pitA: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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{|{{Prettytable}}
{|  id="Z46a9f746e5217"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''pitA''  
''pitA''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Pi transport
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3478, b3493, JW3460, pit, G442''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3478, b3493, JW3460, pit, G442''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='145797'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9f747724e6"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
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MG1655
MG1655
Line 72: Line 76:
78.36 minutes&nbsp;
78.36 minutes&nbsp;
|
|
MG1655: 3635665..3637164<br />{{GBrowseFigureByCoord|3634665|3638164|ecoli|MG1655}}
MG1655: 3635665..3637164<br /><gbrowseImage>
name=NC_000913:3635665..3637164
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12230 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12230 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3634665..3638164 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3634665|3638164|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3635665..3637164&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3635665|3637164|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12230 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12230 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3568331..3569830<br /><gbrowseImage>
name=NC_012967:3568331..3569830
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3568331|3569830|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3568331|3569830|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3524159..3525658<br /><gbrowseImage>
name=NC_012759:3524159..3525658
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3524159|3525658|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3524159|3525658|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4002773..4001274<br />{{GBrowseFigureByCoord|4000274|4003773|ecoli_W3110|W3110}}  
W3110: 4002773..4001274<br /><gbrowseImage>
name=NC_007779:4001274..4002773
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4000274|4003773|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4001274|4002773|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 3733410..3734909<br /><gbrowseImage>
name=NC_010473:3733410..3734909
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4000274..4003773 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3730412|3737907|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4001274..4002773&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3730412|3737907|FASTA Dump}}
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='145798'
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="S46a9f7487d7d0"  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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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108844 CGSC10563]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108844 CGSC10563]<ref name='LIB:cgsc'/>  
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[[PMID:4570598]]<ref name=PMID:4570598/> [[PMID:4568763]]<ref name=PMID:4568763/>
PMID:4570598 PMID:4568763
|
|
[[cgscmutation:5633|CGSC:5633]]
[[cgscmutation:5633|CGSC:5633]]
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[[cgscmutation:102374|CGSC:102374]]
[[cgscmutation:102374|CGSC:102374]]
|
|
   
   
|-
|
''pit'' in strain UR13
|
68 minutes
|
|
Resistant to
|
Resistant to arsenate
|
PMID:4919964
|
Strain: UR13
|
table 1
|-
|
''pit'' in strain 10B5
|
68 minutes
|


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Auxotrophies
|
''sn''-glycerol-3-phosphate auxotroph
|
PMID:4919964
|
Strain: UR13
|
table 1
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17531.S46a9f7487d7d0&page=17531&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17531.A4e04c127332ca-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW3460
JW3460
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCaAGGAACTGCAAGGAGAGCCA  
Primer 2:CCaAGGAACTGCAAGGAGAGCCA  
|-
|-
|
[[:Category:Kohara_Phage:12E4|12E4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=608 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6A4|6A4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=609 Genobase]
|
PMID:3038334
|-  
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zhg-50::Tn10
zhg-50::Tn10
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CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 14% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
|-
|-  
|
|
zic-4901::Tn10
zic-4901::Tn10
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12230 EcoCyc:EG12230]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2142 EchoBASE:EB2142]
EcoCyc:EG12230
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3493 EcoliGenExpDB:b3493]
EcoGene:EG12230
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4291 ECOL199310CYC:C4291]
RegulonDB:ECK120002114
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12230 EcoGene:EG12230]
[http://www.ncbi.nlm.nih.gov/gene?term=948009 GeneID:948009]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PITA ECOO157CYC:PITA]
EchoBASE:EB2142
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011407&formSubmitReturn=1 ASAP:ABE-0011407] 
ASAP:ABE-0011407
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:pit genes]]
[[Category:pit genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:48, 19 September 2013

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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

pitA

Mnemonic

Pi transport

Synonyms

ECK3478, b3493, JW3460, pit, G442[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

78.36 minutes 

MG1655: 3635665..3637164
<gbrowseImage> name=NC_000913:3635665..3637164 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3568331..3569830
<gbrowseImage> name=NC_012967:3568331..3569830 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3524159..3525658
<gbrowseImage> name=NC_012759:3524159..3525658 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4002773..4001274
<gbrowseImage> name=NC_007779:4001274..4002773 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3733410..3734909
<gbrowseImage> name=NC_010473:3733410..3734909 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

ΔpitA (Keio:JW3460)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10563[4]

pitA10

PMID:4570598[5] PMID:4568763[6]

CGSC:5633

pitA1

CGSC:15787

ΔpitA749::kan

PMID:16738554[3]

CGSC:102374

pit in strain UR13

68 minutes

Resistant to

Resistant to arsenate

PMID:4919964[7]

Strain: UR13

table 1

pit in strain 10B5

68 minutes

Auxotrophies

sn-glycerol-3-phosphate auxotroph

PMID:4919964[7]

Strain: UR13

table 1

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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

JW3460

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCCTACATTTGTTTGCTGGCCT

Primer 2:CCaAGGAACTGCAAGGAGAGCCA

12E4

Kohara Phage

Genobase

PMID:3038334[9]

6A4

Kohara Phage

Genobase

PMID:3038334[9]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 14% [10]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: % [10]

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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:EG12230

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12230

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002114

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948009

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2142

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011407

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. ↑ 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. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Willsky, GR et al. (1973) Inorganic phosphate transport in Escherichia coli: involvement of two genes which play a role in alkaline phosphatase regulation. J. Bacteriol. 113 529-39 PubMed
  6. ↑ Bachmann, BJ (1972) Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev 36 525-57 PubMed
  7. ↑ 7.0 7.1 Bennett, RL & Malamy, MH (1970) Arsenate resistant mutants of Escherichia coli and phosphate transport. Biochem. Biophys. Res. Commun. 40 496-503 PubMed
  8. ↑ 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
  9. ↑ 9.0 9.1 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
  10. ↑ 10.0 10.1 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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