{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	secD
Gene Synonym(s)	ECK0402, b0408, JW0398^[1], JW0398
Product Desc.	SecD^[2]^[3]; Component of SecD-SecF-Yajc-YidC Secretion Complex^[2]^[3]; Sec Protein Secretion Complex^[2]^[3] SecDFyajC inner membrane secretion protein trimeric complex; assists the SecYE core translocon to interact with SecA and export protein^[4]
Product Synonyms(s)	SecYEG protein translocase auxillary subunit^[1], EG10938^[2]^[1], B0408^[2]^[1], SecD^[2]^[1] , ECK0402, JW0398, b0408
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yajC-secDF^[2]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

SecYEG complex interacts with SecDFyajC to form a hexameric holocomplex.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	secD
Mnemonic	Secretory
Synonyms	ECK0402, b0408, JW0398^[1], JW0398
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	9.2 minutes	MG1655: 426871..428718 <gbrowseImage> name=NC_000913:426871..428718 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 396070..397917 <gbrowseImage> name=NC_012967:396070..397917 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 329630..331477 <gbrowseImage> name=NC_012759:329630..331477 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 426871..428718 <gbrowseImage> name=NC_007779:426871..428718 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 366202..368049 <gbrowseImage> name=NC_010473:366202..368049 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Phenotype: Description	Availability
secD1		CGSC:44985
secD29(Cs)	cold sensitive	CGSC:38549
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0398	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTAAACCGTTATCCTTTGTG Primer 2:CCGATTGACAGCTTCTTGACGCG
4F3	Kohara Phage	Genobase	PMID:3038334
19F6	Kohara Phage	Genobase	PMID:3038334
zai-3053::Tn10	Linked marker	CAG18091 = CGSC7336^[5]	est. P1 cotransduction: 27% ^[6] Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[5]	est. P1 cotransduction: 86% ^[6]
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10938	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10938	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000927	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:949133	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0931	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001417	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	SecD
Synonyms	SecYEG protein translocase auxillary subunit^[1], EG10938^[2]^[1], B0408^[2]^[1], SecD^[2]^[1] , ECK0402, JW0398, b0408
Product description	SecD^[2]^[3]; Component of SecD-SecF-Yajc-YidC Secretion Complex^[2]^[3]; Sec Protein Secretion Complex^[2]^[3] SecDFyajC inner membrane secretion protein trimeric complex; assists the SecYE core translocon to interact with SecA and export protein^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<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-0997	C	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:0006886	intracellular protein transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005791	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008565	protein transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003335	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015031	protein transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0653	P	Seeded from EcoCyc (v14.0)	complete
	GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005791	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015627	type II protein secretion system complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003335	C	Seeded from EcoCyc (v14.0)	complete
	GO:0015628	protein secretion by the type II secretion system	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003335	P	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:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0015031	protein transport	PMID:3029032	IMP: Inferred from Mutant Phenotype		P		complete
edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes
Protein	Subunits of SecD-SecF-Yajc-YidC Secretion Complex	could be indirect
Protein	Subunits of Sec Protein Secretion Complex	could be indirect
edit table

</protect>

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	C-terminus localized in the cytoplasm with 6 predicted transmembrane domains	Daley et al. (2005) ^[7]
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MLNRYPLWKY VMLIVVIVIG LLYALPNLFG EDPAVQITGA RGVAASEQTL IQVQKTLQEE KITAKSVALE EGAILARFDS TDTQLRAREA LMGVMGDKYV VALNLAPATP RWLAAIHAEP MKLGLDLRGG VHFLMEVDMD TALGKLQEQN IDSLRSDLRE KGIPYTTVRK ENNYGLSITF RDAKARDEAI AYLSKRHPDL VISSQGSNQL RAVMSDARLS EAREYAVQQN INILRNRVNQ LGVAEPVVQR QGADRIVVEL PGIQDTARAK EILGATATLE FRLVNTNVDQ AAAASGRVPG DSEVKQTREG QPVVLYKRVI LTGDHITDST SSQDEYNQPQ VNISLDSAGG NIMSNFTKDN IGKPMATLFV EYKDSGKKDA NGRAVLVKQE EVINIANIQS RLGNSFRITG INNPNEARQL SLLLRAGALI APIQIVEERT IGPTLGMQNI EQGLEACLAG LLVSILFMII FYKKFGLIAT SALIANLILI VGIMSLLPGA TLSMPGIAGI VLTLAVAVDA NVLINERIKE ELSNGRTVQQ AIDEGYRGAF SSIFDANITT LIKVIILYAV GTGAIKGFAI TTGIGVATSM FTAIVGTRAI VNLLYGGKRV KKLSI
Length	615
Mol. Wt	66.634 kDa
pI	8.9 (calculated)
Extinction coefficient	33,350 - 33,475 (calc based on 15 Y, 2 W, and 1 C residues)
edit table

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	427..606	PF02355 Protein export membrane protein	PMID:19920124
Domain	112..143	PF07549 SecD/SecF GG Motif	PMID:19920124
edit table

<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=secD taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128393	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:949133	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001417	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AG90	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10938	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10938	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:949133	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000927	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0931	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	6.38E+02	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	E. coli K-12 MG1655	2699	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	437	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	1250	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
yajC-secDF
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:426851..426891 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0408 (EcoliWiki Page)	NCBI GEO profiles for secD
microarray	GenExpDB:b0408 (EcoliWiki Page)	Summary of data for secD from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to secD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10938	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0931	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0408
EcoGene	EcoGene:EG10938	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000927	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001417	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000027412 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	SECD	From SHIGELLACYC
E. coli O157	SECD	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:82866
Pfam (EcoliWiki Page)	PF02355 Protein export membrane protein
Pfam (EcoliWiki Page)	PF07549 SecD/SecF GG Motif
EcoCyc	EcoCyc:EG10938	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10938	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000927	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0931	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001417	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 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 ^3.4 ^3.5 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 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).
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

secD: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 secD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search