ybdR: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

ybdR

Gene Synonym(s)

ECK0602, b0608, JW0601[1], JW0601

Product Desc.

predicted oxidoreductase, Zn-dependent and NAD(P)-binding[2][3]

Function unknown[4]

Product Synonyms(s)

predicted oxidoreductase, Zn-dependent and NAD(P)-binding[1], B0608[2][1], YbdR[2][1] , ECK0602, JW0601, b0608

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybdR[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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AFMB Structural Genomics target No. (http://afmb.cnrs-mrs.fr/article171.html).[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

ybdR

Mnemonic

Systematic nomenclature

Synonyms

ECK0602, b0608, JW0601[1], JW0601

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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

13.82 minutes 

MG1655: 641311..642549
<gbrowseImage> name=NC_000913:641311..642549 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 624139..625377
<gbrowseImage> name=NC_012967:624139..625377 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 544071..545309
<gbrowseImage> name=NC_012759:544071..545309 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 641311..642549
<gbrowseImage> name=NC_007779:641311..642549 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 580643..581881
<gbrowseImage> name=NC_010473:580643..581881 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 693903..695141
<gbrowseImage> name=NC_010473:693903..695141 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

ΔybdR (Keio:JW0601)

deletion

deletion

PMID:16738554

Shigen
CGSC8716[5]

ΔybdR747::kan

PMID:16738554

CGSC:103726


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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

JW0601

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAAGCATTGACTTATCACGG

Primer 2:CCTATTGTTCCCCCCGGCATCGC

4A5

Kohara Phage

Genobase

PMID:3038334

3G5

Kohara Phage

Genobase

PMID:3038334

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: 83% [6]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 64% [6]
Synonyms:zbe-280::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:G6335

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13537

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002942

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949067

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3307

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002099

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

YbdR

Synonyms

predicted oxidoreductase, Zn-dependent and NAD(P)-binding[1], B0608[2][1], YbdR[2][1] , ECK0602, JW0601, b0608

Product description

predicted oxidoreductase, Zn-dependent and NAD(P)-binding[2][3]

Function unknown[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

P

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013154

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1137403

Protein

groL

PMID:16606699

Experiment(s):EBI-1137403

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1137403

Protein

dnaE

PMID:16606699

Experiment(s):EBI-1137403

Protein

dnaC

PMID:16606699

Experiment(s):EBI-1137403

Protein

ymfD

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.5

Protein

ybgI

PMID:19402753

LCMS(ID Probability):99.6

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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

MKALTYHGPH HVQVENVPDP GVEQADDIIL RITATAICGS DLHLYRGKIP QVKHGDIFGH
EFMGEVVETG KDVKNLQKGD RVVIPFVIAC GDCFFCRLQQ YAACENTNAG KGAALNKKQI
PAPAALFGYS HLYGGVPGGQ AEYVRVPKGN VGPFKVPPLL SDDKALFLSD ILPTAWQAAK
NAQIQQGSSV AVYGAGPVGL LTIACARLLG AEQIFVVDHH PYRLHFAADR YGAIPINFDE
DSDPAQSIIE QTAGHRGVDA VIDAVGFEAK GSTTETVLTN LKLEGSSGKA LRQCIAAVRR
GGIVSVPGVY AGFIHGFLFG DAFDKGLSFK MGQTHVHAWL GELLPLIEKG LLKPEEIVTH
YMPFEEAARG YEIFEKREEE CRKVILVPGA QSAEAAQKAV SGLVNAMPGG TI
Length

412

Mol. Wt

44.175 kDa

pI

6.8 (calculated)

Extinction coefficient

28,880 - 29,880 (calc based on 12 Y, 2 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

197..286

PF00107 Zinc-binding dehydrogenase

PMID:19920124

Domain

25..154

PF08240 Alcohol dehydrogenase GroES-like domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ybdR 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:16128591

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949067

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002099

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77316

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6335

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13537

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949067

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002942

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3307

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

4a

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

53

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)

ybdR

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_000913:641291..641331 source=MG1655 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:b0608 (EcoliWiki Page)

NCBI GEO profiles for ybdR

microarray

GenExpDB:b0608 (EcoliWiki Page)

Summary of data for ybdR 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 (641013..641371) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:A7[7]

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Notes

Accessions Related to ybdR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6335

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3307

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0608

EcoGene

EcoGene:EG13537

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002942

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002099

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

Schizosaccharomyces pombe

  • SPBC11981 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YBDR

From SHIGELLACYC

E. coli O157

YBDR

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)

PF00107 Zinc-binding dehydrogenase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50129

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Panther (EcoliWiki Page)

PTHR11695:SF298

Pfam (EcoliWiki Page)

PF08240 Alcohol dehydrogenase GroES-like domain

EcoCyc

EcoCyc:G6335

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13537

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002942

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3307

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002099

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 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

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