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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Gene Name

ydjA (synonyms: ECK1763, b1765, JW1754)[1]

Product(s)

YdjA product[1]: predicted oxidoreductase product, B1765 product

Description

predicted oxidoreductase[2][3]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ydjA-selD-topB[2]

Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name

ydjA

Mnemonic
Synonyms

ECK1763, b1765, JW1754[1]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

39.79 minutes 

MG1655: 1846700..1846149
gbrowse_img.php?coord=1845149..1847700&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1850390..1849839
gbrowse_img.php?coord=1848839..1851390&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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Notes

Sequence Features

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Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔydjA (Keio:JW1754)

deletion

deletion

PMID:16738554[4]

Shigen

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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW1754

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGATGCACTCGAACTATTGAT

Primer 2:CCGAAATAAGTTACAAACGGCGT

zdj-276::Tn10

Linked marker

CAG18464 = CGSC7387[6]

est. P1 cotransduction: 62% [7]

Synonyms:zdi-276::Tn10

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[6]

est. P1 cotransduction: 41% [7]

Synonyms:zdj-225::Tn10

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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11134

EchoBASE (EcoliWiki Page)

EchoBASE:EB1124

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1765

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2168

EcoGene (EcoliWiki Page)

EcoGene:EG11134

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YDJA

ASAP (EcoliWikiPage)

ASAP:ABE-0005875


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Notes

Links

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NameURLComments
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Categories

Product(s)

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Nomenclature

Standard name

YdjA

Synonyms

predicted oxidoreductase[1], B1765[2][1], YdjA[2][1]

Product description

predicted oxidoreductase[2][3]

EC number (for enzymes)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
GO:0016491

oxidoreductase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000415

F

Seeded from EcoCyc 12.5 [8]

complete

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Interactions

Partner TypePartnerNotesReferences
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Notes

Localization

CompartmentDescriptionEvidenceNotes
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Notes

Structure and Physical Properties

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Physical Properties

Sequence

at EcoCyc 

MDALELLINR RSASRLAEPA PTGEQLQNIL RAGMRAPDHK SMQPWHFFVI EGEGRERFSA
VLEQGAIAAG SDDKAIDKAR NAPFRAPLII TVVAKCEENH KVPRWEQEMS AGCAVMAMQM
AAVAQGFGGI WRSGALTESP VVREAFGCRE QDKIVGFLYL GTPQLKASTS INVPDPTPFV TYF
Mol. Wt

20.06 kDa (calc) [2]

pI
Extinction coefficient

19480 - 19855 (calc based on 2 Y, 3 W, and 3 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes
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Structure

Structures
  • Representative Escherichia coli structure:
    3BM1|A
    1-183 of 183 residues (E-value: 2.1e-96) (Percent Identity: 100.00)
  • Representative homolog:
    2I7H|A (Bacillus cereus)
    17-180 of 183 residues (E-value: 1.4e-12) (Percent Identity: 29.59)
  • View all other structures.
Models

View models at:

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Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11134-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0ACY1

PFAM (EcoliWiki Page)

PFAM:PF00881

RefSeq (EcoliWiki Page)

RefSeq:NP_416279

ModBase (EcoliWiki Page)

ModBase:P0ACY1


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Notes

Links

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NameURLComments
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Categories

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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)

ydjA-selD-topB

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Figure courtesy of RegulonDB
Figure courtesy of RegulonDB

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

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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gbrowse_img.php?coord=1846680..1846720&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&width=400&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression

Allele NameMutationPhenotypeReference
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Expression Studies

TypeReferenceNotes

microarray

GenExpDB:b1765 (EcoliWiki Page)

Summary of data for ydjA from multiple microarray studies

microarray

GEO Profiles:b1765 (EcoliWiki Page)

NCBI GEO profiles for ydjA

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (1846624..1846907) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ13; Well:B3[9]

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Notes

Accessions Related to ydjA Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11134

EchoBASE (EcoliWiki Page)

EchoBASE:EB1124

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b1765

EcoGene (EcoliWiki Page)

EcoGene:EG11134

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Notes

Links

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NameURLComments
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Categories

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Evolution

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Homologs in Other Organisms

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OrganismHomologs (Statistics)Comments

Xenopus tropicalis

  • ENSXETP00000047181 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YDJA

From SHIGELLACYC

E. coli O157

YDJA

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00881

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Notes

Links

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NameURLComments
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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 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 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. ↑ Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
  5. ↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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