ptrA:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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{|   id="I46a9e713a1a47"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9e713a1a47"  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
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W3110: 2957540..2954652<br /><gbrowseImage>
W3110: 2957540..2954652<br /><gbrowseImage>
name=AC_000091:2954652..2957540
name=NC_007779:2954652..2957540
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|2953652|2958540|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2953652|2958540|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|2954652|2957540|FASTA Dump}}  
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{|   id="H46a9e7145cfa3"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9e7145cfa3"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="X46a9e714a4108"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X46a9e714a4108"  class=" tableEdit Gene_allele_table dataTable"   
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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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{|   id="P4e04c1b3074cb"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P4e04c1b3074cb"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="E46a9e7155fd07"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9e7155fd07"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="G46a9e71603faf"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9e71603faf"  class=" tableEdit Gene_accessions_table"   
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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=EG10786 ECOCYC:EG10786]
EcoCyc:EG10786
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10786
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10786 EcoGene:EG10786]
RegulonDB:ECK120000777
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[EchoBASE]]
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EchoBASE:EB0779
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0009252
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:44, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

ptrA

Mnemonic

Protease III

Synonyms

ptr, ECK2817, b2821, JW2789[1][2], JW2789

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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

63.67 minutes 

MG1655: 2956906..2954018
<gbrowseImage> name=NC_000913:2954018..2956906 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2850615..2853503
<gbrowseImage> name=NC_012967:2850615..2853503 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2841166..2844054
<gbrowseImage> name=NC_012759:2841166..2844054 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2957540..2954652
<gbrowseImage> name=NC_007779:2954652..2957540 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3050776..3047888
<gbrowseImage> name=NC_010473:3047888..3050776 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

ptrAH88R

H88R

Loss of activity and of Zn-binding

seeded from UniProt:P05458

ptrAE162Q

E162Q

20% loss of activity

seeded from UniProt:P05458

ptrAE169Q

E169Q

Loss of activity and of Zn-binding

seeded from UniProt:P05458

ptrAE204Q

E204Q

No loss of activity

seeded from UniProt:P05458

ptrAE91Q

E91Q

Loss of activity

seeded from UniProt:P05458

ptrAH92R

H92R

Loss of activity and of Zn-binding

seeded from UniProt:P05458

Δptr::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[3]

Δptr::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[3]

Δptr::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[3]

Δptr::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[3]

ΔptrA746::kan

PMID:16738554[4]

CGSC:113619


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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

10B6

Kohara Phage

Genobase

PMID:3038334[6]

3G11

Kohara Phage

Genobase

PMID:3038334[6]

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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:EG10786

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10786

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000777

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947284

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0779

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009252

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 3.2 3.3 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  4. ↑ 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
  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

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