amiC: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="M46a9e6f89b98f"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''amiC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''amiC''
amidase
Amidase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2813, b2817, JW5449, ygdN''<ref name='LIB:Riley_2006'/>, ygdN''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16201.M46a9e6f89b98f&page=16201&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK2813, b2817, JW5449, ygdN''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16201.M46a9e6f89b98f&page=16201&pagename={{FULLPAGENAMEE}} edit table]
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='141800'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9e6f926039"  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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[[BW2952]]
|
 
|
NC_012759: 2832927..2834180<br /><gbrowseImage>
name=NC_012759:2832927..2834180
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2832927|2834180|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2832927|2834180|FASTA Dump}}
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MG1655
MG1655
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63.49 minutes&nbsp;
63.49 minutes&nbsp;
|
|
MG1655: 2947032..2945779<br />{{GBrowseFigureByCoord|2944779|2948032|ecoli|MG1655}}
MG1655: 2947032..2945779<br /><gbrowseImage>
name=NC_000913:2945779..2947032
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7458 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7458 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2944779..2948032 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2944779|2948032|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2945779..2947032&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2945779|2947032|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7458 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7458 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2843629..2842376<br /><gbrowseImage>
name=NC_012967:2842376..2843629
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2842376|2843629|GBrowse (REL606)}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2947666..2946413<br />{{GBrowseFigureByCoord|2945413|2948666|ecoli_W3110|W3110}}  
W3110: 2947666..2946413<br /><gbrowseImage>
name=NC_007779:2946413..2947666
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2945413|2948666|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2946413|2947666|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2945413..2948666 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2946413..2947666&plugin_action=Go FASTA Dump]
 
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DH10B: 3040902..3039649<br /><gbrowseImage>
name=NC_010473:3039649..3040902
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3037143|3043408|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3037143|3043408|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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====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="Q46a9e6fa28342"  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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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109676 CGSC11395]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109676 CGSC11395]<ref name='LIB:cgsc'/>  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:99994|CGSC:99994]]
[[cgscmutation:99994|CGSC:99994]]
|
|
   
   
|-
|
''∆amiC::Kan''
|
|
|
Colony Morphology
|
20-30% of the population exists as chains of 3 to 6 unseparated cells.
|
PMID:11454209
|
|
|-
|
ΔamiC ΔamiA ΔamiB
|
deletion
|
deletion
|
Cell Shape
|
defect in cell separation
|
PMID:19525345
|
|
|-
|
''amiC(del)''
|
in frame single deletion
|


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Sensitivity to
|
Increase susceptibility to protamine when compared to wild-type. fig 2.
|
PMID:21149452
|
Wildtype parent: BW25113
|
|-
|
''amiABC''(del)
|
 
|
 
|
Growth Phenotype
|
when Supplying cells with the cell-wall precursor murein tripeptide (AeK) labeled with NBD accumulation of AeK-NBD occurs at division site indicating labeled precursors are utilized for septal peptidoglycan synthesis and amiC activity is mainly responsible for the rapid removal of labeled murein peptides at division sites as indicated by double mutant ''amiAB''(del), figure 7.
|
PMID:21472954
|
 
|
|-
|
''amiAB''(del)
|
 
|
 
|
Cell Shape
|
amiC activity is mainly responsible for the rapid removal of labeled murein peptides at division sites as indicated by double mutant ''amiAB''(del), figure 7.
|
 
