trmD:Gene: Difference between revisions

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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=438 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=438 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:22D7|22D7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=439 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10  
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10  
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[[:Category:Kohara_Phage:22D7|22D7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=439 Genobase]
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PMID:3038334


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!|Database!!Accession!!Notes
!|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=EG11023 EcoCyc:EG11023]
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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=EB1016 EchoBASE:EB1016]
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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=b2607 EcoliGenExpDB:b2607]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C3128 ECOL199310CYC:C3128]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11023 EcoGene:EG11023]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=TRMD ECOO157CYC:TRMD]
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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/76 CGSC:76]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0008576&formSubmitReturn=1 ASAP:ABE-0008576]
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Revision as of 21:42, 21 September 2011

{{#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]

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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=AC_000091:2743228..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
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Notes

Links

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<protect>

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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