rutG:On One Page

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

Quickview

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Standard Name

rutG

Gene Synonym(s)

ycdG, ECK0997, b1006, JW5137[1][2], JW5137

Product Desc.

predicted xanthine/uracil transporter[2][3]

Putative pyrimidine permease, pyrimidine nitrogen catabolism[4]

Product Synonyms(s)

predicted transporter[1], B1006[2][1], YcdG[2][1], RutG[2][1] , ECK0997, JW5137, ycdG, b1006

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rutABCDEFG[2]

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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NtrC regulon. The rut operon is required for the utilization of thymidine, uridine and cytidine as nitrogen sources at 37C, but not at room temperature.[4]



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

rutG

Mnemonic

PyRimidine UTilization

Synonyms

ycdG, ECK0997, b1006, JW5137[1][2], JW5137

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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

23.01 minutes 

MG1655: 1069062..1067734
<gbrowseImage> name=NC_000913:1067734..1069062 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1084795..1086123
<gbrowseImage> name=NC_012967:1084795..1086123 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 970702..972030
<gbrowseImage> name=NC_012759:970702..972030 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1070261..1068933
<gbrowseImage> name=NC_007779:1068933..1070261 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1122990..1121662
<gbrowseImage> name=NC_010473:1121662..1122990 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

ΔycdG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

rutG3::FLK2(lacZ,kan)

PMID:12142427

CGSC:87258

ΔrutG4

PMID:12142427

CGSC:87261

ΔrutG750::kan

PMID:16738554

CGSC:103966


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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

5A12

Kohara Phage

Genobase

PMID:3038334

7B5

Kohara Phage

Genobase

PMID:3038334

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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:G6517

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13853

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003117

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946589

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3613

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003401

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

YcdG

Synonyms

predicted transporter[1], B1006[2][1], YcdG[2][1], RutG[2][1] , ECK0997, JW5137, ycdG, b1006

Product description

predicted xanthine/uracil transporter[2][3]

Putative pyrimidine permease, pyrimidine nitrogen catabolism[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:IPR006042

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006043

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:IPR006042

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006043

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:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006042

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006043

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

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006042

P

Seeded from EcoCyc (v14.0)

complete

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006043

P

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

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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

plasma membrane

C-terminus localized in the cytoplasm with 11 predicted transmembrane domains

Daley et al. (2005) [5]


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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

MVRSQLSRAD APCLLTSLRR QLMAMFGFPH WQLKSTSTES GVVAPDERLP FAQTAVMGVQ
HAVAMFGATV LMPILMGLDP NLSILMSGIG TLLFFFITGG RVPSYLGSSA AFVGVVIAAT
GFNGQGINPN ISIALGGIIA CGLVYTVIGL VVMKIGTRWI ERLMPPVVTG AVVMAIGLNL
APIAVKSVSA SAFDSWMAVM TVLCIGLVAV FTRGMIQRLL ILVGLIVACL LYGVMTNVLG
LGKAVDFTLV SHAAWFGLPH FSTPAFNGQA MMLIAPVAVI LVAENLGHLK AVAGMTGRNM
DPYMGRAFVG DGLATMLSGS VGGSGVTTYA ENIGVMAVTK VYSTLVFVAA AVIAMLLGFS
PKFGALIHTI PAAVIGGASI VVFGLIAVAG ARIWVQNRVD LSQNGNLIMV AVTLVLGAGD
FALTLGGFTL GGIGTATFGA ILLNALLSRK LVDVPPPEVV HQEP
Length

464

Mol. Wt

48.054 kDa

pI

9.5 (calculated)

Extinction coefficient

36,440 - 36,940 (calc based on 6 Y, 5 W, and 4 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

30..404

PF00860 Permease family

PMID:19920124

<motif_map/>

tmhmm.php?gene=rutG&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=rutG 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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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:90111201

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946589

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003401

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75892

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6517

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13853

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946589

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003117

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3613

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

2a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

5

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

0a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

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)

rutABCDEFG

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_000913:1069042..1069082 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


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

Type Reference Notes

microarray

GEO Profiles:b1006 (EcoliWiki Page)

NCBI GEO profiles for rutG

microarray

GenExpDB:b1006 (EcoliWiki Page)

Summary of data for rutG 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

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Notes

Accessions Related to rutG Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6517

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3613

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1006

EcoGene

EcoGene:EG13853

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003117

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003401

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Dictyostelium discoideum

  • DDB0215824 (score: 1.000; bootstrap: 100%)
  • DDB0203378 (score: 0.337)

From Inparanoid:20070104

Shigella flexneri

YCDG

From SHIGELLACYC

E. coli O157

YCDG

From ECOO157CYC


Do-It-Yourself Web Tools

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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)

PF00860 Permease family

EcoCyc

EcoCyc:G6517

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13853

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003117

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3613

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003401

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. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

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