panF: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

panF

Gene Synonym(s)

ECK3245, b3258, JW3226[1], JW3226

Product Desc.

PanF sodium/pantothenate SSS transporter[2][3]

Pantothenate permease[4]

Product Synonyms(s)

pantothenate:sodium symporter[1], B3258[2][1], PanF[2][1] , ECK3245, JW3226, b3258

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yhdT-panF-prmA[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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PanF is a symporter.[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

panF

Mnemonic

Pantothenate

Synonyms

ECK3245, b3258, JW3226[1], JW3226

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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

73.4 minutes 

MG1655: 3405629..3407080
<gbrowseImage> name=NC_000913:3405629..3407080 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3335498..3336949
<gbrowseImage> name=NC_012967:3335498..3336949 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3292777..3294228
<gbrowseImage> name=NC_012759:3292777..3294228 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3407462..3408913
<gbrowseImage> name=NC_007779:3407462..3408913 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3503374..3504825
<gbrowseImage> name=NC_010473:3503374..3504825 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

ΔpanF (Keio:JW3226)

deletion

deletion

PMID:16738554

Shigen
CGSC10440[5]

panF::Tn5KAN-I-SceI (FB21087)

Insertion at nt 1277 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21087

contains pKD46

panF::Tn5KAN-I-SceI (FB21088)

Insertion at nt 1277 in Plus orientation

PMID:15262929

E. coli Genome Project:FB21088

does not contain pKD46

panF11

PMID:2995306

CGSC:10713

ΔpanF776::kan

PMID:16738554

CGSC:102254


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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

JW3226

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAGCTTGAAGTAATTCTACC

Primer 2:CCTTTATCAGTAGTCAAAACGGT

6G3

Kohara Phage

Genobase

PMID:3038334

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[5]

est. P1 cotransduction: 17% [6]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[5]

est. P1 cotransduction: 73% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG10685

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10685

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000678

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947752

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0679

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010695

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

PanF

Synonyms

pantothenate:sodium symporter[1], B3258[2][1], PanF[2][1] , ECK3245, JW3226, b3258

Product description

PanF sodium/pantothenate SSS transporter[2][3]

Pantothenate permease[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:IPR001734

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018212

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:IPR001734

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018212

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:0006811

ion transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0406

P

Seeded from EcoCyc (v14.0)

complete

GO:0006814

sodium ion transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

P

Seeded from EcoCyc (v14.0)

complete

GO:0006814

sodium ion transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0739

P

Seeded from EcoCyc (v14.0)

complete

GO:0015081

sodium ion transmembrane transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

F

Seeded from EcoCyc (v14.0)

complete

GO:0015233

pantothenate transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

F

Seeded from EcoCyc (v14.0)

complete

GO:0015293

symporter activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0769

F

Seeded from EcoCyc (v14.0)

complete

GO:0015887

pantothenate transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001734

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018212

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

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:0031402

sodium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011849

F

Seeded from EcoCyc (v14.0)

complete

GO:0031402

sodium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0915

F

Seeded from EcoCyc (v14.0)

complete

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001734

P

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
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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 13 predicted transmembrane domains

Daley et al. (2005) [7]

plasma membrane

From EcoCyc[3]


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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 

MTMQLEVILP LVAYLVVVFG ISVYAMRKRS TGTFLNEYFL GSRSMGGIVL AMTLTATYIS
ASSFIGGPGA AYKYGLGWVL LAMIQLPAVW LSLGILGKKF AILARRYNAV TLNDMLFARY
QSRLLVWLAS LSLLVAFVGA MTVQFIGGAR LLETAAGIPY ETGLLIFGIS IALYTAFGGF
RASVLNDTMQ GLVMLIGTVV LLIGVVHAAG GLSNAVQTLQ TIDPQLVTPQ GADDILSPAF
MTSFWVLVCF GVIGLPHTAV RCISYKDSKA VHRGIIIGTI VVAILMFGMH LAGALGRAVI
PDLTVPDLVI PTLMVKVLPP FAAGIFLAAP MAAIMSTINA QLLQSSATII KDLYLNIRPD
QMQNETRLKR MSAVITLVLG ALLLLAAWKP PEMIIWLNLL AFGGLEAVFL WPLVLGLYWE
RANAKGALSA MIVGGVLYAV LATLNIQYLG FHPIVPSLLL SLLAFLVGNR FGTSVPQATV
LTTDK
Length

