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Gene |

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Expression|

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Standard Name	yafN
Gene Synonym(s)	ECK0233, b0232, JW0222^[1], JW0222
Product Desc.	conserved hypothetical protein with a possible role in spontaneous mutagenesis^[2]^[3] RelB antitoxin homolog, function unknown; no adjacent RelE-like cognate toxin gene; yafO may be a toxin affected by yafN.^[4]
Product Synonyms(s)	predicted antitoxin of the YafO-YafN toxin-antitoxin system^[1], B0232^[2]^[1], YafN^[2]^[1] , ECK0233, JW0222, b0232
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yafN^[2]
Regulation/Activity
Quick Links
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Notes

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YafN is an StbD homolog and a distant homolog of DnaT. Cognate toxin may have been deleted. LexA regulon. dinB-yafNOP operon. The phenotype of some dinB alleles to reduce spontaneous mutations may be due to polarity effects. LexA regulon.^[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	yafN
Mnemonic	Systematic nomenclature
Synonyms	ECK0233, b0232, JW0222^[1], JW0222
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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	5.43 minutes	MG1655: 252005..252298 <gbrowseImage> name=NC_000913:252005..252298 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 256568..256861 <gbrowseImage> name=NC_012967:256568..256861 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 252004..252297 <gbrowseImage> name=NC_012759:252004..252297 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 252005..252298 <gbrowseImage> name=NC_007779:252005..252298 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 226109..226402 <gbrowseImage> name=NC_010473:226109..226402 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

yafN(del) (Keio:JW0222)

deletion

PMID:16738554

Shigen

CGSC8457^[5]

yafN750(del)::kan

PMID:16738554

CGSC:103508

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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
JW0222	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCATCGAATTCTCGCTGAAAA Primer 2:CCTTCCTTAAAGTCATTGAAATC
8F9	Kohara Phage	Genobase	PMID:3038334
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 48% ^[6] Synonyms:zae-502::Tn10
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 77% ^[6]
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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:G6116	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002736	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944920	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2945	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000793	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	YafN
Synonyms	predicted antitoxin of the YafO-YafN toxin-antitoxin system^[1], B0232^[2]^[1], YafN^[2]^[1] , ECK0233, JW0222, b0232
Product description	conserved hypothetical protein with a possible role in spontaneous mutagenesis^[2]^[3] RelB antitoxin homolog, function unknown; no adjacent RelE-like cognate toxin gene; yafO may be a toxin affected by yafN.^[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:0005515	protein binding	PMID:16606699	IPI: Inferred from Physical Interaction	UniProtKB:P0A717	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	PMID:19943910	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0044092	negative regulation of molecular function	PMID:19617347	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		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	Notes	References	Evidence
Protein	prs		PMID:16606699	Experiment(s):EBI-1135968
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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 MHRILAEKSV NITELRKNPA KYFIDQPVAV LSNNRPAGYL LSASAFEALM DMLAEQEEKK PIKARFRPSA ARLEEITRRA EQYLNDMTDD DFNDFKE
Length	97
Mol. Wt	11.233 kDa
pI	5.3 (calculated)
Extinction coefficient	4,470 (calc based on 3 Y, 0 W, and 0 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	7..79	PF02604 Phd_YefM		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=yafN 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:16128218	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944920	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000793	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q47156	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6116	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13151	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944920	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2945	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	311	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	128	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	261	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)
yafN
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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_000913:251985..252025 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:b0232 (EcoliWiki Page)	NCBI GEO profiles for yafN
microarray	GenExpDB:b0232 (EcoliWiki Page)	Summary of data for yafN 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 (251877..252017) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:E11^[7]
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Notes

Accessions Related to yafN Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6116	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2945	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0232
EcoGene	EcoGene:EG13151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002736	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000793	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	YAFN	From SHIGELLACYC
E. coli O157	YAFN	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)	PF02604 Phd_YefM
EcoCyc	EcoCyc:G6116	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13151	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002736	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2945	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000793	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 ^2.6 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yafN: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 yafN Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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