pck:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

pck

Gene Synonym(s)

ECK3390, b3403, JW3366, pckA[1], pckA

Product Desc.

Phosphoenolpyruvate carboxykinase [ATP][2]

Product Synonyms(s)

phosphoenolpyruvate carboxykinase[1], B3403[3][1], Pck[3][1], PckA[3][1] , ECK3390, JW3366, pckA, b3403

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pck[3], OP00192

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

pck

Mnemonic

PEP carboxykinase

Synonyms

ECK3390, b3403, JW3366, pckA[1], pckA

</protect>

Notes

[4][5]

Location(s) and DNA Sequence

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<protect> 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

76.1 minutes 

MG1655: 3530840..3532462
<gbrowseImage> name=NC_000913:3530840..3532462 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3461502..3463124
<gbrowseImage> name=NC_012967:3461502..3463124 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3417997..3419619
<gbrowseImage> name=NC_012759:3417997..3419619 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4107598..4105976
<gbrowseImage> name=NC_007779:4105976..4107598 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3628585..3630207
<gbrowseImage> name=NC_010473:3628585..3630207 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

3530840

Edman degradation

PMID:1701430
PMID:9298646


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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

Δpck (Keio:JW3366)

deletion

deletion

PMID:16738554

Shigen
CGSC10508[6]

pckA::Tn5KAN-I-SceI (FB21164)

Insertion at nt 527 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21164

does not contain pKD46

pckA::Tn5KAN-I-SceI (FB21165)

Insertion at nt 527 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21165

contains pKD46

pckAD268N

D268N

In PCK51; altered-activity mutant that catalyzes the conversion from oxaloacetate to pyruvate (OAA decarboxylase activity)

seeded from UniProt:P22259

pckAG284S

G284S

In PCK53; shows reduced-activity

seeded from UniProt:P22259

ΔpckA::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

pck-2

CGSC:7428

pck-11

CGSC:7825

Δpck-737::kan

PMID:16738554

CGSC:102260


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Notes

Genetic Interactions

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<protect>

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

JW3366

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGCGTTAACAATGGTTTGAC

Primer 2:CCaAGTTTCGGACCAGCCGCTAC

2F6

Kohara Phage

Genobase

PMID:3038334

1C9

Kohara Phage

Genobase

PMID:3038334

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[6]

est. P1 cotransduction: 34% [7]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[6]

est. P1 cotransduction: 28% [7]
Synonyms:zhg-3086::Tn10, zhh-21::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:EG10688

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10688

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000681

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945667

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0682

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011106

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Pck

Synonyms

phosphoenolpyruvate carboxykinase[1], B3403[3][1], Pck[3][1], PckA[3][1] , ECK3390, JW3366, pckA, b3403

Product description

Phosphoenolpyruvate carboxykinase [ATP][2]

EC number (for enzymes)

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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0004611

phosphoenolpyruvate carboxykinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008210

F

Seeded from EcoCyc (v14.0)

complete

GO:0004611

phosphoenolpyruvate carboxykinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013035

F

Seeded from EcoCyc (v14.0)

complete

GO:0004612

phosphoenolpyruvate carboxykinase (ATP) activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00453

F

Seeded from EcoCyc (v14.0)

complete

GO:0004612

phosphoenolpyruvate carboxykinase (ATP) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001272

F

Seeded from EcoCyc (v14.0)

complete

GO:0004612

phosphoenolpyruvate carboxykinase (ATP) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015994

F

Seeded from EcoCyc (v14.0)

complete

GO:0004612

phosphoenolpyruvate carboxykinase (ATP) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.49

