nikA:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12075 ECOCYC:EG12075]
EcoCyc:EG12075
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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://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12075 EcoGene:EG12075]
EcoGene:EG12075
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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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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120001981
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB2000
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0011354
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:30, 27 May 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

nikA

Mnemonic

Nickel

Synonyms

ECK3460, b3476, JW3441, hydC, hydD[1], hydD

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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

77.84 minutes 

MG1655: 3611690..3613264
<gbrowseImage> name=NC_000913:3611690..3613264 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3544355..3545929
<gbrowseImage> name=NC_012967:3544355..3545929 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3500184..3501758
<gbrowseImage> name=NC_012759:3500184..3501758 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4026748..4025174
<gbrowseImage> name=AC_000091:4025174..4026748 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3709435..3711009
<gbrowseImage> name=NC_010473:3709435..3711009 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

3611756

Edman degradation

PMID:7867647[2]


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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

ΔnikA (Keio:JW3441)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10553[4]

nikA::Tn5KAN-I-SceI (FB21228)

Insertion at nt 943 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB21228

contains pKD46

ΔnikA730::kan

PMID:16738554[3]

CGSC:102068


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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

JW3441

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCTCTCCACACTCCGCCGCAC

Primer 2:CCAGGTTTCACCGGTTTAATCTG

5F2

Kohara Phage

Genobase

PMID:3038334[7]

7H7

Kohara Phage

Genobase

PMID:3038334[7]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 47% [8]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

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

EcoCyc

EcoCyc:EG12075

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12075

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947981

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001981

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2000

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011354

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. ↑ de Pina, K et al. (1995) Purification and characterization of the periplasmic nickel-binding protein NikA of Escherichia coli K12. Eur. J. Biochem. 227 857-65 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  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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