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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	yfaY
Gene Synonym(s)	ECK2242, b2249, JW2243^[1], cinA, cinA, JW2243
Product Desc.	conserved protein^[2]^[3] Function unknown^[4]
Product Synonyms(s)	conserved protein^[1], YfaY^[2]^[1], B2249^[2]^[1] , cinA, ECK2242, JW2243, b2249
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfaY^[2]
Regulation/Activity
Quick Links
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Notes

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YfaY is in the gephyrin/MoeA superfamily. YfaY is closely related to the competence damage protein CinA of B. subtilis.^[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	yfaY
Mnemonic	competence induced protein Systematic nomenclature
Synonyms	ECK2242, b2249, JW2243^[1], cinA, cinA, JW2243
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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	50.88 minutes, 50.88 minutes	MG1655: 2361655..2360453 <gbrowseImage> name=NC_000913:2360453..2361655 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2310146..2308944 <gbrowseImage> name=NC_012967:2308944..2310146 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2246258..2247460 <gbrowseImage> name=NC_012759:2246258..2247460 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2368303..2367101 <gbrowseImage> name=NC_007779:2367101..2368303 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2452643..2451441 <gbrowseImage> name=NC_010473:2451441..2452643 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
ΔyfaY (Keio:JW2243)	deletion	deletion	PMID:16738554	Shigen CGSC9809^[5]
ΔyfaY730::kan			PMID:16738554	CGSC:104636
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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
JW2243	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTAAAAGTGGAAATGTTATC Primer 2:CCGACAGATAAGGTCATGGACTC
22C4	Kohara Phage	Genobase	PMID:3038334
4B4	Kohara Phage	Genobase	PMID:3038334
zfa-723::Tn10	Linked marker	CAG12178 gyrA+ = CGSC7526^[5]	est. P1 cotransduction: 54% ^[6] Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 33% ^[6] Synonyms:zej-223::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:G7162	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14087	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003738	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945478	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3840	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007441	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	YfaY
Synonyms	conserved protein^[1], YfaY^[2]^[1], B2249^[2]^[1] , cinA, ECK2242, JW2243, b2249
Product description	conserved protein^[2]^[3] 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	with/from	Aspect	Notes	Status
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001453	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020817	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	dacA	PMID:16606699	Experiment(s):EBI-1142331
Protein	accD	PMID:19402753	LCMS(ID Probability):99.4
Protein	yeiT	PMID:19402753	LCMS(ID Probability):99.6
Protein	yfbN	PMID:19402753	LCMS(ID Probability):99.3
Protein	entF	PMID:19402753	LCMS(ID Probability):99.0
Protein	galF	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):34.299260
Protein	gatD	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):35.871820
Protein	fmt	PMID:19402753	LCMS(ID Probability):99.4
Protein	emrA	PMID:19402753	LCMS(ID Probability):99.6
Protein	galU	PMID:19402753	MALDI(Z-score):36.264075
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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 MLKVEMLSTG DEVLHGQIVD TNAAWLADFF FHQGLPLSRR NTVGDNLDDL VTILRERSQH ADVLIVNGGL GPTSDDLSAL AAATAKGEGL VLHEAWLKEM ERYFHERGRV MAPSNRKQAE LPASAEFINN PVGTACGFAV QLNRCLMFFT PGVPSEFKVM VEHEILPRLR ERFSLPQPPV CLRLTTFGRS ESDLAQSLDT LQLPPGVTMG YRSSMPIIEL KLTGPASEQQ AMEKLWLDVK RVAGQSVIFE GTEGLPAQIS RELQNRQFSL TLSEQFTGGL LALQLSRAGA PLLACEVVPS QEETLAQTAH WITERRANHF AGLALAVSGF ENEHLNFALA TPDGTFALRV RFSTTRYSLA IRQEVCAMMA LNMLRRWLNG QDIASEHGWI EVVESMTLSV
Length	400
Mol. Wt	44.225 kDa
pI	5.6 (calculated)
Extinction coefficient	37,470 - 38,095 (calc based on 3 Y, 6 W, and 5 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	5..171	PF00994 Probable molybdopterin binding domain		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=yfaY 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:16130184	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945478	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007441	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77808	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7162	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14087	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945478	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003738	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3840	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	653	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	182	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	458	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)
yfaY
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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_000913:2361635..2361675 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:b2249 (EcoliWiki Page)	NCBI GEO profiles for yfaY
microarray	GenExpDB:b2249 (EcoliWiki Page)	Summary of data for yfaY 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 (2361578..2361832) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:H4^[7]
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Notes

Accessions Related to yfaY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7162	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3840	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2249
EcoGene	EcoGene:EG14087	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003738	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007441	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
Anopheles gambiae	ENSANGP00000029134 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000022956 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000021377 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YMR178W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	S2461	From SHIGELLACYC
E. coli O157	Z3507	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)	PF00994 Probable molybdopterin binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53218
EcoCyc	EcoCyc:G7162	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14087	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003738	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3840	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007441	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

yfaY: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 yfaY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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