lptD:Gene Product(s): Difference between revisions

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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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^[4]	IPI: Inferred from Physical Interaction	EcoliWiki:rlpB	F		complete
	GO:0005515	protein binding	PMID:16861298^[4]	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^[4]	IGI: Inferred from Genetic Interaction	EcoliWiki:rlpB	P		complete
	GO:0015920	lipopolysaccharide transport	PMID:16861298^[4]	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009279	cell outer membrane	PMID:12207697^[5]	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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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^[6]
Domain	308..697	PF04453 Organic solvent tolerance protein		PMID:19920124^[6]
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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

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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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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 ^4.3 Wu, T et al. (2006) Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103 11754-9 PubMed
↑ Braun, M & Silhavy, TJ (2002) Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol. Microbiol. 45 1289-302 PubMed
↑ ^6.0 ^6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-exported protein required for envelope biosynthesis and integrity<ref name='LIB:Riley_2006'/>, B0054<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YabG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OstA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Imp<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''exported protein required for envelope biosynthesis and integrity<ref name='LIB:Riley_2006'/>, B0054<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YabG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OstA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Imp<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0055, imp, JW0053, ostA, yabG, b0054''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 74: / Line 74: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="H46aa186aed1c2"  class=" tableEdit GO_table_product dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46aa186aed1c2"  class=" tableEdit GO_table_product dataTable"
 |- {{table_heading_style}}
 !|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
@@ Line 136: / Line 136: @@
 |
-|
-complete
-|-
-|
-|
-GO:0005886
-|
-plasma membrane
-|
-GOA:spkw<br />SP_KW:GO_REF:0000004
-|
-IEA: Inferred from Electronic Annotation
-|
-SP_KW:KW-1003
-|
-C
-|
-Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 184: / Line 165: @@
 cell outer membrane
 |
-GOA:hamap<br />GO_REF:0000020
+PMID:12207697
-|
-IEA: Inferred from Electronic Annotation
-|
-HAMAP:MF_01411
-|
-C
-|
-Seeded from [[EcoCyc]] (v14.0)
-|
-complete
-|-
-|
-|
-GO:0009279
-|
-cell outer membrane
-|
-GOA:interpro<br />GO_REF:0000002
-|
-IEA: Inferred from Electronic Annotation
-|
-InterPro:IPR020889
-|
-C
-|
-Seeded from [[EcoCyc]] (v14.0)
-|
-complete
-|-
-|
-|
-GO:0009279
-|
-cell outer membrane
-|
-GOA:spkw<br />SP_KW:GO_REF:0000004
 |
-IEA: Inferred from Electronic Annotation
+IDA: Inferred from Direct Assay
-|
-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)
+Fig. 2
 |
 complete
@@ Line 342: / Line 266: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="W46aa187023903"  class=" tableEdit Product_interactions_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aa187023903"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 365: / Line 289: @@
 {|   id="M46aa1870c7396"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |-
 |
@@ Line 537: / Line 461: @@
 View models at:
 * [http://www.proteinmodelportal.org/query/uniprot/P31554 Protein Model Portal]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P31554 PSI-PRED (P31554)]
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P31554 Genomes TO Protein (P31554)] (GTOP)
 |- class="tableEdit_footer"
@@ Line 601: / Line 525: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="D46aa187375122"  class=" tableEdit Gene_accessions_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46aa187375122"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|Database!!Accession!!Notes
 |-
 |
-[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11569-MONOMER EcoCyc:EG11569-MONOMER]
+[http://www.ncbi.nlm.nih.gov/protein/16128048 GI:16128048]
 |
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
+|
+[http://www.ncbi.nlm.nih.gov/protein/NP_414596.1 GeneID:945011]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P31554 UniProtKB/Swiss-Prot:P31554]
+|
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[http://www.uniprot.org/uniprot/P31554 UniProt:P31554]
+[http://www.ncbi.nlm.nih.gov/gene?term=945011 GeneID:945011]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
+RegulonDB:
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
+[[EchoBASE]]
 |
-[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414596 RefSeq:NP_414596]
+EchoBASE:
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"

lptD:Gene Product(s): Difference between revisions

Latest revision as of 22:52, 20 May 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

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lptD:Gene Product(s): Difference between revisions

Latest revision as of 22:52, 20 May 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

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