hdeA:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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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

hdeA

Mnemonic

H-NS-determined expression

Synonyms

ECK3494, b3510, JW3478, yhhC, yhiB[1], yhiB

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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

78.76 minutes 

MG1655: 3654763..3654431
<gbrowseImage> name=NC_000913:3654431..3654763 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3586231..3585899
<gbrowseImage> name=NC_012967:3585899..3586231 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3542925..3543257
<gbrowseImage> name=NC_012759:3542925..3543257 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3983675..3984007
<gbrowseImage> name=NC_007779:3983675..3984007 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3752508..3752176
<gbrowseImage> name=NC_010473:3752176..3752508 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

Coding Start (SO:0000323)

MG1655

3654434

Edman degradation

PMID:8455549[2]
PMID:9298646[3]
PMID:9868784[4]


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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

ΔhdeA (Keio:JW3478)

deletion

deletion

PMID:16738554[5]

Shigen
CGSC10576[6]

hdeA::Tn5KAN-I-SceI (FB21247)

Insertion at nt 225 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB21247

does not contain pKD46

hdeA::Tn5KAN-I-SceI (FB21248)

Insertion at nt 225 in Plus orientation

PMID:15262929[7]

E. coli Genome Project:FB21248

contains pKD46

ΔhdeA765::kan

PMID:16738554[5]

CGSC:101328


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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

JW3478

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAAAAAAGTATTAGGCGTTAT

Primer 2:CCCATATCTTTCTTAATTTTGTC

4D9

Kohara Phage

Genobase

PMID:3038334[9]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[6]

est. P1 cotransduction: 3% [10]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[6]

est. P1 cotransduction: % [10]

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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:EG11398

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11398

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001364

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948025

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1370

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011464

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. Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. Yoshida, T et al. (1993) Function of the Escherichia coli nucleoid protein, H-NS: molecular analysis of a subset of proteins whose expression is enhanced in a hns deletion mutant. Mol. Gen. Genet. 237 113-22 PubMed
  3. Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. Wasinger, VC & Humphery-Smith, I (1998) Small genes/gene-products in Escherichia coli K-12. FEMS Microbiol. Lett. 169 375-82 PubMed
  5. 5.0 5.1 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
  6. 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. 7.0 7.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  8. 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
  9. Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  10. 10.0 10.1 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).

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