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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	ygeR
Gene Synonym(s)	ECK2861, b2865, JW2833^[1], JW2833
Product Desc.	putative lipoprotein^[2]; putative lipoprotein; predicted DNA-binding transcriptional regulator^[3] Novel lipoprotein, function unknown, metalloprotease homolog; M23 family^[4]
Product Synonyms(s)	Tetratricopeptide repeat transcriptional regulator^[1], B2865^[2]^[1], YgeR^[2]^[1] , ECK2861, JW2833, b2865
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ygeR^[2]
Regulation/Activity
Quick Links
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Notes

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nlpD, ygeR, yebA and envC are paralogs. ygeR is a backbone gene flanking the insertion of the type three secretion system pathogenicity island ETT2. 18 kb of ETT2 has been deleted from K-12, leaving a 10 kb remnant. First 25 aa are a type II signal peptide.^[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	ygeR
Mnemonic	Systematic nomenclature
Synonyms	ECK2861, b2865, JW2833^[1], JW2833
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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	64.6 minutes	MG1655: 2997913..2997158 <gbrowseImage> name=NC_000913:2997158..2997913 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2885646..2884891 <gbrowseImage> name=NC_012967:2884891..2885646 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2884306..2885061 <gbrowseImage> name=NC_012759:2884306..2885061 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2998547..2997792 <gbrowseImage> name=NC_007779:2997792..2998547 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3091783..3091028 <gbrowseImage> name=NC_010473:3091028..3091783 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
ΔygeR (Keio:JW2833)	deletion	deletion			PMID:16738554	Shigen CGSC10203^[5]
ΔygeR787::kan					PMID:16738554	CGSC:104954
ΔygeR	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔenvC	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔnlpD	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔyebA	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔnlpD ΔenvC	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔyebA ΔenvC	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔyebA ΔnlpD	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
ΔygeR ΔyebA ΔnlpD ΔenvC	deletion	deletion	Cell Shape	defect in cell separation	PMID:19525345
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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
JW2833	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTGCGGGACGCCTGAATAA Primer 2:CCGCATTTTGGCTTGCTGCCCTG
15G6	Kohara Phage	Genobase	PMID:3038334
10D8	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: 13% ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: % ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:G7484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13048	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004047	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947352	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2860	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009407	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	YgeR
Synonyms	Tetratricopeptide repeat transcriptional regulator^[1], B2865^[2]^[1], YgeR^[2]^[1] , ECK2861, JW2833, b2865
Product description	putative lipoprotein^[2]; putative lipoprotein; predicted DNA-binding transcriptional regulator^[3] Novel lipoprotein, function unknown, metalloprotease homolog; M23 family^[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:0000920	septum digestion after cytokinesis	PMID:19525345	IGI: Inferred from Genetic Interaction	UniProtKB:P0ADA3 UniProtKB:P37690 UniProtKB:P0AFS9	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004222	metalloendopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002886	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002886	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000920	cytokinetic cell separation	PMID:19525345	IGI: Inferred from Genetic Interaction	UniProtKB:P37690	P		complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016998	cell wall macromolecule catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002482	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000920	cytokinetic cell separation	PMID:19525345	IGI: Inferred from Genetic Interaction	UniProtKB:P0ADA3 UniProtKB:P37690 UniProtKB:Q46798	P		complete
	GO:0016998	cell wall macromolecule catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018392	P	Seeded from EcoCyc (v14.0)	complete
	GO:0031225	anchored to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9901	C	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
Protein	rplL		PMID:19402753	LCMS(ID Probability):99.6
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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
Outer membrane		PMID:15174130	EchoLocation:ygeR
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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 MFFKRGKILS AGRLNKKSLG IVMLLSVGLL LAGCSGSKSS DTGTYSGSVY TVKRGDTLYR ISRTTGTSVK ELARLNGISP PYTIEVGQKL KLGGAKSSSI TRKSTAKSTT KTASVTPSSA VPKSSWPPVG QRCWLWPTTG KVIMPYSTAD GGNKGIDISA PRGTPIYAAG AGKVVYVGNQ LRGYGNLIMI KHSEDYITAY AHNDTMLVNN GQSVKAGQKI ATMGSTDAAS VRLHFQIRYR ATAIDPLRYL PPQGSKPKC
Length	259
Mol. Wt	27.555 kDa
pI	10.6 (calculated)
Extinction coefficient	34,380 - 34,755 (calc based on 12 Y, 3 W, and 3 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
motif	1-25	UniProt Manual:Signal Peptides	UniProt:Q46798
Domain	42..85	PF01476 LysM domain		PMID:19920124
Domain	143..238	PF01551 Peptidase family M23		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=ygeR 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:90111503	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947352	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009407	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:Q46798	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13048	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947352	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004047	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2860	Escherichia coli str. K-12 substr. MG1655
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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	298	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	125	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	262	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)
ygeR
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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_000913:2997893..2997933 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:b2865 (EcoliWiki Page)	NCBI GEO profiles for ygeR
microarray	GenExpDB:b2865 (EcoliWiki Page)	Summary of data for ygeR 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 ygeR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7484	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2860	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2865
EcoGene	EcoGene:EG13048	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004047	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009407	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	S3067	From SHIGELLACYC
E. coli O157	Z4203	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)	PF01551 Peptidase family M23
Pfam (EcoliWiki Page)	PF01476 LysM domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:51261
EcoCyc	EcoCyc:G7484	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13048	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004047	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2860	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009407	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).

ygeR: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 ygeR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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