rdgC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0388, b0393, JW0384, yaiD''<ref name='LIB:Riley_2006'/>
''ECK0388, b0393, JW0384, yaiD''<ref name='LIB:Riley_2006'/>, yaiD''


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9af0909c4b"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 409243..408332<br /><gbrowseImage>
W3110: 409243..408332<br /><gbrowseImage>
name=AC_000091:408332..409243
name=NC_007779:408332..409243
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|407332|410243|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|407332|410243|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|408332|409243|FASTA Dump}}  
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="I46a9af0a68e03"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46a9af0a68e03"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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rdgC
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deletion
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Sensitivity to
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increases sensitivity to bicyclomycin
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PMID:21357484
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mutation didn't affect sensitivity to any of 22 other antibiotics tested.
fig 2


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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:EG12158
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG12158
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[RegulonDB]]
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RegulonDB:ECK120002055
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''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]])
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[http://www.ncbi.nlm.nih.gov/gene?term=948585 GeneID:948585]
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Escherichia coli str. K-12 substr. MG1655
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[[EchoBASE]]
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EchoBASE:EB2078
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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-0001366
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:28, 19 September 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

rdgC

Mnemonic

Recombination-dependent growth

Synonyms

ECK0388, b0393, JW0384, yaiD[1], yaiD

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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

8.8 minutes 

MG1655: 409243..408332
<gbrowseImage> name=NC_000913:408332..409243 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 378442..377531
<gbrowseImage> name=NC_012967:377531..378442 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 311091..312002
<gbrowseImage> name=NC_012759:311091..312002 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 409243..408332
<gbrowseImage> name=NC_007779:408332..409243 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 348574..347663
<gbrowseImage> name=NC_010473:347663..348574 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

408332

Edman degradation

PMID:10368163[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

ΔrdgC (Keio:JW0384)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8560[4]

yaiD::Tn5KAN-I-SceI (FB20168)

Insertion at nt 339 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20168

does not contain pKD46

yaiD::Tn5KAN-I-SceI (FB20169)

Insertion at nt 339 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20169

contains pKD46

ΔyaiD::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[6]

ΔrdgC758::kan

PMID:16738554[3]

CGSC:102618

rdgC

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[7]

mutation didn't affect sensitivity to any of 22 other antibiotics tested. fig 2

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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

JW0384

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCCTGTGGTTCAAAAATTTAAT

Primer 2:CCACGTTGTGCTTCGCCACCTAA

6A12

Kohara Phage

Genobase

PMID:3038334[9]

9G9

Kohara Phage

Genobase

PMID:3038334[9]

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[4]

est. P1 cotransduction: 61% [10]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 42% [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:EG12158

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12158

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002055

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948585

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2078

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001366

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. ↑ Murphy, LD et al. (1999) Identification of two new proteins in spermidine nucleoids isolated from Escherichia coli. J. Bacteriol. 181 3842-4 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. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  6. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  7. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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. ↑ 9.0 9.1 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
  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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