LmrA - Revision history

Jstuelk: /* Reviews */

2014-09-19T10:55:33Z

‎Reviews

134.76.38.147 at 12:55, 2 April 2014

2014-04-02T12:55:09Z

Jstuelk at 16:30, 6 September 2013

2013-09-06T16:30:31Z

Jstuelk: /* References */

2013-07-13T16:07:15Z

‎References

134.76.70.252 at 12:28, 16 May 2013

2013-05-16T12:28:44Z

134.76.70.252 at 09:24, 14 May 2013

2013-05-14T09:24:26Z

134.76.70.252 at 12:04, 13 May 2013

2013-05-13T12:04:32Z

134.76.70.252 at 09:27, 8 August 2012

2012-08-08T09:27:06Z

134.76.70.252 at 08:31, 8 August 2012

2012-08-08T08:31:48Z

134.76.70.252 at 15:16, 7 August 2012

2012-08-07T15:16:41Z

← Older revision		Revision as of 10:55, 19 September 2014
Line 1:		Line 1:
−	* '''Description:~~''' transcriptional regulator ([[TetR family]]), control of ''[[qdoI]]-[[yxaH]]'' and ''[[lmrA]]-[[lmrB]]'' <br/><br/>~~	+	{{#bank: LmrA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''lmrA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''lin-2, yccB ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| transcriptional regulator~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| regulation of lincomycin resistance~~
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02680 lmrA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 20 kDa, 5.033~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 564 bp, 188 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[lmrB]]'', ''[[ansZ]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02680 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02680 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02680 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:lmrA_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lmrA_290132_290698_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:lmrA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02680]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transcription factors and their control]]}},~~
−	~~{{SubtiWiki category\|[[resistance against toxins/ antibiotics]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[LmrA regulon]]}}~~
−	~~=The [[LmrA regulon]]:=~~
−	* ''[[lmrA]]-[[lmrB]]'', ''[[qdoR]]'', ''[[qdoI]]-[[yxaH]]''
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02680
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02680&redirect=T BSU02680]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lmrAB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12612]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' [[TetR family]]
−
−	* '''Paralogous protein(s):''' [[QdoR]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:''' flavonoids such as quercetin serve as inducers, binding results in release from DNA {{PubMed\|17483215}}
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU02680&redirect=T BSU02680]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34619 O34619]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02680]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[lmrA]]-[[lmrB]]'' {{PubMed\|15317768}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lmrA_290132_290698_-1 lmrA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|12499232}}
−
−	* '''Regulation:'''
−	** induced by flavonoids such as quercetin ([[LmrA]]){{PubMed\|17483215}}
−
−	* '''Regulatory mechanism:'''
−	** [[LmrA]]: transcription repression {{PubMed\|15317768}}
−
−	* '''Additional information:'''
−	** the mRNA is substantially stabilized upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>24006471 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>15317768,17483215,12499232 , 21815947 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/lmrAB.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 1: / Line 1: @@
-* '''Description:''' transcriptional regulator, control of ''[[qdoI]]-[[yxaH]]'' and ''[[lmrA]]-[[lmrB]]'' <br/><br/>
+* '''Description:''' transcriptional regulator ([[TetR family]]), control of ''[[qdoI]]-[[yxaH]]'' and ''[[lmrA]]-[[lmrB]]'' <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 72: / Line 68: @@
 * '''Catalyzed reaction/ biological activity:'''
-* '''Protein family:'''
+* '''Protein family:''' [[TetR family]]
 * '''Paralogous protein(s):''' [[QdoR]]
@@ Line 109: / Line 105: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lmrA_290132_290698_-1 lmrA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|12499232}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|12499232}}
 * '''Regulation:'''
@@ Line 139: / Line 135: @@
 =References=
 <pubmed>15317768,17483215,12499232 , 21815947 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 139: / Line 139: @@
 =References=
- <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
+<pubmed>15317768,17483215,12499232 , 21815947 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 27: / Line 27: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lmrA_290132_290698_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:lmrA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=lmrA_290132_290698_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:lmrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02680]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lmrB]]'', ''[[ansZ]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02680 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02680 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02680 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02680 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02680 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02680 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:lmrA_context.gif]]

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of lincomycin resistance
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02680 lmrA]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02680 lmrA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 5.033
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[lmrB]]'', ''[[ansZ]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12062&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02680 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02680 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02680 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:lmrA_context.gif]]