aspA:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa0817e934a"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 4373007..4371571<br /><gbrowseImage>
W3110: 4373007..4371571<br /><gbrowseImage>
name=AC_000091:4371571..4373007
name=NC_007779:4371571..4373007
source=W3110
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preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|4370571|4374007|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|4371571|4373007|FASTA Dump}}  
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{|   id="M46aa0818b1171"  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="M46aa0818b1171"  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="Z46aa08190866b"  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="Z46aa08190866b"  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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{|   id="P4e04b7e14ea6b"  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="P4e04b7e14ea6b"  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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!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="R46aa081a73af4"  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="R46aa081a73af4"  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=EG10095 ECOCYC:EG10095]
EcoCyc:EG10095
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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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[[EcoGene]]
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EcoGene:EG10095
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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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10095 EcoGene:EG10095]
RegulonDB:ECK120000091
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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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[[EchoBASE]]
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EchoBASE:EB0093
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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-0013551
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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 20:51, 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

aspA

Mnemonic

Aspartate

Synonyms

ECK4133, b4139, JW4099[1], JW4099

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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

94.08 minutes, 94.08 minutes 

MG1655: 4366350..4364914
<gbrowseImage> name=NC_000913:4364914..4366350 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4347048..4345612
<gbrowseImage> name=NC_012967:4345612..4347048 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4303649..4305085
<gbrowseImage> name=NC_012759:4303649..4305085 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4373007..4371571
<gbrowseImage> name=NC_007779:4371571..4373007 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4466712..4465276
<gbrowseImage> name=NC_010473:4465276..4466712 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

4364917

Edman degradation

PMID:2987841[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

aspAK327R

K327R

Auxotrophies

Reduces activity by 99.7%. Increases KM for aspartic acid 5-fold

seeded from UniProt:P0AC38

aspAR29A

R29A

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 40-fold

seeded from UniProt:P0AC38

aspAK55R

K55R

Auxotrophies

Loss of activity

seeded from UniProt:P0AC38

aspAH124L

H124L

Auxotrophies

Reduces activity by 30%

seeded from UniProt:P0AC38

aspAS143G

S143G

Auxotrophies

Reduces Kcat by 90%. Increases KM for aspartic acid 4-fold

seeded from UniProt:P0AC38

aspAS143T

S143T

Auxotrophies

Reduces Kcat by 98.5%. Increases KM for aspartic acid 2-fold

seeded from UniProt:P0AC38

aspAD10A

D10A

Auxotrophies

Loss of activity

seeded from UniProt:P0AC38

aspAD10N

D10N

Auxotrophies

Reduces Kcal by 80%. Increases KM for aspartic acid 3-fold

seeded from UniProt:P0AC38

aspAR15A

R15A

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 2.5-fold

seeded from UniProt:P0AC38

aspAH26N

H26N

Auxotrophies

No effect on Kcat. Increases KM for aspartic acid 3-fold

seeded from UniProt:P0AC38

ΔaspA (Keio:JW4099)

deletion

deletion

Auxotrophies

PMID:16738554[3]

Shigen

CGSC8324[4]

aspA22

Auxotrophies

CGSC:5112

aspA23

Auxotrophies

CGSC:5113

ΔaspA765::kan

deletion

deletion

Auxotrophies

PMID:16738554[3]

CGSC:100110


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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

JW4099

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAAACAACATTCGTATCGA

Primer 2:CCtTGTTCGCTTTCATCAGTATA

5G7

Kohara Phage

Genobase

PMID:3038334[6]

9B1

Kohara Phage

Genobase

PMID:3038334[6]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[4]

est. P1 cotransduction: 76% [7]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[4]

est. P1 cotransduction: 4% [7]

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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:EG10095

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10095

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000091

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948658

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0093

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013551

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. ↑ Takagi, JS et al. (1985) Cloning and nucleotide sequence of the aspartase gene of Escherichia coli W. Nucleic Acids Res. 13 2063-74 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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