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On One Page

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Expression|

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Standard Name	yafO
Gene Synonym(s)	ECK0234, b0233, JW0223^[1], JW0223
Product Desc.	conserved protein with a possible role in spontaneous mutagenesis; toxin of a putative toxin-antitoxin pair^[2]^[3] Possible toxin, function unknown^[4]
Product Synonyms(s)	predicted toxin of the YafO-YafN toxin-antitoxin system^[1], B0233^[2]^[1], YafO^[2]^[1] , ECK0234, JW0223, b0233
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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LexA regulon. dinB-yafNOP operon. The phenotype of some dinB alleles to reduce spontaneous mutations may be due to polarity effects on yafO. Overexpression causes filamentous biofilm formation and increased CV staining. Overexpression also reported to inhibit growth (Brown, 2003). YafN may be antitoxin for possible toxin YafO.^[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	yafO
Mnemonic	Systematic nomenclature
Synonyms	ECK0234, b0233, JW0223^[1], JW0223
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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	5.44 minutes	MG1655: 252301..252699 <gbrowseImage> name=NC_000913:252301..252699 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 256864..257262 <gbrowseImage> name=NC_012967:256864..257262 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 252300..252698 <gbrowseImage> name=NC_012759:252300..252698 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 252301..252699 <gbrowseImage> name=NC_007779:252301..252699 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 226405..226803 <gbrowseImage> name=NC_010473:226405..226803 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
yafO(del) (Keio:JW0223)	deletion	deletion			PMID:16738554	Shigen CGSC8458^[5]
yafO::Tn5KAN-I-SceI (FB20064)	Insertion at nt 300 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20064	does not contain pKD46
yafO::Tn5KAN-I-SceI (FB20065)	Insertion at nt 300 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20065	contains pKD46
yafO(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
yafO751(del)::kan					PMID:16738554	CGSC:103510
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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
JW0223	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGGGTATTCAAAACAAAACT Primer 2:CCAAAACGCATGCGAAACGCTTC
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: 78% ^[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:G6117	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13152	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002737	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944916	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2946	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000795	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	YafO
Synonyms	predicted toxin of the YafO-YafN toxin-antitoxin system^[1], B0233^[2]^[1], YafO^[2]^[1] , ECK0234, JW0223, b0233
Product description	conserved protein with a possible role in spontaneous mutagenesis; toxin of a putative toxin-antitoxin pair^[2]^[3] Possible toxin, function unknown^[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	Aspect	Notes	Status
	GO:0017148	negative regulation of translation	PMID:19617347	IDA: Inferred from Direct Assay	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043023	ribosomal large subunit binding	PMID:19617347	IDA: Inferred from Direct Assay	F	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	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 MRVFKTKLIR LQLTAEELDA LTADFISYKR DGVLPDIFGR DALYDDSFTW PLIKFERVAH IHLANENNPF PPQLRQFSRT NDEAHLVYCQ GAFDEQAWLL IAILKPEPHK LARDNNQMHK IGKMAEAFRM RF
Length	132
Mol. Wt	15.488 kDa
pI	7.6 (calculated)
Extinction coefficient	15,470 - 15,595 (calc based on 3 Y, 2 W, and 1 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
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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=yafO 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:16128219	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944916	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000795	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q47157	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6117	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13152	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944916	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002737	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2946	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	2.34+/-0.066	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.00879397	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	63	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	30	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	66	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_000913:252281..252321 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:b0233 (EcoliWiki Page)	NCBI GEO profiles for yafO
microarray	GenExpDB:b0233 (EcoliWiki Page)	Summary of data for yafO 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 yafO Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6117	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2946	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0233
EcoGene	EcoGene:EG13152	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002737	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000795	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	YAFO	From SHIGELLACYC
E. coli O157	YAFO	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
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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).

yafO: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 yafO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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