murA:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|murA}}{{Tab On|Gene|murA}}{{Tab|Gene Product(s)|murA}}{{Tab|Expression|murA}}{{Tab|Evolution|murA}}{{Tab|On One Page|murA}}{{TabsBottom}}
{{Tab|Quickview|murA}}{{Tab On|Gene|murA}}{{Tab|Gene Product(s)|murA}}{{Tab|Expression|murA}}{{Tab|Evolution|murA}}{{Tab|On One Page|murA}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''murA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''murA''
Murein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3178, b3189, JW3156, mrbA, murZ''<ref name='LIB:Riley_2006'/>, murZ''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16931.V46a9efc65953e&page=16931&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3178, b3189, JW3156, mrbA, murZ''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9efc6d923f"  class=" tableEdit Gene_location_table" 
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
|
|
71.84 minutes&nbsp;
71.84 minutes 
|
|
MG1655: 3334516..3333257<br />{{GBrowseFigureByCoord|3332257|3335516|ecoli|MG1655}}
MG1655: 3334516..3333257<br /><gbrowseImage>
name=NC_000913:3333257..3334516
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11358 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11358 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3332257..3335516 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3332257|3335516|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3333257..3334516&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3333257|3334516|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11358 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11358 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3271729..3270470<br /><gbrowseImage>
name=NC_012967:3270470..3271729
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3270470|3271729|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3270470|3271729|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3220405..3221664<br /><gbrowseImage>
name=NC_012759:3220405..3221664
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3220405|3221664|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3220405|3221664|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3336349..3335090<br />{{GBrowseFigureByCoord|3334090|3337349|ecoli_W3110|W3110}}
W3110: 3336349..3335090<br /><gbrowseImage>
name=NC_007779:3335090..3336349
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3334090..3337349 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3334090|3337349|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3335090..3336349&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3335090|3336349|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9efc797fde"  class=" tableEdit Gene_sequence_features_table" 
|- {{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]]
|
3333257
|
Edman degradation
|
PMID:1512209<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9efc7e01dd"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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Strain DH10B
|
 
|
I28N
|
 
|
Nonsynonomous mutation
|
PMID:18245285
|
[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
|
This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
|-
|
murA C115D
|
 
|
C115D
|
Resistant to
|
Fosfomycin
|
PMID:8075065
|
 
|
|-
|
''murZ Fos<sup>r</sup>''
|
Mapped to 69.3 min
|
 
|
Resistant to
|
Resistant to phosphomycin
|
PMID:1512209
|
 
|
See figure 1 for chemical reaction. 
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3156
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGATAAATTTCGTGTTCAGGG
 
Primer 2:CCTTCGCCTTTCACACGCTCAAT
|-
|
[[:Category:Kohara_Phage:14F11|14F11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=521 Genobase]
|
PMID:3038334
|-
|
[[sfsB:Gene|sfsB203::Tn10]]
|
Linked marker
|
CAG12072 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38770 CGSC7440]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 94% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgj-203::Tn10, zha-203::Tn10
|-
|
[[yhcF:Gene|zhc-6::Tn10]]
|
Linked marker
|
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zha-6::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11358 EcoCyc:EG11358]
[[EcoCyc]]
|
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EcoCyc:EG11358
|-
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
|-  
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1333 EchoBASE:EB1333]
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3189 EcoliGenExpDB:b3189] 
EcoGene:EG11358
|
|
''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=C3947 ECOL199310CYC:C3947] 
RegulonDB:ECK120001327
|
|
''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=EG11358 EcoGene:EG11358]
[http://www.ncbi.nlm.nih.gov/gene?term=947703 GeneID:947703]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=MURA ECOO157CYC:MURA] 
EchoBASE:EB1333
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33518 CGSC:33518] 
ASAP:ABE-0010479
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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==Links==
==Links==
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==References==
==References==
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<references />
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:mur genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

murA

Mnemonic

Murein

Synonyms

ECK3178, b3189, JW3156, mrbA, murZ[1], murZ

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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

71.84 minutes 

MG1655: 3334516..3333257
<gbrowseImage> name=NC_000913:3333257..3334516 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3271729..3270470
<gbrowseImage> name=NC_012967:3270470..3271729 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3220405..3221664
<gbrowseImage> name=NC_012759:3220405..3221664 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3336349..3335090
<gbrowseImage> name=NC_007779:3335090..3336349 source=W3110 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

3333257

Edman degradation

PMID:1512209[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

Strain DH10B

I28N

Nonsynonomous mutation

PMID:18245285[3]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

murA C115D

C115D

Resistant to

Fosfomycin

PMID:8075065[4]

murZ Fosr

Mapped to 69.3 min

Resistant to

Resistant to phosphomycin

PMID:1512209[2]

See figure 1 for chemical reaction.

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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

JW3156

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGATAAATTTCGTGTTCAGGG

Primer 2:CCTTCGCCTTTCACACGCTCAAT

14F11

Kohara Phage

Genobase

PMID:3038334[6]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[7]

est. P1 cotransduction: 94% [8]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[7]

est. P1 cotransduction: 30% [8]
Synonyms:zha-6::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:EG11358

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11358

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001327

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947703

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1333

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010479

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 Marquardt, JL et al. (1992) Cloning and sequencing of Escherichia coli murZ and purification of its product, a UDP-N-acetylglucosamine enolpyruvyl transferase. J. Bacteriol. 174 5748-52 PubMed
  3. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  4. ↑ Marquardt, JL et al. (1994) Kinetics, stoichiometry, and identification of the reactive thiolate in the inactivation of UDP-GlcNAc enolpyruvoyl transferase by the antibiotic fosfomycin. Biochemistry 33 10646-51 PubMed
  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. ↑ 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 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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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