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Standard Name	exbD
Gene Synonym(s)	ECK2998, b3005, JW2973^[1], JW2973
Product Desc.	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]
Product Synonyms(s)	membrane spanning protein in TonB-ExbB-ExbD complex^[1], B3005^[2]^[1], ExbD^[2]^[1] , ECK2998, JW2973, b3005
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): exbD^[2], exbBD^[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	exbD
Mnemonic	Export
Synonyms	ECK2998, b3005, JW2973^[1], JW2973
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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	67.87 minutes	MG1655: 3149265..3148840 <gbrowseImage> name=NC_000913:3148840..3149265 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3085415..3084990 <gbrowseImage> name=NC_012967:3084990..3085415 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3035988..3036413 <gbrowseImage> name=NC_012759:3035988..3036413 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3149899..3149474 <gbrowseImage> name=NC_007779:3149474..3149899 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3247010..3246585 <gbrowseImage> name=NC_010473:3246585..3247010 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)	Reference	Availability
ΔexbD (Keio:JW2973)	deletion	deletion	PMID:16738554	Shigen CGSC10284^[5]
ΔexbD778::kan			PMID:16738554	CGSC:100766
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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
JW2973	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCAATGCATCTTAACGAAAA Primer 2:CCtTTCGCTTTGGCGGTTTCTTC
5C10	Kohara Phage	Genobase	PMID:3038334
6H4	Kohara Phage	Genobase	PMID:3038334
nupG511::Tn10	Linked marker	CAG18472 = CGSC7433^[5]	est. P1 cotransduction: 14% ^[6]
metC162::Tn10	Linked marker	CAG18475 = CGSC7435^[5]	est. P1 cotransduction: 95% ^[6]
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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:EG10272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000266	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946345	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0268	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009866	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	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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<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: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	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
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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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 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
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<motif_map/>

Structure
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Structures

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

Models

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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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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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	Reference(s)
Protein	E. coli K-12 MG1655	941	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	298	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	182	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)
exbD
exbBD
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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_000913:3149245..3149285 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:b3005 (EcoliWiki Page)	NCBI GEO profiles for exbD
microarray	GenExpDB:b3005 (EcoliWiki Page)	Summary of data for exbD 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 exbD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10272	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0268	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3005
EcoGene	EcoGene:EG10272	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000266	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009866	Escherichia coli str. K-12 substr. MG1655
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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	EXBD	From SHIGELLACYC
E. coli O157	EXBD	From ECOO157CYC
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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)	PF02472 Biopolymer transport protein ExbD/TolR
EcoCyc	EcoCyc:EG10272	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10272	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
ASAP	ASAP:ABE-0009866	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 ^1.5 ^1.6 ^1.7 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 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 ^3.10 ^3.11 ^3.12 ^3.13 ^3.14 ^3.15 ^3.16 ^3.17 ^3.18 ^3.19 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

exbD:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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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 exbD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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