fadB:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3838, b3846, JW3822, oldB''<ref name='LIB:Riley_2006'/>
''ECK3838, b3846, JW3822, oldB''<ref name='LIB:Riley_2006'/>, oldB''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="K46aa0069efc01"  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="K46aa0069efc01"  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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10279 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10279 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4025805|4029994|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4025805|4029994|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|4026805|4028994|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4026805|4028994|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10279 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10279 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3916474|NC_3918663|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3916474|3918663|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3916474|NC_3918663|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3916474|3918663|FASTA Dump}}  
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W3110: 3605710..3607899<br /><gbrowseImage>
W3110: 3605710..3607899<br /><gbrowseImage>
name=AC_000091:3605710..3607899
name=NC_007779:3605710..3607899
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3604710|3608899|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3604710|3608899|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3605710|3607899|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3605710|3607899|FASTA Dump}}  
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{{GBrowseLink|ecoli_DH10B|NC_010473|4121347|4132292|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4121347|4132292|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4121347|4132292|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4121347|4132292|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="E46aa006ab4e0a"  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="E46aa006ab4e0a"  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="O46aa006b0b6ae"  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="O46aa006b0b6ae"  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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&Delta;fadB (Keio:JW3822)
''fadB(del)'' (Keio:JW3822)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109045 CGSC10764]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=109045 CGSC10764]<ref name='LIB:cgsc'/>  
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''&#916;fadB786::kan''
''fadB786(del)::kan''
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{|   id="Z4e04baad1ce3b"  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="Z4e04baad1ce3b"  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="C46aa006bc4fe3"  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="C46aa006bc4fe3"  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:CCAGCCGTTTTCAGGTCGCCAA  
Primer 2:CCAGCCGTTTTCAGGTCGCCAA  
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[[:Category:Kohara_Phage:9B11|9B11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=549 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:16G1|16G1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=550 Genobase]
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PMID:3038334
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{|   id="B46aa006c713dd"  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="B46aa006c713dd"  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]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10279 EcoCyc:EG10279]
EcoCyc:EG10279
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0275 EchoBASE:EB0275]
EcoGene:EG10279
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3846 EcoliGenExpDB:b3846]
RegulonDB:ECK120000273
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4793 ECOL199310CYC:C4793]
[http://www.ncbi.nlm.nih.gov/gene?term=948336 GeneID:948336]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10279 EcoGene:EG10279]
EchoBASE:EB0275
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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=FADB ECOO157CYC:FADB]
ASAP:ABE-0012564
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/793 CGSC:793]
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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=0012564&formSubmitReturn=1 ASAP:ABE-0012564]
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{|   id="Q46a71a3fc2291"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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Latest revision as of 20:50, 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

fadB

Mnemonic

Fatty acid degradation

Synonyms

ECK3838, b3846, JW3822, oldB[1], oldB

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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

86.79 minutes 

MG1655: 4028994..4026805
<gbrowseImage> name=NC_000913:4026805..4028994 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4009344..4007155
<gbrowseImage> name=NC_012967:4007155..4009344 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3916474..3918663
<gbrowseImage> name=NC_012759:3916474..3918663 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3605710..3607899
<gbrowseImage> name=NC_007779:3605710..3607899 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4127914..4125725
<gbrowseImage> name=NC_010473:4125725..4127914 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

4026805

Edman degradation

PMID:2191949[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

fadB(del) (Keio:JW3822)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC10764[4]

fadB786(del)::kan

PMID:16738554[3]

CGSC:100778


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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

JW3822

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCCTTTACAAAGGCGACACCCT

Primer 2:CCAGCCGTTTTCAGGTCGCCAA

9B11

Kohara Phage

Genobase

PMID:3038334[6]

16G1

Kohara Phage

Genobase

PMID:3038334[6]

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[4]

est. P1 cotransduction: 52% [7]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[4]

est. P1 cotransduction: 99% [7]
Synonyms:fadAB101::Tn10

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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:EG10279

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10279

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000273

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948336

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0275

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012564

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. ↑ Yang, SY et al. (1990) Nucleotide sequence of the fadA gene. Primary structure of 3-ketoacyl-coenzyme A thiolase from Escherichia coli and the structural organization of the fadAB operon. J. Biol. Chem. 265 10424-9 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. ↑ 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. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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