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Gene |

Product(s) |

Expression|

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References |

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Standard Name	ubiH
Gene Synonym(s)	ECK2902, b2907, JW2875, visB, acd^[1], acd
Product Desc.	OCTAPRENYL-METHOXYPHENOL-OH^[2]^[3] 2-octaprenyl-6-methoxyphenol hydroxylase; produces 2-octaprenyl-6-methoxy-1,4-benzoquinone^[4]
Product Synonyms(s)	2-octaprenyl-6-methoxyphenol hydroxylase, FAD/NAD(P)-binding^[1], B2907^[2]^[1], Acd^[2]^[1], VisB^[2]^[1], UbiH^[2]^[1] , acd, ECK2902, JW2875, visB, b2907
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): visC^[2]
Regulation/Activity
Quick Links
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Notes

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visC, ubiH, ubiF and mhpA are paralogs.^[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	ubiH
Mnemonic	Ubiquinone
Synonyms	ECK2902, b2907, JW2875, visB, acd^[1], acd
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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	65.75 minutes	MG1655: 3051540..3050362 <gbrowseImage> name=NC_000913:3050362..3051540 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2939269..2938091 <gbrowseImage> name=NC_012967:2938091..2939269 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2937510..2938688 <gbrowseImage> name=NC_012759:2937510..2938688 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3052174..3050996 <gbrowseImage> name=NC_007779:3050996..3052174 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3145410..3144232 <gbrowseImage> name=NC_010473:3144232..3145410 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
ubiH(del) (Keio:JW2875)	deletion	deletion			PMID:16738554	Shigen CGSC10230^[5]
ubiH101						CGSC:7477
ubiH758(del)::kan					PMID:16738554	CGSC:103272
visB103			Sensitivity to	visible light (460nm)	PMID:1339425		Strains VS550 and VS551
visB(del)	deletion	deletion	Sensitivity to	visible light (460nm)	PMID:1339425		Strain VS560 and VS005
visB(del):KmR ubiA	deletion	deletion		not photosensitive	PMID:1339425		Strain VS561
ubiH758(del)::FRT	deletion		Mutagenesis Rate	Decrease in Stress Induced Mutagenesis (SIM)	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12260	The mutation caused a strong decrease in the level of SIM, over 90 percent decrease of the Wild Type levels. See Table S3 for full experimental results.
ubiH758(del)::FRT	deletion		Sensitivity to	Increase in SDS-EDTA sensitivity	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12260	SDS-EDTA sensitivity increased relative toward the wild type. See table S7 and S1 for a summary of experimental results.
SMR4562 yiaG-yfp FRTcatFRT ubiH758(del)::FRTKanFRT	Deletion		Sigma ^S activity	Decrease in Sigma^S activity	PMID:23224554	Parental Strain: SMR10582 Experimental Strain: SMR12686	See table S8 for full experimental strain
CAG45114 ubiH758(del)::FRTKanFRT	deletion		Sigma^E activity	Decrease in Sigma^E activity	PMID:23224554	Parental Strain: CAG45114 Experimental Strain: SMR15295	See table S11 for full experimental calculations.
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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
JW2875	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGTAATCATCGTCGGTGG Primer 2:CCACGCGCCACCCAACCGAGGGT
5E11	Kohara Phage	Genobase	PMID:3038334
10B4	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: % ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: 24% ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:EG11324	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11324	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001295	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947388	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1300	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009545	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	UbiH
Synonyms	2-octaprenyl-6-methoxyphenol hydroxylase, FAD/NAD(P)-binding^[1], B2907^[2]^[1], Acd^[2]^[1], VisB^[2]^[1], UbiH^[2]^[1] , acd, ECK2902, JW2875, visB, b2907
Product description	OCTAPRENYL-METHOXYPHENOL-OH^[2]^[3] 2-octaprenyl-6-methoxyphenol hydroxylase; produces 2-octaprenyl-6-methoxy-1,4-benzoquinone^[4]
EC number (for enzymes)	1.14.3.-^[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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004497	monooxygenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002938	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004497	monooxygenase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0503	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006744	ubiquinone biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010971	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006744	ubiquinone biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0831	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006979	response to oxidative stress	PMID:1339425	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010971	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010971	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002938	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010971	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006979	response to oxidative stress	PMID:1339425	IMP: Inferred from Mutant Phenotype		P	sensitive to paraquat	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
	GO:0009416	response to light stimulus	PMID:1339425	IMP: Inferred from Mutant Phenotype		P		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	References	Evidence
Protein	hldD	PMID:15690043	Experiment(s):EBI-883179
Protein	groL	PMID:16606699	Experiment(s):EBI-1144266
Protein	dnaJ	PMID:16606699	Experiment(s):EBI-1144266
Protein	paaE	PMID:16606699	Experiment(s):EBI-1144266
Protein	rho	PMID:16606699	Experiment(s):EBI-1144266
Protein	rfaD	PMID:19402753	MALDI(Z-score):41.254245
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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 MSVIIVGGGM AGATLALAIS RLSHGALPVH LIEATAPESH AHPGFDGRAI ALAAGTCQQL ARIGVWQSLA DCATAITTVH VSDRGHAGFV TLAAEDYQLA ALGQVVELHN VGQRLFALLR KAPGVTLHCP DRVANVARTQ SHVEVTLESG ETLTGRVLVA ADGTHSALAT ACGVDWQQEP YEQLAVIANV ATSVAHEGRA FERFTQHGPL AMLPMSDGRC SLVWCHPLER REEVLSWSDE KFCRELQSAF GWRLGKITHA GKRSAYPLAL THAARSITHR TVLVGNAAQT LHPIAGQGFN LGMRDVMSLA ETLTQAQERG EDMGDYGVLC RYQQRRQSDR EATIGVTDSL VHLFANRWAP LVVGRNIGLM TMELFTPARD VLAQRTLGWV AR
Length	392
Mol. Wt	42.286 kDa
pI	7.3 (calculated)
Extinction coefficient	45,950 - 46,950 (calc based on 5 Y, 7 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	1..345	PF01494 FAD 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=ubiH 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:16130809	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947388	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009545	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P25534	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11324	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11324	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947388	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001295	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1300	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	12.71+/-0.069	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.058998302	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	295	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	132	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	244	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)
visC
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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_000913:3051520..3051560 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:b2907 (EcoliWiki Page)	NCBI GEO profiles for ubiH
microarray	GenExpDB:b2907 (EcoliWiki Page)	Summary of data for ubiH 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 ubiH Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11324	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1300	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2907
EcoGene	EcoGene:EG11324	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001295	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009545	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	YGR255C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	UBIH	From SHIGELLACYC
E. coli O157	UBIH	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)	PF01494 FAD binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51905
Panther (EcoliWiki Page)	PTHR13789:SF27
EcoCyc	EcoCyc:EG11324	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11324	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001295	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1300	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009545	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 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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 ^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).

ubiH: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 ubiH Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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