rlmE:Gene: Difference between revisions

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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9ef84653b0"  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: 3327519..3326890<br /><gbrowseImage>
W3110: 3327519..3326890<br /><gbrowseImage>
name=AC_000091:3326890..3327519
name=NC_007779:3326890..3327519
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|ecoli_W3110|AC_000091|3325890|3328519|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|3325890|3328519|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3326890|3327519|FASTA Dump}}  
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rlmE
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deletion
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Sensitivity to
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increases sensitivity to bicyclomycin
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PMID:21357484
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fig 2


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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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!|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=EG11507 EcoCyc:EG11507]
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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=EB1470 EchoBASE:EB1470]
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[http://BioCyc.org/ECOL199310/new-image?object=C3936 ECOL199310CYC:C3936]
[http://BioCyc.org/ECOL199310/new-image?object=C3936 ECOL199310CYC:C3936]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11507 EcoGene:EG11507]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33511 CGSC:33511]
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33511 CGSC:33511]
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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=0010447&formSubmitReturn=1 ASAP:ABE-0010447]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:46, 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

rlmE

Mnemonic

rRNA large-subunit methylation

Synonyms

ECK3168, b3179, JW3146, ftsJ, mrsF, rrmJ[1], mrsF, rrmJ

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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

71.67 minutes 

MG1655: 3325686..3325057
<gbrowseImage> name=NC_000913:3325057..3325686 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3212205..3212834
<gbrowseImage> name=NC_012759:3212205..3212834 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3327519..3326890
<gbrowseImage> name=NC_007779:3326890..3327519 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3423431..3422802
<gbrowseImage> name=NC_010473:3422802..3423431 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

ΔrrmJ (Keio:JW3146)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10390[3]

rlmED83A

D83A

5-fold decrease in activity. Increase in Km for 50S subunit and for S- adenosyl-L-methionine. Loss of S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmES197A

S197A

No change in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEE199A

E199A

16-fold decrease in activity. No change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED20A

D20A

2-fold decrease in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEY22A

Y22A

No change in activity

seeded from UniProt:P0C0R7

rlmER32A

R32A

4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-34

seeded from UniProt:P0C0R7

rlmER34A

R34A

4-fold decrease in activity and increase in Km for 50S subunit; when associated with A-32

seeded from UniProt:P0C0R7

rlmEK38A

K38A

Loss of activity. Almost no change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED124A

D124A

Loss of activity. Loss of S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmED136N

D136N

2-fold decrease in activity

seeded from UniProt:P0C0R7

rlmEK164A

K164A

Loss of activity. No change in S- adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

rlmEK189A

K189A

9-fold decrease in activity

seeded from UniProt:P0C0R7

rlmER194A

R194A

No change in activity. Increase in Km for 50S subunit

seeded from UniProt:P0C0R7

rlmEY201A

Y201A

5-fold decrease in activity. Almost no change in S-adenosyl-L-methionine binding

seeded from UniProt:P0C0R7

ΔrrmJ786::kan

PMID:16738554[2]

CGSC:102804

rlmE

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[4]

fig 2

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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

JW3146

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACAGGTAAGAAGCGTTCTGC

Primer 2:CCGGGTTTACGCCCGGTCGCTAC

18H7

Kohara Phage

Genobase

PMID:3038334[6]

14F11

Kohara Phage

Genobase

PMID:3038334[6]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[3]

est. P1 cotransduction: % [7]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[3]

est. P1 cotransduction: 81% [7]
Synonyms:zgj-203::Tn10, zha-203::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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3179

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3936

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:FTSJ

CGSC (EcoliWiki Page)

CGSC:33511

EcoCyc (EcoliWiki Page)

ECOCYC:EG11507

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947689

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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
  7. ↑ 7.0 7.1 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).

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