ybjX: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

ybjX

Gene Synonym(s)

ECK0868, b0877, JW0861[1], JW0861

Product Desc.

conserved protein[2][3]

Function unknown, homologous to somA (S.t.) and virK (S.f.)[4]

Product Synonyms(s)

conserved protein[1], B0877[2][1], YbjX[2][1] , ECK0868, JW0861, b0877

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybjX[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]


The ybjX homolog somA is an msbB (lpxM) suppressor mutation in Salmonella.[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

ybjX

Mnemonic

Systematic nomenclature

Synonyms

ECK0868, b0877, JW0861[1], JW0861

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

19.77 minutes 

MG1655: 918343..917351
<gbrowseImage> name=NC_000913:917351..918343 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 935826..934834
<gbrowseImage> name=NC_012967:934834..935826 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 820319..821311
<gbrowseImage> name=NC_012759:820319..821311 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 919542..918550
<gbrowseImage> name=NC_007779:918550..919542 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 972271..971279
<gbrowseImage> name=NC_010473:971279..972271 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

ΔybjX (Keio:JW0861)

deletion

deletion

PMID:16738554

Shigen
CGSC8893[5]

ΔybjX::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔybjX778::kan

PMID:16738554

CGSC:103894


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

JW0861

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGTGAAATCGACGCCATGTAT

Primer 2:CCACCGCGAAACATCGTGGCCAT

1E5

Kohara Phage

Genobase

PMID:3038334

1H1

Kohara Phage

Genobase

PMID:3038334

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: % [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 32% [6]
Synonyms:zbj-1230::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:G6460

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13693

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003060

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946025

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3457

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002982

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

YbjX

Synonyms

conserved protein[1], B0877[2][1], YbjX[2][1] , ECK0868, JW0861, b0877

Product description

conserved protein[2][3]

Function unknown, homologous to somA (S.t.) and virK (S.f.)[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:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

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

lpdA

PMID:15690043

Experiment(s):EBI-879208

Protein

pssA

PMID:15690043

Experiment(s):EBI-879208

Protein

rplA

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplB

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplC

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplD

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplE

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplF

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplM

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rplV

PMID:15690043

Experiment(s):EBI-879208

Protein

rpoC

PMID:15690043

Experiment(s):EBI-879208

Protein

rpsA

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rpsB

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rpsC

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rpsD

PMID:15690043

Experiment(s):EBI-879208

Protein

rpsG

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

srmB

PMID:15690043

Experiment(s):EBI-879208

Protein

tufA

PMID:15690043

Experiment(s):EBI-879208, EBI-882921

Protein

rnr

PMID:15690043

Experiment(s):EBI-879208

Protein

rluB

PMID:15690043

Experiment(s):EBI-879208

Protein

rplX

PMID:15690043

Experiment(s):EBI-882921

Protein

rpmB

PMID:15690043

Experiment(s):EBI-882921

Protein

rpmC

PMID:15690043

Experiment(s):EBI-882921

Protein

rpmG

PMID:15690043

Experiment(s):EBI-882921

Protein

rpsE

PMID:15690043

Experiment(s):EBI-882921

Protein

rpsF

PMID:15690043

Experiment(s):EBI-882921

Protein

rpsM

PMID:15690043

Experiment(s):EBI-882921

Protein

rpsS

PMID:15690043

Experiment(s):EBI-882921

Protein

rpsT

PMID:15690043

Experiment(s):EBI-882921

Protein

aceF

PMID:15690043

Experiment(s):EBI-882921

Protein

dnaJ

PMID:15690043

Experiment(s):EBI-882921

Protein

hupA

PMID:15690043

Experiment(s):EBI-882921

Protein

hupB

PMID:15690043

Experiment(s):EBI-882921

Protein

rplI

PMID:15690043

Experiment(s):EBI-882921

Protein

rplJ

PMID:15690043

Experiment(s):EBI-882921

Protein

rplL

PMID:15690043

Experiment(s):EBI-882921

Protein

rplO

PMID:15690043

Experiment(s):EBI-882921

Protein

rplQ

PMID:15690043

Experiment(s):EBI-882921

Protein

rplS

PMID:15690043

Experiment(s):EBI-882921

Protein

rplT

PMID:15690043

Experiment(s):EBI-882921

Protein

rplU

PMID:15690043

Experiment(s):EBI-882921

Protein

perM

PMID:16606699

Experiment(s):EBI-1138231

Protein

yciH

PMID:16606699

Experiment(s):EBI-1138231

Protein

rplB

PMID:16606699

Experiment(s):EBI-1138231

Protein

appY

PMID:16606699

Experiment(s):EBI-1138231

Protein

groL

PMID:16606699

Experiment(s):EBI-1138231

Protein

mutH

PMID:16606699

Experiment(s):EBI-1138231

Protein

rpmC

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.224236

Protein

rplJ

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):3.385515

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.323521

Protein

rfaD

PMID:19402753

MALDI(Z-score):38.502110

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753

MALDI(Z-score):20.676555

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):29.180248

Protein

rplQ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.654204

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):32.496120

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):34.058088

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.378458

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.679102

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):37.287562

Protein

srmB

PMID:19402753

MALDI(Z-score):24.880466

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):18.911757

Protein

yfiF

PMID:19402753

LCMS(ID Probability):97.8 MALDI(Z-score):7.664643

Protein

rnr

PMID:19402753

MALDI(Z-score):26.041938

Protein

rplL

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 

MVKSTPCITI DFMNMSQLTE RTFTPSESLS SLSLFLSLAR GQCRPGKFWH RRSFRQKFLL
RSLIMPRLSV EWMNELSHWP NLNVLLTRQP RLPVRLHRPY LAANLSRKQL LEALRYHYAL
LRECMSAEEF SLYLNTPGLQ LAKLEGKNGE QFTLELTMMI SMDKEGDSTI LFRNSEGIPL
AEITFTLCEY QGKRTMFIGG LQGAKWEIPH QEIQNATKAC HGLFPKRLVM EAACLFAQRL
QVEQIIAVSN ETHIYRSLRY RDKEGKIHAD YNAFWESVGG VCDAERHYRL PAQIARKEIA
EIASKKRAEY RRRYEMLDAI QPQMATMFRG
Length

330

Mol. Wt

38.358 kDa

pI

9.7 (calculated)

Extinction coefficient

43,890 - 44,765 (calc based on 11 Y, 5 W, and 7 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

40..328

PF04393 Protein of unknown function (DUF535)

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=ybjX 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:16128845

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946025

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002982

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75829

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6460

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13693

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3457

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

Ecoli K-12

9.267+/-0.083

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.106854839

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

2797

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

507

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

2424

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)

ybjX

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_000913:918323..918363 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:b0877 (EcoliWiki Page)

NCBI GEO profiles for ybjX

microarray

GenExpDB:b0877 (EcoliWiki Page)

Summary of data for ybjX 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
edit table

<protect></protect>

Notes

Accessions Related to ybjX Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G6460

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3457

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0877

EcoGene

EcoGene:EG13693

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003060

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002982

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

YBJX

From SHIGELLACYC

E. coli O157

YBJX

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)

PF04393 Protein of unknown function (DUF535)

EcoCyc

EcoCyc:G6460

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13693

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3457

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002982

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 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).

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ybjX:On_One_Page&oldid=219268"