EcoliWiki - User contributions [en]

PMID:9776741

2007-11-08T18:28:06Z

Bhahn: New PMID: Page!

<protect>
{{RightTOC}}

 '''Davies, GP, Powell, LM, Webb, JL, Cooper, LP and Murray, NE''' (1998) EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities.''Nucleic Acids Res.'' '''26''':4828-36

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || For type I restriction systems, recently determined nucleotide sequences predict conserved amino acids in the subunit that is essential for restriction but not modification (HsdR). The conserved sequences emphasize motifs characteristic of the DEAD-box family of proteins which comprises putative helicases, and they identify a new candidate for motif IV. We provide evidence based on an analysis of Eco KI which supports both the relevance of DEAD-box motifs to the mechanism of restriction and the new definition of motif IV. Amino acid substitutions within the newly identified motif IV and those in six other previously identified DEAD-box motifs, but not in the original motif IV, confer restriction-deficient phenotypes. We have examined the relevance of the DEAD-box motifs to the restriction pathway by determining the steps permitted in vitro by the defective enzymes resulting from amino acid substitutions in each of the seven motifs. Eco KI purified from the seven restriction-deficient mutants binds to an unmethylated target sequence and, in the presence of AdoMet, responds to ATP by undergoing the conformational change essential for the pathway of events leading to DNA cleavage. The seven enzymes have little or no ATPase activity and no endonuclease activity, but they retain the ability to nick unmodified DNA, though at reduced rates. Nicking of a DNA strand could therefore be an essential early step in the restriction pathway, facilitating the ATP-dependent translocation of DNA, particularly if this involves DNA helicase activity.
</noinclude>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9776741 PubMed]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' {{Prettytable}} id='221864'
|- {{table heading style}}
!Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.V4733553607909&page=0&pagename={{FULLPAGENAMEE}} edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==References==
{{RefHelp}}
<references/>

hsdR:Gene

2007-11-08T18:27:56Z

Bhahn: edited by Bhahn via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|hsdR}}{{Tab On|Gene|hsdR}}{{Tab|Gene Product(s)|hsdR}}{{Tab|Expression|hsdR}}{{Tab|Evolution|hsdR}}{{Tab|On One Page|hsdR}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''hsdR''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024&page=19251&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='150964'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
98.74 minutes 
|
MG1655: 4584838..4581272 {{GBrowseFigureByCoord|4580272|4585838|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10459 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4580272..4585838 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4581272..4584838&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG10459 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 4591495..4587929 {{GBrowseFigureByCoord|4586929|4592495|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4586929..4592495 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4587929..4591495&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150965'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150966'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔhsdR (Keio:JW4313)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] [http://cgsc2.biology.yale.edu/Strain.php?ID=109364 CGSC11083]<ref name='LIB:cgsc'/>
|

|-
|
hsdRΔ4
|
deletion
|
deletion
|

|
Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity
|
[[PMID:9776741]]<ref name=PMID:9776741/>
|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.D46aa0d47dca5e&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150967'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW4313
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCTTATGGGCgTTAAATATTTGGACAGGCCCG

Primer 2:CCGGCCAGCTCGTCCCAGATATA
|-
|
[[ytfN:Gene|zjf-920::Tn10]]
|
Linked marker
|
CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zjh-901::Tn10, zjg-920::Tn10
|-
|
[[mdoB:Gene|mdoB202::Tn10]]
|
Linked marker
|
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zjj-202::Tn10, zji-202::Tn10
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150968'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10459 EcoCyc:EG10459]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0454 EchoBASE:EB0454]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4350 EcoliGenExpDB:b4350]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C5425 ECOL199310CYC:C5425]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10459 EcoGene:EG10459]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=Z5948 ECOO157CYC:Z5948]
|

|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/620 CGSC:620]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.F46aa0d4955d6d&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='100446'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

