ydeO: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

ydeO

Gene Synonym(s)

ECK1493, b1499, JW1494[1], JW1494

Product Desc.

YdeO transcriptional activator[2][3]

Required for acid resistance conferred by EvgA overexpression; AraC family transcriptional activator[4]

Product Synonyms(s)

predicted DNA-binding transcriptional acfivator[1], B1499[2][1], YdeO[2][1] , ECK1493, JW1494, b1499

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ydeO[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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EvgAS regulon. YdeO induces GadE expression. YdeO and YdeP repress the type III secretion system (TTSS) of EPEC E. coli (Nadler, 2006).[4]



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

ydeO

Mnemonic

Systematic nomenclature

Synonyms

ECK1493, b1499, JW1494[1], JW1494

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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

34.07 minutes 

MG1655: 1581711..1580950
<gbrowseImage> name=NC_000913:1580950..1581711 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1557638..1556877
<gbrowseImage> name=NC_012967:1556877..1557638 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1473009..1473770
<gbrowseImage> name=NC_012759:1473009..1473770 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1585401..1584640
<gbrowseImage> name=NC_007779:1584640..1585401 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1672306..1671545
<gbrowseImage> name=NC_010473:1671545..1672306 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

ΔydeO (Keio:JW1494)

deletion

deletion

PMID:16738554

Shigen


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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

JW1494

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCGCTCGTTTGTTCTGTTAT

Primer 2:CCAATAGCTAAAGCATTCATCGT

6E8

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 13% [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::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:G6789

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13797

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003378

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945922

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3558

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004992

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

YdeO

Synonyms

predicted DNA-binding transcriptional acfivator[1], B1499[2][1], YdeO[2][1] , ECK1493, JW1494, b1499

Product description

YdeO transcriptional activator[2][3]

Required for acid resistance conferred by EvgA overexpression; AraC family transcriptional activator[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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012287

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012287

P

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0805

P

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

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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

MSLVCSVIFI HHAFNANILD KDYAFSDGEI LMVDNAVRTH FEPYERHFKE IGFTENTIKK
YLQCTNIQTV TVPVPAKFLR ASNVPTGLLN EMIAYLNSEE RNHHNFSELL LFSCLSIFAA
CKGFITLLTN GVLSVSGKVR NIVNMKPAHP WKLKDICDCL YISESLLKKK LKQEQTTFSQ
ILLDARMQHA KNLIRVEGSV NKIAEQCGYA STSYFIYAFR KHFGNSPKRV SKEYRCQSHT
GMNTGNTMNA LAI
Length

253

Mol. Wt

28.725 kDa

pI

9.0 (calculated)

Extinction coefficient

18,910 - 19,910 (calc based on 9 Y, 1 W, and 8 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

143..183

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

PMID:19920124

Domain

199..230

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ydeO 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:16129458

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945922

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004992

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76135

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6789

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13797

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945922

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003378

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3558

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

8a

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

8

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

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)

ydeO

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_000913:1581691..1581731 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:b1499 (EcoliWiki Page)

NCBI GEO profiles for ydeO

microarray

GenExpDB:b1499 (EcoliWiki Page)

Summary of data for ydeO 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 (1581628..1581825) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:B8[7]

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Notes

Accessions Related to ydeO Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6789

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3558

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1499

EcoGene

EcoGene:EG13797

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003378

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004992

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

S1654

From SHIGELLACYC

E. coli O157

Z2209

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)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Pfam (EcoliWiki Page)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

EcoCyc

EcoCyc:G6789

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13797

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003378

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3558

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004992

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 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 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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