ThdF - Revision history

Jstuelk at 10:33, 1 June 2015

2015-06-01T10:33:45Z

134.76.70.252 at 09:41, 17 April 2014

2014-04-17T09:41:58Z

134.76.38.147 at 15:19, 2 April 2014

2014-04-02T15:19:04Z

134.76.70.252 at 09:49, 12 November 2013

2013-11-12T09:49:50Z

134.76.70.252 at 15:03, 16 May 2013

2013-05-16T15:03:48Z

134.76.70.252 at 11:46, 14 May 2013

2013-05-14T11:46:43Z

134.76.70.252 at 14:21, 13 May 2013

2013-05-13T14:21:30Z

Jstuelk at 17:25, 30 April 2013

2013-04-30T17:25:17Z

134.76.70.252 at 17:56, 7 August 2012

2012-08-07T17:56:54Z

134.76.70.252 at 13:19, 23 April 2012

2012-04-23T13:19:34Z

← Older revision		Revision as of 10:33, 1 June 2015
Line 1:		Line 1:
−	* '''Description:~~''' GTP-binding protein, putative tRNA modification GTPase<br/><br/>~~	+	{{#bank: ThdF}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''thdF''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''mnmE ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| putative tRNA modification GTPase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| tRNA modification~~
−	\|-
−	\|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=BSU41020 thdF]
−	\|-
−	\|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=ThdF ThdF]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 50 kDa, 4.643~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1377 bp, 459 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[gidA]]'', ''[[jag]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU41020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU41020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU41020 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]~~
−	~~<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=trmE_4211510_4212889_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:thdF_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU41020]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[translation]]}},~~
−	~~{{SubtiWiki category\|[[GTP-binding proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[ComK regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU41020
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU41020&redirect=T BSU41020]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thdF-gidAB-yyaA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10060]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Binds and hydrolyzes GTP and readily exchanges GDP for GTP
−
−	* '''Protein family:''' MnmE subfamily (according to Swiss-Prot) Era/Obg family
−
−	* '''Paralogous protein(s):''' [[Era]], [[Obg]], [[YphC]], [[YsxC]], [[RbgA]], [[YqeH]], [[ThdF]], [[YyaF]], [[YnbA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[GidA]]-[[ThdF]] (suggested by interaction of ''E. coli'' counterparts {{PubMed\|19801413}} and by co-localization on the chromosome)
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU41020&redirect=T BSU41020]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P25811 P25811]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU41020]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~Information on the corresponding protein from ''E. coli'': [http://BioCyc.org/ECOLI/NEW-IMAGE?type=ENZYME&object=EG10997-MONOMER EcoCyc]~~
−	MnmE required for wild-type 5-methylaminomethyl-2-thiouridine modification of tRNA, interacts with [[GidA]]. MnmE also appears to play a role in oxidation of thiophene and furan compounds and regulates glutamate-dependent acid resistance.
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[thdF]]-[[gidA]]-[[rsmG]]-[[noc]]'' {{PubMed\|11807071}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=trmE_4211510_4212889_-1 thdF] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[ComK]]: transcription activation {{PubMed\|11948146}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 180 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 507 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Naotake Ogasawara]], Nara, Japan~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed> 21885683</pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>12427945, 11807071 11948146 23630314 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 09:41, 17 April 2014
Line 122:		Line 122:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 180 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 507 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thdF-gidAB-yyaA.html]
@@ Line 93: / Line 94: @@
 === 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=BSU41020 thdF]
 |-
-|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/ThdF ThdF]
+|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=ThdF ThdF]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 4.643

@@ 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=trmE_4211510_4212889_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:thdF_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=trmE_4211510_4212889_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:thdF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU41020]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gidA]]'', ''[[jag]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU41020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU41020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU41020 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU41020 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU41020 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU41020 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]

@@ Line 6: / Line 6: @@
 |''thdF''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mnmE ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 149: / Line 145: @@
 <pubmed> 21885683</pubmed>
 ==Original publications==
-<pubmed>12427945, 11807071 11948146</pubmed>
+<pubmed>12427945, 11807071 11948146 23630314 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 |-
 |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/ThdF ThdF]