F

Seeded from EcoCyc (v14.0)

complete

GO:0005509

calcium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0106

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00453

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001272

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015994

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00453

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00453

P

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001272

P

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008210

P

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013035

P

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015994

P

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0312

P

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0016831

carboxy-lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0210

F

Seeded from EcoCyc (v14.0)

complete

GO:0017076

purine nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008210

F

Seeded from EcoCyc (v14.0)

complete

GO:0017076

purine nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013035

F

Seeded from EcoCyc (v14.0)

complete

GO:0006094

gluconeogenesis

PMID:6986370

TAS: Traceable Author Statement

P

complete

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1145805

Protein

metR

PMID:16606699

Experiment(s):EBI-1145805

Protein

yebT

PMID:16606699

Experiment(s):EBI-1145805

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

Cytoplasm

PMID:1701430

EchoLocation:pckA


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc

MRVNNGLTPQ ELEAYGISDV HDIVYNPSYD LLYQEELDPS LTGYERGVLT NLGAVAVDTG
IFTGRSPKDK YIVRDDTTRD TFWWADKGKG KNDNKPLSPE TWQHLKGLVT RQLSGKRLFV
VDAFCGANPD TRLSVRFITE VAWQAHFVKN MFIRPSDEEL AGFKPDFIVM NGAKCTNPQW
KEQGLNSENF VAFNLTERMQ LIGGTWYGGE MKKGMFSMMN YLLPLKGIAS MHCSANVGEK
GDVAVFFGLS GTGKTTLSTD PKRRLIGDDE HGWDDDGVFN FEGGCYAKTI KLSKEAEPEI
YNAIRRDALL ENVTVREDGT IDFDDGSKTE NTRVSYPIYH IDNIVKPVSK AGHATKVIFL
TADAFGVLPP VSRLTADQTQ YHFLSGFTAK LAGTERGITE PTPTFSACFG AAFLSLHPTQ
YAEVLVKRMQ AAGAQAYLVN TGWNGTGKRI SIKDTRAIID AILNGSLDNA ETFTLPMFNL
AIPTELPGVD TKILDPRNTY ASPEQWQEKA ETLAKLFIDN FDKYTDTPAG AALVAAGPKL
Length

540

Mol. Wt

59.644 kDa

pI

5.5 (calculated)

Extinction coefficient

74,830 - 75,455 (calc based on 17 Y, 9 W, and 5 C residues)


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Modification Site

250

phosphorylation site at S250

probability less than 75%

PMID:17938405

Modification Site

252

phosphorylation site at T252

probability less than 75%

PMID:17938405

Domain

19..493

PF01293 Phosphoenolpyruvate carboxykinase

PMID:19920124

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=pck taxon=562,83333 </beststructure>

Models

View models at:

</protect>

Structure figures

<protect>

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

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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 (Protein) (EcoliWiki Page)

GI:16131280

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945667

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011106

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P22259

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10688

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10688

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000681

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0682

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

7029

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

639

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2989

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

pck

Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3530820..3530860 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3403 (EcoliWiki Page)

NCBI GEO profiles for pck

microarray

GenExpDB:b3403 (EcoliWiki Page)

Summary of data for pck from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3529985..3530474) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:A10[8]

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Notes

Accessions Related to pck Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10688

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0682

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3403

EcoGene

EcoGene:EG10688

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000681

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011106

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT4G37870 (score: 1.000; bootstrap: 100%)
  • AT5G65690 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231108 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q7XAU8 (score: 1.000; bootstrap: 100%)
  • Q5KQS7 (score: 0.799)
  • P49292 (score: 0.789)
  • Q9XFA2 (score: 0.785)
  • Q9SLZ0 (score: 0.778)
  • Q8RV78 (score: 0.616)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YKR097W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

PCKA

From SHIGELLACYC

E. coli O157

PCKA

From ECOO157CYC


Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:53795

Superfamily (EcoliWiki Page)

SUPERFAMILY:68923

Pfam (EcoliWiki Page)

PF01293 Phosphoenolpyruvate carboxykinase

EcoCyc

EcoCyc:EG10688

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10688

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000681

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0682

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011106

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. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. 3.0 3.1 3.2 3.3 3.4 3.5 3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. Medina, V et al. (1990) Sequence of the pckA gene of Escherichia coli K-12: relevance to genetic and allosteric regulation and homology of E. coli phosphoenolpyruvate carboxykinase with the enzymes from Trypanosoma brucei and Saccharomyces cerevisiae. J. Bacteriol. 172 7151-6 PubMed
  5. Goldie, H & Medina, V (1990) Physical and genetic analysis of the phosphoenolpyruvate carboxykinase (pckA) locus from Escherichia coli K12. Mol. Gen. Genet. 220 191-6 PubMed
  6. 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  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).
  8. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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