485

Mol. Wt

51.951 kDa

pI

9.9 (calculated)

Extinction coefficient

66,350 - 66,600 (calc based on 15 Y, 8 W, and 2 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

36..432

PF00474 Sodium:solute symporter family

PMID:19920124

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<motif_map/>

tmhmm.php?gene=panF&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=panF 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:90111565

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947752

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010695

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P16256

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10685

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10685

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947752

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000678

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0679

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

382

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

29

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

58

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)

yhdT-panF-prmA

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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_000913:3405609..3405649 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:b3258 (EcoliWiki Page)

NCBI GEO profiles for panF

microarray

GenExpDB:b3258 (EcoliWiki Page)

Summary of data for panF 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 panF Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10685

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0679

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3258

EcoGene

EcoGene:EG10685

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000678

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010695

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

  • ENSANGP00000011580 (score: 1.000; bootstrap: 69%)
  • ENSANGP00000011955 (score: 0.570)
  • ENSANGP00000023805 (score: 0.356)
  • ENSANGP00000010569 (score: 0.321)
  • ENSANGP00000002287 (score: 0.304)
  • ENSANGP00000019520 (score: 0.282)
  • ENSANGP00000012870 (score: 0.266)
  • ENSANGP00000019502 (score: 0.257)
  • ENSANGP00000022454 (score: 0.166)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000010240 (score: 1.000; bootstrap: 61%)
  • ENSAPMP00000007743 (score: 0.441)
  • ENSAPMP00000003219 (score: 0.295)
  • ENSAPMP00000007399 (score: 0.274)
  • ENSAPMP00000016151 (score: 0.167)
  • ENSAPMP00000032180 (score: 0.100)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00028503 (score: 1.000; bootstrap: 56%)
  • WBGene00025216 (score: 0.060)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00014092 (score: 1.000; bootstrap: 57%)
  • WBGene00018716 (score: 0.056)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0037895 (score: 1.000; bootstrap: 75%)
  • FBgn0035293 (score: 1.000; bootstrap: 73%)
  • FBgn0029950 (score: 0.471)
  • FBgn0051090 (score: 0.384)
  • FBgn0031998 (score: 0.315)
  • FBgn0017448 (score: 0.277)
  • FBgn0039872 (score: 0.253)
  • FBgn0039873 (score: 0.247)
  • FBgn0039394 (score: 0.245)
  • FBgn0053124 (score: 0.244)
  • FBgn0052669 (score: 0.219)
  • FBgn0034494 (score: 0.207)
  • FBgn0051668 (score: 0.190)
  • FBgn0051262 (score: 0.176)
  • FBgn0039391 (score: 0.167)
  • FBgn0039393 (score: 0.135)
  • FBgn0038652 (score: 0.116)
  • FBgn0039390 (score: 0.073)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21946-PA (score: 1.000; bootstrap: 65%)
  • GA21442-PA (score: 0.273)
  • GA15290-PA (score: 0.223)
  • GA17054-PA (score: 0.213)
  • GA21420-PA (score: 0.172)
  • GA20543-PA (score: 0.161)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC8693c (score: 1.000; bootstrap: 100%)
  • SPBPB8B62c (score: 0.454)
  • SPBC23G73c (score: 0.352)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000132536 (score: 1.000; bootstrap: 47%)
  • NEWSINFRUP00000139147 (score: 0.363)
  • NEWSINFRUP00000165007 (score: 0.340)
  • NEWSINFRUP00000165433 (score: 0.337)
  • NEWSINFRUP00000143770 (score: 0.303)
  • NEWSINFRUP00000181937 (score: 0.297)
  • NEWSINFRUP00000182500 (score: 0.262)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000044878 (score: 1.000; bootstrap: 82%)

From Inparanoid:20070104

Shigella flexneri

PANF

From SHIGELLACYC

E. coli O157

PANF

From ECOO157CYC

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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

Panther (EcoliWiki Page)

PTHR11819:SF14

Pfam (EcoliWiki Page)

PF00474 Sodium:solute symporter family

EcoCyc

EcoCyc:EG10685

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10685

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000678

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0679

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010695

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 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 3.2 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. ↑ 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).
  7. ↑ 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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