{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	idnD
Gene Synonym(s)	ECK4260, b4267, JW4224, yjgV^[1], yjgV
Product Desc.	IDONDEHYD- L-idonate 5-dehydrogenase^[2]
Product Synonyms(s)	L-idonate 5-dehydrogenase, NAD-binding^[1], B4267^[3]^[1], YjgV^[3]^[1], IdnD^[3]^[1] , ECK4260, JW4224, yjgV, b4267
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): idnDOTR^[3], idnD
Regulation/Activity
Quick Links
edit table

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

Notes

[back to top]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

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

Standard name	idnD
Mnemonic	Idonate
Synonyms	ECK4260, b4267, JW4224, yjgV^[1], yjgV
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	96.8 minutes	MG1655: 4492429..4491398 <gbrowseImage> name=NC_000913:4491398..4492429 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4477634..4476603 <gbrowseImage> name=NC_012967:4476603..4477634 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4430133..4431164 <gbrowseImage> name=NC_012759:4430133..4431164 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4499086..4498055 <gbrowseImage> name=NC_007779:4498055..4499086 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4594237..4593206 <gbrowseImage> name=NC_010473:4593206..4594237 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔidnD (Keio:JW4224)	deletion	deletion	PMID:16738554	Shigen CGSC11039^[4]
ΔidnD738::kan			PMID:16738554	CGSC:101528
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

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

Resource	Resource Type	Source	Notes/Reference
JW4224	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAGTGAAAACACAGTCCTG Primer 2:CCGAAAACAAGCTGGACTTTTGC
5C4	Kohara Phage	Genobase	PMID:3038334
E4D8	Kohara Phage	Genobase	PMID:3038334
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[4]	est. P1 cotransduction: 12% ^[5] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[4]	est. P1 cotransduction: % ^[5] Synonyms:zjj-202::Tn10, zji-202::Tn10
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12541	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004388	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944769	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2430	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013975	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	IdnD
Synonyms	L-idonate 5-dehydrogenase, NAD-binding^[1], B4267^[3]^[1], YjgV^[3]^[1], IdnD^[3]^[1] , ECK4260, JW4224, yjgV, b4267
Product description	IDONDEHYD- L-idonate 5-dehydrogenase^[2]
EC number (for enzymes)	1.1.1.264^[1]
edit table

Notes

Function

[back to top]

<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: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: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:0019521	D-gluconate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0311	P	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:0050572	L-idonate 5-dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.264	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: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
edit table

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

Partner Type	Partner	References	Evidence
Protein	lpdA	PMID:15690043	Experiment(s):EBI-890292
Protein	lysS	PMID:15690043	Experiment(s):EBI-895247
Protein	yecC	PMID:15690043	Experiment(s):EBI-895247
Protein	rplB	PMID:16606699	Experiment(s):EBI-1147786
Protein	ycgE	PMID:16606699	Experiment(s):EBI-1147786
Protein	lysS	PMID:19402753	LCMS(ID Probability):99.6
Protein	yecC	PMID:19402753	LCMS(ID Probability):99.6
edit table

</protect>

Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MQVKTQSCVV AGKKTVAVTE QTIDWNNNGT LVQITRGGIC GSDLHYYQEG KVGNFMIKAP MVLGHEVIGK VIHSDSSELH EGQTVAINPS KPCGHCKYCI EHNENQCTDM RFFGSAMYFP HVDGGFTRYK MVETSQCVPY PAKADEKVMA FAEPLAVAIH AAHQAGELQG KRVFISGVGP IGCLIVSAVK TLGAAEIVCA DVSPRSLSLG KEMGADVLVN PQNDDMDHWK AEKGYFDVSF EVSGHPSSVN TCLEVTRARG VMVQVGMGGA MAEFPMMTLI GKEISLRGSF RFTSEFNTAV SWLANGVINP LPLLSAEYPF TDLEEALRFA GDKTQAAKVQ LVF
Length	343
Mol. Wt	37.145 kDa
pI	6.3 (calculated)
Extinction coefficient	28,420 - 29,670 (calc based on 8 Y, 3 W, and 10 C residues)
edit table

Domains/Motifs/Modification Sites

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

Type	Residues	Description	References
Domain	180..305	PF00107 Zinc-binding dehydrogenase	PMID:19920124
Domain	27..140	PF08240 Alcohol dehydrogenase GroES-like domain	PMID:19920124
edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

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

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16132089	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944769	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013975	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39346	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12541	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944769	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004388	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2430	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	8^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	9	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	1^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
idnDOTR
edit table

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

[back to top]

<protect><gbrowseImage> name=NC_000913:4492409..4492449 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

[back to top]

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

Allele Name	Mutation	Phenotype	Reference
edit table

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

Type	Reference	Notes
microarray	GEO Profiles:b4267 (EcoliWiki Page)	NCBI GEO profiles for idnD
microarray	GenExpDB:b4267 (EcoliWiki Page)	Summary of data for idnD from multiple microarray studies
edit table

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

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to idnD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7893	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2430	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4267
EcoGene	EcoGene:EG12541	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004388	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013975	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

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

Organism	Homologs (Statistics)	Comments
Macaca mulatta	ENSMMUP00000021010 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014201 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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:G7893	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12541	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004388	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2430	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013975	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^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
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

idnD:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to idnD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search