Latest revision as of 05:20, 29 July 2007

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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	gspD
Gene Synonym(s)	ECK3312, b3325, JW5707, yheF^[1], yheF
Product Desc.	putative protein secretion protein for export^[2]^[3]; Component of GspC-O secreton complex^[3] Part of H-NS-silenced gsp divergon, type II protein secretion; OM secretin; cloned gsp divergon secretes ChiA^[4]
Product Synonyms(s)	general secretory pathway component, cryptic^[1], B3325^[2]^[1], YheF^[2]^[1], GspD^[2]^[1] , ECK3312, JW5707, yheF, b3325
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gspC^[2]^[3]
Regulation/Activity
Quick Links
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See Help:Quickview for help with entering information in the Quickview table.

Notes

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A divergon is a regulon comprised of two adjacent divergent operons or genes.^[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	gspD
Mnemonic	General secretory pathway
Synonyms	ECK3312, b3325, JW5707, yheF^[1], yheF
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Notes

Location(s) and DNA Sequence

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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	74.45 minutes, 74.45 minutes	MG1655: 3454399..3456351 <gbrowseImage> name=NC_000913:3454399..3456351 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3384282..3386234 <gbrowseImage> name=NC_012967:3384282..3386234 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3341556..3343508 <gbrowseImage> name=NC_012759:3341556..3343508 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4184039..4182087 <gbrowseImage> name=NC_007779:4182087..4184039 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3552144..3554096 <gbrowseImage> name=NC_010473:3552144..3554096 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
ΔgspD (Keio:JW5707)	deletion	deletion			PMID:16738554	Shigen CGSC11532^[5]
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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
JW5707	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAGGACTCAATAAAATCAC Primer 2:CCaCGTGACGATGGCGCAGGGGC
9H3	Kohara Phage	Genobase	PMID:3038334
E1H9	Kohara Phage	Genobase	PMID:3038334
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[5]	est. P1 cotransduction: 38% ^[6] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[5]	est. P1 cotransduction: 11% ^[6] Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
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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:G7703	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12890	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004248	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947822	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2727	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010879	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	GspD
Synonyms	general secretory pathway component, cryptic^[1], B3325^[2]^[1], YheF^[2]^[1], GspD^[2]^[1] , ECK3312, JW5707, yheF, b3325
Product description	putative protein secretion protein for export^[2]^[3]; Component of GspC-O secreton complex^[3] Part of H-NS-silenced gsp divergon, type II protein secretion; OM secretin; cloned gsp divergon secretes ChiA^[4]
EC number (for enzymes)
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Notes

Function

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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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008565	protein transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004845	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008565	protein transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013356	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0998	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009279	cell outer membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0040	C	Seeded from EcoCyc (v14.0)	complete
	GO:0009306	protein secretion	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001775	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009306	protein secretion	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004846	P	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:IPR013356	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:IPR013356	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001775	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:0019867	outer membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013356	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	Subunits of GspC-O secreton complex	could be indirect
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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
Periplasm		PMID:11266368	EchoLocation:gspD
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Notes

Structure and Physical Properties

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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 MDCVMKGLNK ITCCLLAALL MPCAGHAENE QYGANFNNAD IRQFVEIVGQ HLGKTILIDP SVQGTISVRS NDTFSQQEYY QFFLSILDLY GYSVITLDNG FLKVVRSANV KTSPGMIADS SRPGVGDELV TRIVPLENVP ARDLAPLLRQ MMDAGSVGNV VHYEPSNVLI LTGRASTINK LIEVIKRVDV IGTEKQQIIH LEYASAEDLA EILNQLISES HGKSQMPALL SAKIVADKRT NSLIISGPEK ARQRITSLLK SLDVEESEEG NTRVYYLKYA KATNLVEVLT GVSEKLKDEK GNARKPSSSG AMDNVAITAD EQTNSLVITA DQSVQEKLAT VIARLDIRRA QVLVEAIIVE VQDGNGLNLG VQWANKNVGA QQFTNTGLPI FNAAQGVADY KKNGGITSAN PAWDMFSAYN GMAAGFFNGD WGVLLTALAS NNKNDILATP SIVTLDNKLA SFNVGQDVPV LSGSQTTSGD NVFNTVERKT VGTKLKVTPQ VNEGDAVLLE IEQEVSSVDS SSNSTLGPTF NTRTIQNAVL VKTGETVVLG GLLDDFSKEQ VSKVPLLGDI PLVGQLFRYT STERAKRNLM VFIRPTIIRD DDVYRSLSKE KYTRYRQEQQ QRIDGKSKAL VGSEDLPVLD ENTFNSHAPA PSSR
Length	654
Mol. Wt	71.146 kDa
pI	5.3 (calculated)
Extinction coefficient	40,340 - 40,840 (calc based on 16 Y, 3 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
motif	1-23	UniProt Manual:Signal Peptides	UniProt:P45758
Domain	433..595	PF00263 Bacterial type II and III secretion system protein		PMID:19920124^[7]
Domain	127..189	PF03958 Bacterial type II/III secretion system short domain		PMID:19920124^[7]
Domain	192..264	PF03958 Bacterial type II/III secretion system short domain		PMID:19920124^[7]
Domain	268..347	PF03958 Bacterial type II/III secretion system short domain		PMID:19920124^[7]
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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=gspD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:90111569	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947822	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010879	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P45758	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7703	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12890	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947822	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004248	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2727	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 MG1655	3^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	5	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	0^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)
gspC
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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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<gbrowseImage> name=NC_000913:3454379..3454419 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

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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:b3325 (EcoliWiki Page)	NCBI GEO profiles for gspD
microarray	GenExpDB:b3325 (EcoliWiki Page)	Summary of data for gspD 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 gspD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7703	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2727	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3325
EcoGene	EcoGene:EG12890	Escherichia coli str. K-12 substr. MG1655
EcoCyc (EcoliWiki Page)	EcoCyc:TU0-14373
RegulonDB	RegulonDB:ECK120004248	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010879	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
Xenopus tropicalis	ENSXETP00000000933 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	ESCC	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)	PF00263 Bacterial type II and III secretion system protein
Pfam (EcoliWiki Page)	PF03958 Bacterial type II/III secretion system short domain
Pfam (EcoliWiki Page)	PF03958 Bacterial type II/III secretion system short domain
Pfam (EcoliWiki Page)	PF03958 Bacterial type II/III secretion system short domain
EcoCyc	EcoCyc:G7703	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12890	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004248	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2727	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010879	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 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 ^3.4 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).
↑ ^7.0 ^7.1 ^7.2 ^7.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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gspD:On One Page: Difference between revisions

Latest revision as of 05:20, 29 July 2007

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 gspD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

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