yhhK:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3443, b3459, JW3424, livL''<ref name='LIB:Riley_2006'/>
''ECK3443, b3459, JW3424, livL''<ref name='LIB:Riley_2006'/>, livL''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="P46a9f66c4468e"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a9f66c4468e"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655: 3596007..3596390<br /><gbrowseImage>
MG1655: 3596007..3596390<br /><gbrowseImage>
name=NC_000913:3596007..3596390
name=NC_000913:3596007..3596390
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12211 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12211 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3595007|3597390|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3595007|3597390|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3596007|3596390|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3596007|3596390|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12211 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12211 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3484501|NC_3484884|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3484501|3484884|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3484501|NC_3484884|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3484501|3484884|FASTA Dump}}  
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W3110: 4042431..4042048<br /><gbrowseImage>
W3110: 4042431..4042048<br /><gbrowseImage>
name=AC_000091:4042048..4042431
name=NC_007779:4042048..4042431
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|4041048|4043431|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4041048|4043431|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|4042048|4042431|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|4042048|4042431|FASTA Dump}}  
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DH10B: 3693752..3694135<br /><gbrowseImage>
DH10B: 3693752..3694135<br /><gbrowseImage>
name=NC_010473:3693752..3694135
name=NC_010473:3693752..3694135
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|3692986|3694901|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3692986|3694901|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3692986|3694901|FASTA Dump}}  
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{|   id="M46a9f66d05b0d"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9f66d05b0d"  class=" tableEdit Gene_sequence_features_table"   
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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="S46a9f66d4ed05"  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="S46a9f66d4ed05"  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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contains [[pKD46]]  
contains [[pKD46]]  
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''yhhK''::Tn''10''dCam
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR12134
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Mutation Rate was comparatively moderate, to other strains, with decrease only happening in 68-89% of wild type population.


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{|   id="K4e04ca61e3b47"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K4e04ca61e3b47"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="W46a9f66e0ff34"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9f66e0ff34"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCACACTTCTCCCAGCCGCCCTG  
Primer 2:CCACACTTCTCCCAGCCGCCCTG  
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[[:Category:Kohara_Phage:1B6|1B6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=613 Genobase]
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PMID:3038334
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****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="K46a9f66eacdfc"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9f66eacdfc"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|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]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2125 EchoBASE:EB2125]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3459 EcoliGenExpDB:b3459]
[http://www.ncbi.nlm.nih.gov/gene?term=947963 GeneID:947963]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C4251 ECOL199310CYC:C4251]
RegulonDB:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[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. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=YHHK ECOO157CYC:YHHK]
ASAP:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011296&formSubmitReturn=1 ASAP:ABE-0011296]
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{|   id="X46a7114d5f45b"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a7114d5f45b"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:47, 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

yhhK

Mnemonic

Systematic nomenclature

Synonyms

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

edit table


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=NC_007779:4042048..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.

edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


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).

Categories

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