msrA: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="B46aa0a375e8ae"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''msrA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''msrA''
Methionine sulfoxide reductase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4215, b4219, JW4178, pmsR, pms''<ref name='LIB:Riley_2006'/>, pms''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19003.B46aa0a375e8ae&page=19003&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK4215, b4219, JW4178, pmsR, pms''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46aa0a37e29ac"  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
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95.69 minutes&nbsp;
95.69 minutes&nbsp;
|
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MG1655: 4440199..4439561<br />{{GBrowseFigureByCoord|4438561|4441199|ecoli|MG1655}}
MG1655: 4440199..4439561<br /><gbrowseImage>
name=NC_000913:4439561..4440199
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11433 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11433 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4438561|4441199|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4438561|4441199|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4439561..4440199&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4439561|4440199|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11433 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11433 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 4425933..4425295<br /><gbrowseImage>
name=NC_012967:4425295..4425933
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4425295|4425933|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4425295|4425933|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4378296..4378934<br /><gbrowseImage>
name=NC_012759:4378296..4378934
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4378296|4378934|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|4378296|4378934|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4446856..4446218<br />{{GBrowseFigureByCoord|4445218|4447856|ecoli_W3110|W3110}}  
W3110: 4446856..4446218<br /><gbrowseImage>
name=NC_007779:4446218..4446856
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4445218|4447856|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|4446218|4446856|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 4540561..4539923<br /><gbrowseImage>
name=NC_010473:4539923..4540561
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|4445218|4447856|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|4538647|4541837|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4446218..4446856&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4538647|4541837|FASTA Dump}}
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===Notes===
===Notes===
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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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Coding Start (SO:0000323)
|
[[MG1655]]
|
4439564
|
Edman degradation
|
PMID:1386361<br />
|
 
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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="P46aa0a3902da0"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!|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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|
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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=109289 CGSC11008]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109289 CGSC11008]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
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msrAC52S
|
|
C52S
|
|
Loss of activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A744 UniProt:P0A744]
|-
|
msrAC87S
|
|
C87S
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A744 UniProt:P0A744]
|-
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msrAC199S
|
|
C199S
|
|
Decrease in activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A744 UniProt:P0A744]
|-
|
msrAC207S
|
|
C207S
|
|
Decrease in activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A744 UniProt:P0A744]
|-  
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:101958|CGSC:101958]]
[[cgscmutation:101958|CGSC:101958]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19003.P46aa0a3902da0&page=19003&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}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H4e04bfa788604"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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!Resource!!Resource Type!!Source!!Notes/Reference
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JW4178
JW4178
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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:CCTGCTTCCGGCGGCAGACAGAC  
Primer 2:CCTGCTTCCGGCGGCAGACAGAC  
|-
|-
|
[[:Category:Kohara_Phage:5B5|5B5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=656 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:E1H3|E1H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=657 Genobase]
|
PMID:3038334
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[[cycA:Gene|cycA30::Tn10]]
[[cycA:Gene|cycA30::Tn10]]
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|
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est. P1 cotransduction: 63% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 63% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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[[ytfN:Gene|zjf-920::Tn10]]
[[ytfN:Gene|zjf-920::Tn10]]
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CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 84% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 84% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjh-901::Tn10, zjg-920::Tn10


Synonyms:zjh-901::Tn10, zjg-920::Tn10
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===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aa0a3a6e866"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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!|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=EG11433 EcoCyc:EG11433]
EcoCyc:EG11433
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1403 EchoBASE:EB1403]
EcoGene:EG11433
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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]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4219 EcoliGenExpDB:b4219]
RegulonDB:ECK120001397
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5317 ECOL199310CYC:C5317]
[http://www.ncbi.nlm.nih.gov/gene?term=948734 GeneID:948734]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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|
[http://ecogene.org/geneinfo.php?eg_id=EG11433 EcoGene:EG11433]
EchoBASE:EB1403
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
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[http://BioCyc.org/ECOO157/new-image?object=MSRA ECOO157CYC:MSRA]
ASAP:ABE-0013804
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/34400 CGSC:34400]
|
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013804&formSubmitReturn=1 ASAP:ABE-0013804]
|


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===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:msr genes]]
[[Category:msr genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:52, 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

msrA

Mnemonic

Methionine sulfoxide reductase

Synonyms

ECK4215, b4219, JW4178, pmsR, pms[1], pms

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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

95.69 minutes 

MG1655: 4440199..4439561
<gbrowseImage> name=NC_000913:4439561..4440199 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4425933..4425295
<gbrowseImage> name=NC_012967:4425295..4425933 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4378296..4378934
<gbrowseImage> name=NC_012759:4378296..4378934 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4446856..4446218
<gbrowseImage> name=NC_007779:4446218..4446856 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4540561..4539923
<gbrowseImage> name=NC_010473:4539923..4540561 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

4439564

Edman degradation

PMID:1386361[2]


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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

ΔmsrA (Keio:JW4178)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC11008[4]

msrAC52S

C52S

Loss of activity

seeded from UniProt:P0A744

msrAC87S

C87S

No effect

seeded from UniProt:P0A744

msrAC199S

C199S

Decrease in activity

seeded from UniProt:P0A744

msrAC207S

C207S

Decrease in activity

seeded from UniProt:P0A744

ΔmsrA768::kan

PMID:16738554[3]

CGSC:101958


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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

JW4178

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGTTTATTTGATAAAAAGCA

Primer 2:CCTGCTTCCGGCGGCAGACAGAC

5B5

Kohara Phage

Genobase

PMID:3038334[6]

E1H3

Kohara Phage

Genobase

PMID:3038334[6]

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[4]

est. P1 cotransduction: 63% [7]

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[4]

est. P1 cotransduction: 84% [7]
Synonyms:zjh-901::Tn10, zjg-920::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:EG11433

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11433

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001397

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948734

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1403

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013804

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. ↑ Rahman, MA et al. (1992) Cloning, sequencing, and expression of the Escherichia coli peptide methionine sulfoxide reductase gene. J. Biol. Chem. 267 15549-51 PubMed
  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. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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