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Standard Name	secB
Gene Synonym(s)	ECK3599, b3609, JW3584^[1], JW3584
Product Desc.	SecB^[2]^[3]; Component of Sec Protein Secretion Complex^[2]^[3] Protein export chaperone; SecB helps SecA deliver proteins to the SecYE core translocon; general protein chaperone^[4]
Product Synonyms(s)	protein export chaperone^[1], B3609^[2]^[1], SecB^[2]^[1] , ECK3599, JW3584, b3609
Function from GO	<GO_nr />
Knock-Out Phenotype	non lethal. SecB null strains are deficient in post translational targeting of some secretion and outer membrane proteins.^[5]
Regulation/Expression	transcription unit(s): gpsA^[2]
Regulation/Activity
Quick Links
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Notes

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Penultimate Ser residue missing from purified protein could be a proteolytic artifact.^[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	secB
Mnemonic	secretion Secretory
Synonyms	ECK3599, b3609, JW3584^[1], JW3584
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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	81.51 minutes	MG1655: 3782151..3781684 <gbrowseImage> name=NC_000913:3781684..3782151 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3724894..3724427 <gbrowseImage> name=NC_012967:3724427..3724894 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3670010..3670477 <gbrowseImage> name=NC_012759:3670010..3670477 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3856287..3856754 <gbrowseImage> name=NC_007779:3856287..3856754 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3879728..3879261 <gbrowseImage> name=NC_010473:3879261..3879728 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	3781687	Edman degradation	PMID:2644258
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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	Comments
ΔsecB (Keio:JW3584)	deletion	deletion	PMID:16738554	Shigen CGSC10640^[6]
secB8			PMID:6403503		null
ΔsecB721::kan			PMID:16738554	CGSC:102902
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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
JW3584	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAGAACAAAACAACACTGA Primer 2:CCGGCATCCTGATGTTCTTCAGT
5D2	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[6]	est. P1 cotransduction: % ^[7] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[6]	est. P1 cotransduction: 13% ^[7]
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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:EG10937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10937	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000926	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948123	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0930	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011798	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	SecB
Synonyms	protein export chaperone^[1], B3609^[2]^[1], SecB^[2]^[1] , ECK3599, JW3584, b3609
Product description	SecB^[2]^[3]; Component of Sec Protein Secretion Complex^[2]^[3] Protein export chaperone; SecB helps SecA deliver proteins to the SecYE core translocon; general protein chaperone^[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:0005515	protein binding	PMID:2649892	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00821	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006457	protein folding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00821	P	Seeded from EcoCyc (v14.0)	complete
	GO:0051082	unfolded protein binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003708	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051262	protein tetramerization	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003708	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006605	protein targeting	PMID:6403503	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0015031	protein transport	PMID:6403503	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0043952	protein transport by the Sec complex	PMID:6403503	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0005515	protein binding	PMID:2649892	IDA: Inferred from Direct Assay		F	E. coli SecB is a homotetramer.	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 Sec Protein Secretion Complex	could be indirect
Protein	yaiX		PMID:15690043	Experiment(s):EBI-886253
Protein	ybgK		PMID:16606699	Experiment(s):EBI-1146244
Protein	rpsC		PMID:16606699	Experiment(s):EBI-1146244
Protein	nrdI		PMID:16606699	Experiment(s):EBI-1146244
Protein	motB		PMID:16606699	Experiment(s):EBI-1146244
Protein	lon		PMID:15690043	Experiment(s):EBI-880504, EBI-886253
Protein	cpxR		PMID:15690043	Experiment(s):EBI-886253
Protein	lon		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.283587
Protein	cpxR		PMID:19402753	LCMS(ID Probability):99.2
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Notes

SecB substrates have been examined in a comparative proteomics experiment^[8]. Intracellular aggregates of proteins that depend on SecB for secretion were formed in a secB mutant.

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 MSEQNNTEMT FQIQRIYTKD ISFEAPNAPH VFQKDWQPEV KLDLDTASSQ LADDVYEVVL RVTVTASLGE ETAFLCEVQQ GGIFSIAGIE GTQMAHCLGA YCPNILFPYA RECITSMVSR GTFPQLNLAP VNFDALFMNY LQQQAGEGTE EHQDA
Length	155
Mol. Wt	17.276 kDa
pI	4.1 (calculated)
Extinction coefficient	12,950 - 13,450 (calc based on 5 Y, 1 W, and 4 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
Modification Site	22	phosphorylation site at S22	probability greater than 75%	PMID:17938405
Domain	1..146	PF02556 Preprotein translocase subunit SecB		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=secB 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:16131480	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948123	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011798	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AG86	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10937	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948123	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000926	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0930	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	3.19E+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	672.937+/-5.812	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.48273+/-0.01589	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.375802998	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	21205	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	5193	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	17840	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)
gpsA
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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_000913:3782131..3782171 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:b3609 (EcoliWiki Page)	NCBI GEO profiles for secB
microarray	GenExpDB:b3609 (EcoliWiki Page)	Summary of data for secB 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 (3781678..3781836) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:F5^[9]
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Notes

Accessions Related to secB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10937	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0930	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3609
EcoGene	EcoGene:EG10937	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000926	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011798	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	ENSANGP00000028748 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	SECB	From SHIGELLACYC
E. coli O157	SECB	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:54611
Pfam (EcoliWiki Page)	PF02556 Preprotein translocase subunit SecB
EcoCyc	EcoCyc:EG10937	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10937	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000926	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0930	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011798	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 ^2.7 ^2.8 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 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Kumamoto, CA & Beckwith, J (1985) Evidence for specificity at an early step in protein export in Escherichia coli. J. Bacteriol. 163 267-74 PubMed
↑ ^6.0 ^6.1 ^6.2 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).
↑ Baars, L et al. (2006) Defining the role of the Escherichia coli chaperone SecB using comparative proteomics. J. Biol. Chem. 281 10024-34 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

secB: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

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 secB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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