yibF: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

yibF

Gene Synonym(s)

ECK3581, b3592, JW3565[1], JW3565

Product Desc.

glutathione transferase-like protein possibly involved in selenium metabolism[2][3]

Function unknown, glutathione S-transferase homolog[4]

Product Synonyms(s)

predicted glutathione S-transferase[1], B3592[2][1], YibF[2][1] , ECK3581, JW3565, b3592

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yibF[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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

yibF

Mnemonic

Systematic nomenclature

Synonyms

ECK3581, b3592, JW3565[1], JW3565

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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

81.03 minutes 

MG1655: 3759978..3759370
<gbrowseImage> name=NC_000913:3759370..3759978 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3696648..3696040
<gbrowseImage> name=NC_012967:3696040..3696648 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3647696..3648304
<gbrowseImage> name=NC_012759:3647696..3648304 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3878460..3879068
<gbrowseImage> name=NC_007779:3878460..3879068 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3857555..3856947
<gbrowseImage> name=NC_010473:3856947..3857555 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

ΔyibF (Keio:JW3565)

deletion

deletion

PMID:16738554

Shigen

yibF::Tn5KAN-I-SceI (FB21324)

Insertion at nt 104 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21324

does not contain pKD46

yibF::Tn5KAN-I-SceI (FB21325)

Insertion at nt 104 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21325

contains pKD46

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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

JW3565

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAACTCGTCGGTAGCTACAC

Primer 2:CCAGCCTTTGGCGGTTCGGTGCG

17G2

Kohara Phage

Genobase

PMID:3038334

2C10

Kohara Phage

Genobase

PMID:3038334

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: % [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 2% [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:EG11762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001698

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948113

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1712

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011736

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

YibF

Synonyms

predicted glutathione S-transferase[1], B3592[2][1], YibF[2][1] , ECK3581, JW3565, b3592

Product description

glutathione transferase-like protein possibly involved in selenium metabolism[2][3]

Function unknown, glutathione S-transferase homolog[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:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

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

lacZ

PMID:16606699

Experiment(s):EBI-1146189

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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

MKLVGSYTSP FVRKLSILLL EKGITFEFIN ELPYNADNGV AQFNPLGKVP VLVTEEGECW
FDSPIIAEYI ELMNVAPAML PRDPLESLRV RKIEALADGI MDAGLVSVRE QARPAAQQSE
DELLRQREKI NRSLDVLEGY LVDGTLKTDT VNLATIAIAC AVGYLNFRRV APGWCVDRPH
LVKLVENLFS RESFARTEPP KA
Length

202

Mol. Wt

22.545 kDa

pI

5.0 (calculated)

Extinction coefficient

18,450 - 18,825 (calc based on 5 Y, 2 W, and 3 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

96..192

PF00043 Glutathione S-transferase, C-terminal domain

PMID:19920124

Domain

2..71

PF02798 Glutathione S-transferase, N-terminal domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=yibF 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:16131463

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948113

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011736

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACA1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11762

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948113

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001698

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1712

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

3.15E+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

326

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

386

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

251

molecules/cell/generation

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

Ribosome Profiling

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)

yibF

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_000913:3759958..3759998 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:b3592 (EcoliWiki Page)

NCBI GEO profiles for yibF

microarray

GenExpDB:b3592 (EcoliWiki Page)

Summary of data for yibF 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 (3759292..3759622) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:B1[7]

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Notes

Accessions Related to yibF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11762

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1712

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3592

EcoGene

EcoGene:EG11762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001698

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011736

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

  • AT2G29450 (score: 1.000; bootstrap: 100%)
  • AT2G29440 (score: 0.775)
  • AT2G29490 (score: 0.682)
  • AT2G29460 (score: 0.659)
  • AT2G29480 (score: 0.638)
  • AT2G29470 (score: 0.587)
  • AT2G29420 (score: 0.488)
  • AT3G09270 (score: 0.359)
  • AT1G59700 (score: 0.240)
  • AT5G62480 (score: 0.233)
  • AT1G59670 (score: 0.222)
  • AT1G74590 (score: 0.220)
  • AT1G27130 (score: 0.217)
  • AT1G69920 (score: 0.191)
  • AT1G10370 (score: 0.181)
  • AT1G69930 (score: 0.165)
  • AT1G27140 (score: 0.163)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000013573 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000013676 (score: 0.604)

