trmD:Gene: Difference between revisions

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W3110: 2743995..2743228<br /><gbrowseImage>
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name=NC_007779:2743228..2743995
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{{GBrowseLink|W3110|AC_000091|2742228|2744995|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|2743228|2743995|FASTA Dump}}  
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/gene?term=947099 GeneID:947099]
RegulonDB:ECK120001012
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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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[[RegulonDB]]
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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RegulonDB:ECK120001012
[http://www.ncbi.nlm.nih.gov/gene?term=947099 GeneID:947099]
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
Escherichia coli str. K-12 substr. MG1655  
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Latest revision as of 20:43, 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

trmD

Mnemonic

tRNA methyltransferase

Synonyms

ECK2604, b2607, JW2588[1], JW2588

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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

59.11 minutes, 59.11 minutes 

MG1655: 2743361..2742594
<gbrowseImage> name=NC_000913:2742594..2743361 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2666746..2665979
<gbrowseImage> name=NC_012967:2665979..2666746 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2628406..2629173
<gbrowseImage> name=NC_012759:2628406..2629173 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2743995..2743228
<gbrowseImage> name=NC_007779:2743228..2743995 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2835126..2834359
<gbrowseImage> name=NC_010473:2834359..2835126 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

2742594

Edman degradation

PMID:6337136[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

trmDD169A

D169A

Loss of activity

seeded from UniProt:P0A873

trmDL197A

L197A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDF171A

F171A

Loss of activity

seeded from UniProt:P0A873

trmDP184A

P184A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDG59A

G59A

Loss of activity

seeded from UniProt:P0A873

trmDG91A

G91A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDR114A

R114A

Loss of activity

seeded from UniProt:P0A873

trmDY115A

Y115A

Increases Km for S-adenosyl-L- methionine 24-fold

seeded from UniProt:P0A873

trmDG117A

G117A

Loss of activity

seeded from UniProt:P0A873

trmDD119A

D119A

Loss of activity

seeded from UniProt:P0A873

trmDR121A

R121A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDL196A

L196A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDV192A

V192A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDG141A

G141A

Increases Km for S-adenosyl-L- methionine 82-fold

seeded from UniProt:P0A873

trmDR154A

R154A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDD135A

D135A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDY136A

Y136A

Increases Km for S-adenosyl-L- methionine 68-fold

seeded from UniProt:P0A873

trmDP193A

P193A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDD128A

D128A

Loss of activity

seeded from UniProt:P0A873

trmDW207A

W207A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDW207F,H

W207F,H

Small decrease in activity

seeded from UniProt:P0A873

trmDR208A

R208A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

trmDI204A

I204A

Loss of activity; no effect on tRNA binding

seeded from UniProt:P0A873

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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

JW2588

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCTGGATTGGCATAATTAGCCT

Primer 2:CCgGCCATCCCATCATGTTTATG

E8F2

Kohara Phage

Genobase

PMID:3038334[4]

22D7

Kohara Phage

Genobase

PMID:3038334[4]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 84% [6]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: % [6]
Synonyms:zfh-3131::Tn10, zfi-3131::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:EG11023

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11023

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001012

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947099

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1016

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008576

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. ↑ Hjalmarsson, KJ et al. (1983) Purification and characterization of transfer RNA (guanine-1)methyltransferase from Escherichia coli. J. Biol. Chem. 258 1343-51 PubMed
  3. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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