hsdR:Gene

2007-11-08T18:27:26Z

Bhahn: edited by Bhahn via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|hsdR}}{{Tab On|Gene|hsdR}}{{Tab|Gene Product(s)|hsdR}}{{Tab|Expression|hsdR}}{{Tab|Evolution|hsdR}}{{Tab|On One Page|hsdR}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''hsdR''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024&page=19251&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='150964'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
98.74 minutes 
|
MG1655: 4584838..4581272 {{GBrowseFigureByCoord|4580272|4585838|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10459 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4580272..4585838 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4581272..4584838&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG10459 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 4591495..4587929 {{GBrowseFigureByCoord|4586929|4592495|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4586929..4592495 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4587929..4591495&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150965'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150966'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔhsdR (Keio:JW4313)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] [http://cgsc2.biology.yale.edu/Strain.php?ID=109364 CGSC11083]<ref name='LIB:cgsc'/>
|

|-
|
hsdRΔ4
|
deletion
|
deletion
|

|
Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity
|

|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.D46aa0d47dca5e&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150967'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW4313
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCTTATGGGCgTTAAATATTTGGACAGGCCCG

Primer 2:CCGGCCAGCTCGTCCCAGATATA
|-
|
[[ytfN:Gene|zjf-920::Tn10]]
|
Linked marker
|
CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zjh-901::Tn10, zjg-920::Tn10
|-
|
[[mdoB:Gene|mdoB202::Tn10]]
|
Linked marker
|
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zjj-202::Tn10, zji-202::Tn10
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='150968'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10459 EcoCyc:EG10459]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0454 EchoBASE:EB0454]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4350 EcoliGenExpDB:b4350]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C5425 ECOL199310CYC:C5425]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10459 EcoGene:EG10459]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=Z5948 ECOO157CYC:Z5948]
|

|-
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/620 CGSC:620]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.F46aa0d4955d6d&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='100446'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

<noinclude><protect>
==References==
{{BacktoTop}}
{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

ompT:Gene

2007-11-06T19:59:16Z

Bhahn: edited by Bhahn via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|ompT}}{{Tab On|Gene|ompT}}{{Tab|Gene Product(s)|ompT}}{{Tab|Expression|ompT}}{{Tab|Evolution|ompT}}{{Tab|On One Page|ompT}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''ompT''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK0557, b0565, JW0554''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11691.J46a9b395bf746&page=11691&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='128273'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
12.58 minutes 
|
MG1655: 584856..583903 {{GBrowseFigureByCoord|582903|585856|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10673 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:582903..585856 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:583903..584856&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=EG10673 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 584856..583903 {{GBrowseFigureByCoord|582903|585856|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:582903..585856 GBrowse(W3110)]
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:583903..584856&plugin_action=Go FASTA Dump]
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</protect>
===Notes===

==Sequence Features==
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|- {{table_heading_style}}
!Feature type!!Location!!Description
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{{Gene_sequence_features_help}}
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====Notes====

==Alleles and Phenotypes==
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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ΔompT (Keio:JW0554)
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deletion
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deletion
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[[PMID:16738554]]<ref name=PMID:16738554/>
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] [http://cgsc2.biology.yale.edu/Strain.php?ID=106961 CGSC8680]<ref name='LIB:cgsc'/>
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|-
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ΔompT
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deletion
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deletion
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lack ompT protease activity. lack the ability to cleave between specific paired basic amino acids
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[[PMID:17880914]]<ref name=PMID:17880914/>
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===Notes===

==Genetic Resources==
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{|class = 'sortable' {{Prettytable}} id='128276'
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW0554
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Plasmid clone
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCCGGGCGAAACTTCTGGGAAT

Primer 2:CCAAATGTGTACTTAAGACCAGC
|-
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[[purK:Gene|purK79::Tn10]]
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Linked marker
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:purE79::Tn10
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[[dsbG:Gene|dsbG601::Tn10]]
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Linked marker
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CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zbd-601::Tn10, zbe-601::Tn10
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{{Gene_resources_help}}
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===Notes===

==Accessions in Other Databases==
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{|class = 'sortable' {{Prettytable}} id='128277'
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!Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10673 EcoCyc:EG10673]
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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=EB0667 EchoBASE:EB0667]
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|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0565 EcoliGenExpDB:b0565]
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|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C0652 ECOL199310CYC:C0652]
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|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG10673 EcoGene:EG10673]
|

|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=Z1931 ECOO157CYC:Z1931]
|

|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/4984 CGSC:4984]
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{{Gene_accessions_help}}
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===Notes===

==Links==
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!Name!!URL!!Comments
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{{Links_help}}

<noinclude><protect>
==References==
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{{RefHelp}}
<references/>
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]