glgX:On One Page

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

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Standard Name

glgX

Gene Synonym(s)

ECK3417, b3431, JW3394[1], JW3394

Product Desc.

EG10381[2][3]

Glycogen debranching enzyme[4]

Product Synonyms(s)

glycogen debranching enzyme[1], B3431[2][1], GlgX[2][1] , ECK3417, JW3394, b3431

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s):

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

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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], JW3394

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Notes

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

76.89 minutes 

MG1655: 3569342..3567369
<gbrowseImage> name=NC_000913:3567369..3569342 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3502773..3500800
<gbrowseImage> name=NC_012967:3500800..3502773 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3455863..3457836
<gbrowseImage> name=NC_012759:3455863..3457836 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4069096..4071069
<gbrowseImage> name=NC_007779:4069096..4071069 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3667087..3665114
<gbrowseImage> name=NC_010473:3665114..3667087 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

ΔglgX (Keio:JW3394)

deletion

deletion

PMID:16738554

Shigen
CGSC10527[5]

glgX::Tn5KAN-I-SceI (FB21201)

Insertion at nt 1449 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21201

contains pKD46

glgX::Tn5KAN-I-SceI (FB21202)

Insertion at nt 1449 in Minus orientation

PMID:15262929

E. coli Genome Project:FB21202

does not contain pKD46

ΔglgX764::kan

PMID:16738554

CGSC:101148


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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

JW3394

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACACAACTCGCCATTGGCAA

Primer 2:CCTCTCTGGAACACACACAATCC

16A5

Kohara Phage

Genobase

PMID:3038334

E5B4

Kohara Phage

Genobase

PMID:3038334

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.

Database Accession Notes

EcoCyc

EcoCyc:EG10381

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10381

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000374

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947941

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0376

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011206

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

GlgX

Synonyms

glycogen debranching enzyme[1], B3431[2][1], GlgX[2][1] , ECK3417, JW3394, b3431

Product description

EG10381[2][3]

Glycogen debranching enzyme[4]

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:0016052

carbohydrate catabolic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000271

polysaccharide biosynthetic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013780

F

Seeded from EcoCyc (v14.0)

complete

GO:0004133

glycogen debranching enzyme activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01248

F

Seeded from EcoCyc (v14.0)

complete

GO:0004133

glycogen debranching enzyme activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011837

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004193

F

Seeded from EcoCyc (v14.0)

complete

GO:0004553

hydrolase activity, hydrolyzing O-glycosyl compounds

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011837

F

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004193

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013780

P

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc (v14.0)

complete

GO:0005977

glycogen metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0321

P

Seeded from EcoCyc (v14.0)

complete

GO:0005980

glycogen catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01248

P

Seeded from EcoCyc (v14.0)

complete

GO:0005980

glycogen catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011837

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0016798

hydrolase activity, acting on glycosyl bonds

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

F

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006047

F

Seeded from EcoCyc (v14.0)

complete

GO:0043169

cation binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013780

F

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

P

complete

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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 Type Partner Notes References Evidence

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.

Compartment Description Evidence Reference/Source Notes
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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 

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.

Type Residues Description Notes References

Domain

11..97

PF02922 Carbohydrate-binding module 48 (Isoamylase N-terminal domain)

PMID:19920124

Domain

183..527

PF00128 Alpha amylase, catalytic domain

PMID:19920124

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<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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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:16131305

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947941

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011206

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P15067

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10381

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10381

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947941

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000374

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0376

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

47

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

180

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

85

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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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)
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Figure courtesy of RegulonDB

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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_000913:3569322..3569362 source=MG1655 flip=1 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

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

Type Reference Notes

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 Name Resource Type Description Source Notes
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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.

Database Accession Notes

EcoCyc

EcoCyc:EG10381

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0376

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3431

EcoGene

EcoGene:EG10381

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000374

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011206

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (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

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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

Pfam (EcoliWiki Page)

PF02922 Carbohydrate-binding module 48 (Isoamylase N-terminal domain)

Pfam (EcoliWiki Page)

PF00128 Alpha amylase, catalytic domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:51445

Panther (EcoliWiki Page)

PTHR10357:SF74

Superfamily (EcoliWiki Page)

SUPERFAMILY:81296

EcoCyc

EcoCyc:EG10381

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10381

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000374

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0376

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011206

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 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 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).

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