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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	lrhA
Gene Synonym(s)	ECK2283, b2289, JW2284, genR^[1], genR
Product Desc.	LrhA transcriptional repressor^[2]; LrhA transcriptional dual regulator^[3] Transcriptional repressor of flagellar and motility master regulator FlhDC; autoregulator; mutation confers lower RpoS levels, modulates rssB activity^[4]
Product Synonyms(s)	DNA-binding transcriptional repressor of flagellar, motility and chemotaxis genes^[1], B2289^[2]^[1], GenR^[2]^[1], LrhA^[2]^[1] , ECK2283, genR, JW2284, b2289
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lrhA^[2]
Regulation/Activity
Quick Links
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Notes

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LysR family. LhrA is upstream of the nuo operon, but is not part of the nuo operon and does not regulate the nuo operon.^[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	lrhA
Mnemonic	LysR homolog
Synonyms	ECK2283, b2289, JW2284, genR^[1], genR
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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	51.81 minutes	MG1655: 2404663..2403725 <gbrowseImage> name=NC_000913:2403725..2404663 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2350232..2349294 <gbrowseImage> name=NC_012967:2349294..2350232 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2289530..2290468 <gbrowseImage> name=NC_012759:2289530..2290468 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2411311..2410373 <gbrowseImage> name=NC_007779:2410373..2411311 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2496428..2495490 <gbrowseImage> name=NC_010473:2495490..2496428 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	Comments
ΔlrhA (Keio:JW2284)	deletion	deletion	PMID:16738554	Shigen
lrhA::Tn5KAN-2 (FB20751)	Insertion at nt 108 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20751	contains pKD46
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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
JW2284	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATAAGTGCAAATCGTCCGAT Primer 2:CCtTCGATATCCCTTTCAATCAA
9C2	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 61% ^[6] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[5]	est. P1 cotransduction: % ^[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:EG12123	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002026	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946769	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2044	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007555	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	LrhA
Synonyms	DNA-binding transcriptional repressor of flagellar, motility and chemotaxis genes^[1], B2289^[2]^[1], GenR^[2]^[1], LrhA^[2]^[1] , ECK2283, genR, JW2284, b2289
Product description	LrhA transcriptional repressor^[2]; LrhA transcriptional dual regulator^[3] Transcriptional repressor of flagellar and motility master regulator FlhDC; autoregulator; mutation confers lower RpoS levels, modulates rssB activity^[4]
EC number (for enzymes)
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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:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	PMID: 12123461	IDA: Inferred from Direct Assay		F		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 MISANRPIIN LDLDLLRTFV AVADLNTFAA AAAAVCRTQS AVSQQMQRLE QLVGKELFAR HGRNKLLTEH GIQLLGYARK ILRFNDEACS SLMFSNLQGV LTIGASDESA DTILPFLLNR VSSVYPKLAL DVRVKRNAYM AEMLESQEVD LMVTTHRPSA FKALNLRTSP THWYCAAEYI LQKGEPIPLV LLDDPSPFRD MVLATLNKAD IPWRLAYVAS TLPAVRAAVK AGLGVTARPV EMMSPDLRVL SGVDGLPPLP DTEYLLCYDP SSNNELAQVI YQAMESYHNP WQYSPMSAPE GDDSLLIERD IE
Length	312
Mol. Wt	34.594 kDa
pI	5.1 (calculated)
Extinction coefficient	32,890 - 33,390 (calc based on 11 Y, 3 W, and 4 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	References
Domain	95..288	PF03466 LysR substrate binding domain	PMID:19920124
Domain	13..72	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family	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=lrhA 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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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:16130224	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946769	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007555	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36771	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12123	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12123	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946769	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002026	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2044	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 MG1655	962	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	174	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	400	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)
lrhA
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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_000913:2404643..2404683 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	GenExpDB:b2289 (EcoliWiki Page)	Summary of data for lrhA from multiple microarray studies
microarray	PMID: 12123461	Microarray study in MG1655 and MG1655 lrhA-.
microarray	GEO Profiles:b2289 (EcoliWiki Page)	NCBI GEO profiles for lrhA
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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
Reporter		lrhA'-'lacZ	PMID: 12123461
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Notes

Accessions Related to lrhA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2044	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2289
EcoGene	EcoGene:EG12123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002026	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007555	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
Xenopus tropicalis	ENSXETP00000011052 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	LRHA	From SHIGELLACYC
E. coli O157	LRHA	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)	PF03466 LysR substrate binding domain
Pfam (EcoliWiki Page)	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
EcoCyc	EcoCyc:EG12123	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002026	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2044	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007555	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 ^1.9 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 ^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 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).

lrhA: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 lrhA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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