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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	idnO
Gene Synonym(s)	ECK4259, b4266, JW4223, yjgU^[1], yjgU
Product Desc.	5-keto-D-gluconate 5-reductase^[2]^[3] 5-keto-D-gluconate 5-reductase^[4]
Product Synonyms(s)	5-keto-D-gluconate-5-reductase^[1], B4266^[2]^[1], YjgU^[2]^[1], IdnO^[2]^[1] , ECK4259, JW4223, yjgU, b4266
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): idnDOTR^[2], idnD
Regulation/Activity
Quick Links
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</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	idnO
Mnemonic	Idonate
Synonyms	ECK4259, b4266, JW4223, yjgU^[1], yjgU
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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	96.79 minutes, 96.79 minutes	MG1655: 4491374..4490610 <gbrowseImage> name=NC_000913:4490610..4491374 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4476579..4475815 <gbrowseImage> name=NC_012967:4475815..4476579 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4429345..4430109 <gbrowseImage> name=NC_012759:4429345..4430109 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4498031..4497267 <gbrowseImage> name=NC_007779:4497267..4498031 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4593182..4592418 <gbrowseImage> name=NC_010473:4592418..4593182 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability
ΔidnO (Keio:JW4223)	deletion	deletion	PMID:16738554	Shigen CGSC11038^[5]
ΔidnO737::kan			PMID:16738554	CGSC:101530
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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
JW4223	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACGATCTATTTTCACTGGC Primer 2:CCAACAGCCACTAACATGCCGCC
5C4	Kohara Phage	Genobase	PMID:3038334
E4D8	Kohara Phage	Genobase	PMID:3038334
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[5]	est. P1 cotransduction: 13% ^[6] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: % ^[6] Synonyms:zjj-202::Tn10, zji-202::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:G7892	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12540	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004387	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947109	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2429	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013971	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	IdnO
Synonyms	5-keto-D-gluconate-5-reductase^[1], B4266^[2]^[1], YjgU^[2]^[1], IdnO^[2]^[1] , ECK4259, JW4223, yjgU, b4266
Product description	5-keto-D-gluconate 5-reductase^[2]^[3] 5-keto-D-gluconate 5-reductase^[4]
EC number (for enzymes)	1.1.1.69^[1]
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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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	F	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:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008874	gluconate 5-dehydrogenase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.1.1.69	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002198	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020904	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	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:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002347	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
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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 MNDLFSLAGK NILITGSAQG IGFLLATGLG KYGAQIIIND ITAERAELAV EKLHQEGIQA VAAPFNVTHK HEIDAAVEHI EKDIGPIDVL VNNAGIQRRH PFTEFPEQEW NDVIAVNQTA VFLVSQAVTR HMVERKAGKV INICSMQSEL GRDTITPYAA SKGAVKMLTR GMCVELARHN IQVNGIAPGY FKTEMTKALV EDEAFTAWLC KRTPAARWGD PQELIGAAVF LSSKASDFVN GHLLFVDGGM LVAV
Length	254
Mol. Wt	27.562 kDa
pI	6.3 (calculated)
Extinction coefficient	20,970 - 21,345 (calc based on 3 Y, 3 W, and 3 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	10..177	PF00106 short chain dehydrogenase		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=idnO 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:16132088	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947109	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013971	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9P9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7892	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12540	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947109	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004387	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2429	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Ecoli K-12	3.147+/-0.092	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	50	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	19	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	24^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
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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)
idnDOTR
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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_000913:4491354..4491394 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

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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:b4266 (EcoliWiki Page)	NCBI GEO profiles for idnO
microarray	GenExpDB:b4266 (EcoliWiki Page)	Summary of data for idnO 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 idnO Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7892	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2429	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4266
EcoGene	EcoGene:EG12540	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004387	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013971	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	ENSAPMP00000030681 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000000813 (score: 1.000; bootstrap: 63%) ENSBTAP00000011525 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000019987 (score: 1.000; bootstrap: 75%) ENSCINP00000010325 (score: 0.069)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1498 (score: 1.000; bootstrap: 87%) ZDB-CDNA-040425-2432 (score: 1.000; bootstrap: 87%) ZDB-CDNA-040425-2431 (score: 0.315)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0186029 (score: 1.000; bootstrap: 64%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA20258-PA (score: 1.000; bootstrap: 64%) GA11451-PA (score: 0.050)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000012515 (score: 1.000; bootstrap: 81%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000014296 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000020810 (score: 1.000; bootstrap: 71%) ENSMODP00000004520 (score: 1.000; bootstrap: 73%) ENSMODP00000004616 (score: 0.429) ENSMODP00000004553 (score: 0.422) ENSMODP00000019429 (score: 0.057) ENSMODP00000019424 (score: 0.052)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000024782 (score: 1.000; bootstrap: 70%) ENSRNOP00000024484 (score: 0.385)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC17398c (score: 1.000; bootstrap: 98%) SPAC22A127c (score: 0.333) SPAC8E110 (score: 0.185)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000137832 (score: 1.000; bootstrap: 78%) NEWSINFRUP00000148738 (score: 0.126)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00005495001 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014202 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	Z1533	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF00106 short chain dehydrogenase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51735
EcoCyc	EcoCyc:G7892	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12540	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004387	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2429	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013971	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

idnO:On One Page

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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 idnO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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