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Expression|

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Standard Name	oppD
Gene Synonym(s)	ECK1240, b1246, JW1238^[1], JW1238
Product Desc.	OppD^[2]^[3]; Component of oligopeptide ABC transporter^[2]^[3] Oligopeptide transport, ATP-binding protein^[4]
Product Synonyms(s)	oligopeptide transporter subunit^[1], ATP-binding component of ABC superfamily^[1], B1246^[2]^[1], OppD^[2]^[1] , ECK1240, JW1238, b1246
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): oppABCDF^[2], OP00313, oppABCD
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	oppD
Mnemonic	Oligopeptide permease
Synonyms	ECK1240, b1246, JW1238^[1], JW1238
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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	28.08 minutes	MG1655: 1302778..1303791 <gbrowseImage> name=NC_000913:1302778..1303791 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1302348..1303361 <gbrowseImage> name=NC_012967:1302348..1303361 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1193627..1194640 <gbrowseImage> name=NC_012759:1193627..1194640 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1306468..1307481 <gbrowseImage> name=NC_007779:1306468..1307481 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1343796..1344809 <gbrowseImage> name=NC_010473:1343796..1344809 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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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	Comments
ΔoppD (Keio:JW1238)	deletion	deletion	PMID:16738554	Shigen CGSC9117^[5]
oppD::Tn5KAN-2 (FB20274)	Insertion at nt 731 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20274	does not contain pKD46
ΔoppD753::kan			PMID:16738554	CGSC:102196
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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
JW1238	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGTAATTGAAACTGCAAC Primer 2:CCTAACAGTTCCTCCACCGGTTT
3D5	Kohara Phage	Genobase	PMID:3038334
14C4	Kohara Phage	Genobase	PMID:3038334
fadR13::Tn10	Linked marker	CAG18497 = CGSC7365^[5]	est. P1 cotransduction: 2% ^[6]
oppC506::Tn10	Linked marker	CAG12169 = CGSC7369^[5]	est. P1 cotransduction: 97% ^[6] Synonyms:zch-506::Tn10, zci-506::Tn10
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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:EG10677	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10677	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000670	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945802	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0671	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004178	Escherichia coli str. K-12 substr. MG1655
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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	OppD
Synonyms	oligopeptide transporter subunit^[1], ATP-binding component of ABC superfamily^[1], B1246^[2]^[1], OppD^[2]^[1] , ECK1240, JW1238, b1246
Product description	OppD^[2]^[3]; Component of oligopeptide ABC transporter^[2]^[3] Oligopeptide transport, ATP-binding protein^[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:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010066	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013563	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	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: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:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003439	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016887	ATPase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017871	F	Seeded from EcoCyc (v14.0)	complete
	GO:0017111	nucleoside-triphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	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 oligopeptide ABC transporter	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
Cytoplasm		PMID:3926486	EchoLocation:oppD
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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 MSVIETATVP LAQQQADALL NVKDLRVTFS TPDGDVTAVN DLNFSLRAGE TLGIVGESGS GKSQTAFALM GLLAANGRIG GSATFNGREI LNLPEHELNK LRAEQISMIF QDPMTSLNPY MRVGEQLMEV LMLHKNMSKA EAFEESVRML DAVKMPEARK RMKMYPHEFS GGMRQRVMIA MALLCRPKLL IADEPTTALD VTVQAQIMTL LNELKREFNT AIIMITHDLV VVAGICDKVL VMYAGRTMEY GNARDVFYQP VHPYSIGLLN AVPRLDAEGE TMLTIPGNPP NLLRLPKGCP FQPRCPHAME ICSSAPPLEE FTPGRLRACF KPVEELL
Length	337
Mol. Wt	37.188 kDa
pI	6.0 (calculated)
Extinction coefficient	8,940 - 9,690 (calc based on 6 Y, 0 W, and 6 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	References
Domain	65..197	PF00005 ABC transporter	PMID:19920124
Domain	248..312	PF08352 Oligopeptide/dipeptide transporter, C-terminal region	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=oppD 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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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:49176090	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945802	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004178	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76027	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10677	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10677	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945802	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000670	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0671	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	Reference(s)
Protein	E. coli K-12 MG1655	3522	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	474	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	3431	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)
oppABCDF
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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_000913:1302758..1302798 source=MG1655 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:b1246 (EcoliWiki Page)	NCBI GEO profiles for oppD
microarray	GenExpDB:b1246 (EcoliWiki Page)	Summary of data for oppD 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 oppD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10677	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0671	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1246
EcoGene	EcoGene:EG10677	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000670	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004178	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	OPPD	From SHIGELLACYC
E. coli O157	OPPD	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)	PF00005 ABC transporter
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Panther (EcoliWiki Page)	PTHR24220:SF108
Pfam (EcoliWiki Page)	PF08352 Oligopeptide/dipeptide transporter, C-terminal region
EcoCyc	EcoCyc:EG10677	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10677	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000670	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0671	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0004178	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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↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 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 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).

oppD: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 oppD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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