TsaE - Revision history

134.76.70.252 at 11:24, 17 April 2014

2014-04-17T11:24:42Z

134.76.38.147 at 13:05, 2 April 2014

2014-04-02T13:05:55Z

134.76.70.252 at 14:14, 18 November 2013

2013-11-18T14:14:23Z

134.76.70.252 at 12:40, 16 May 2013

2013-05-16T12:40:24Z

134.76.70.252 at 09:35, 14 May 2013

2013-05-14T09:35:43Z

134.76.70.252 at 12:15, 13 May 2013

2013-05-13T12:15:39Z

Jstuelk at 15:24, 18 October 2012

2012-10-18T15:24:41Z

Jstuelk at 11:38, 18 October 2012

2012-10-18T11:38:33Z

Jstuelk at 11:24, 18 October 2012

2012-10-18T11:24:18Z

Jstuelk at 11:12, 18 October 2012

2012-10-18T11:12:49Z

← Older revision		Revision as of 11:24, 17 April 2014
Line 1:		Line 1:
−	* '''Description:''' P-loop ATPase, required for threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA <br/><br/>	+	{{#bank: TsaE}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tsaE''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ydiB ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| tRNA modification enzyme~~
−	\|-
−	~~\|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=BSU05910 tsaE]~~
−	\|-
−	\|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=TsaE ~~TsaE]~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 17 kDa, 4.597~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 474 bp, 158 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[thiL]]'', ''[[tsaB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05910 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ydiB_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=ydiB_641654_642130_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:ydiB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05910]]~~
−	\|-
−	\|}

−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[translation]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU05910
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~reduced growth rate [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU05910&redirect=T BSU05910]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12199]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** biosynthesis of the threonylcarbamoyladenosine (t6A) residue at position 37 of ANN-decoding tRNAs using L-threonylcarbamoyl-AMP ([[TsaB]]-[[TsaD]]-[[TsaE]]) {{PubMed\|23072323,21183954}}
−
−	* '''Protein family:''' UPF0079 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:''' K(M) for ATP: 60 myM, V(max) 10 nmol/min [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** dimerizes and oligomerizes [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
−	** [[TsaB]]-[[TsaE]] {{PubMed\|23072323}}
−	** [[TsaD]]-[[TsaE]] {{PubMed\|23072323}}
−
−	* '''[[Localization]]:'''
−	** cytoplasm with the exception of the nucleoid region [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU05910&redirect=T BSU05910]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O05515 O05515]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU05910]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~ATPase activity is required for ''in vivo'' function of the protein [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[thiL]]-[[tsaE]]-[[tsaB]]-[[ydiD]]-[[tsaD]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 tsaE] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−	** for expression/ purification from ''B. subtilis'' with N-terminal Strep-tag, for [[SPINE]], in [[pGP380]]: pGP833, available in [[Stülke]] lab
−	** for expression/ purification from ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP841, available in [[Stülke]] lab
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed> 17005971, 19246765 23072323 22383849</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 55: / Line 55: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 97: / Line 98: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU05910 tsaE]
 |-
-|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/TsaE TsaE]
+|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=TsaE TsaE]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597

@@ Line 28: / Line 28: @@
   <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=ydiB_641654_642130_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydiB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ydiB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05910]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[tsaB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05910 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05910 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ydiB_context.gif]]

@@ Line 3: / Line 3: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''ydiB''
+|''tsaE''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydiB ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no

@@ Line 13: / Line 13: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 ydiB]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 tsaE]
 |-
 |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/TsaE TsaE]

@@ Line 15: / Line 15: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 ydiB]
 |-
-|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/YdiB YdiB]
+|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/TsaE TsaE]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 17 kDa, 4.597
@@ Line 21: / Line 21: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 474 bp, 158 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[ydiC]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[thiL]]'', ''[[tsaB]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12410&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
@@ Line 94: / Line 94: @@
 * '''[[Localization]]:'''
-** cytoplasm with the excepton of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
+** cytoplasm with the exception of the nucleoid region  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
 === Database entries ===
@@ Line 112: / Line 112: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:'''  ''[[thiL]]-[[tsaE]]-[[tsaB]]-[[ydiD]]-[[tsaD]]'' {{PubMed|22383849}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 ydiB] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ydiB_641654_642130_1 tsaE] {{PubMed|22383849}}
 * '''Sigma factor:'''
@@ Line 146: / Line 146: @@
 =References=
-<pubmed> 17005971, 19246765 23072323</pubmed>
+<pubmed> 17005971, 19246765 23072323 22383849</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 1: / Line 1: @@
-* '''Description:''' P-loop ATPase <br/><br/>
+* '''Description:''' P-loop ATPase, required for threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA  <br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
@@ Line 9: / Line 9: @@
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || P-loop ATPase
+|style="background:#ABCDEF;" align="center"| '''Product''' || tRNA modification enzyme
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || tRNA modification
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU05910 ydiB]
@@ Line 36: / Line 36: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[proteins of unknown function]]}}
+{{SubtiWiki category|[[translation]]}}
 = This gene is a member of the following [[regulons]] =
@@ Line 73: / Line 69: @@
 === Basic information/ Evolution ===
-* '''Catalyzed reaction/ biological activity:'''  the corresponding ''E. coli'' protein is involved in the control of the activity of the [[Gcp]] homolog [http://www.ncbi.nlm.nih.gov/sites/entrez/19376873 PubMed]
+* '''Catalyzed reaction/ biological activity:'''
 * '''Protein family:''' UPF0079 family (according to Swiss-Prot)
@@ Line 93: / Line 90: @@
 * '''[[SubtInteract|Interactions]]:'''
 ** dimerizes and oligomerizes  [http://www.ncbi.nlm.nih.gov/sites/entrez/19246765 PubMed]
-** the corresponding ''E. coli'' protein interacts with the protein corresponding to [[YdiC]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19376873 PubMed]
+** [[TsaB]]-[[TsaE]] {{PubMed|23072323}}
 * '''[[Localization]]:'''
@@ Line 148: / Line 146: @@
 =References=
-<pubmed> 17005971, 19246765 </pubmed>
+<pubmed> 17005971, 19246765 23072323</pubmed>
 [[Category:Protein-coding genes]]