yojI:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

yojI

Gene Synonym(s)

ECK2203, b2211, JW2199, yojJ[1], yojJ

Product Desc.

YojI[2][3]

Microcin J25 efflux pump, TolC-dependent; non-essential gene[4]

Product Synonyms(s)

fused predicted multidrug transport subunits of ABC superfamily: membrane component[1], ATP-binding component[1], B2211[2][1], YojJ[2][1], YojI[2][1] , ECK2203, JW2199, yojJ, b2211

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yojI[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

edit table

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

Notes

[back to top]


Overexpressed YojI confers Microcin J25 resistance and a yojI mutation confers Microcin J25 sensistivity. YojI is homologous to ABC-type transporters. No other overexpression resistances found among 26 inhibitors tested.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

yojI

Mnemonic

Systematic nomenclature

Synonyms

ECK2203, b2211, JW2199, yojJ[1], yojJ

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

49.68 minutes 

MG1655: 2306637..2304994
<gbrowseImage> name=NC_000913:2304994..2306637 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2258719..2257076
<gbrowseImage> name=NC_012967:2257076..2258719 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2190799..2192442
<gbrowseImage> name=NC_012759:2190799..2192442 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2311949..2310306
<gbrowseImage> name=NC_007779:2310306..2311949 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2397625..2395982
<gbrowseImage> name=NC_010473:2395982..2397625 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔyojI (Keio:JW2199)

deletion

deletion

PMID:16738554

Shigen
CGSC9778[5]

yojI::Tn5KAN-I-SceI (FB20705)

Insertion at nt 563 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20705

contains pKD46

ΔyojI764::kan

PMID:16738554

CGSC:105896


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2199

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAACTTCTTGTACTTGTCTG

Primer 2:CCTGCCGTCCGGGCAACGGCATC

19D1

Kohara Phage

Genobase

PMID:3038334

22A6

Kohara Phage

Genobase

PMID:3038334

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[5]

est. P1 cotransduction: 88% [6]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[5]

est. P1 cotransduction: 59% [6]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12070

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001979

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946705

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1997

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007303

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

YojI

Synonyms

fused predicted multidrug transport subunits of ABC superfamily: membrane component[1], ATP-binding component[1], B2211[2][1], YojJ[2][1], YojI[2][1] , ECK2203, JW2199, yojJ, b2211

Product description

YojI[2][3]

Microcin J25 efflux pump, TolC-dependent; non-essential gene[4]

EC number (for enzymes)


edit table

<protect></protect>

Notes

Function

[back to top]


<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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005898

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011527

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0015197

peptide transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005898

F

Seeded from EcoCyc (v14.0)

complete

GO:0015833

peptide transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005898

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005898

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011527

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0042626

ATPase activity, coupled to transmembrane movement of substances

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011527

F

Seeded from EcoCyc (v14.0)

complete

GO:0046677

response to antibiotic

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0046

P

Seeded from EcoCyc (v14.0)

complete

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011527

P

Seeded from EcoCyc (v14.0)

complete

GO:0042884

microcin transport

PMID:15866933

IMP: Inferred from Mutant Phenotype

P

complete

edit table

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

atpD

PMID:16606699

Experiment(s):EBI-1142177

Protein

mqo

PMID:16606699

Experiment(s):EBI-1142177

Protein

fumB

PMID:16606699

Experiment(s):EBI-1142177

Protein

groL

PMID:16606699

Experiment(s):EBI-1142177

Protein

rho

PMID:16606699

Experiment(s):EBI-1142177
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

plasma membrane

From EcoCyc[3]


edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

MELLVLVWRQ YRWPFISVMA LSLASAALGI GLIAFINQRL IETADTSLLV LPEFLGLLLL
LMAVTLGSQL ALTTLGHHFV YRLRSEFIKR ILDTHVERIE QLGSASLLAG LTSDVRNITI
AFVRLPELVQ GIILTIGSAA YLWMLSGKML LVTAIWMAIT IWGGFVLVAR VYKHMATLRE
TEDKLYTDFQ TVLEGRKELT LNRERAEYVF NNLYIPDAQE YRHHIIRADT FHLSAVNWSN
IMMLGAIGLV FWMANSLGWA DTNVAATYSL TLLFLRTPLL SAVGALPTLL TAQVAFNKLN
KFALAPFKAE FPRPQAFPNW QTLELRNVTF AYQDNAFSVG PINLTIKRGE LLFLIGGNGS
GKSTLAMLLT GLYQPQSGEI LLDGKPVSGE QPEDYRKLFS AVFTDVWLFD QLLGPEGKPA
NPQLVEKWLA QLKMAHKLEL SNGRIVNLKL SKGQKKRVAL LLALAEERDI ILLDEWAADQ
DPHFRREFYQ VLLPLMQEMG KTIFAISHDD HYFIHADRLL EMRNGQLSEL TGEERDAASR
DAVARTA
Length

547

Mol. Wt

61.555 kDa

pI

7.2 (calculated)

Extinction coefficient

86,860 (calc based on 14 Y, 12 W, and 0 C residues)

edit table


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

363..478

PF00005 ABC transporter

PMID:19920124

edit table

<motif_map/>

tmhmm.php?gene=yojI&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=yojI taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130148

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946705

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007303

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33941

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12070

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12070

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946705

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001979

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1997

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

332

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

84

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

76

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

yojI

edit table
Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:2306617..2306657 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

microarray

GEO Profiles:b2211 (EcoliWiki Page)

NCBI GEO profiles for yojI

microarray

GenExpDB:b2211 (EcoliWiki Page)

Summary of data for yojI from multiple microarray studies

edit table


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 (2306567..2306738) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:D1[7]

edit table

<protect></protect>

Notes

Accessions Related to yojI Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG12070

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1997

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2211

EcoGene

EcoGene:EG12070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001979

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007303

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000044382 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YOJI

From SHIGELLACYC

E. coli O157

YOJI

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR24223:SF212

Superfamily (EcoliWiki Page)

SUPERFAMILY:90123

EcoCyc

EcoCyc:EG12070

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12070

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001979

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1997

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007303

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 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 2.7 2.8 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 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

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=yojI:On_One_Page&oldid=220601"