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Standard Name	ytjB
Gene Synonym(s)	ECK4379, b4387, JW4350, smp^[1], smp
Product Desc.	membrane protein^[2]^[3] Function unknown, membrane protein; transcribed divergently from serB, overlapping promoters; homologous to ahpA of P. multocida, which induces anaerobic expression of the cryptic hemolysin HlyE(SheA) when cloned in E. coli^[4]
Product Synonyms(s)	conserved protein ^[1], B4387 ^[2]^[1], YtjB ^[2]^[1], Smp ^[2]^[1] , ECK4379, JW4350, smp, b4387
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lplA^[2], ytjB^[2], smp
Regulation/Activity
Quick Links
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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	ytjB
Mnemonic	Systematic nomenclature
Synonyms	ECK4379, b4387, JW4350, smp^[1], smp
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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	99.62 minutes	MG1655: 4622812..4622168 <gbrowseImage> name=NC_000913:4622168..4622812 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4612359..4613003 <gbrowseImage> name=NC_012967:4612359..4613003 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4560652..4561296 <gbrowseImage> name=NC_012759:4560652..4561296 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4629469..4628825 <gbrowseImage> name=NC_007779:4628825..4629469 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4669274..4668630 <gbrowseImage> name=NC_010473:4668630..4669274 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
ΔytjB (Keio:JW4350)	deletion	deletion			PMID:16738554	Shigen CGSC11105^[5]
ΔytjB783::kan					PMID:16738554	CGSC:106096
ytjB(P)::Tn10dCam			Mutagenesis rate	Decreased stress-induced mutagenesis (SIM) phenotype.	PMID:23224554	Parental Strain: SMR4562 Experimental Strain: SMR11981	Mutation was comparatively weak with decrease only happening to 33-67% of population.
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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
JW4350	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTCGCACAAAACTGAAATT Primer 2:CCtTCTTTTTTCTCGCTTTCTTC
15C9	Kohara Phage	Genobase	PMID:3038334
12A4	Kohara Phage	Genobase	PMID:3038334
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[5]	est. P1 cotransduction: 33% ^[6] Synonyms:zjj-202::Tn10, zji-202::Tn10
thrA34::Tn10	Linked marker	CAG18442 = CGSC7320^[5]	est. P1 cotransduction: 53% ^[6] Synonyms:thr-34::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:EG10951	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10951	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000940	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946089	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0944	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014387	Escherichia coli str. K-12 substr. MG1655
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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	YtjB
Synonyms	conserved protein ^[1], B4387 ^[2]^[1], YtjB ^[2]^[1], Smp ^[2]^[1] , ECK4379, JW4350, smp, b4387
Product description	membrane protein^[2]^[3] Function unknown, membrane protein; transcribed divergently from serB, overlapping promoters; homologous to ahpA of P. multocida, which induces anaerobic expression of the cryptic hemolysin HlyE(SheA) when cloned in E. coli^[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: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: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:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	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	References	Evidence
Protein	glyS	PMID:16606699	Experiment(s):EBI-1147968
Protein	glgB	PMID:16606699	Experiment(s):EBI-1147968
Protein	clpB	PMID:16606699	Experiment(s):EBI-1147968
Protein	dnaB	PMID:16606699	Experiment(s):EBI-1147968
Protein	rpmB	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
plasma membrane			From EcoCyc^[3]
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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 MARTKLKFRL HRAVIVLFCL ALLVALMQGA SWFSQNHQRQ RNPQLEELAR TLARQVTLNV APLMRTDSPD EKRIQAILDQ LTDESRILDA GVYDEQGDLI ARSGESVEVR DRLALDGKKA GGYFNQQIVE PIAGKNGPLG YLRLTLDTHT LATEAQQVDN TTNILRLMLL LSLAIGVVLT RTLLQGKRTR WQQSPFLLTA SKPVPEEEES EKKE
Length	214
Mol. Wt	24.083 kDa
pI	8.9 (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
motif	1-30	UniProt Manual:Signal Peptides	UniProt:P0AGC7
Domain	1..210	PF10144 Bacterial virulence factor haemolysin		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=ytjB 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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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:16132204	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946089	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014387	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AGC7	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10951	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10951	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946089	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000940	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0944	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	6.357+/-0.061	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	119	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	43	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)
lplA
ytjB
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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_000913:4622792..4622832 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:b4387 (EcoliWiki Page)	NCBI GEO profiles for ytjB
microarray	GenExpDB:b4387 (EcoliWiki Page)	Summary of data for ytjB 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 (4622275..4622499) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:D12^[7]
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Notes

Accessions Related to ytjB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10951	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0944	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4387
EcoGene	EcoGene:EG10951	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000940	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014387	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	SMP	From SHIGELLACYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF03099
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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)	PF10144 Bacterial virulence factor haemolysin
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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 ^1.8 ^1.9 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 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 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 ^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

ytjB:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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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 ytjB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Families

Notes

Links

References

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