From Inparanoid:20070104

Oryza gramene

  • O04941 (score: 1.000; bootstrap: 100%)
  • Q8LL15 (score: 0.947)
  • Q8LGS9 (score: 0.947)
  • Q9FUE4 (score: 0.659)
  • Q6WSC3 (score: 0.657)
  • Q8S714 (score: 0.654)
  • Q9FQ97 (score: 0.654)
  • Q8LGS8 (score: 0.647)
  • Q9SB98 (score: 0.642)
  • Q8S715 (score: 0.642)
  • Q9ZS20 (score: 0.624)
  • Q945X0 (score: 0.617)
  • Q8S7T0 (score: 0.614)
  • Q945W9 (score: 0.614)
  • Q8S712 (score: 0.612)
  • Q8S703 (score: 0.604)
  • Q9ZS19 (score: 0.602)
  • Q6WSC2 (score: 0.599)
  • Q9FQ99 (score: 0.596)
  • Q8RUJ2 (score: 0.596)
  • Q9FUE3 (score: 0.594)
  • Q8RUS1 (score: 0.594)
  • Q8S702 (score: 0.584)
  • Q945W6 (score: 0.581)
  • Q945W4 (score: 0.581)
  • Q8S710 (score: 0.576)
  • Q9FQA4 (score: 0.569)
  • Q945W2 (score: 0.566)
  • Q8S711 (score: 0.564)
  • Q9FUE2 (score: 0.559)
  • Q945X1 (score: 0.556)
  • Q9FQB7 (score: 0.541)
  • Q8H8I8 (score: 0.536)
  • Q8S717 (score: 0.524)
  • Q9FQA2 (score: 0.489)
  • Q9FQB2 (score: 0.489)
  • Q8RW01 (score: 0.486)
  • Q9FQA1 (score: 0.486)
  • Q9FQA9 (score: 0.479)
  • Q06398 (score: 0.471)
  • Q945W5 (score: 0.469)
  • Q8RZY8 (score: 0.469)
  • Q8LMJ0 (score: 0.469)
  • Q8L4V6 (score: 0.464)
  • Q8S718 (score: 0.459)
  • Q8LGN6 (score: 0.451)
  • Q9FQB4 (score: 0.451)
  • Q9FQA7 (score: 0.449)
  • Q8S9U5 (score: 0.444)
  • Q8W2T8 (score: 0.444)
  • Q9FQA6 (score: 0.431)
  • Q69LE6 (score: 0.416)
  • Q6QN17 (score: 0.414)
  • Q9FQB3 (score: 0.406)
  • Q8RW00 (score: 0.386)
  • Q9FQA8 (score: 0.368)
  • Q9FQA5 (score: 0.363)
  • Q8LMI9 (score: 0.356)
  • Q9FQA0 (score: 0.353)
  • Q6QN18 (score: 0.351)
  • Q945W3 (score: 0.348)
  • Q8S7S9 (score: 0.346)
  • Q6AUB4 (score: 0.316)
  • Q9FQB9 (score: 0.313)
  • Q9FQA3 (score: 0.303)
  • Q9FQ98 (score: 0.298)
  • Q9AV55 (score: 0.296)
  • Q9FQB6 (score: 0.291)
  • Q8RZB1 (score: 0.288)
  • Q9ZP60 (score: 0.278)
  • Q9FQB0 (score: 0.276)
  • Q5JKX6 (score: 0.271)
  • Q851H8 (score: 0.268)
  • Q93WY5 (score: 0.263)
  • Q9FQB5 (score: 0.261)
  • Q5JKY3 (score: 0.258)
  • Q5GAR4 (score: 0.253)
  • P50472 (score: 0.251)
  • Q9FQB1 (score: 0.251)
  • Q8L576 (score: 0.251)
  • Q5JKY4 (score: 0.251)
  • Q8RZA8 (score: 0.248)
  • Q945W8 (score: 0.243)
  • Q8GSQ7 (score: 0.241)
  • Q8RZB3 (score: 0.238)
  • Q5GAV2 (score: 0.238)
  • Q9FQB8 (score: 0.236)
  • Q6R4K3 (score: 0.158)
  • Q6R4J7 (score: 0.158)
  • Q6R4I9 (score: 0.158)
  • Q6R4K6 (score: 0.158)
  • Q6R4K5 (score: 0.158)
  • Q6R4J8 (score: 0.155)
  • Q6R4J1 (score: 0.153)
  • Q6R4J6 (score: 0.153)
  • Q6R4I6 (score: 0.153)
  • Q6R4K8 (score: 0.150)
  • Q6R4J0 (score: 0.150)
  • Q6R4I1 (score: 0.150)
  • Q93W19 (score: 0.150)
  • Q93W18 (score: 0.150)
  • Q93VZ7 (score: 0.148)
  • Q6R4J2 (score: 0.148)
  • Q94FD1 (score: 0.145)
  • Q6QHA4 (score: 0.145)
  • Q93W69 (score: 0.138)
  • Q6R4H9 (score: 0.118)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000037094 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YIBF

From SHIGELLACYC

E. coli O157

YIBF

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)

PF02798 Glutathione S-transferase, N-terminal domain

Pfam (EcoliWiki Page)

PF00043 Glutathione S-transferase, C-terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47616

Superfamily (EcoliWiki Page)

SUPERFAMILY:52833

Panther (EcoliWiki Page)

PTHR11260:SF41

EcoCyc

EcoCyc:EG11762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001698

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1712

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011736

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 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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