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Expression|

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Standard Name	sspB
Gene Synonym(s)	ECK3217, b3228, JW3197^[1], JW3197
Product Desc.	EG10978^[2]^[3]; Component of ClpXP protease specificity-enhancing factor^[3] Specificity-enhancing factor for ClpXP protease, binds ssrA-tagged proteins; ribosome-associated stress response protein; homodimeric^[4]
Product Synonyms(s)	ClpXP protease specificity-enhancing factor^[1], B3228^[2]^[1], SspB^[2]^[1] , ECK3217, JW3197, b3228
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): sspAB^[2]
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	sspB
Mnemonic	Stringent starvation protein
Synonyms	ECK3217, b3228, JW3197^[1], JW3197
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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	72.73 minutes	MG1655: 3374798..3374301 <gbrowseImage> name=NC_000913:3374301..3374798 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3304674..3304177 <gbrowseImage> name=NC_012967:3304177..3304674 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3261449..3261946 <gbrowseImage> name=NC_012759:3261449..3261946 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3376631..3376134 <gbrowseImage> name=NC_007779:3376134..3376631 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3472543..3472046 <gbrowseImage> name=NC_010473:3472046..3472543 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
Coding Start (SO:0000323)	MG1655	3374301	Edman degradation	PMID:11009422
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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
sspB(del) (Keio:JW3197)	deletion	deletion	PMID:16738554	Shigen CGSC10426^[5]
sspB756(del)::kan			PMID:16738554	CGSC:103030
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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
JW3197	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATTTGTCACAGCTAACACC Primer 2:CCtTTCACAACGCGTAATGCCGG
7C8	Kohara Phage	Genobase	PMID:3038334
1E3	Kohara Phage	Genobase	PMID:3038334
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 70% ^[6] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 18% ^[6] Synonyms:zhd-3083::Tn10, zhe-3083::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:EG10978	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10978	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000967	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944774	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0971	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010591	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	SspB
Synonyms	ClpXP protease specificity-enhancing factor^[1], B3228^[2]^[1], SspB^[2]^[1] , ECK3217, JW3197, b3228
Product description	EG10978^[2]^[3]; Component of ClpXP protease specificity-enhancing factor^[3] Specificity-enhancing factor for ClpXP protease, binds ssrA-tagged proteins; ribosome-associated stress response protein; homodimeric^[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:0006950	response to stress	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0346	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	Notes	References	Evidence
Protein	Subunits of ClpXP protease specificity-enhancing factor	could be indirect
Protein	dnaE		PMID:15690043	Experiment(s):EBI-879764
Protein	tufA		PMID:15690043	Experiment(s):EBI-879764
Protein	slyD		PMID:16606699	Experiment(s):EBI-1145192
Protein	rpsD		PMID:16606699	Experiment(s):EBI-1145192
Protein	rplE		PMID:16606699	Experiment(s):EBI-1145192
Protein	cheA		PMID:16606699	Experiment(s):EBI-1145192
Protein	lrp		PMID:16606699	Experiment(s):EBI-1145192
Protein	lon		PMID:16606699	Experiment(s):EBI-1145192
Protein	htpG		PMID:16606699	Experiment(s):EBI-1145192
Protein	malZ		PMID:16606699	Experiment(s):EBI-1145192
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1145192
Protein	greA		PMID:16606699	Experiment(s):EBI-1145192
Protein	rnc		PMID:16606699	Experiment(s):EBI-1145192
Protein	infB		PMID:16606699	Experiment(s):EBI-1145192
Protein	rplF		PMID:16606699	Experiment(s):EBI-1145192
Protein	clpB		PMID:16606699	Experiment(s):EBI-1145192
Protein	ydbH		PMID:16606699	Experiment(s):EBI-1145192
Protein	rpsC		PMID:16606699	Experiment(s):EBI-1145192
Protein	thrS		PMID:16606699	Experiment(s):EBI-1145192
Protein	surE		PMID:16606699	Experiment(s):EBI-1145192
Protein	ves		PMID:16606699	Experiment(s):EBI-1145192
Protein	rplJ		PMID:16606699	Experiment(s):EBI-1145192
Protein	clpA		PMID:15690043	Experiment(s):EBI-884360
Protein	dnaK		PMID:15690043	Experiment(s):EBI-884360
Protein	elaB		PMID:15690043	Experiment(s):EBI-884360
Protein	rho		PMID:15690043	Experiment(s):EBI-884360
Protein	rplD		PMID:15690043	Experiment(s):EBI-884360
Protein	rpsG		PMID:15690043	Experiment(s):EBI-884360
Protein	slyD		PMID:15690043	Experiment(s):EBI-884360
Protein	ybdN		PMID:15690043	Experiment(s):EBI-884360
Protein	aegA		PMID:15690043	Experiment(s):EBI-884360
Protein	elaB		PMID:19402753	LCMS(ID Probability):99.6
Protein	aegA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rho		PMID:19402753	LCMS(ID Probability):99.6
Protein	clpA		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplD		PMID:19402753	LCMS(ID Probability):99.6
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Notes

Localization

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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 MDLSQLTPRR PYLLRAFYEW LLDNQLTPHL VVDVTLPGVQ VPMEYARDGQ IVLNIAPRAV GNLELANDEV RFNARFGGIP RQVSVPLAAV LAIYARENGA GTMFEPEAAY DEDTSIMNDE EASADNETVM SVIDGDKPDH DDDTHPDDEP PQPPRGGRPA LRVVK
Length	165
Mol. Wt	18.261 kDa
pI	4.2 (calculated)
Extinction coefficient	12,950 (calc based on 5 Y, 1 W, and 0 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..165	PF04386 Stringent starvation protein B		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=sspB 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:16131118	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944774	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010591	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFZ3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10978	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10978	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944774	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000967	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0971	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 MC4100	1.04E+03	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	45.473+/-0.266	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.262575453	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	2957	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	553	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	1081	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)
sspAB
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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_000913:3374778..3374818 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:b3228 (EcoliWiki Page)	NCBI GEO profiles for sspB
microarray	GenExpDB:b3228 (EcoliWiki Page)	Summary of data for sspB 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 sspB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10978	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0971	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3228
EcoGene	EcoGene:EG10978	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000967	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010591	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
Apis mellifera	ENSAPMP00000019722 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	SSPB	From SHIGELLACYC
E. coli O157	SSPB	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:101738
Pfam (EcoliWiki Page)	PF04386 Stringent starvation protein B
EcoCyc	EcoCyc:EG10978	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10978	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000967	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0971	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010591	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 ^3.2 ^3.3 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).

sspB: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 sspB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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