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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	yfaS
Gene Synonym(s)	Note that this is a pseudogene in K12 strains., ECK2220, JW2221, JW2222, yfaR, b4500
Product Desc.	Note that this is a pseudogene in K12 strains. hypothetical protein^[1]; putative membrane protein^[1]; predicted protein, C-ter fragment^[2]; predicted protein, N-ter fragment^[2]
Product Synonyms(s)	YfaS^[1], YfaS_2^[1], B2227^[1], YfaR^[1], YfaS_1^[1], B2228^[1] , ECK2220, JW2221, JW2222, yfaR, b4500
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfaP^[1]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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This is a pseudogene in K12 strains.

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	yfaS
Mnemonic
Synonyms	Note that this is a pseudogene in K12 strains., ECK2220, JW2221, JW2222, yfaR, b4500
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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	50.17 minutes	MG1655: 2328305..2327820 <gbrowseImage> name=NC_000913:2327820..2328305 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2334953..2334468 <gbrowseImage> name=NC_007779:2334468..2334953 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
MG1655	50.18 minutes	MG1655: 2332424..2328321 <gbrowseImage> name=NC_000913:2328321..2332424 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 2339072..2334969 <gbrowseImage> name=NC_007779:2334969..2339072 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	FASTA Dump
MG1655		MG1655: 2332424..2327820 <gbrowseImage> name=NC_000913:2327820..2332424 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 2339072..2334468 <gbrowseImage> name=NC_007779:2334468..2339072 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	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	Reference	Availability
ΔyfaS782::kan	PMID:16738554	CGSC:104624
ΔyfaS781::kan	PMID:16738554	CGSC:104622
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
5A1	Kohara Phage	Genobase	PMID:3038334
4F12	Kohara Phage	Genobase	PMID:3038334
E13A5	Kohara Phage	Genobase	PMID:3038334
atoS298::Tn10	Linked marker	CAG12177 gyrA+ = CGSC7525^[3]	est. P1 cotransduction: 75% ^[4] Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
zfa-723::Tn10	Linked marker	CAG12178 gyrA+ = CGSC7526^[3]	est. P1 cotransduction: 60% ^[4] Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2228
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C2770
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:Z3481
ASAP (EcoliWikiPage)	ASAP:ABE-0007364
NCBI (EcoliWiki Page)	GeneID:1450231	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003732	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	YfaS
Synonyms	YfaS^[1], YfaS_2^[1], B2227^[1], YfaR^[1], YfaS_1^[1], B2228^[1] , ECK2220, JW2221, JW2222, yfaR, b4500
Product description	Note that this is a pseudogene in K12 strains. hypothetical protein^[1]; putative membrane protein^[1]; predicted protein, C-ter fragment^[2]; predicted protein, N-ter fragment^[2]
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:0004866	endopeptidase inhibitor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001599	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004866	endopeptidase inhibitor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002890	F	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	References	Evidence
Protein	gapA	PMID:16606699	Experiment(s):EBI-1142232
Protein	alaS	PMID:16606699	Experiment(s):EBI-1142232
Protein	bcsB	PMID:16606699	Experiment(s):EBI-1142232
Protein	fabA	PMID:16606699	Experiment(s):EBI-1142232
Protein	pepD	PMID:16606699	Experiment(s):EBI-1142232
Protein	rho	PMID:16606699	Experiment(s):EBI-1142232
Protein	ydbH	PMID:16606699	Experiment(s):EBI-1142232
Protein	ykgF	PMID:16606699	Experiment(s):EBI-1142232
Protein	yidF	PMID:16606699	Experiment(s):EBI-1142232
Protein	pldA	PMID:16606699	Experiment(s):EBI-1142232
Protein	udk	PMID:16606699	Experiment(s):EBI-1142232
Protein	rob	PMID:16606699	Experiment(s):EBI-1142232
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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
Length
Mol. Wt
pI
Extinction coefficient
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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
motif	1-38	UniProt Manual:Signal Peptides	UniProt:P76464
Domain	871..960	PF00207 Alpha-2-macroglobulin family		PMID:19920124
Domain	344..440	PF01835 MG2 domain		PMID:19920124
Domain	660..806	PF07703 Alpha-2-macroglobulin family N-terminal region		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=yfaS_1 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)	GeneID:1450231	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0007364	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0285101	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76464	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:1450231	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003732	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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)
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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)
yfaP
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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_000913:2328285..2328325 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:b2228 (EcoliWiki Page)	NCBI GEO profiles for yfaS_1
microarray	GenExpDB:b2228 (EcoliWiki Page)	Summary of data for yfaS_1 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 yfaS Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2228
RegulonDB	RegulonDB:ECK120003732	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	S2436	From SHIGELLACYC
E. coli O157	Z3481	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
Pfam (EcoliWiki Page)	PF00207 Alpha-2-macroglobulin family
Pfam (EcoliWiki Page)	PF01835 MG2 domain
Pfam (EcoliWiki Page)	PF07703 Alpha-2-macroglobulin family N-terminal region
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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 ^1.14 ^1.15 ^1.16 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^2.0 ^2.1 ^2.2 ^2.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 CGSC: The Coli Genetics Stock Center
↑ ^4.0 ^4.1 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).

yfaS: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 yfaS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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