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Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

glgX

Gene Synonym(s)

ECK3417, b3431, JW3394[1]

Product Desc.

EG10381[2][3]

Glycogen debranching enzyme[4]

Product Synonyms(s)

glycogen debranching enzyme[1], B3431[2][1], GlgX[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s):

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(glgX)    Textpresso(glgX)

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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

glgX

Mnemonic

Glycogen

Synonyms

ECK3417, b3431, JW3394[1]

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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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

76.89 minutes 

MG1655: 3569342..3567369
gbrowse_img.php?coord=3567369..3569342&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3502773..3500800
gbrowse_img.php?coord=3500800..3502773&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4069096..4071069
gbrowse_img.php?coord=4069096..4071069&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3667087..3665114
gbrowse_img.php?coord=3665114..3667087&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3455863..3457836
gbrowse_img.php?coord=3455863..3457836&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔglgX (Keio:JW3394)

deletion

deletion

PMID:16738554

Shigen
CGSC10527[5]

glgX::Tn5KAN

PMID:12519969

ASAP

At position 1449 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB21201

glgX::Tn5KAN

PMID:12519969

ASAP

At position 1449 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21202

ΔglgX764::kan

PMID:16738554

CGSC:101148


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3394

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACACAACTCGCCATTGGCAA

Primer 2:CCTCTCTGGAACACACACAATCC

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[5]

est. P1 cotransduction: 87% [6]
Synonyms:zhg-3086::Tn10, zhh-21::Tn10

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: 41% [6]
Synonyms:zhf-50::Tn10, zhf-5::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10381

EchoBASE (EcoliWiki Page)

EchoBASE:EB0376

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3431

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4218

EcoGene (EcoliWiki Page)

EcoGene:EG10381

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:GLGX

ASAP (EcoliWikiPage)

ASAP:ABE-0011206


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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

GlgX

Synonyms

glycogen debranching enzyme[1], B3431[2][1], GlgX[2][1]

Product description

EG10381[2][3]

Glycogen debranching enzyme[4]

EC number (for enzymes)
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Notes

Function

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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0003824

catalytic activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047
InterPro:IPR013780

F

Seeded from EcoCyc [7]

complete

GO:0004133

glycogen debranching enzyme activity

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR011837
HAMAP:MF_01248

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004193
InterPro:IPR011837

F

Seeded from EcoCyc [7]

complete

GO:0005975

carbohydrate metabolic process

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004193
InterPro:IPR006047
InterPro:IPR013780
SP_KW:KW-0119

P

Seeded from EcoCyc [7]

complete

GO:0005977

glycogen metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0321

P

Seeded from EcoCyc [7]

complete

GO:0005980

glycogen catabolic process

GO_REF:0000002
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR011837
HAMAP:MF_01248

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0008152

metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc [7]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc [7]

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc [7]

complete

GO:0043169

cation binding

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047
InterPro:IPR013780

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016052

carbohydrate catabolic process

P

Seeded from Riley et al 2006 [1].

required fields missing

GO:0000271

polysaccharide biosynthetic process

P

Seeded from Riley et al 2006 [1].

required fields missing

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

Partner TypePartnerNotesReferencesEvidence

Protein

groL

PMID:16606699

Experiment(s):EBI-1145878

Protein

sprT

PMID:16606699

Experiment(s):EBI-1145878

Protein

rplN

PMID:16606699

Experiment(s):EBI-1145878

Protein

trpE

PMID:16606699

Experiment(s):EBI-1145878

Protein

ygjQ

PMID:16606699

Experiment(s):EBI-1145878

Protein

aceB

PMID:16606699

Experiment(s):EBI-1145878

Protein

yhhX

PMID:16606699

Experiment(s):EBI-1145878

Protein

waaU

PMID:16606699

Experiment(s):EBI-1145878

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MTQLAIGKPA PLGAHYDGQG VNFTLFSAHA ERVELCVFDA NGQEHRYDLP GHSGDIWHGY
LPDARPGLRY GYRVHGPWQP AEGHRFNPAK LLIDPCARQI DGEFKDNPLL HAGHNEPDYR
DNAAIAPKCV VVVDHYDWED DAPPRTPWGS TIIYEAHVKG LTYLHPEIPV EIRGTYKALG
HPVMINYLKQ LGITALELLP VAQFASEPRL QRMGLSNYWG YNPVAMFALH PAYACSPETA
LDEFRDAIKA LHKAGIEVIL DIVLNHSAEL DLDGPLFSLR GIDNRSYYWI REDGDYHNWT
GCGNTLNLSH PAVVDYASAC LRYWVETCHV DGFRFDLAAV MGRTPEFRQD APLFTAIQNC
PVLSQVKLIA EPWDIAPGGY QVGNFPPLFA EWNDHFRDAA RRFWLHYDLP LGAFAGRFAA
SSDVFKRNGR LPSAAINLVT AHDGFTLRDC VCFNHKHNEA NGEENRDGTN NNYSNNHGKE
GLGGSLDLVE RRRDSIHALL TTLLLSQGTP MLLAGDEHGH SQHGNNNAYC QDNQLTWLDW
SQASSGLTAF TAALIHLRKR IPALVENRWW EEGDGNVRWL NRYAQPLSTD EWQNGPKQLQ
ILLSDRFLIA INATLEVTEI VLPAGEWHAI PPFAGEDNPV ITAVWQGPAH GLCVFQR
Length

657

Mol. Wt

73.577 kDa

pI

6.1 (calculated)

Extinction coefficient

140,260 - 141,760 (calc based on 24 Y, 19 W, and 12 C residues)

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Domains/Motifs/Modification Sites

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

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10381-MONOMER

UniProt (EcoliWiki Page)

UniProt:P15067

PFAM (EcoliWiki Page)

PFAM:PF02922

RefSeq (EcoliWiki Page)

RefSeq:NP_417889


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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
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Figure courtesy of RegulonDB

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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gbrowse_img.php?coord=3569322..3569362&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b3431 (EcoliWiki Page)

NCBI GEO profiles for glgX

microarray

GenExpDB:b3431 (EcoliWiki Page)

Summary of data for glgX from multiple microarray studies

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

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to glgX Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10381

EchoBASE (EcoliWiki Page)

EchoBASE:EB0376

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3431

EcoGene (EcoliWiki Page)

EcoGene:EG10381


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Notes

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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.

OrganismHomologs (Statistics)Comments

Arabidopsis thaliana

  • AT2G39930 (score: 1.000; bootstrap: 99%)
  • AT4G09020 (score: 0.174)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000007671 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • O80403 (score: 1.000; bootstrap: 99%)
  • Q84L53 (score: 0.993)
  • Q8VWN0 (score: 0.818)
  • Q8W547 (score: 0.818)
  • Q7XA16 (score: 0.814)
  • Q8VWM3 (score: 0.813)
  • Q7XA15 (score: 0.812)
  • Q8LKZ7 (score: 0.807)
  • Q8VWM4 (score: 0.804)
  • O22637 (score: 0.796)
  • Q41742 (score: 0.784)
  • Q9XFG6 (score: 0.605)
  • Q8W546 (score: 0.290)
  • Q8LKZ6 (score: 0.255)
  • Q9XFG7 (score: 0.242)
  • Q84UE5 (score: 0.170)
  • Q6K4A4 (score: 0.169)
  • Q5FBD0 (score: 0.159)
  • Q8LKZ5 (score: 0.105)

From Inparanoid:20070104

Shigella flexneri

GLGX

From SHIGELLACYC

E. coli O157

GLGX

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02922


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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 2.2 2.3 2.4 2.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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