|
 
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW5449
JW5449
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTCCCCTTCTCGCCAGCGTCGC  
Primer 2:CCTCCCCTTCTCGCCAGCGTCGC  
|-
|-
|
[[:Category:Kohara_Phage:9A12|9A12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=458 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10B6|10B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=459 Genobase]
|
PMID:3038334
|-  
|
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[[fucP:Gene|fucP3072::Tn10]]
[[fucP:Gene|fucP3072::Tn10]]
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CAG12079 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38034 CGSC7427]<ref name='LIB:cgsc'/>
CAG12079 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38034 CGSC7427]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:fuc-3072::Tn10  
Synonyms:fuc-3072::Tn10  
|-
|-  
|
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[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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|
|
est. P1 cotransduction: 85% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 85% <ref name='LIB:Nichols_linked_Tn'/>  
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===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=G7458 EcoCyc:G7458] 
EcoCyc:G7458
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2895 EchoBASE:EB2895] 
EcoGene:EG13086
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2817 EcoliGenExpDB:b2817] 
RegulonDB:ECK120004021
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=C3411 ECOL199310CYC:C3411]
[http://www.ncbi.nlm.nih.gov/gene?term=947293 GeneID:947293]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13086 EcoGene:EG13086] 
EchoBASE:EB2895
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z4134 ECOO157CYC:Z4134] 
ASAP:ABE-0009238
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:ami genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

amiC

Mnemonic

amidase Amidase

Synonyms

ECK2813, b2817, JW5449, ygdN[1], ygdN

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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

BW2952

NC_012759: 2832927..2834180
<gbrowseImage> name=NC_012759:2832927..2834180 source=BW2952 preset=GeneLocation </gbrowseImage>

MG1655

63.49 minutes 

MG1655: 2947032..2945779
<gbrowseImage> name=NC_000913:2945779..2947032 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2843629..2842376
<gbrowseImage> name=NC_012967:2842376..2843629 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2947666..2946413
<gbrowseImage> name=NC_007779:2946413..2947666 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3040902..3039649
<gbrowseImage> name=NC_010473:3039649..3040902 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

ΔamiC (Keio:JW5449)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11395[3]

ΔamiC742::kan

PMID:16738554[2]

CGSC:99994

∆amiC::Kan

Colony Morphology

20-30% of the population exists as chains of 3 to 6 unseparated cells.

PMID:11454209[4]

ΔamiC ΔamiA ΔamiB

deletion

deletion

Cell Shape

defect in cell separation

PMID:19525345[5]

amiC(del)

in frame single deletion

Sensitivity to

Increase susceptibility to protamine when compared to wild-type. fig 2.

PMID:21149452[6]

Wildtype parent: BW25113

amiABC(del)

Growth Phenotype

when Supplying cells with the cell-wall precursor murein tripeptide (AeK) labeled with NBD accumulation of AeK-NBD occurs at division site indicating labeled precursors are utilized for septal peptidoglycan synthesis and amiC activity is mainly responsible for the rapid removal of labeled murein peptides at division sites as indicated by double mutant amiAB(del), figure 7.

PMID:21472954[7]

amiAB(del)

Cell Shape

amiC activity is mainly responsible for the rapid removal of labeled murein peptides at division sites as indicated by double mutant amiAB(del), figure 7.


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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

JW5449

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCTCAGGATCCAACACTGCAAT

Primer 2:CCTCCCCTTCTCGCCAGCGTCGC

9A12

Kohara Phage

Genobase

PMID:3038334[9]

10B6

Kohara Phage

Genobase

PMID:3038334[9]

fucP3072::Tn10

Linked marker

CAG12079 = CGSC7427[3]

est. P1 cotransduction: 62% [10]
Synonyms:fuc-3072::Tn10

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 85% [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:G7458

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13086

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004021

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947293

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2895

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009238

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ Heidrich, C et al. (2001) Involvement of N-acetylmuramyl-L-alanine amidases in cell separation and antibiotic-induced autolysis of Escherichia coli. Mol. Microbiol. 41 167-78 PubMed
  5. ↑ Uehara, T et al. (2009) LytM-domain factors are required for daughter cell separation and rapid ampicillin-induced lysis in Escherichia coli. J. Bacteriol. 191 5094-107 PubMed
  6. ↑ Weatherspoon-Griffin, N et al. (2011) The CpxR/CpxA two-component system up-regulates two Tat-dependent peptidoglycan amidases to confer bacterial resistance to antimicrobial peptide. J. Biol. Chem. 286 5529-39 PubMed
  7. ↑ Olrichs, NK et al. (2011) A novel in vivo cell-wall labeling approach sheds new light on peptidoglycan synthesis in Escherichia coli. Chembiochem 12 1124-33 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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