yeeX: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

yeeX

Gene Synonym(s)

ECK2001, b2007, JW1989[1], JW1989

Product Desc.

conserved protein[2][3]

Function unknown[4]

Product Synonyms(s)

conserved protein[1], YeeX[2][1], B2007[2][1] , ECK2001, JW1989, b2007

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yeeX[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]





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

yeeX

Mnemonic

Systematic nomenclature

Synonyms

ECK2001, b2007, JW1989[1], JW1989

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

44.77 minutes, 44.77 minutes 

MG1655: 2077451..2077056
<gbrowseImage> name=NC_000913:2077056..2077451 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2009870..2009475
<gbrowseImage> name=NC_012967:2009475..2009870 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1969539..1969868
<gbrowseImage> name=NC_012759:1969539..1969868 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2081564..2081169
<gbrowseImage> name=NC_007779:2081169..2081564 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2168459..2168064
<gbrowseImage> name=NC_010473:2168064..2168459 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

Coding Start (SO:0000323)

MG1655

2077056

Edman degradation

PMID:9868784


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

ΔyeeX (Keio:JW1989)

deletion

deletion

PMID:16738554

Shigen
CGSC9640[5]

ΔyeeX776::kan

PMID:16738554

CGSC:104508


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

JW1989

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTGGCCCTAACGAATAGCGG

Primer 2:CCtTTCGCTTCGCCGTTTTTCAT

3B12

Kohara Phage

Genobase

PMID:3038334

2G4

Kohara Phage

Genobase

PMID:3038334

zed-3069::Tn10

Linked marker

CAG18451 = CGSC7395[5]

est. P1 cotransduction: 18% [6]

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[5]

est. P1 cotransduction: 81% [6]
Synonyms:zee-3129::Tn10

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:G7087

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13391

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003673

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946541

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3172

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006663

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

YeeX

Synonyms

conserved protein[1], YeeX[2][1], B2007[2][1] , ECK2001, JW1989, b2007

Product description

conserved protein[2][3]

Function unknown[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
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

tig

PMID:19402753

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.705543

Protein

rplN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.5

Protein

secA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.898492

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):6.253198

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.106052

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):15.474095

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.304559

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):20.409675

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.483955

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.795438

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.161132

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):32.180897

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):13.198885

Protein

rpoB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.6

Protein

accA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):31.420320

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):16.325900

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):19.872659

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

lon

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.008480

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.627877

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsO

PMID:19402753

LCMS(ID Probability):99.5

Protein

pdxH

PMID:19402753

LCMS(ID Probability):99.2

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.1 MALDI(Z-score):4.774822

Protein

rpmA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rlmL

PMID:19402753

LCMS(ID Probability):98.0 MALDI(Z-score):8.389847

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753

LCMS(ID Probability):99.6

Protein

malP

PMID:19402753

LCMS(ID Probability):99.6

Protein

srmB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.472980

Protein

rpoA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yhiR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.967277

Protein

fadI

PMID:19402753

LCMS(ID Probability):99.6

Protein

skp

PMID:19402753

LCMS(ID Probability):99.0

Protein

ycaO

PMID:19402753

MALDI(Z-score):27.663915

Protein

hrpA

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfiF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.034632

Protein

lpxD

PMID:19402753

LCMS(ID Probability):99.6

Protein

infC

PMID:19402753

LCMS(ID Probability):99.6

Protein

yibL

PMID:19402753

LCMS(ID Probability):99.6

Protein

pssA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):25.011184

Protein

norV

PMID:19402753

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.377997

Protein

rsuA

PMID:19402753

LCMS(ID Probability):99.6

Protein

spoT

PMID:19402753

MALDI(Z-score):26.807712

Protein

rimP

PMID:19402753

LCMS(ID Probability):99.6

Protein

yadE

PMID:19402753

LCMS(ID Probability):99.2

Protein

yihA

PMID:19402753

LCMS(ID Probability):99.6

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
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 

MLALTNSGCL NESDSHIIRG IKMETTKPSF QDVLEFVRLF RRKNKLQREI QDVEKKIRDN
QKRVLLLDNL SDYIKPGMSV EAIQGIIASM KGDYEDRVDD YIIKNAELSK ERRDISKKLK
AMGEMKNGEA K
Length

131

Mol. Wt

15.133 kDa

pI

9.5 (calculated)

Extinction coefficient

4,470 - 4,595 (calc based on 3 Y, 0 W, and 1 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

8..102

PF04363 Protein of unknown function (DUF496)

PMID:19920124

edit table

<motif_map/>

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

Structures

<beststructure> gene=yeeX 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:145698283

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946541

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006663

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8M6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7087

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13391

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946541

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003673

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3172

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 MC4100

2.66E+03

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

Ecoli K-12

269.523+/-4.362

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.418987342

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

13270

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

6787

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

8581

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)

yeeX

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_000913:2077431..2077471 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:b2007 (EcoliWiki Page)

NCBI GEO profiles for yeeX

microarray

GenExpDB:b2007 (EcoliWiki Page)

Summary of data for yeeX 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 (2077356..2077608) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ17; Well:G10[7]

edit table

<protect></protect>

Notes

Accessions Related to yeeX Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7087

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3172

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2007

EcoGene

EcoGene:EG13391

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003673

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006663

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

Shigella flexneri

YEEX

From SHIGELLACYC

E. coli O157

YEEX

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)

PF04363 Protein of unknown function (DUF496)

EcoCyc

EcoCyc:G7087

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13391

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003673

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3172

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006663

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. ↑ 1.0 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).
  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=yeeX:On_One_Page&oldid=220400"