tdcA: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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!|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=EG10989 ECOCYC:EG10989]
EcoCyc:EG10989
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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=EG10989 EcoGene:EG10989]
EcoGene:EG10989
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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:ECK120000978
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0982
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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-0010252
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:28, 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

tdcA

Mnemonic

Threonine dehydratase, catabolic

Synonyms

ECK3107, b3118, JW3089[1], JW3089

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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

70.35 minutes 

MG1655: 3265087..3264149
<gbrowseImage> name=NC_000913:3264149..3265087 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3200099..3199161
<gbrowseImage> name=NC_012967:3199161..3200099 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3151297..3152235
<gbrowseImage> name=NC_012759:3151297..3152235 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3266920..3265982
<gbrowseImage> name=AC_000091:3265982..3266920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3362832..3361894
<gbrowseImage> name=NC_010473:3361894..3362832 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

ΔtdcA (Keio:JW3089)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10353[3]

ΔtdcA::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938[4]

ΔtdcA::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔtdcA::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔtdcA::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔtdcA::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔtdcA734::kan

PMID:16738554[2]

CGSC:103110


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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

JW3089

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGCACTATTCTTCTTCCGAA

Primer 2:CCACCAACTTCTATTAATTGCCT

8F8

Kohara Phage

Genobase

PMID:3038334[6]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[3]

est. P1 cotransduction: 11% [7]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[3]

est. P1 cotransduction: 2% [7]
Synonyms:zgj-203::Tn10, zha-203::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:EG10989

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10989

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947494

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000978

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0982

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010252

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 4.3 4.4 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
  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 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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