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Standard Name	nemR
Gene Synonym(s)	ECK1645, b1649, JW5874, ydhM^[1], JW5874, ydhM
Product Desc.	hypothetical protein^[2]; predicted DNA-binding transcriptional regulator^[3]. YdhM binding to the ydhM-nemA promoter is reduced by addition of NEM. Genomic SELEX identifies a binding site for YdhM in the ydhM-nemA promoter region. ^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B1649^[2]^[1], YdhM^[2]^[1] , ECK1645, JW5874, ydhM, b1649
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
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	nemR
Mnemonic	N-Ethylmaleimide
Synonyms	ECK1645, b1649, JW5874, ydhM^[1], JW5874, ydhM
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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	37.16 minutes	MG1655: 1724131..1724646 <gbrowseImage> name=NC_000913:1724131..1724646 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 1727821..1728336 <gbrowseImage> name=NC_007779:1727821..1728336 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
BW2952		NC_012759: 1616106..1616705 <gbrowseImage> name=NC_012759:1616106..1616705 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse(BW2952)	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
ΔydhM (Keio:JW5874)	deletion	deletion			PMID:16738554	Shigen
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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
JW5874	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGGGCTAAGCGAATTACTAAA Primer 2:CCAACGGCAGGCGTCGCAATAATct
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[5]	est. P1 cotransduction: % ^[6] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[5]	est. P1 cotransduction: 8% ^[6] Synonyms:zdh-925::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:G6889	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13947	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003478	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946166	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3705	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005514	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	YdhM
Synonyms	predicted DNA-binding transcriptional regulator^[1], B1649^[2]^[1], YdhM^[2]^[1] , ECK1645, JW5874, ydhM, b1649
Product description	hypothetical protein^[2]; predicted DNA-binding transcriptional regulator^[3]. YdhM binding to the ydhM-nemA promoter is reduced by addition of NEM. Genomic SELEX identifies a binding site for YdhM in the ydhM-nemA promoter region. ^[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. 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:IPR001647	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:18567656	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:18567656	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACS9	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:18567656	IDA: Inferred from Direct Assay		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	References	Evidence
Protein	kdsB	PMID:15690043	Experiment(s):EBI-890408
Protein	kdsB	PMID:19402753	LCMS(ID Probability):99.4
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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 MNKHTEHDTR EHLLATGEQL CLQRGFTGMG LSELLKTAEV PKGSFYHYFR SKEAFGVAML ERHYAAYHQR LTELLQSGEG NYRDRILAYY QQTLNQFCQH GTISGCLTVK LSAEVCDLSE DMRSAMDKGA RGVIALLSQA LENGRENHCL TFCGEPLQQA QVLYALWLGA NLQAKISRSF EPLENALAHV KNIIATPAV
Length	199
Mol. Wt	22.275 kDa
pI	3.5 (calculated)
Extinction coefficient	17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 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	13..59	PF00440 Bacterial regulatory proteins, tetR 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=nemR taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:145698269	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946166	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005514	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P67430	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6889	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13947	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946166	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003478	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3705	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	E. coli K-12 MG1655	90	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	27	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	58^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)
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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_000913:1724111..1724151 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:b1649 (EcoliWiki Page)	NCBI GEO profiles for ydhM
microarray	GenExpDB:b1649 (EcoliWiki Page)	Summary of data for ydhM 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 nemR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6889	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3705	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1649
EcoGene	EcoGene:EG13947	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003478	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005514	Escherichia coli str. K-12 substr. MG1655
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Links

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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	S1807	From SHIGELLACYC
E. coli O157	Z2666	From ECOO157CYC
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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)	PF00440 Bacterial regulatory proteins, tetR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46689
Superfamily (EcoliWiki Page)	SUPERFAMILY:48498
EcoCyc	EcoCyc:G6889	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13947	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003478	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3705	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005514	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 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 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 Umezawa, Y et al. (2008) The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. J. Bacteriol. 190 5890-7 PubMed
↑ ^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).

nemR: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 nemR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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