YlnE - Revision history

134.76.70.252 at 14:19, 17 April 2014

2014-04-17T14:19:26Z

134.76.70.252 at 09:42, 17 April 2014

2014-04-17T09:42:07Z

134.76.38.147 at 13:41, 2 April 2014

2014-04-02T13:41:03Z

134.76.70.252 at 10:44, 7 January 2014

2014-01-07T10:44:58Z

134.76.70.252 at 13:18, 16 May 2013

2013-05-16T13:18:42Z

134.76.70.252 at 10:11, 14 May 2013

2013-05-14T10:11:17Z

134.76.70.252 at 12:47, 13 May 2013

2013-05-13T12:47:40Z

134.76.70.252 at 09:32, 7 August 2012

2012-08-07T09:32:05Z

134.76.70.252 at 09:16, 19 April 2012

2012-04-19T09:16:05Z

134.76.70.252 at 08:41, 13 April 2012

2012-04-13T08:41:17Z

← Older revision		Revision as of 14:19, 17 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' probable siroheme ferrochelatase <br/><br/>~~	+	{{#bank: YlnE}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ylnE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| probable siroheme ferrochelatase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| siroheme biosynthesis, sulfite reduction~~
−	\|-
−	\|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=BSU15620 ylnE]
−	\|-
−	\|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=ylnE ylnE]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 28 kDa, 6.063~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 783 bp, 261 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ylnD]]'', ''[[ylnF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15620 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ylnE_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=sirB_1634837_1635622_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ylnE_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15620]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<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\|[[biosynthesis of cofactors]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CymR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[S-box]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU15620
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15620&redirect=T BSU15620]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cysHP-sat-cysC-ylnDEF.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13381]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Siroheme + 2 H<sup>+</sup> = sirohydrochlorin + Fe<sup>2+</sup> (according to Swiss-Prot)
−
−	* '''Protein family:''' SirB subfamily (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]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU15620&redirect=T BSU15620]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34632 O34632]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU15620]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[cysH]]-[[cysP]]-[[sat]]-[[cysC]]-[[ylnD]]-[[ylnE]]-[[ylnF]]'' {{PubMed\|11004190}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sirB_1634837_1635622_1 ylnE] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|11004190}}
−
−	* '''Regulation:'''
−	** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** repressed in the presence of cysteine ([[CymR]])
−	** induced by methionine starvation ([[S-box]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[S-box]]: transcription termination/ antitermination, the [[S-box]] [[riboswitch]] binds S-adenosylmethionine resulting in termination [http://www.ncbi.nlm.nih.gov/sites/entrez/10094622 PubMed]
−	** [[CymR]]: transcription repression
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 192 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 542 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>16267287,11004190,12107147, 18039762 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:42, 17 April 2014
Line 127:		Line 127:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 192 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 542 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 59: / Line 59: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cysHP-sat-cysC-ylnDEF.html]
@@ Line 96: / Line 97: @@
 === 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=BSU15620 ylnE]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''
+|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=ylnE ylnE]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 6.063

@@ 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=sirB_1634837_1635622_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ylnE_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sirB_1634837_1635622_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ylnE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU15620]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ylnD]]'', ''[[ylnF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15620 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU15620 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU15620 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU15620 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ylnE_context.gif]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || siroheme biosynthesis, sulfite reduction
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/cys_meth_and_sulfate_assimilation.html Cys, Met & Sulfate assimilation]'''

@@ Line 101: / Line 101: @@
 * '''Operon:''' ''[[cysH]]-[[cysP]]-[[sat]]-[[cysC]]-[[ylnD]]-[[ylnE]]-[[ylnF]]'' {{PubMed|11004190}}
-* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|11004190}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sirB_1634837_1635622_1 ylnE] {{PubMed|22383849}}
 * '''Regulation:'''