TsaC - Revision history

Jstuelk: /* References */

2015-08-14T08:09:23Z

‎References

Jstuelk: /* References */

2015-06-01T09:35:40Z

‎References

134.76.70.252 at 11:26, 17 April 2014

2014-04-17T11:26:24Z

134.76.38.147 at 15:02, 2 April 2014

2014-04-02T15:02:58Z

134.76.70.252 at 14:48, 16 May 2013

2013-05-16T14:48:51Z

134.76.70.252 at 11:30, 14 May 2013

2013-05-14T11:30:38Z

134.76.70.252 at 14:05, 13 May 2013

2013-05-13T14:05:16Z

Jstuelk at 15:22, 18 October 2012

2012-10-18T15:22:17Z

Jstuelk: /* References */

2012-10-18T08:09:28Z

‎References

Jstuelk: /* Expression and regulation */

2012-10-18T08:08:46Z

‎Expression and regulation

← Older revision		Revision as of 08:09, 14 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' L-threonylcarbamoyl-AMP synthase, biosynthesis of the hypermodified base threonylcarbamoyladenosine (t(6)A) (together with [[TsaB]]-[[TsaD]]-[[TsaE]]) <br/><br/>~~	+	{{#bank: TsaC}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''tsaC''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ipc-29d, ywlC ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| L-threonylcarbamoyl-AMP synthase~~
−	\|-
−	~~\|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=BSU36950 tsaC]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 36 kDa, 5.82~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1038 bp, 346 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ywlD]]'', ''[[ywlB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36950 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ywlC_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=ywlC_3792969_3794009_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ywlC_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36950]]
−	\|-
−	\|}
−
−	~~__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]] =~~
−	~~{{SubtiWiki regulon\|[[DnaA regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU36950
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36950&redirect=T BSU36950]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10939]
−
−	~~=== Additional information===~~
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−	** conversion of L-threonine, bicarbonate/CO2 and ATP to give the intermediate L-threonylcarbamoyl-AMP (TC-AMP) and pyrophosphate as products {{PubMed\|23072323}}
−	** biosynthesis of the hypermodified base threonylcarbamoyladenosine (t(6)A), a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro (shown for the corresponding ''E. coli'' protein YrdC) {{PubMed\|19287007}}
−
−	* '''Protein family:''' SUA5 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU36950&redirect=T BSU36950]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=1HRU 1HRU] (the homolog from ''E. coli'') {{PubMed\|19287007}}
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P39153 P39153]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36950]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''''' [[tsaC]]'' {{PubMed\|22383849}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlC_3792969_3794009_-1 tsaC] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−	** [[DnaA]]: transcription repression {{PubMed\|17932079}}
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 209 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>17005971 17932079 19287007 23072323 22383849 26020636</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 138: / Line 138: @@
 =References=
-<pubmed>17005971 17932079 19287007 23072323 22383849</pubmed>
+<pubmed>17005971 17932079 19287007 23072323 22383849 26020636</pubmed>
 [[Category:Protein-coding genes]]

← Older revision		Revision as of 11:26, 17 April 2014
Line 116:		Line 116:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 209 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 52: / Line 52: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=1HRU 1HRU] (the homolog from ''E. coli'') {{PubMed|19287007}}

@@ 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=ywlC_3792969_3794009_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ywlC_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlC_3792969_3794009_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ywlC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU36950]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlD]]'', ''[[ywlB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36950 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36950 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ywlC_context.gif]]

@@ Line 14: / Line 14: @@
 |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/BSU36950 tsaC]
+|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=BSU36950 tsaC]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36 kDa, 5.82
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywlD]]'', ''[[ywlB]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15712&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU36950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU36950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU36950 Advanced_DNA]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ywlC_context.gif]]

@@ Line 4: / Line 4: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''ywlC''
+|''tsaC''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-29d ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ipc-29d, ywlC ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no

@@ Line 102: / Line 102: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''''' [[tsaC]]'' {{PubMed|22383849}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlC_3792969_3794009_-1 ywlC] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ywlC_3792969_3794009_-1 tsaC] {{PubMed|22383849}}
 * '''Sigma factor:'''