oppC:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

oppC

Gene Synonym(s)

ECK1239, b1245, JW1237[1], JW1237, stkB

Product Desc.

OppC[2][3];

Component of oligopeptide ABC transporter[2][3]

Oligopeptide transport, permease[4]

Product Synonyms(s)

oligopeptide transporter subunit[1], membrane component of ABC superfamily[1], B1245[2][1], OppC[2][1] , ECK1239, JW1237, stkB, b1245

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  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

oppC

Mnemonic

Oligopeptide permease

Synonyms

ECK1239, b1245, JW1237[1], JW1237, stkB

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

28.06 minutes 

MG1655: 1301858..1302766
<gbrowseImage> name=NC_000913:1301858..1302766 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1301428..1302336
<gbrowseImage> name=NC_012967:1301428..1302336 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1190894..1191076
<gbrowseImage> name=NC_012759:1190894..1191076 source=BW2952 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1192707..1193615
<gbrowseImage> name=NC_012759:1192707..1193615 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1305548..1306456
<gbrowseImage> name=NC_007779:1305548..1306456 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1342876..1343784
<gbrowseImage> name=NC_010473:1342876..1343784 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔoppC (Keio:JW1237)

deletion

deletion

PMID:16738554

Shigen
CGSC9116[5]

oppC506::Tn10

Insertion at 1,302,475 bp in MG1655 (NC_000913)

adapted from Nichols et al.[6]

CAG12169 = CGSC7369[5]

Synonyms: zch-506::Tn10, zci-506::Tn10

oppC506::Tn10

PMID:9829956

CGSC:9940

oppC3117::Tn10kan

PMID:2540407 PMID:9829956

CGSC:38030

ΔoppC752::kan

PMID:16738554

CGSC:102194


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

</protect>

Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW1237

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATGTTAAGTAAGAAAAACAG

Primer 2:CCACGATCTTTCGGGTCGAGGGC

3D5

Kohara Phage

Genobase

PMID:3038334

14C4

Kohara Phage

Genobase

PMID:3038334

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[5]

est. P1 cotransduction: 2% [6]

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[5]

est. P1 cotransduction: 57% [6]
Synonyms:trpB83::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10676

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10676

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000669

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945810

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0670

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004176

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

OppC

Synonyms

oligopeptide transporter subunit[1], membrane component of ABC superfamily[1], B1245[2][1], OppC[2][1] , ECK1239, JW1237, stkB, b1245

Product description

OppC[2][3];

Component of oligopeptide ABC transporter[2][3]

Oligopeptide transport, permease[4]

EC number (for enzymes)


<protect></protect>

Notes

Function

[back to top]


<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:IPR000515

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:IPR000515

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:IPR000515

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-9909

C

Seeded from EcoCyc (v14.0)

complete

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


</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

plasma membrane

C-terminus localized in the cytoplasm with 6 predicted transmembrane domains

Daley et al. (2005) [7]


<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MMLSKKNSET LENFSEKLEV EGRSLWQDAR RRFMHNRAAV ASLIVLVLIA LFVILAPMLS
QFAYDDTDWA MMSSAPDMES GHYFGTDSSG RDLLVRVAIG GRISLMVGVA AALVAVVVGT
LYGSLSGYLG GKVDSVMMRL LEILNSFPFM FFVILLVTFF GQNILLIFVA IGMVSWLDMA
RIVRGQTLSL KRKEFIEAAQ VGGVSTSGIV IRHIVPNVLG VVVVYASLLV PSMILFESFL
SFLGLGTQEP LSSWGALLSD GANSMEVSPW LLLFPAGFLV VTLFCFNFIG DGLRDALDPK DR
Length

302

Mol. Wt

33.022 kDa

pI

5.4 (calculated)

Extinction coefficient

34,950 - 35,075 (calc based on 5 Y, 5 W, and 1 C residues)


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

115..302

PF00528 Binding-protein-dependent transport system inner membrane component

PMID:19920124

<motif_map/>

tmhmm.php?gene=oppC&show=pic&.jpg
Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129206

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945810

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004176

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFH6

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10676

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10676

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945810

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000669

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0670

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

2612

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

261

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

1586

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

oppABCDF

Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:1301838..1301878 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1245 (EcoliWiki Page)

NCBI GEO profiles for oppC

microarray

GenExpDB:b1245 (EcoliWiki Page)

Summary of data for oppC from multiple microarray studies


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to oppC Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10676

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0670

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1245

EcoGene

EcoGene:EG10676

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000669

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004176

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Apis mellifera

  • ENSAPMP00000032452 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

OPPC

From SHIGELLACYC

E. coli O157

OPPC

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00528 Binding-protein-dependent transport system inner membrane component

EcoCyc

EcoCyc:EG10676

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10676

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000669

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0670

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004176

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 5.3 CGSC: The Coli Genetics Stock Center
  6. 6.0 6.1 6.2 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).
  7. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

[back to top]