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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	bioD
Gene Synonym(s)	ECK0767, b0778, JW0761^[1], JW0761
Product Desc.	dethiobiotin synthetase subunit^[2]; dethiobiotin synthetase^[3]; Component of dethiobiotin synthetase^[2]^[3] Dethiobiotin synthase^[4]
Product Synonyms(s)	dethiobiotin synthetase^[1], B0778^[2]^[1], BioD^[2]^[1] , ECK0767, JW0761, b0778
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): bioBFCD^[2], OP00157
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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False positive lipoprotein prediction, verified amino terminus, Met is cleaved. BioD is 50% identical to paralog YnfK.^[4]

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	bioD
Mnemonic	Biotin
Synonyms	ECK0767, b0778, JW0761^[1], JW0761
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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	17.49 minutes	MG1655: 811493..812170 <gbrowseImage> name=NC_000913:811493..812170 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 804896..805573 <gbrowseImage> name=NC_012967:804896..805573 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 714461..715138 <gbrowseImage> name=NC_012759:714461..715138 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 812692..813369 <gbrowseImage> name=NC_007779:812692..813369 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 865421..866098 <gbrowseImage> name=NC_010473:865421..866098 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
Coding Start (SO:0000323)	MG1655	811496	Edman degradation	PMID:8289297
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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: Description	Reference	Availability	Comments
bioDE13A,D		E13A,D	Almost no change in activity			seeded from UniProt:P13000
bioDK16Q		K16Q	Complete loss of activity			seeded from UniProt:P13000
bioDK38L,Q,R		K38L,Q,R	Complete loss of activity			seeded from UniProt:P13000
bioDS42A,C		S42A,C	Almost no change in activity			seeded from UniProt:P13000
bioDT12V		T12V	24000-fold increase in KM(ATP); little or no change in the Kd(ATP), KM(DAPA) and DTBS Kcat; essential role for this residue in the steady-state affinity for ATP			seeded from UniProt:P13000
ΔbioD (Keio:JW0761)	deletion	deletion		PMID:16738554	Shigen CGSC8320^[5]
bioD19					CGSC:7573
bioD302					CGSC:66558
ΔbioD750::kan				PMID:16738554	CGSC:100200
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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
JW0761	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTAAACGTTATTTTGTCAC Primer 2:CCCAACAAGGCAAGGTTTATGTA
4H7	Kohara Phage	Genobase	PMID:3038334
3D4	Kohara Phage	Genobase	PMID:3038334
nadA57::Tn10	Linked marker	CAG12147 = CGSC7351^[5]	est. P1 cotransduction: 28% ^[6]
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: 72% ^[6] Synonyms:zbi-29::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:EG10120	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000116	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945387	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0118	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002650	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	BioD
Synonyms	dethiobiotin synthetase^[1], B0778^[2]^[1], BioD^[2]^[1] , ECK0767, JW0761, b0778
Product description	dethiobiotin synthetase subunit^[2]; dethiobiotin synthetase^[3]; Component of dethiobiotin synthetase^[2]^[3] Dethiobiotin synthase^[4]
EC number (for enzymes)	6.3.3.3^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00336	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004472	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004141	dethiobiotin synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00336	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004141	dethiobiotin synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004472	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004141	dethiobiotin synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:6.3.3.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00336	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004472	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	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:0009102	biotin biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00336	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004472	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0093	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009236	cobalamin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002586	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042242	cobyrinic acid a,c-diamide synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002586	F	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	Subunits of dethiobiotin synthetase	could be indirect
Protein	yghT		PMID:16606699	Experiment(s):EBI-1137938
Protein	groL		PMID:16606699	Experiment(s):EBI-1137938
Protein	dld		PMID:16606699	Experiment(s):EBI-1137938
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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 MSKRYFVTGT DTEVGKTVAS CALLQAAKAA GYRTAGYKPV ASGSEKTPEG LRNSDALALQ RNSSLQLDYA TVNPYTFAEP TSPHIISAQE GRPIESLVMS AGLRALEQQA DWVLVEGAGG WFTPLSDTFT FADWVTQEQL PVILVVGVKL GCINHAMLTA QVIQHAGLTL AGWVANDVTP PGKRHAEYMT TLTRMIPAPL LGEIPWLAEN PENAATGKYI NLALL
Length	225
Mol. Wt	24.139 kDa
pI	5.7 (calculated)
Extinction coefficient	37,930 - 38,180 (calc based on 7 Y, 5 W, and 2 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
Initiator Methionine	1	Removed	UniProt:P13000
Domain	5..217	PF01656 CobQ/CobB/MinD/ParA nucleotide binding 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=bioD 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:16128746	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945387	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002650	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P13000	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10120	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10120	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945387	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000116	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0118	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	Reference(s)
Protein	E. coli K-12 MC4100	6.64E+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	2362	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	675	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	2994	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
bioBFCD
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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_000913:811473..811513 source=MG1655 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:b0778 (EcoliWiki Page)	NCBI GEO profiles for bioD
microarray	GenExpDB:b0778 (EcoliWiki Page)	Summary of data for bioD 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 bioD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10120	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0118	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0778
EcoGene	EcoGene:EG10120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000116	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002650	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
Shigella flexneri	BIOD	From SHIGELLACYC
E. coli O157	BIOD	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)	PF01656 CobQ/CobB/MinD/ParA nucleotide binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
EcoCyc	EcoCyc:EG10120	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10120	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000116	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0118	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002650	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 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 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 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).

bioD: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 bioD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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