fpr:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{| id="Y46aa02632dea8"  class=" tableEdit Gene_nomenclature_table"   
{|   id="Y46aa02632dea8"  class=" tableEdit Gene_nomenclature_table"   


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{|   id="P46aa0263b0d82"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46aa0263b0d82"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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88.62 minutes 
88.62 minutes 
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MG1655: 4112495..4111749<br />{{GBrowseFigureByCoord|4111749|4112495|ecoli|MG1655}}
MG1655: 4112495..4111749<br /><gbrowseImage>
name=NC_000913:4111749..4112495
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10628 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10628 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4110749|4113495|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4110749|4113495|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|4111749|4112495|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4111749|4112495|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10628 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10628 EcoCyc Sequence Dump]  
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NC_012967: 4093954..4093208<br />{{GBrowseFigureByCoord|4093208|4093954|REL606|NC_012967}}
NC_012967: 4093954..4093208<br /><gbrowseImage>
name=NC_012967:4093208..4093954
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|4093208|4093954|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|4093208|4093954|GBrowse (REL606)}}
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NC_012759: 4001418..4002164<br />{{GBrowseFigureByCoord|4001418|4002164|BW2952|NC_012759}}
NC_012759: 4001418..4002164<br /><gbrowseImage>
name=NC_012759:4001418..4002164
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|4001418|NC_4002164|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|4001418|4002164|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|4001418|NC_4002164|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|4001418|4002164|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 3522209..3522955<br />{{GBrowseFigureByCoord|3522209|3522955|ecoli_W3110|W3110}}
W3110: 3522209..3522955<br /><gbrowseImage>
name=NC_007779:3522209..3522955
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|3521209|3523955|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3521209|3523955|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3522209|3522955|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3522209|3522955|FASTA Dump}}  
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DH10B: 4212192..4211446<br />{{GBrowseFigureByCoord|4211446|4212192|ecoli_DH10B|DH10B}}
DH10B: 4212192..4211446<br /><gbrowseImage>
name=NC_010473:4211446..4212192
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|4209954|4213684|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4209954|4213684|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4209954|4213684|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4209954|4213684|FASTA Dump}}  


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{|   id="N46aa026476837"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aa026476837"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4111752
|
Edman degradation
|
PMID:7642583<br />PMID:7961651<br />PMID:8449868<br />
|


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{| {{Prettytable}} id="T46aa0264c1886"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="T46aa0264c1886"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18407.M4e04bb61efbe7-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04bb61efbe7"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18407.M4e04bb61efbe7&page=18407&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="J46aa0265883f4"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46aa0265883f4"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCCCAGTAATGCTCCGCTGTCAT  
Primer 2:CCCCAGTAATGCTCCGCTGTCAT  
|-
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[[:Category:Kohara_Phage:4H12|4H12]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=539 Genobase]
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PMID:3038334
|-
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[[:Category:Kohara_Phage:8B10|8B10]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=540 Genobase]
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PMID:3038334
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{|   id="M46aa026634db9"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa026634db9"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10628 EcoCyc:EG10628]
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|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1480 EchoBASE:EB1480]
EcoCyc:EG10628
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3924 EcoliGenExpDB:b3924]
EcoGene:EG10628
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C4876 ECOL199310CYC:C4876]
RegulonDB:ECK120000621
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10628 EcoGene:EG10628]
[http://www.ncbi.nlm.nih.gov/gene?term=948414 GeneID:948414]
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=FPR ECOO157CYC:FPR]
EchoBASE:EB1480
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012818&formSubmitReturn=1 ASAP:ABE-0012818]
ASAP:ABE-0012818
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a71bfee79c2"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:50, 19 September 2013

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

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

fpr

Mnemonic

Ferredoxin NADP+ reductase

Synonyms

ECK3916, b3924, JW3895, mvrA, flxR, G7964[1][2]

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Notes

Location(s) and DNA Sequence

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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

88.62 minutes 

MG1655: 4112495..4111749
<gbrowseImage> name=NC_000913:4111749..4112495 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4093954..4093208
<gbrowseImage> name=NC_012967:4093208..4093954 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4001418..4002164
<gbrowseImage> name=NC_012759:4001418..4002164 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3522209..3522955
<gbrowseImage> name=NC_007779:3522209..3522955 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4212192..4211446
<gbrowseImage> name=NC_010473:4211446..4212192 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

Coding Start (SO:0000323)

MG1655

4111752

Edman degradation

PMID:7642583[3]
PMID:7961651[4]
PMID:8449868[5]


edit table


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

Δfpr (Keio:JW3895)

deletion

deletion

PMID:16738554[6]

Shigen
CGSC10810[7]

Δfpr-783::kan

PMID:16738554[6]

CGSC:100988

Strain BW2952

G126A

PMID:19376874[8]

Relative to MG1655.

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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

[back to top]


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

Resource Resource Type Source Notes/Reference

JW3895

Plasmid clone

Shigen

PMID:16769691[9]

Status:Clone OK

Primer 1:GCCGCTGATTGGGTAACAGGCAA

Primer 2:CCCCAGTAATGCTCCGCTGTCAT

4H12

Kohara Phage

Genobase

PMID:3038334[10]

8B10

Kohara Phage

Genobase

PMID:3038334[10]

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[7]

est. P1 cotransduction: 12% [11]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[7]

est. P1 cotransduction: 29% [11]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG10628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000621

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948414

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1480

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012818

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Birch, OM et al. (1995) Biotin synthase from Escherichia coli, an investigation of the low molecular weight and protein components required for activity in vitro. J. Biol. Chem. 270 19158-65 PubMed
  4. ↑ Jenkins, CM & Waterman, MR (1994) Flavodoxin and NADPH-flavodoxin reductase from Escherichia coli support bovine cytochrome P450c17 hydroxylase activities. J. Biol. Chem. 269 27401-8 PubMed
  5. ↑ Bianchi, V et al. (1993) Escherichia coli ferredoxin NADP+ reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein. J. Bacteriol. 175 1590-5 PubMed
  6. ↑ 6.0 6.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  7. ↑ 7.0 7.1 7.2 CGSC: The Coli Genetics Stock Center
  8. ↑ Ferenci, T et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191 4025-9 PubMed
  9. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
  10. ↑ 10.0 10.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  11. ↑ 11.0 11.1 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).

Categories

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