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Standard Name	ubiX
Gene Synonym(s)	ECK2305, b2311, JW2308, dedF^[1], dedF
Product Desc.	3-octaprenyl-4-hydroxybenzoate decarboxylase 2^[2]^[3] 3-octaprenyl-4-hydroxybenzoate carboxylyase; UbiD isozyme^[4]
Product Synonyms(s)	3-octaprenyl-4-hydroxybenzoate carboxy-lyase^[1], B2311^[2]^[1], DedF^[2]^[1], UbiX^[2]^[1] , dedF, ECK2305, JW2308, b2311
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cvpA-purF-ubiX^[2]
Regulation/Activity
Quick Links
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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	ubiX
Mnemonic	Ubiquinone
Synonyms	ECK2305, b2311, JW2308, dedF^[1], dedF
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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	52.29 minutes	MG1655: 2426648..2426079 <gbrowseImage> name=NC_000913:2426079..2426648 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2372218..2371649 <gbrowseImage> name=NC_012967:2371649..2372218 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2311884..2312453 <gbrowseImage> name=NC_012759:2311884..2312453 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2434072..2433503 <gbrowseImage> name=NC_007779:2433503..2434072 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2518413..2517844 <gbrowseImage> name=NC_010473:2517844..2518413 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ubiX(del) (Keio:JW2308)	deletion	deletion			PMID:16738554	Shigen CGSC9853^[5]
ubiX732(del)::kan					PMID:16738554	CGSC:103274
ubiX732(del)::FRTKanFRT			Mutagenesis rate	Decreased stress-induced mutagenesis (SIM) phenotype.	PMID:23224554	Parental Strain: SMR4562 Experimental Strain: SMR11967	Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
SMR4562 yiaG-yfp FRTcatFRT ubiX732(del)::FRTKanFRT	deletion		Sigma^S activity	Decrease in Sigma^S activity	PMID:23224554	Parental Strain: SMR:10582 Experimental Strain: SMR12699	See table S8 for full experimental results.
CAG45114 ubiX732(del)::FRTKanFRT	Deletion		Sigma^E activity	Decrease of Sigma^E activity	PMID:23224554	Parental strain: CAG45114 Experimental Strain: SMR15317	See table S11 for full experimental data.
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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
JW2308	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACGACTCATTGTAGGCAT Primer 2:CCTGCGCCCTGCCAGCGGGCAAA
9D2	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 22% ^[6] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[5]	est. P1 cotransduction: 3% ^[6] Synonyms:zfb-1::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:EG11044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001033	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949033	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1037	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007628	Escherichia coli str. K-12 substr. MG1655
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Notes

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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	UbiX
Synonyms	3-octaprenyl-4-hydroxybenzoate carboxy-lyase^[1], B2311^[2]^[1], DedF^[2]^[1], UbiX^[2]^[1] , dedF, ECK2305, JW2308, b2311
Product description	3-octaprenyl-4-hydroxybenzoate decarboxylase 2^[2]^[3] 3-octaprenyl-4-hydroxybenzoate carboxylyase; UbiD isozyme^[4]
EC number (for enzymes)	4.1.1.-^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
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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	References	Evidence
Protein	rplB	PMID:16606699	Experiment(s):EBI-1142527
Protein	rpsD	PMID:16606699	Experiment(s):EBI-1142527
Protein	groL	PMID:16606699	Experiment(s):EBI-1142527
Protein	ribB	PMID:16606699	Experiment(s):EBI-1142527
Protein	tyrA	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):39.963401
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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 MKRLIVGISG ASGAIYGVRL LQVLRDVTDI ETHLVMSQAA RQTLSLETDF SLREVQALAD VTHDARDIAA SISSGSFQTL GMVILPCSIK TLSGIVHSYT DGLLTRAADV VLKERRPLVL CVRETPLHLG HLRLMTQAAE IGAVIMPPVP AFYHRPQSLD DVINQTVNRV LDQFAITLPE DLFARWQGA
Length	189
Mol. Wt	20.694 kDa
pI	6.9 (calculated)
Extinction coefficient	9,970 - 10,220 (calc based on 3 Y, 1 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
Domain	2..123	PF02441 Flavoprotein		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=ubiX 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:16130246	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949033	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007628	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AG03	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11044	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949033	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001033	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1037	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	36.02+/-0.46	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.014059754	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	268	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	124	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	206	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)
cvpA-purF-ubiX
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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_000913:2426628..2426668 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:b2311 (EcoliWiki Page)	NCBI GEO profiles for ubiX
microarray	GenExpDB:b2311 (EcoliWiki Page)	Summary of data for ubiX 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
	GFP Fusion	Intergenic region (2426567..2426785) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ06; Well:B10^[7]
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Notes

Accessions Related to ubiX Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11044	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1037	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2311
EcoGene	EcoGene:EG11044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001033	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007628	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
Saccharomyces cerevisiae	YDR538W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	UBIX	From SHIGELLACYC
E. coli O157	UBIX	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)	PF02441 Flavoprotein
Superfamily (EcoliWiki Page)	SUPERFAMILY:52507
EcoCyc	EcoCyc:EG11044	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11044	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001033	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1037	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007628	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 ^1.11 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ubiX: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 ubiX Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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