oppF:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

oppF

Gene Synonym(s)

ECK1241, b1247, JW1239[1], JW1239

Product Desc.

OppF[2][3];

Component of oligopeptide ABC transporter[2][3]

Oligopeptide transpor, ATP-binding protein[4]

Product Synonyms(s)

oligopeptide transporter subunit[1], ATP-binding component of ABC superfamily[1], B1247[2][1], OppF[2][1] , ECK1241, JW1239, b1247

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): oppABCDF[2], OP00313, oppABCD

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

oppF

Mnemonic

Oligopeptide permease

Synonyms

ECK1241, b1247, JW1239[1], JW1239

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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

28.1 minutes 

MG1655: 1303788..1304792
<gbrowseImage> name=NC_000913:1303788..1304792 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1303358..1304362
<gbrowseImage> name=NC_012967:1303358..1304362 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1194637..1195641
<gbrowseImage> name=NC_012759:1194637..1195641 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1307478..1308482
<gbrowseImage> name=NC_007779:1307478..1308482 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1344806..1345810
<gbrowseImage> name=NC_010473:1344806..1345810 source=DH10B preset=GeneLocation </gbrowseImage>

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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) Phenotype: Type Phenotype: Description Reference Availability Comments

Strain DH10B

S325A

Nonsynonomous mutation

PMID:18245285

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔoppF (Keio:JW1239)

deletion

deletion

PMID:16738554

Shigen
CGSC9118[5]

ΔoppF754::kan

PMID:16738554

CGSC:102198


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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

JW1239

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATGCTGTAACTGAAGGAAG

Primer 2:CCAAGCGGATCGACTTTCAGGCA

14C4

Kohara Phage

Genobase

PMID:3038334

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[5]

est. P1 cotransduction: 100% [6]
Synonyms:zch-506::Tn10, zci-506::Tn10

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[5]

est. P1 cotransduction: 62% [6]
Synonyms:trpB83::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:EG10678

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10678

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000671

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945818

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0672

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004182

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

OppF

Synonyms

oligopeptide transporter subunit[1], ATP-binding component of ABC superfamily[1], B1247[2][1], OppF[2][1] , ECK1241, JW1239, b1247

Product description

OppF[2][3];

Component of oligopeptide ABC transporter[2][3]

Oligopeptide transpor, 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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013563

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

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: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:0015197

peptide transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010066

F

Seeded from EcoCyc (v14.0)

complete

GO:0015833

peptide transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010066

P

Seeded from EcoCyc (v14.0)

complete

GO:0015833

peptide transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013563

P

Seeded from EcoCyc (v14.0)

complete

GO:0015833

peptide transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0571

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

Protein

nadE

PMID:16606699

Experiment(s):EBI-1139302

Protein

groL

PMID:16606699

Experiment(s):EBI-1139302

Protein

mglB

PMID:16606699

Experiment(s):EBI-1139302

Protein

lrp

PMID:16606699

Experiment(s):EBI-1139302
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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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<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 

MNAVTEGRKV LLEIADLKVH FEIKDGKQWF WQPPKTLKAV DGVTLRLYEG ETLGVVGESG
CGKSTFARAI IGLVKATDGH VAWLGKELLG MKPDEWRAVR SDIQMIFQDP LASLNPRMTI
GEIIAEPLRT YHPKMSRQEV RERVKAMMLK VGLLPNLINR YPHEFSGGQC QRIGIARALI
LEPKLIICDE PVSALDVSIQ AQVVNLLQQL QREMGLSLIF IAHDLAVVKH ISDRVLVMYL
GHAVELGTYD EVYHNPLHPY TRALMSAVPI PDPDLEKNKT IQLLEGELPS PINPPSGCVF
RTRCPIAGPE CAKTRPVLEG SFRHSVSCLK VDPL
Length

334

Mol. Wt

37.197 kDa

pI

7.8 (calculated)

Extinction coefficient

32,430 - 33,305 (calc based on 7 Y, 4 W, and 7 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

64..193

PF00005 ABC transporter

PMID:19920124

Domain

244..311

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=oppF 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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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:16129208

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945818

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004182

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77737

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10678

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10678

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945818

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000671

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0672

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

E. coli K-12 MG1655

3935

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

485

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

2830

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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<protect>

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_000913:1303768..1303808 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:b1247 (EcoliWiki Page)

NCBI GEO profiles for oppF

microarray

GenExpDB:b1247 (EcoliWiki Page)

Summary of data for oppF 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 oppF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10678

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0672

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1247

EcoGene

EcoGene:EG10678

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000671

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004182

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

Anopheles gambiae

  • ENSANGP00000000682 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022364001 (score: 1.000; bootstrap: 56%)
  • GSTENP00030600001 (score: 0.153)
  • GSTENP00019589001 (score: 0.144)
  • GSTENP00022664001 (score: 0.133)
  • GSTENP00012322001 (score: 0.120)
  • GSTENP00012676001 (score: 0.120)
  • GSTENP00011937001 (score: 0.119)
  • GSTENP00008809001 (score: 0.087)
  • GSTENP00036523001 (score: 0.082)
  • GSTENP00029830001 (score: 0.064)
  • GSTENP00006944001 (score: 0.063)
  • GSTENP00019587001 (score: 0.058)
  • YP_025300 (score: 0.098)

From Inparanoid:20070104

Shigella flexneri

OPPF

From SHIGELLACYC

E. coli O157

OPPF

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

Pfam (EcoliWiki Page)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF08352 Oligopeptide/dipeptide transporter, C-terminal region

EcoCyc

EcoCyc:EG10678

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10678

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000671

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0672

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004182

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 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. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).

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