YxeM - Revision history

134.76.70.252 at 10:07, 17 April 2014

2014-04-17T10:07:05Z

134.76.70.252 at 11:54, 8 April 2014

2014-04-08T11:54:29Z

134.76.38.147 at 15:12, 2 April 2014

2014-04-02T15:12:38Z

134.76.70.252 at 09:44, 12 November 2013

2013-11-12T09:44:11Z

Jstuelk at 12:05, 18 August 2013

2013-08-18T12:05:15Z

Jstuelk: /* Expression and regulation */

2013-08-18T11:50:18Z

‎Expression and regulation

Jstuelk: /* References */

2013-07-13T16:40:30Z

‎References

134.76.70.252 at 14:58, 16 May 2013

2013-05-16T14:58:37Z

134.76.70.252 at 11:40, 14 May 2013

2013-05-14T11:40:59Z

134.76.70.252 at 14:15, 13 May 2013

2013-05-13T14:15:31Z

← Older revision		Revision as of 10:07, 17 April 2014
Line 1:		Line 1:
−	* '''Description:''' putative cysteine [[ABC transporter]] (binding protein), the ''[[yxeK]]-[[snaB]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[sndB]]-[[yxeQ]]'' operon may be implicated in the utilization of a modified cysteine variant <br/><br/>	+	{{#bank: YxeM}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yxeM''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| putative cysteine [[ABC transporter]] (binding protein)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| uptake of cysteine~~
−	\|-
−	\|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=BSU39500 yxeM]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=YxeM YxeM]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=YxeM YxeM]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 29 kDa, 9.086~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 792 bp, 264 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yxeN]]'', ''[[yxeL]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39500 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yxeM_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=yxeM_4059488_4060282_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yxeM_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39500]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[ABC transporters]]}},~~
−	~~{{SubtiWiki category\|[[biosynthesis/ acquisition of amino acids]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CymR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU39500
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU39500&redirect=T BSU39500]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11889]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' bacterial solute-binding protein 3 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[YxeO]]-[[YxeN]]-[[YxeM]] {{PubMed\|10092453}}
−
−	* '''[[Localization]]:''' associated to the membrane (via [[YxeN]]) {{PubMed\|10092453}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU39500&redirect=T BSU39500]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P54952 P54952]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39500]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[yxeK]]-[[snaB]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[sndB]]-[[yxeQ]]'' {{PubMed\|10746760}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeM_4059488_4060282_-1 yxeM] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|16513748}}
−
−	* '''Regulation:'''
−	** repressed in the presence of cysteine ([[CymR]]) {{PubMed\|16513748}}
−
−	* '''Regulatory mechanism:'''
−	** [[CymR]]: transcription repression {{PubMed\|16513748}}
−
−	* '''Additional information:'''
−	** the amount of the mRNA is substantially decreased upon depletion of [[Rny\|RNase Y]] {{PubMed\|21815947}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** 1A950 ( ''yxeM''::''cat''), {{PubMed\|15262924}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A950&Search=1A950 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>10092453,12193636,16513748, 10746760 21815947</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 17: / Line 17: @@
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=YxeM YxeM]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 9.086

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 16: / Line 16: @@
 |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=BSU39500 yxeM]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/YxeM YxeM]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=YxeM YxeM]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 9.086

← Older revision		Revision as of 12:05, 18 August 2013
Line 1:		Line 1:
−	* '''Description:''' putative cysteine [[ABC transporter]] (binding protein) <br/><br/>	+	* '''Description:''' putative cysteine [[ABC transporter]] (binding protein), the ''[[yxeK]]-[[snaB]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[sndB]]-[[yxeQ]]'' operon may be implicated in the utilization of a modified cysteine variant <br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

@@ Line 106: / Line 106: @@
 =Expression and regulation=
-* '''Operon:''' ''[[yxeK]]-[[yxeL]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[yxeP]]-[[yxeQ]]'' {{PubMed|10746760}}
+* '''Operon:''' ''[[yxeK]]-[[snaB]]-[[yxeM]]-[[yxeN]]-[[yxeO]]-[[sndB]]-[[yxeQ]]'' {{PubMed|10746760}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeM_4059488_4060282_-1 yxeM] {{PubMed|22383849}}

@@ Line 141: / Line 141: @@
 =References=
- <big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
- <big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
+<pubmed>10092453,12193636,16513748, 10746760 21815947</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 29: / Line 29: @@
   <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=yxeM_4059488_4060282_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yxeM_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yxeM_4059488_4060282_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yxeM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU39500]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yxeN]]'', ''[[yxeL]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39500 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU39500 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU39500 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU39500 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yxeM_context.gif]]