yhfW: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

yhfW

Gene Synonym(s)

ECK3367, b3380, JW3343[1], JW3343

Product Desc.

predicted mutase[2][3]

Function unknown[4]

Product Synonyms(s)

predicted mutase[1], B3380[2][1], YhfW[2][1] , ECK3367, JW3343, b3380

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yhfS[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

yhfW

Mnemonic

Systematic nomenclature

Synonyms

ECK3367, b3380, JW3343[1], JW3343

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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

75.58 minutes 

MG1655: 3507835..3506609
<gbrowseImage> name=NC_000913:3506609..3507835 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3438495..3437269
<gbrowseImage> name=NC_012967:3437269..3438495 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3393766..3394992
<gbrowseImage> name=NC_012759:3393766..3394992 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4130603..4131829
<gbrowseImage> name=NC_007779:4130603..4131829 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3605580..3604354
<gbrowseImage> name=NC_010473:3604354..3605580 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

ΔyhfW (Keio:JW3343)

deletion

deletion

PMID:16738554

Shigen
CGSC10496[5]

yhfW::Tn5KAN-I-SceI (FB21142)

Insertion at nt 536 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21142

contains pKD46

yhfW::Tn5KAN-I-SceI (FB21143)

Insertion at nt 536 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21143

does not contain pKD46

ΔyhfW787::kan

PMID:16738554

CGSC:105196


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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

JW3343

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGCGATTTGTGGTGTTAGT

Primer 2:CCTAGGGTGTCTCCTGCAAACCG

6F9

Kohara Phage

Genobase

PMID:3038334

15C3

Kohara Phage

Genobase

PMID:3038334

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[5]

est. P1 cotransduction: 89% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 6% [6]
Synonyms:zhg-3086::Tn10, zhh-21::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:G7732

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12918

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004275

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947890

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2754

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011046

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

YhfW

Synonyms

predicted mutase[1], B3380[2][1], YhfW[2][1] , ECK3367, JW3343, b3380

Product description

predicted mutase[2][3]

Function unknown[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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006124

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017849

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017850

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

C

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017849

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017850

P

Seeded from EcoCyc (v14.0)

complete

GO:0008973

phosphopentomutase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

F

Seeded from EcoCyc (v14.0)

complete

GO:0009117

nucleotide metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

P

Seeded from EcoCyc (v14.0)

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0043094

cellular metabolic compound salvage

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010045

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006124

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

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

xseA

PMID:16606699

Experiment(s):EBI-1145716

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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

MARFVVLVID SFGVGAMKDV TLVRPQDAGA NTCGHILSQL PHLQLPTLET LGLINALGYA
PGDMQPSDSA TWGVAELQHE GGDTFMGHQE ILGTRPLPPL RMPFRDVIDR VEQALVSAGW
QVERRGDDLQ FLWVNQAVAI GDNLEADLGQ VYNITANLSV ISFDDAIKIG RIVREQVQVG
RVITFGGLLT DSQRILDAAE SKEGRFIGIN APRSGAYDNG FQVVHMGYGV DEKVQVPQKL
YEAGVPTVLV GKVADIVNNP YGVSWQNLVD SQRIMDITLN EFNTHPTAFI CTNIQETDLA
GHAEDVARYA ERLQVVDRNL ARLVEAMQPD DCLVVMADHG NDPTIGHSHH TREVVPVLVY
QQGMIATQLG VRTTLSDVGA TVCEFFRAPP PQNGRSFLSS LRFAGDTL
Length

408

Mol. Wt

44.558 kDa

pI

4.8 (calculated)

Extinction coefficient

33,920 - 34,420 (calc based on 8 Y, 4 W, and 4 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

Domain

2..397

PF01676 Metalloenzyme superfamily

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=yhfW 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:16131258

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947890

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011046

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P45549

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7732

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12918

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947890

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004275

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2754

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 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

0a

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

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)

yhfS

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_000913:3507815..3507855 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


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

Type Reference Notes

microarray

GEO Profiles:b3380 (EcoliWiki Page)

NCBI GEO profiles for yhfW

microarray

GenExpDB:b3380 (EcoliWiki Page)

Summary of data for yhfW 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

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Notes

Accessions Related to yhfW Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7732

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2754

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3380

EcoGene

EcoGene:EG12918

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004275

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011046

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

Shigella flexneri

YHFW

From SHIGELLACYC


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)

PF01676 Metalloenzyme superfamily

Superfamily (EcoliWiki Page)

SUPERFAMILY:53649

EcoCyc

EcoCyc:G7732

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12918

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004275

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2754

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011046

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).

Categories

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