YkuP - Revision history

Jstuelk at 15:44, 26 May 2014

2014-05-26T15:44:51Z

Jstuelk at 15:33, 26 May 2014

2014-05-26T15:33:59Z

134.76.70.252 at 09:24, 17 April 2014

2014-04-17T09:24:09Z

134.76.38.147 at 13:35, 2 April 2014

2014-04-02T13:35:12Z

134.76.70.252 at 10:39, 7 January 2014

2014-01-07T10:39:51Z

134.76.70.252 at 16:08, 11 November 2013

2013-11-11T16:08:43Z

134.76.70.252 at 13:09, 16 May 2013

2013-05-16T13:09:18Z

134.76.70.252 at 10:05, 14 May 2013

2013-05-14T10:05:01Z

134.76.70.252 at 12:42, 13 May 2013

2013-05-13T12:42:15Z

Jstuelk at 19:51, 3 November 2012

2012-11-03T19:51:24Z

← Older revision		Revision as of 15:44, 26 May 2014
Line 1:		Line 1:
−	* '''Description:~~''' flavodoxin, binds FMN, replaces ferredoxin under conditions of iron limitation <br/><br/>~~	+	{{#bank: YkuP}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ykuP''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| flavodoxin~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| electron transfer~~
−	\|-
−	\|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=BSU14170 ykuP]
−	\|-
−	\|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=YkuP YkuP]
−	\|-
−	\|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=ykuP ykuP]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 20 kDa, 4.098~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 534 bp, 178 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ykuO]]'', ''[[ykuQ]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14170 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ykuP_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=ykuP_1488413_1488868_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ykuP_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14170]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[electron transport/ other]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[Fur regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU14170
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14170&redirect=T BSU14170]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuNOP.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13300]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' flavodoxin-like domain (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[YkuN]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:''' FMN
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[YkuP]]-[[BioI]] {{PubMed\|15449930}}
−	** [[YjiB]]-[[YkuP]] {{PubMed\|20186410}}
−	** [[Des]]-[[YkuP]] (electron transfer to [[Des]]) {{PubMed\|21665975}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14170&redirect=T BSU14170]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34589 O34589]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14170]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[ykuN]]-[[ykuO]]-[[ykuP]]'' {{PubMed\|12354229}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykuP_1488413_1488868_1 ykuP] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|12354229}}
−
−	* '''Regulation:'''
−	** induced upon iron starvation ([[Fur]]) {{PubMed\|12354229}}
−	** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** expressed under anaerobic conditions ([[ResD]]) {{PubMed\|24214949}}
−	** induced by nitric oxide under anaerobic conditions ([[NsrR]]) {{PubMed\|24214949}}
−
−	* '''Regulatory mechanism:'''
−	** [[Fur]]: transcription repression {{PubMed\|12354229}}
−	** [[ResD]]: transcription activation {{PubMed\|24214949}}
−	** [[NsrR]]: transcription repression {{PubMed\|24214949}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 4675 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1156 {{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>15449930,17127770 ,12354229,12107147, 20186410 24214949 21665975</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 83: / Line 83: @@
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:''' FMN
 * '''Effectors of protein activity:'''
@@ Line 118: / Line 118: @@
 ** induced upon iron starvation ([[Fur]]) {{PubMed|12354229}}
 ** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
 * '''Regulatory mechanism:'''
 ** [[Fur]]: transcription repression {{PubMed|12354229}}
 * '''Additional information:'''
@@ Line 145: / Line 149: @@
 =References=
-'''Additional publications:''' {{PubMed|21665975}}
+<pubmed>15449930,17127770 ,12354229,12107147, 20186410 24214949 21665975</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 09:24, 17 April 2014
Line 123:		Line 123:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 4675 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1156 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ykuNOP.html]
@@ Line 94: / Line 95: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 18: / Line 18: @@
 |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=YkuP YkuP]
 |-
-|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/lys_threo.html Lys, Thr]'''
+|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=ykuP ykuP]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.098

@@ 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=BSU14170 ykuP]
 |-
-|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/YkuP YkuP]
+|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=YkuP YkuP]
 |-
 |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/lys_threo.html Lys, Thr]'''

@@ Line 31: / Line 31: @@
   <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=ykuP_1488413_1488868_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ykuP_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykuP_1488413_1488868_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ykuP_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14170]]
 |-
 |}

@@ Line 26: / Line 26: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuO]]'', ''[[ykuQ]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14170 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14170 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ykuP_context.gif]]

@@ Line 39: / Line 39: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 115: / Line 111: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ykuP_1488413_1488868_1 ykuP] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|12354229}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|12354229}}
 * '''Regulation:'''
-** repressed unless the cells enter an iron starvation ([[Fur]]) {{PubMed|12354229}}
+** induced upon iron starvation ([[Fur]]) {{PubMed|12354229}}
 ** repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]