TopA - Revision history

Jstuelk at 07:57, 3 August 2015

2015-08-03T07:57:57Z

Jstuelk at 09:26, 6 August 2014

2014-08-06T09:26:22Z

134.76.70.252 at 09:46, 17 April 2014

2014-04-17T09:46:12Z

134.76.38.147 at 13:43, 2 April 2014

2014-04-02T13:43:04Z

Jstuelk: /* References */

2013-11-17T18:55:15Z

‎References

134.76.70.252 at 13:21, 16 May 2013

2013-05-16T13:21:05Z

134.76.70.252 at 10:13, 14 May 2013

2013-05-14T10:13:25Z

134.76.70.252 at 12:49, 13 May 2013

2013-05-13T12:49:42Z

Jstuelk at 19:33, 29 April 2013

2013-04-29T19:33:28Z

134.76.70.252 at 09:41, 7 August 2012

2012-08-07T09:41:35Z

← Older revision		Revision as of 07:57, 3 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' DNA topoisomerase I <br/><br/>~~	+	{{#bank: TopA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''topA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''topI ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| yes {{PubMed\|25092907}}~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| DNA topoisomerase I~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| [[DNA replication]]~~
−	\|-
−	\|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=BSU16120 topA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 78 kDa, 9.023~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 2073 bp, 691 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[dprA]]'', ''[[trmFO]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16120 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:topA_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=topA_1683661_1685736_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:topA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16120]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[DNA condensation/ segregation]]}},~~
−	~~{{SubtiWiki category\|[[essential genes]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~[[Efp-dependent proteins]]~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16120
−
−	~~===Phenotypes of a mutant ===~~
−	* essential {{PubMed\|25092907}}
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16120&redirect=T BSU16120]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/topA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11007]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' ATP-independent breakage of single-stranded DNA, followed by passage and rejoining (according to Swiss-Prot)
−
−	* '''Protein family:''' prokaryotic type I/III topoisomerase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[TopB]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** TopA interacts with the [[RNA polymerase]] {{PubMed\|21710567}}
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16120&redirect=T BSU16120]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P39814 P39814]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16120]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''topA'' (according to [http://dbtbs.hgc.jp/COG/prom/topA.html DBTBS])
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=topA_1683661_1685736_1 topA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:'''
−
−	* '''Regulation:'''
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed\|23239624,23239623}}
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 324 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 1123 {{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>17114254,21710567 25092907</pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 8: / Line 8: @@
 |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''topI ''
 |-
-|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+|style="background:#ABCDEF;" align="center"| '''Essential''' || yes {{PubMed|25092907}}
 |-
 |style="background:#ABCDEF;" align="center"| '''Product''' || DNA topoisomerase I
@@ Line 40: / Line 40: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[DNA condensation/ segregation]]}}
+{{SubtiWiki category|[[DNA condensation/ segregation]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 52: / Line 53: @@
 ===Phenotypes of a mutant ===
 === Database entries ===
@@ Line 70: / Line 72: @@
 * '''Protein family:''' prokaryotic type I/III topoisomerase family (according to Swiss-Prot)
-* '''Paralogous protein(s):''' [[TopB]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
+* '''Paralogous protein(s):''' [[TopB]]
 === Extended information on the protein ===
@@ Line 138: / Line 140: @@
 =References=
-<pubmed>17114254,21710567 </pubmed>
+<pubmed>17114254,21710567 25092907</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 116: / Line 116: @@
 * '''Additional information:'''
 ** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed|23239624,23239623}}
 =Biological materials =

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/topA.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:'''

@@ Line 134: / Line 134: @@
 =References=
-'''Additional publications:''' {{PubMed|21710567}}
+<pubmed>17114254,21710567 </pubmed>
 [[Category:Protein-coding genes]]

@@ 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=topA_1683661_1685736_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:topA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=topA_1683661_1685736_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:topA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16120]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dprA]]'', ''[[trmFO]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16120 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16120 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16120 topA]
+|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=BSU16120 topA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 78 kDa, 9.023
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dprA]]'', ''[[trmFO]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13485&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16120 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16120 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16120 Advanced_DNA]
 |-
 |-

@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || DNA topoisomerase I
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || replication
+|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU16120 topA]
@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
 <br/><br/>
@@ Line 47: / Line 43: @@
 = This gene is a member of the following [[regulons]] =
+[[Efp-dependent proteins]]
 =The gene=
@@ Line 110: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=topA_1683661_1685736_1 topA] {{PubMed|22383849}}
-* '''Sigma factor:'''
+* '''[[Sigma factor]]:'''
 * '''Regulation:'''
@@ Line 117: / Line 113: @@
 * '''Additional information:'''
 =Biological materials =