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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12211 ECOCYC:EG12211]
[http://www.ncbi.nlm.nih.gov/gene?term=947963 GeneID:947963]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12211 EcoGene:EG12211]
EchoBASE:
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
[[ASAP]]
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[http://www.ncbi.nlm.nih.gov/gene?term=947963 GeneID:947963]
ASAP:
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:30, 27 May 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

yhhK

Mnemonic

Systematic nomenclature

Synonyms

ECK3443, b3459, JW3424, livL[1], livL

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Notes

Location(s) and DNA Sequence

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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

77.51 minutes 

MG1655: 3596007..3596390
<gbrowseImage> name=NC_000913:3596007..3596390 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3528658..3529041
<gbrowseImage> name=NC_012967:3528658..3529041 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3484501..3484884
<gbrowseImage> name=NC_012759:3484501..3484884 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4042431..4042048
<gbrowseImage> name=AC_000091:4042048..4042431 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3693752..3694135
<gbrowseImage> name=NC_010473:3693752..3694135 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

ΔyhhK (Keio:JW3424)

deletion

deletion

PMID:16738554[2]

Shigen

yhhK::Tn5KAN-I-SceI (FB21221)

Insertion at nt 109 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB21221

contains pKD46

yhhK::Tn10dCam

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[4]

Parental Strain: SMR4562

Experimental Strain: SMR12134

Mutation Rate was comparatively moderate, to other strains, with decrease only happening in 68-89% of wild type population.

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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

JW3424

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAGCTGACCATCATTCGATT

Primer 2:CCACACTTCTCCCAGCCGCCCTG

1B6

Kohara Phage

Genobase

PMID:3038334[6]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[7]

est. P1 cotransduction: 85% [8]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[7]

est. P1 cotransduction: % [8]

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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 (EcoliWiki Page)

GeneID:947963

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ 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
  3. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  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
  6. ↑ 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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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