yggW: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

yggW

Gene Synonym(s)

ECK2950, b2955, JW2922[1], JW2922

Product Desc.

predicted oxidoreductase[2][3]

Function unknown, Radical SAM superfamily[4]

Product Synonyms(s)

predicted oxidoreductase[1], B2955[2][1], YggW[2][1] , ECK2950, JW2922, b2955

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yggS[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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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

yggW

Mnemonic

Systematic nomenclature

Synonyms

ECK2950, b2955, JW2922[1], JW2922

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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

66.71 minutes 

MG1655: 3095289..3096425
<gbrowseImage> name=NC_000913:3095289..3096425 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2983018..2984154
<gbrowseImage> name=NC_012967:2983018..2984154 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2982437..2983573
<gbrowseImage> name=NC_012759:2982437..2983573 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3095923..3097059
<gbrowseImage> name=NC_007779:3095923..3097059 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3190358..3191494
<gbrowseImage> name=NC_010473:3190358..3191494 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

ΔyggW (Keio:JW2922)

deletion

deletion

PMID:16738554

Shigen
CGSC10260[5]

ΔyggW729::kan

PMID:16738554

CGSC:105012


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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

JW2922

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTTAAATTACCTCCGCTGAG

Primer 2:CCtTCAGCCAGAAAAAGCTCCAG

23G4S

Kohara Phage

Genobase

PMID:3038334

12C6

Kohara Phage

Genobase

PMID:3038334

3A9

Kohara Phage

Genobase

PMID:3038334

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 71% [6]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[5]

est. P1 cotransduction: 75% [6]

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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:G7531

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12983

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004092

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947446

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2808

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009694

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

YggW

Synonyms

predicted oxidoreductase[1], B2955[2][1], YggW[2][1] , ECK2950, JW2922, b2955

Product description

predicted oxidoreductase[2][3]

Function unknown, Radical SAM superfamily[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007197

F

Seeded from EcoCyc (v14.0)

complete

GO:0004109

coproporphyrinogen oxidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004559

F

Seeded from EcoCyc (v14.0)

complete

GO:0004109

coproporphyrinogen oxidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010723

F

Seeded from EcoCyc (v14.0)

complete

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:IPR004559

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010723

C

Seeded from EcoCyc (v14.0)

complete

GO:0006779

porphyrin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004559

P

Seeded from EcoCyc (v14.0)

complete

GO:0006779

porphyrin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010723

P

Seeded from EcoCyc (v14.0)

complete

GO:0006779

porphyrin biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0627

P

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: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:IPR007197

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:IPR004559

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010723

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

rpsB

PMID:16606699

Experiment(s):EBI-1144435

Protein

blc

PMID:16606699

Experiment(s):EBI-1144435

Protein

fnr

PMID:16606699

Experiment(s):EBI-1144435

Protein

ymfM

PMID:16606699

Experiment(s):EBI-1144435

Protein

rplF

PMID:16606699

Experiment(s):EBI-1144435

Protein

fdnH

PMID:16606699

Experiment(s):EBI-1144435

Protein

nadE

PMID:16606699

Experiment(s):EBI-1144435

Protein

groL

PMID:16606699

Experiment(s):EBI-1144435

Protein

glcC

PMID:16606699

Experiment(s):EBI-1144435
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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 

MVKLPPLSLY IHIPWCVQKC PYCDFNSHAL KGEVPHDDYV QHLLNDLDND VAYAQGREVK
TIFIGGGTPS LLSGPAMQTL LDGVRARLPL AADAEITMEA NPGTVEADRF VDYQRAGVNR
ISIGVQSFSE EKLKRLGRIH GPQEAKRAAK LASGLGLRSF NLDLMHGLPD QSLEEALGDL
RQAIELNPPH LSWYQLTIEP NTLFGSRPPV LPDDDALWDI FEQGHQLLTA AGYQQYETSA
YAKPGYQCQH NLNYWRFGDY IGIGCGAHGK VTFPDGRILR TTKTRHPRGF MQGRYLESQR
DVEATDKPFE FFMNRFRLLE AAPRVEFIAY TGLCEDVIRP QLDEAIAQGY LTECADYWQI
TEHGKLFLNS LLELFLAE
Length

378

Mol. Wt

42.585 kDa

pI

5.5 (calculated)

Extinction coefficient

51,340 - 52,215 (calc based on 16 Y, 5 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

Domain

10..180

PF04055 Radical SAM superfamily

PMID:19920124

Domain

252..366

PF06969 HemN C-terminal region

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=yggW 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:16130856

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947446

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009694

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52062

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7531

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12983

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947446

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004092

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2808

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

Ecoli K-12

8.838+/-0.182

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.03125

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

310

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

99

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

140

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)

yggS

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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_000913:3095269..3095309 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
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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:b2955 (EcoliWiki Page)

NCBI GEO profiles for yggW

microarray

GenExpDB:b2955 (EcoliWiki Page)

Summary of data for yggW 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 yggW Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7531

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2808

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2955

EcoGene

EcoGene:EG12983

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004092

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009694

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

Arabidopsis thaliana

  • AT5G63290 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000028387 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000025128 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0205185 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000258955 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000022675 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000026136 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:3039628 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000015966 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000135550 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00019744001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000022002 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YGGW

From SHIGELLACYC

E. coli O157

YGGW

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)

PF04055 Radical SAM superfamily

Panther (EcoliWiki Page)

PTHR13932:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:102114

Pfam (EcoliWiki Page)

PF06969 HemN C-terminal region

EcoCyc

EcoCyc:G7531

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12983

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004092

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2808

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009694

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 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 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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