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Product(s) |

Expression|

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Standard Name	yagI
Gene Synonym(s)	ECK0273, b0272, JW0265^[1], JW0265
Product Desc.	putative regulator^[2]^[3] Function unknown, CP4-6 putative prophage remnant^[4]
Product Synonyms(s)	CP4-6 prophage; predicted DNA-binding transcriptional regulator^[1], B0272^[2]^[1], YagI^[2]^[1] , ECK0273, JW0265, b0272
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yagI^[2]
Regulation/Activity
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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	yagI
Mnemonic	Systematic nomenclature
Synonyms	ECK0273, b0272, JW0265^[1], JW0265
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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	6.2 minutes	MG1655: 288386..287628 <gbrowseImage> name=NC_000913:287628..288386 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 288386..287628 <gbrowseImage> name=NC_007779:287628..288386 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 263936..261732 <gbrowseImage> name=NC_010473:261732..263936 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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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	Comments
yagI(del) (Keio:JW0265)	deletion	deletion	PMID:16738554	Shigen
yagI::Tn5KAN-I-SceI (FB20111)	Insertion at nt 541 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20111	contains pKD46
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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
JW0265	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCGATTATTCAGTCTGTTGA Primer 2:CCGGCCGGGTAGCCCAGCGCGCG
3C7	Kohara Phage	Genobase	PMID:3038334
21C10	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 34% ^[6]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[5]	est. P1 cotransduction: % ^[6] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (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
EcoCyc	EcoCyc:G6144	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13349	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945016	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002764	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3133	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000933	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	YagI
Synonyms	CP4-6 prophage; predicted DNA-binding transcriptional regulator^[1], B0272^[2]^[1], YagI^[2]^[1] , ECK0273, JW0265, b0272
Product description	putative regulator^[2]^[3] Function unknown, CP4-6 putative prophage remnant^[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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005471	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P16528	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005471	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P16528	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	References	Evidence
Protein	puuE	PMID:16606699	Experiment(s):EBI-1136056
Protein	lacZ	PMID:16606699	Experiment(s):EBI-1136056
Protein	yjjK	PMID:16606699	Experiment(s):EBI-1136056
Protein	fdnG	PMID:16606699	Experiment(s):EBI-1136056
Protein	btuD	PMID:16606699	Experiment(s):EBI-1136056
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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 MPIIQSVERA LQILDLFNEQ ATELKITDIS KLMGLSKSTL HSLLKTLQLH GYIDQNPENG KYRLGMKLVE RGHFVVGSID IRQKAKGWLT ELSRRTGQTT HLGILDGREG VYIEKIEGKL AAIAYSRIGR RLPVHATAIG KVLIAWLGEA ELNALLEGYQ YTTFTPATLA SREALMSALA QTREQGYALD SEENEQGVRC VAVPVWNHES RVIAALSLST LTSRVDDAEL ANFREQLQQA GLALSRALGY PA
Length	252
Mol. Wt	27.838 kDa
pI	7.5 (calculated)
Extinction coefficient	28,420 - 28,545 (calc based on 8 Y, 3 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	References
Domain	120..247	PF01614 Bacterial transcriptional regulator	PMID:19920124
Domain	6..57	PF09339 IclR helix-turn-helix 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=yagI 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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Resource type	Source	Notes/Reference
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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:16128257	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000933	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77300	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6144	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13349	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945016	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002764	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3133	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	101	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	74	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	60^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)
yagI
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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_000913:288366..288406 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:b0272 (EcoliWiki Page)	NCBI GEO profiles for yagI
microarray	GenExpDB:b0272 (EcoliWiki Page)	Summary of data for yagI 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 (288312..288603) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:D3^[7]
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Notes

Accessions Related to yagI Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6144	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3133	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0272
EcoGene	EcoGene:EG13349	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002764	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000933	Escherichia coli str. K-12 substr. MG1655
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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
Xenopus tropicalis	ENSXETP00000011286 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
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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)	PF01614 Bacterial transcriptional regulator
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:55781
Pfam (EcoliWiki Page)	PF09339 IclR helix-turn-helix domain
EcoCyc	EcoCyc:G6144	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13349	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002764	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3133	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000933	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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yagI: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 yagI Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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