xanQ: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

xanQ

Gene Synonym(s)

ECK2878, b2882, JW2850, ygfO[1], JW2850, ygfO

Product Desc.

YgfO NCS2 transporter[2][3]

Xanthine permease[4] [5]

Product Synonyms(s)

predicted transporter[1], B2882[2][1], YgfO[2][1][6] , ECK2878, JW2850, ygfO, b2882

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): xanQ[2]

Regulation/Activity
Quick Links

porteco.png

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

edit table

</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

xanQ

Mnemonic

Xanthine

Synonyms

ECK2878, b2882, JW2850, ygfO[1], JW2850, ygfO

edit table

</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

65.14 minutes 

MG1655: 3022373..3023773
<gbrowseImage> name=NC_000913:3022373..3023773 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2910105..2911505
<gbrowseImage> name=NC_012967:2910105..2911505 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2909521..2910921
<gbrowseImage> name=NC_012759:2909521..2910921 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3023007..3024407
<gbrowseImage> name=NC_007779:3023007..3024407 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3116243..3117643
<gbrowseImage> name=NC_010473:3116243..3117643 source=DH10B preset=GeneLocation </gbrowseImage>

edit table

</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
edit table

<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

ΔygfO (Keio:JW2850)

deletion

deletion

PMID:16738554

Shigen
CGSC10214[7]

ΔygfO733::kan

PMID:16738554

CGSC:104972


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</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

JW2850

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGATATAAACCATGCAGG

Primer 2:CCATCCATCTCTTCCGCTGAGGT

6A1

Kohara Phage

Genobase

PMID:3038334

5B4

Kohara Phage

Genobase

PMID:3038334

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[7]

est. P1 cotransduction: 1% [8]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[7]

est. P1 cotransduction: 3% [8]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

edit table

<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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2882

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3460

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YGFO

EcoCyc (EcoliWiki Page)

ECOCYC:G7501

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949075

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

edit table

<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

XanQ

Synonyms

predicted transporter[1], B2882[2][1], YgfO[2][1][6] , ECK2878, JW2850, ygfO, b2882

Product description

YgfO NCS2 transporter[2][3]

Xanthine permease[4] [5]

EC number (for enzymes)


edit table

<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:0005887

integral to plasma membrane

PMID:16096267

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0042906

xanthine transport

PMID:16096267

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0042907

xanthine transmembrane transporter activity

PMID:16096267

IDA: Inferred from Direct Assay

F

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

edit table

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
edit table

</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 12 predicted transmembrane domains

Daley et al. (2005) [9]

plasma membrane


edit table

<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 

M SDINHAGSDL IFELEDRPPF HQALVGAITH LLAIFVPMVT
PALIVGAALQ LSAETTAYLV SMAMIASGIG TWLQVNRYGI VGSGLLSIQS VNFSFVTVMI
ALGSSMKSDG FHEELIMSSL LGVSFVGAFL VVGSSFILPY LRRVITPTVS GIVVLMIGLS
LIKVGIIDFG GGFAAKSSGT FGNYEHLGVG LLVLIVVIGF NCCRSPLLRM GGIAIGLCVG
YIASLCLGMV DFSSMRNLPL ITIPHPFKYG FSFSFHQFLV VGTIYLLSVL EAVGDITATA
MVSRRPIQGE EYQSRLKGGV LADGLVSVIA SAVGSLPLTT FAQNNGVIQM TGVASRYVGR
TIAVMLVILG LFPMIGGFFT TIPSAVLGGA MTLMFSMIAI AGIRIIITNG LKRRETLIVA
TSLGLGLGVS YDPEIFKILP ASIYVLVENP ICAGGLTAIL LNIILPGGYR QENVLPGITS
AEEMD
Length

466

Mol. Wt

49.109 kDa

pI

6.9 (calculated)

Extinction coefficient

23,380 - 24,005 (calc based on 12 Y, 1 W, and 5 C residues)

edit table


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

22..416

PF00860 Permease family

PMID:19920124

edit table

<motif_map/>

tmhmm.php?gene=ygfO&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=ygfO taxon=562,83333 </beststructure>

Models

View models at:

edit table
</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
edit table

<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:90111507

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949075

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P67444

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949075

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

edit table

<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

1a

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

3

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

edit table

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)

ygfO

edit table
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_000913:3022353..3022393 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
edit table


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

Type Reference Notes

microarray

GEO Profiles:b2882 (EcoliWiki Page)

NCBI GEO profiles for ygfO

microarray

GenExpDB:b2882 (EcoliWiki Page)

Summary of data for ygfO from multiple microarray studies

edit table


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

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to xanQ Expression

[back to top]


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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2882

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

edit table

<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

Caenorhabditis briggsae

  • WBGene00031101 (score: 1.000; bootstrap: 100%)
  • WBGene00039175 (score: 0.307)
  • WBGene00030168 (score: 0.291)
  • WBGene00030171 (score: 0.288)
  • WBGene00024937 (score: 0.277)
  • WBGene00030153 (score: 0.253)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00011595 (score: 1.000; bootstrap: 100%)
  • WBGene00011593 (score: 0.812)
  • WBGene00011596 (score: 0.492)
  • WBGene00020004 (score: 0.431)
  • WBGene00021994 (score: 0.308)
  • WBGene00008252 (score: 0.247)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0037807 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19493-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000026307 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000001345 (score: 0.233)
  • ENSMMUP00000003100 (score: 0.089)
  • ENSMMUP00000001065 (score: 0.056)

From Inparanoid:20070104

Mus musculus

  • MGI:1859682 (score: 1.000; bootstrap: 100%)
  • MGI:1341903 (score: 0.562)
  • MGI:1917272 (score: 0.158)
  • MGI:104516 (score: 0.137)

From Inparanoid:20070104

Oryza gramene

  • Q6Z257 (score: 1.000; bootstrap: 100%)
  • Q6ZIE6 (score: 1.000; bootstrap: 100%)
  • Q6H5A2 (score: 0.874)
  • Q6Z7R7 (score: 0.827)
  • Q94DT2 (score: 0.808)
  • Q852B5 (score: 0.798)
  • Q41760 (score: 0.547)
  • Q851K4 (score: 0.529)
  • Q7XHQ9 (score: 0.081)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000028885 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000027048 (score: 0.564)
  • ENSRNOP00000030381 (score: 0.157)
  • ENSRNOP00000024667 (score: 0.133)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC13991c (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

YGFO

From ECOO157CYC

edit table


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

Panther (EcoliWiki Page)

PTHR11119:SF3

Pfam (EcoliWiki Page)

PF00860 Permease family

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

edit table

<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 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 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 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 Karatza, P & Frillingos, S () Cloning and functional characterization of two bacterial members of the NAT/NCS2 family in Escherichia coli. Mol. Membr. Biol. 22 251-61 PubMed
  6. ↑ 6.0 6.1 Karena, E & Frillingos, S (2009) Role of intramembrane polar residues in the YgfO xanthine permease: HIS-31 and ASN-93 are crucial for affinity and specificity, and ASP-304 and GLU-272 are irreplaceable. J. Biol. Chem. 284 24257-68 PubMed
  7. ↑ 7.0 7.1 7.2 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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).
  9. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=xanQ:On_One_Page&oldid=944413"