exbD:Gene Product(s): Difference between revisions

Standard name	ExbD
Synonyms	membrane spanning protein in TonB-ExbB-ExbD complex^[1], B3005^[2]^[1], ExbD^[2]^[1] , ECK2998, JW2973, b3005
Product description	ExbD uptake of enterochelin; tonB-dependent uptake of B colicins^[2]^[3]; Component of TonB energy transducing system^[3]; Outer Membrane Ferric Citrate Transport System^[3]; Outer Membrane Ferrichrome Transport System^[3]; Outer Membrane Ferric Enterobactin Transport System^[3]; vitamin B12 outer membrane transport complex^[3]; ferric dicitrate uptake system^[3]; ferrichrome uptake system^[3]; Ferric Enterobactin Transport System^[3]; vitamin B12 transport system^[3] Uptake of enterochelin; resistance or sensitivity to colicins; similarity with TolR^[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:0005215	transporter activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003400	F	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-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:0006810	transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003400	P	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: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:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003400	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: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-9906	C	Seeded from EcoCyc (v14.0)	complete
	GO:0043213	bacteriocin transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0080	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
Protein	Subunits of TonB energy transducing system	could be indirect
Protein	groS		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	ihfA		PMID:19402753^[5]	LCMS(ID Probability):99.4
Protein	cspC		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	dps		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	rplJ		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	acpP		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	ompA		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	fimA		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	arpA		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	adk		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	efp		PMID:19402753^[5]	LCMS(ID Probability):99.0
Protein	osmY		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	rplL		PMID:19402753^[5]	LCMS(ID Probability):99.6
Protein	Subunits of Outer Membrane Ferric Citrate Transport System	could be indirect
Protein	Subunits of Outer Membrane Ferrichrome Transport System	could be indirect
Protein	Subunits of Outer Membrane Ferric Enterobactin Transport System	could be indirect
Protein	Subunits of vitamin B12 outer membrane transport complex	could be indirect
Protein	Subunits of ferric dicitrate uptake system	could be indirect
Protein	Subunits of ferrichrome uptake system	could be indirect
Protein	Subunits of Ferric Enterobactin Transport System	could be indirect
Protein	Subunits of vitamin B12 transport system	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
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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 MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP EKPVYLSVKA DNSMFIGNDP VTDETMITAL NALTEGKKDT TIFFRADKTV DYETLMKVMD TLHQAGYLKI GLVGEETAKA K
Length	141
Mol. Wt	15.526 kDa
pI	4.6 (calculated)
Extinction coefficient	4,470 (calc based on 3 Y, 0 W, and 0 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
Domain	11..137	PF02472 Biopolymer transport protein ExbD/TolR		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=exbD 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:16130903	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946345	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009866	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABV2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10272	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946345	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000266	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0268	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.00 ^5.01 ^5.02 ^5.03 ^5.04 ^5.05 ^5.06 ^5.07 ^5.08 ^5.09 ^5.10 ^5.11 ^5.12 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

exbD:Gene Product(s): Difference between revisions

Latest revision as of 20:58, 17 February 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

@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-membrane spanning protein in TonB-ExbB-ExbD complex<ref name='LIB:Riley_2006'/>, B3005<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ExbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''membrane spanning protein in TonB-ExbB-ExbD complex<ref name='LIB:Riley_2006'/>, B3005<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, ExbD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2998, JW2973, b3005''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 77: / Line 77: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="P46aacbdb0c784"  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="P46aacbdb0c784"  class=" tableEdit GO_table_product dataTable"
 |- {{table_heading_style}}
-!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
+!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
 |-
 |
@@ Line 303: / Line 303: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="N46aacbe122baf"  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="N46aacbe122baf"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 317: / Line 317: @@
 |
+|-
+|
+Protein
+|
+groS
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+ihfA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.4
+|-
+|
+Protein
+|
+cspC
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+dps
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rplJ
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+acpP
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+ompA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+fimA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+arpA
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+adk
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+efp
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.0
+|-
+|
+Protein
+|
+osmY
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rplL
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
 |-
 |
@@ Line 423: / Line 566: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="E46a860b1d3602"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a860b1d3602"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 449: / Line 592: @@
 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="N46aacbe9b6fb2"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 472: / Line 619: @@
 !align=left {{table heading style}} |Extinction coefficient
 ||
-,470 (calc based on 3 Y,  W, and  C residues)
+,470 (calc based on 3 Y, 0 W, and 0 C residues)
 |- class="tableEdit_footer"
@@ Line 489: / Line 636: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="H46aacbea33ecf"  class=" tableEdit Product_motif_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46aacbea33ecf"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
@@ Line 500: / Line 647: @@
 [http://pfam.janelia.org/family/PF02472 PF02472  Biopolymer transport protein ExbD/TolR]
 |
-[http://pfam.janelia.org/protein/P0ABV2 Pfam:P0ABV2]
 |
+PMID:19920124
 |- class="tableEdit_footer"
@@ Line 538: / Line 685: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P0ABV2 Protein Model Portal]
-* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
+* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0ABV2 PSI-PRED (P0ABV2)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0ABV2 Genomes TO Protein (P0ABV2)] (GTOP)
-* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
-* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
 |- class="tableEdit_footer"
@@ Line 583: / Line 728: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="K46aacbeb038a8"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aacbeb038a8"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 605: / Line 750: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="Z46aacbeb6345e"  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="Z46aacbeb6345e"  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=EG10272-MONOMER EcoCyc:EG10272-MONOMER]
+[http://www.ncbi.nlm.nih.gov/protein/16130903 GI:16130903]
 |
+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_417478.1 GeneID:946345]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0009866
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P0ABV2 UniProtKB/Swiss-Prot:P0ABV2]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG10272
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG10272
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[[uniprot:P0ABV2|UniProt:P0ABV2]]
+[http://www.ncbi.nlm.nih.gov/gene?term=946345 GeneID:946345]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.sanger.ac.uk/family?acc=PF02472 PFAM:PF02472]
+RegulonDB:ECK120000266
 |
+''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_417478 RefSeq:NP_417478]
+EchoBASE:EB0268
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 655: / Line 835: @@
 *
 ****************************************************************************************** -->
-{|   id="Z46a860b6337a6"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a860b6337a6"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
@@ Line 676: / Line 856: @@
 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0015404_!_ion-gradient-driven energizer activity]][[Category:GO:0006826_!_iron ion transport]][[Category:Complex:TonB energy transducing system]][[Category:Complex:Outer Membrane Ferric Citrate Transport System]][[Category:Complex:Outer Membrane Ferrichrome Transport System]][[Category:Complex:Outer Membrane Ferric Enterobactin Transport System]][[Category:Complex:vitamin B12 outer membrane transport complex]][[Category:Complex:ferric dicitrate uptake system]][[Category:Complex:ferrichrome uptake system]][[Category:Complex:Ferric Enterobactin Transport System]][[Category:Complex:vitamin B12 transport system]]
-[[Category:Pfam:PF02472_!_Biopolymer transport protein ExbD/TolR]]

exbD:Gene Product(s): Difference between revisions

Latest revision as of 20:58, 17 February 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

Search