TsaD - Revision history

134.76.70.252 at 11:25, 17 April 2014

2014-04-17T11:25:16Z

134.76.38.147 at 13:06, 2 April 2014

2014-04-02T13:06:03Z

134.76.70.252 at 14:14, 18 November 2013

2013-11-18T14:14:29Z

134.76.70.252 at 12:40, 16 May 2013

2013-05-16T12:40:33Z

134.76.70.252 at 09:35, 14 May 2013

2013-05-14T09:35:53Z

134.76.70.252 at 12:15, 13 May 2013

2013-05-13T12:15:47Z

Jstuelk: /* Publications on the corresponding protein from other species */

2012-11-14T12:35:44Z

‎Publications on the corresponding protein from other species

Jstuelk: /* References */

2012-11-14T12:32:56Z

‎References

Jstuelk at 11:37, 18 October 2012

2012-10-18T11:37:55Z

Jstuelk: /* Expression and regulation */

2012-10-18T11:17:17Z

‎Expression and regulation

← Older revision		Revision as of 11:25, 17 April 2014
Line 1:		Line 1:
−	* '''Description:''' required for threonyl carbamoyl adenosine (t6A) modification of tRNAs that pair with ANN codons in mRNA (together with [[TsaC]]), [[universally conserved protein]] <br/><br/>	+	{{#bank: TsaD}}
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tsaD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ydiE, gcp ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]~~
−	\|-
−	~~\|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=BSU05940 tsaD]~~
−	\|-
−	\|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=TsaD TsaD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 36 kDa, 5.016~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1038 bp, 346 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ydiD]]'', ''[[ydiF]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05940 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05940 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05940 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:gcp_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=gcp_643258_644298_1 Expression at a glance]'''   {{PubMed\|22383849~~}~~}<br/>[[Image:gcp_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05940]]~~
−	\|-
−	\|}

−	~~__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\|[[essential genes]]}},~~
−	~~{{SubtiWiki category\|[[universally conserved proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU05940
−
−	~~===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=BSU05940&redirect=T BSU05940]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12202]
−
−	~~=== 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:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[TsaB]]-[[TsaD]] {{PubMed\|23072323,21285948}}
−	** [[TsaD]]-[[TsaE]] {{PubMed\|23072323}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU05940&redirect=T BSU05940]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O05518 O05518]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU05940]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−	~~[[universally conserved protein]]~~
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[thiL]]-[[tsaE]]-[[tsaB]]-[[ydiD]]-[[tsaD]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gcp_643258_644298_1 tsaD] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed> 23072323 22383849</pubmed>~~
−	~~==Publications on the corresponding protein from other species==~~
−	~~<pubmed> 21183954 19376873 20824107 21619589 21285948 21625506 23056478 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 95: / Line 96: @@
 === 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=BSU05940 tsaD]
 |-
-|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/TsaD TsaD]
+|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=TsaD TsaD]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.016

@@ 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=gcp_643258_644298_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gcp_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gcp_643258_644298_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gcp_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05940]]
 |-
 |}

@@ Line 23: / Line 23: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydiD]]'', ''[[ydiF]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05940 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05940 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05940 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05940 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05940 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05940 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:gcp_context.gif]]

@@ Line 141: / Line 141: @@
 <pubmed> 23072323 22383849</pubmed>
 ==Publications on the corresponding protein from other species==
-<pubmed> 21183954 19376873 20824107 21619589 21285948 21625506 </pubmed>
+<pubmed> 21183954 19376873 20824107 21619589 21285948 21625506 23056478 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 108: / Line 108: @@
 =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=gcp_643258_644298_1 tsaD] {{PubMed|22383849}}
@@ Line 139: / Line 139: @@
 =References=
-<pubmed> 23072323 </pubmed>
+<pubmed> 23072323 22383849</pubmed>
 ==Publications on the corresponding'' E. coli'' protein, YgjD==
 <pubmed> 21183954 19376873 20824107 21619589 21285948 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 110: / Line 110: @@
 * '''Operon:'''
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gcp_643258_644298_1 gcp] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gcp_643258_644298_1 tsaD] {{PubMed|22383849}}
 * '''Sigma factor:'''