gatD: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

gatD

Gene Synonym(s)

ECK2084, b2091, JW2075[1], JW2075

Product Desc.

Galactitol-1-phosphate dehydrogenase[2]

Product Synonyms(s)

galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding[1], B2091[3][1], GatD[3][1] , ECK2084, JW2075, b2091

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): gatYZABCD[3], OP00231

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

gatD

Mnemonic

Galactitol

Synonyms

ECK2084, b2091, JW2075[1], JW2075

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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

46.77 minutes 

MG1655: 2170897..2169857
<gbrowseImage> name=NC_000913:2169857..2170897 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2126235..2125195
<gbrowseImage> name=NC_012967:2125195..2126235 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2062340..2063380
<gbrowseImage> name=NC_012759:2062340..2063380 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2175010..2173970
<gbrowseImage> name=NC_007779:2173970..2175010 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2261905..2260865
<gbrowseImage> name=NC_010473:2260865..2261905 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

ΔgatD (Keio:JW2075)

deletion

deletion

PMID:16738554

Shigen
CGSC9695[4]

gatD::Tn5KAN-2 (FB20609)

Insertion at nt 479 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20609

contains pKD46

gatD::Tn5KAN-2 (FB20610)

Insertion at nt 479 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20610

does not contain pKD46

ΔgatD786::kan

PMID:16738554

CGSC:101106


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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

JW2075

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAAATCAGTGGTGAATGATAC

Primer 2:CCGGGAATGAGCAACACTTTGCC

1H4

Kohara Phage

Genobase

PMID:3038334

10H4

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: % [5]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: 81% [5]
Synonyms:zbc-3105::Tn10, zbd-3105::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:EG12417

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12417

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002277

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946598

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2316

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006924

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

GatD

Synonyms

galactitol-1-phosphate dehydrogenase, Zn-dependent and NAD(P)-binding[1], B2091[3][1], GatD[3][1] , ECK2084, JW2075, b2091

Product description

Galactitol-1-phosphate dehydrogenase[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005488

binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR016040

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0008868

galactitol-1-phosphate 5-dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.251

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002085

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002328

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013149

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

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

baeR

PMID:16606699

Experiment(s):EBI-1141898

Protein

mukB

PMID:16606699

Experiment(s):EBI-1141898

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1141898

Protein

rpsB

PMID:16606699

Experiment(s):EBI-1141898

Protein

groL

PMID:16606699

Experiment(s):EBI-1141898

Protein

glpD

PMID:16606699

Experiment(s):EBI-1141898

Protein

nadE

PMID:16606699

Experiment(s):EBI-1141898

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1141898

Protein

mrcA

PMID:16606699

Experiment(s):EBI-1141898

Protein

rplB

PMID:16606699

Experiment(s):EBI-1141898

Protein

topA

PMID:16606699

Experiment(s):EBI-1141898

Protein

yegQ

PMID:16606699

Experiment(s):EBI-1141898

Protein

barA

PMID:16606699

Experiment(s):EBI-1141898

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1141898

Protein

nuoG

PMID:16606699

Experiment(s):EBI-1141898
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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 

MKSVVNDTDG IVRVAESVIP EIKHQDEVRV KIASSGLCGS DLPRIFKNGA HYYPITLGHE
FSGYIDAVGS GVDDLHPGDA VACVPLLPCF TCPECLKGFY SQCAKYDFIG SRRDGGFAEY
IVVKRKNVFA LPTDMPIEDG AFIEPITVGL HAFHLAQGCE NKNVIIIGAG TIGLLAIQCA
VALGAKSVTA IDISSEKLAL AKSFGAMQTF NSSEMSAPQM QSVLRELRFN QLILETAGVP
QTVELAVEIA GPHAQLALVG TLHQDLHLTS ATFGKILRKE LTVIGSWMNY SSPWPGQEWE
TASRLLTERK LSLEPLIAHR GSFESFAQAV RDIARNAMPG KVLLIP
Length

346

Mol. Wt

37.39 kDa

pI

6.4 (calculated)

Extinction coefficient

26,930 - 27,930 (calc based on 7 Y, 3 W, and 8 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

171..308

PF00107 Zinc-binding dehydrogenase

PMID:19920124

Domain

25..131

PF08240 Alcohol dehydrogenase GroES-like 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=gatD 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:16130029

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946598

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006924

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9S3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12417

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12417

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946598

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002277

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2316

Escherichia coli str. K-12 substr. MG1655

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Notes

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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 MC4100

5.82E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

643

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

2360

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

465

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)

gatYZABCD

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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_000913:2170877..2170917 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:b2091 (EcoliWiki Page)

NCBI GEO profiles for gatD

microarray

GenExpDB:b2091 (EcoliWiki Page)

Summary of data for gatD 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 gatD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12417

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2316

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2091

EcoGene

EcoGene:EG12417

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002277

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006924

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

Apis mellifera

  • ENSAPMP00000025434 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000021010 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Shigella flexneri

GATD

From SHIGELLACYC

E. coli O157

GATD

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)

PF00107 Zinc-binding dehydrogenase

Superfamily (EcoliWiki Page)

SUPERFAMILY:50129

Superfamily (EcoliWiki Page)

SUPERFAMILY:51735

Pfam (EcoliWiki Page)

PF08240 Alcohol dehydrogenase GroES-like domain

EcoCyc

EcoCyc:EG12417

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12417

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002277

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2316

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006924

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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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