YhaM - Revision history

134.76.70.252 at 14:17, 17 April 2014

2014-04-17T14:17:50Z

134.76.70.252 at 09:45, 17 April 2014

2014-04-17T09:45:03Z

134.76.38.147 at 13:19, 2 April 2014

2014-04-02T13:19:32Z

134.76.70.252 at 12:53, 16 May 2013

2013-05-16T12:53:43Z

134.76.70.252 at 09:49, 14 May 2013

2013-05-14T09:49:38Z

134.76.70.252 at 12:27, 13 May 2013

2013-05-13T12:27:59Z

Jstuelk: /* Extended information on the protein */

2012-08-25T19:27:45Z

‎Extended information on the protein

Raphael2215 at 08:19, 10 August 2012

2012-08-10T08:19:26Z

134.76.70.252 at 16:24, 6 August 2012

2012-08-06T16:24:03Z

134.76.70.252 at 16:51, 18 April 2012

2012-04-18T16:51:32Z

← Older revision		Revision as of 14:17, 17 April 2014
Line 1:		Line 1:
−	* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease <br/><br/>	+	{{#bank: YhaM}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yhaM''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:~~#~~ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background~~:~~#ABCDEF;" align="center"\| '''Product''' \|\| [[RNase]]~~ YhaM
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| RNA degradation~~
−	\|-
−	\|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=BSU09930 yhaM]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 35 kDa, 5.851~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 942 bp, 314 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[sbcE]]'', ''[[yhaL]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09930 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yhaM_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=yhaM_1069042_1069986_1 Expression at a glance]'''   {{PubMed\|22383849}~~}~~<br/>[[Image:yhaM_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09930]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−
−
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[Rnases]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[LexA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU09930
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09930&redirect=T BSU09930]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yhaONM.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12989]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 3'-5' exoribonuclease
−
−	* '''Protein family:''' OB DNA-binding domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU09930&redirect=T BSU09930]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O07521 O07521]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09930]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~:* subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]~~
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[yhaO]]-[[sbcE]]-[[yhaM]]'' {{PubMed\|16267290}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhaM_1069042_1069986_1 yhaM] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−	** induced by DNA damage ([[LexA]]) {{PubMed\|16267290}}
−	** putatively regulated by [[CcpN]] {{PubMed\|19732150}}
−
−	* '''Regulatory mechanism:'''
−	** [[LexA]]: transcription repression {{PubMed\|16267290}}
−
−	* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation {{PubMed\|17981983}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 292 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 948 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed> 19732150 12399495 19553197, 16267290, 16479537,17981983, 15805522 19880604 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:45, 17 April 2014
Line 121:		Line 121:

	* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation {{PubMed\|17981983}}		* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation {{PubMed\|17981983}}
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 292 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 948 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yhaONM.html]
@@ Line 91: / Line 92: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 26: / Line 26: @@
   <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=yhaM_1069042_1069986_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yhaM_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yhaM_1069042_1069986_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yhaM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU09930]]
 |-
 |}

@@ Line 21: / Line 21: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09930 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09930 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yhaM_context.gif]]

@@ Line 13: / Line 13: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || RNA degradation
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU09930 yhaM]
+|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=BSU09930 yhaM]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.851
@@ Line 21: / Line 21: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sbcE]]'', ''[[yhaL]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12833&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU09930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU09930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU09930 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:yhaM_context.gif]]

@@ Line 85: / Line 85: @@
 * '''Effectors of protein activity:'''
-* '''Interactions:'''
+* '''[[SubtInteract|Interactions]]:'''
-* '''Localization:''' Cytoplasm (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
+* '''[[Localization]]:'''
 === Database entries ===

@@ Line 1: / Line 1: @@
+* '''Description:''' [[RNase]], 3'-> 5' exoribonuclease <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-