YodF - Revision history

Jstuelk at 09:35, 30 July 2015

2015-07-30T09:35:27Z

Jstuelk: /* References */

2015-07-30T09:23:11Z

‎References

Jstuelk: /* Biological materials */

2014-09-19T20:13:54Z

‎Biological materials

Dreuss1: /* Biological materials */

2014-09-18T13:11:10Z

‎Biological materials

Dreuss1: /* Biological materials */

2014-09-18T13:05:53Z

‎Biological materials

134.76.70.252 at 09:33, 17 April 2014

2014-04-17T09:33:09Z

134.76.70.252 at 11:54, 8 April 2014

2014-04-08T11:54:42Z

134.76.38.147 at 13:55, 2 April 2014

2014-04-02T13:55:52Z

Jstuelk at 17:47, 14 March 2014

2014-03-14T17:47:38Z

Jstuelk at 12:26, 28 November 2013

2013-11-28T12:26:51Z

← Older revision		Revision as of 09:35, 30 July 2015
Line 1:		Line 1:
−	* '''Description:~~''' similar to amino acid permease <br/><br/>~~	+	{{#bank: YodF}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yodF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| unknown~~
−	\|-
−	\|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=BSU19580 yodF]
−	\|-
−	\|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=YodF YodF]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 53 kDa, 9.682~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1488 bp, 496 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[yoyD]]'', ''[[ctpA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19580 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19580 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19580 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yodF_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=yodF_2130377_2131867_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yodF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19580]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[transporters/ other]]}},~~
−	~~{{SubtiWiki category\|[[putative amino acid transporter]]}},~~
−	~~{{SubtiWiki category\|[[membrane proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[TnrA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU19580
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19580&redirect=T BSU19580]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13535]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** in some database, the protein is annotated as being similar to proline permease, however, it is not involved in proline transport {{PubMed\|24142252}}
−
−	* '''Protein family:''' solute:sodium symporter family (SSS family)
−
−	* '''Paralogous protein(s):''' [[YhjB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''[[Domains]]:'''
−
−	* '''Modification:'''
−
−	* '''[[Cofactors]]:'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19580&redirect=T BSU19580]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34745 O34745]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19580]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=yodF_2130377_2131867_1 yodF] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed]
−	** repressed in the absence of good nitrogen sources (glutamine or ammonium) ([[TnrA]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[TnrA]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12823818 PubMed]
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 445 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 807 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−	** available in [[Erhard Bremer]]'s lab {{PubMed\|24142252}}
−	** GP1887 (kan) available in [[Jörg Stülke]]'s lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>12823818,,12823818,12107147 18763711, 24142252 25755103</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 145: / Line 145: @@
 =References=
-<pubmed>12823818,,12823818,12107147 18763711, 24142252</pubmed>
+<pubmed>12823818,,12823818,12107147 18763711, 24142252 25755103</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 128: / Line 128: @@
 ** available in [[Erhard Bremer]]'s lab {{PubMed|24142252}}
 ** GP1887 (kan) available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 128: / Line 128: @@
 ** available in [[Erhard Bremer]]'s lab {{PubMed|24142252}}
 ** GP1887 (kan) available in [[Jörg Stülke]]'s lab
 * '''Expression vector:'''

@@ Line 127: / Line 127: @@
 * '''Mutant:'''
 ** available in [[Erhard Bremer]]'s lab {{PubMed|24142252}}
 * '''Expression vector:'''

← Older revision		Revision as of 09:33, 17 April 2014
Line 120:		Line 120:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 445 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 807 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ 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=BSU19580 yodF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 53 kDa, 9.682

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 90: / Line 91: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 60: / Line 60: @@
 === Additional information===
 =The protein=
@@ Line 71: / Line 70: @@
 * '''Protein family:''' solute:sodium symporter family (SSS family)
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[YhjB]]
 === Extended information on the protein ===
@@ Line 77: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''[[Domains]]:'''
 * '''Modification:'''
-* '''Cofactor(s):'''
+* '''[[Cofactors]]:'''
 * '''Effectors of protein activity:'''