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Expression|

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Standard Name	lptD
Gene Synonym(s)	ECK0055, b0054, JW0053, ostA, yabG, imp^[1], imp, yabG
Product Desc.	exported protein required for envelope biosynthesis and integrity^[2]^[3]
Product Synonyms(s)	exported protein required for envelope biosynthesis and integrity^[1], B0054^[2]^[1], YabG^[2]^[1], OstA^[2]^[1], Imp^[2]^[1] , ECK0055, imp, JW0053, ostA, yabG, b0054
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lptD-surA-pdxA^[2], lptD^[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	lptD
Mnemonic	LPS transport
Synonyms	ECK0055, b0054, JW0053, ostA, yabG, imp^[1], imp, yabG
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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	1.18 minutes	MG1655: 57109..54755 <gbrowseImage> name=NC_000913:54755..57109 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 58950..61304 <gbrowseImage> name=NC_012967:58950..61304 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 54755..57109 <gbrowseImage> name=NC_012759:54755..57109 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 57109..54755 <gbrowseImage> name=NC_007779:54755..57109 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 57109..54755 <gbrowseImage> name=NC_010473:54755..57109 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	54758	Edman degradation	PMID:9298646
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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	Comments
imp-4213	in-frame deletion of 23 codons^[4]	deletion of amino acids 330 to 352	Sensitivity to	variety of detergents, antibiotics, and dyes (Table 2)	PMID:2547691
lptD allele in JA300			Resistant to	n-hexane	PMID:7811102
imp-4213	in-frame deletion of 23 codons^[4]	deletion of amino acids 330-352	Growth Phenotype	growth on maltodextrins in the absence of LamB	PMID:2547691
attB::P_T7 lacO-imp+ imp(del)::kan			Essential		PMID:12207697
imp-208	in-frame deletion of 25 codons ^[4]	deletion of amino acids 335-359	Sensitivity to	variety of detergents, antibiotics, and dyes (Table 2)	PMID:2547691
imp+ overexpression			Colony Morphology	colonies have high surface tension; "can be pushed around on agar plates like hockey pucks"	PMID:12207697	imp under control of T7 promoter and lacO grown in the presence of IPTG
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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
JW0053	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAACGTATCCCCACTCT Primer 2:CCCAAAGTGTTTTGATACGGCAG
8D2	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 44% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 33% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0054
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0067
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:G7E-6
CGSC (EcoliWiki Page)	CGSC:36754
EcoCyc (EcoliWiki Page)	ECOCYC:EG11569	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945011	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	LptD
Synonyms	exported protein required for envelope biosynthesis and integrity^[1], B0054^[2]^[1], YabG^[2]^[1], OstA^[2]^[1], Imp^[2]^[1] , ECK0055, imp, JW0053, ostA, yabG, b0054
Product description	exported protein required for envelope biosynthesis and integrity^[2]^[3]
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:16861298	IPI: Inferred from Physical Interaction	EcoliWiki:rlpB	F		complete
	GO:0005515	protein binding	PMID:16861298	IPI: Inferred from Physical Interaction	UniProtKB:P0ADC1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043165	Gram-negative-bacterium-type cell outer membrane assembly	PMID:16861298	IGI: Inferred from Genetic Interaction	EcoliWiki:rlpB	P		complete
	GO:0015920	lipopolysaccharide transport	PMID:16861298	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009279	cell outer membrane	PMID:12207697	IDA: Inferred from Direct Assay		C	Fig. 2	complete
	GO:0010033	response to organic substance	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007543	P	Seeded from EcoCyc (v14.0)	complete
	GO:0010033	response to organic substance	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020889	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043165	Gram-negative-bacterium-type cell outer membrane assembly	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01411	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043165	Gram-negative-bacterium-type cell outer membrane assembly	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020889	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
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
outer membrane
Outer Membrane	PMID:9298646	EchoLocation:imp
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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 MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK GDYPDDAVFT GSVDIMQGNS RLQADEVQLH QKEAPGQPEP VRTVDALGNV HYDDNQVILK GPKGWANLNT KDTNVWEGDY QMVGRQGRGK ADLMKQRGEN RYTILDNGSF TSCLPGSDTW SVVGSEIIHD REEQVAEIWN ARFKVGPVPI FYSPYLQLPV GDKRRSGFLI PNAKYTTTNY FEFYLPYYWN IAPNMDATIT PHYMHRRGNI MWENEFRYLS QAGAGLMELD YLPSDKVYED EHPNDDSSRR WLFYWNHSGV MDQVWRFNVD YTKVSDPSYF NDFDNKYGSS TDGYATQKFS VGYAVQNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ NDVGPFDTRI YGQAVHFVNT RDDMPEATRV HLEPTINLPL SNNWGSINTE AKLLATHYQQ TNLDWYNSRN TTKLDESVNR VMPQFKVDGK MVFERDMEML APGYTQTLEP RAQYLYVPYR DQSDIYNYDS SLLQSDYSGL FRDRTYGGLD RIASANQVTT GVTSRIYDDA AVERFNISVG QIYYFTESRT GDDNITWEND DKTGSLVWAG DTYWRISERW GLRGGIQYDT RLDNVATSNS SIEYRRDEDR LVQLNYRYAS PEYIQATLPK YYSTAEQYKN GISQVGAVAS WPIADRWSIV GAYYYDTNAN KQADSMLGVQ YSSCCYAIRV GYERKLNGWD NDKQHAVYDN AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL
Length
Mol. Wt
pI
Extinction coefficient
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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	1-24	UniProt Manual:Signal Peptides	UniProt:P31554
Domain	6..195	PF03968 OstA-like protein		PMID:19920124
Domain	308..697	PF04453 Organic solvent tolerance protein		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=lptD 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:16128048	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945011	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31554	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945011	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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		60	Molecules/cell	Medium:MOPS minimal glucose Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other: aerobic	protein sequencing	culture harvested at OD600=0.2 to 0.25	PMID:9298646
Protein	E. coli K-12 EMG2	50	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: M62	PMID: 9298646
Protein	E. coli K-12 MG1655	2267	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	1037	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	1500	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)
lptD-surA-pdxA
imp
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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_000913:57089..57129 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:b0054 (EcoliWiki Page)	NCBI GEO profiles for imp
microarray	GenExpDB:b0054 (EcoliWiki Page)	Summary of data for imp 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 (57013..57395) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:D6^[7]
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Notes

Accessions Related to lptD Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0054
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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	G7V-674	From SHIGELLACYC
E. coli O157	G7E-6	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)	PFAM:PF04453
Pfam (EcoliWiki Page)	PF03968 OstA-like protein
Pfam (EcoliWiki Page)	PF04453 Organic solvent tolerance protein
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 ^1.10 ^1.11 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 Braun, M & Silhavy, TJ (2002) Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol. Microbiol. 45 1289-302 PubMed
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

lptD: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 lptD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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