YumC - Revision history

Jstuelk: /* References */

2015-02-24T08:59:45Z

‎References

Jstuelk at 11:32, 19 September 2014

2014-09-19T11:32:18Z

Jstuelk at 11:12, 19 September 2014

2014-09-19T11:12:52Z

134.76.70.252 at 14:21, 17 April 2014

2014-04-17T14:21:35Z

134.76.70.252 at 09:32, 17 April 2014

2014-04-17T09:32:30Z

134.76.38.147 at 14:40, 2 April 2014

2014-04-02T14:40:04Z

Jstuelk: /* Basic information/ Evolution */

2014-02-18T18:41:55Z

‎Basic information/ Evolution

Jstuelk at 18:40, 18 February 2014

2014-02-18T18:40:56Z

Jstuelk: /* Database entries */

2014-02-18T18:37:44Z

‎Database entries

134.76.70.252 at 14:28, 16 May 2013

2013-05-16T14:28:54Z

← Older revision		Revision as of 08:59, 24 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' ferredoxin/flavodoxin-NAD(P)+ oxidoreductase<br/><br/>~~	+	{{#bank: YumC}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yumC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| ferredoxin/flavodoxin reductase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| redox reactions that involve ferredoxin and flavodoxin~~
−	\|-
−	\|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=BSU32110 yumC]
−	\|-
−	\|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=YumC YumC]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 36 kDa, 5.573~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 996 bp, 332 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yumB]]'', ''[[yuzG]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU32110 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU32110 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU32110 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yumC_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=yumC_3301586_3302584_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yumC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32110]]
−	\|-
−	\|}
−
−	~~__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]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU32110
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32110&redirect=T BSU32110]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12391]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin or flavodoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin or flavodoxin + NADPH (according to Swiss-Prot)
−
−	* '''Protein family:''' ferredoxin-NADP reductase type 2 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[YcgT]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in ''B. subtilis'' and other ''Bacillus'' species [http://www.ncbi.nlm.nih.gov/pubmed/22938038 PubMed]
−
−	* '''[[Cofactors]]:''' FAD {{PubMed\|20878669}}
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** dimeric protein {{PubMed\|20878669}}
−	** [[YumC]]-[[YkuN]] (electron transfer from NADPH via [[YumC]] to [[YkuN]]) {{PubMed\|25194416}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU32110&redirect=T BSU32110]
−
−	* '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3LZW 3LZW] {{PubMed\|20878669}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O05268 O05268]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32110]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.18.1.2 1.18.1.2]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 yumC] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 5753 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 9972 {{PubMed\|24696501}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 5216 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 2849 {{PubMed\|21395229}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 3293 {{PubMed\|21395229}}
−
−	~~=Biological materials =~~
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 24529496 25194416 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 1: / Line 1: @@
-* '''Description:''' ferredoxin-NAD(P)+ oxidoreductase<br/><br/>
+* '''Description:''' ferredoxin/flavodoxin-NAD(P)+ oxidoreductase<br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 15: / Line 15: @@
 |-
 |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=BSU32110 yumC]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.573
@@ Line 67: / Line 69: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin + NADPH (according to Swiss-Prot)
+* '''Catalyzed reaction/ biological activity:''' 2 reduced ferredoxin or flavodoxin + NADP<sup>+</sup> + H<sup>+</sup> = 2 oxidized ferredoxin or flavodoxin + NADPH (according to Swiss-Prot)
-* '''Protein family:''' ferredoxin--NADP reductase type 2 family (according to Swiss-Prot)
+* '''Protein family:''' ferredoxin-NADP reductase type 2 family (according to Swiss-Prot)
 * '''Paralogous protein(s):''' [[YcgT]]
@@ Line 79: / Line 81: @@
 * '''[[Domains]]:'''
-* '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species[http://www.ncbi.nlm.nih.gov/pubmed/22938038  PubMed]
+* '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in ''B. subtilis'' and other ''Bacillus'' species [http://www.ncbi.nlm.nih.gov/pubmed/22938038  PubMed]
 * '''[[Cofactors]]:''' FAD {{PubMed|20878669}}
@@ Line 87: / Line 89: @@
 * '''[[SubtInteract|Interactions]]:'''
 ** dimeric protein {{PubMed|20878669}}
 * '''[[Localization]]:'''
@@ Line 141: / Line 144: @@
 =References=
-<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 24529496 </pubmed>
+<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 24529496 25194416 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 10: / Line 10: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || ferredoxin-NAD(P)+ oxidoreductase
+|style="background:#ABCDEF;" align="center"| '''Product''' || ferredoxin/flavodoxin reductase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || redox reactions that involve ferredoxin
+|style="background:#ABCDEF;" align="center"|'''Function''' || redox reactions that involve ferredoxin and flavodoxin
 |-
 |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=BSU32110 yumC]

@@ Line 118: / Line 118: @@
 ** number of protein molecules per cell (minimal medium with glucose and ammonium): 5753 {{PubMed|24696501}}
 ** number of protein molecules per cell (complex medium with amino acids, without glucose): 9972 {{PubMed|24696501}}
 =Biological materials =
 * '''Mutant:'''

← Older revision		Revision as of 09:32, 17 April 2014
Line 116:		Line 116:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 5753 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 9972 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:''' [http://www.pdb.org/pdb/search/structidSearch.do?structureId=3LZW 3LZW]	{{PubMed|20878669}}

@@ Line 35: / Line 35: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 65: / Line 61: @@
 === Additional information===
 =The protein=
@@ Line 83: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:''' active site Cys85 is S-bacillithiolated by NaOCl stress in B. subtilis and other Bacillus species[http://www.ncbi.nlm.nih.gov/pubmed/22938038  PubMed]
-* '''Cofactor(s):''' FAD, NADPH {{PubMed|20878669}}
+* '''[[Cofactors]]:''' FAD {{PubMed|20878669}}
 * '''Effectors of protein activity:'''
-* '''Interactions:''' dimeric protein {{PubMed|20878669}}
+* '''[[SubtInteract|Interactions]]:'''
-* '''Localization:'''
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 113: / Line 107: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 yumC] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 141: / Line 135: @@
 =References=
-<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 </pubmed>
+<pubmed>22938038, 20208166, 20878669, 19162251, 15252706 24529496 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 103: / Line 103: @@
 * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU32110]
-* '''E.C. number:'''
+* '''E.C. number:''' [http://www.expasy.org/enzyme/1.18.1.2 1.18.1.2]
 === Additional information===

@@ 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=yumC_3301586_3302584_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yumC_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yumC_3301586_3302584_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:yumC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU32110]]
 |-
 |}