcoCyc:G7506

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004068

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2881

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009473

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 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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