XynA - Revision history

Jstuelk: /* Original publications */

2015-08-19T15:20:24Z

‎Original publications

Jstuelk: /* Original publications */

2014-08-11T09:13:20Z

‎Original publications

134.76.38.147 at 13:53, 2 April 2014

2014-04-02T13:53:31Z

134.76.70.252 at 10:56, 7 January 2014

2014-01-07T10:56:11Z

Jstuelk at 10:28, 28 November 2013

2013-11-28T10:28:14Z

134.76.70.252 at 13:32, 16 May 2013

2013-05-16T13:32:34Z

134.76.70.252 at 10:24, 14 May 2013

2013-05-14T10:24:07Z

134.76.70.252 at 12:59, 13 May 2013

2013-05-13T12:59:32Z

Jstuelk at 09:00, 6 March 2013

2013-03-06T09:00:28Z

Awiechert at 10:52, 3 December 2012

2012-12-03T10:52:54Z

← Older revision		Revision as of 15:20, 19 August 2015
Line 1:		Line 1:
−	* '''Description:~~''' endo-1,4-beta-xylanase <br/><br/>~~	+	{{#bank: XynA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''xynA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| endo-1,4-beta-xylanase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| xylan degradation~~
−	\|-
−	\|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=BSU18840 xynA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Metabolic function and regulation of this protein in [[SubtiPathways\|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=xynA xynA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 23 kDa, 9.644~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 639 bp, 213 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[pps]]'', ''[[yozV]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18840 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:xynA_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=xynA_2054599_2055240_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:xynA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18840]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[utilization of specific carbon sources]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU18840
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18840&redirect=T BSU18840]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynA.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10808]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans (according to Swiss-Prot)
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18840&redirect=T BSU18840]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2QZ3 2QZ3] (complex with xylotetraose), [http://www.rcsb.org/pdb/explore.do?structureId=2Z79 2Z79], [http://www.rcsb.org/pdb/explore.do?structureId=3EXU 3EXU]
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P18429 P18429]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU18840]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.8 3.2.1.8]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''xynA'' {{PubMed\|8628241}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xynA_2054599_2055240_-1 xynA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|8628241}}
−
−	* '''Regulation:'''
−	**constitutively expressed {{PubMed\|8012596}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** A [[ncRNA]] is predicted between ''[[pps]]'' and ''[[xynA]]'' {{PubMed\|20525796}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20735481 </pubmed>~~
−	~~==Original publications==~~
−	~~<pubmed>19531602 ,8012596, 18957862, 19422059 19994888 20096384 20188130 21466172 8628241 20525796 21966517 21785938 24271172 21964501 23459129 25096197 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 140: / Line 140: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-<pubmed>19531602 ,8012596, 18957862, 19422059  19994888 20096384 20188130 21466172 8628241 20525796 21966517 21785938 24271172 21964501 23459129 </pubmed>
+<pubmed>19531602 ,8012596, 18957862, 19422059  19994888 20096384 20188130 21466172 8628241 20525796 21966517 21785938 24271172 21964501 23459129 25096197 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 54: / Line 54: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynA.html]
@@ Line 89: / Line 90: @@
 === Database entries ===
 * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2QZ3 2QZ3] (complex with xylotetraose),  [http://www.rcsb.org/pdb/explore.do?structureId=2Z79 2Z79], [http://www.rcsb.org/pdb/explore.do?structureId=3EXU 3EXU]

@@ 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=BSU18840 xynA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism]'''
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=xynA xynA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 9.644

@@ Line 138: / Line 138: @@
 <pubmed>20735481 </pubmed>
 ==Original publications==
-'''Additional publications:''' {{PubMed|21785938}}
+<pubmed>19531602 ,8012596, 18957862, 19422059  19994888 20096384 20188130 21466172 8628241 20525796 21966517 21785938 24271172 21964501 23459129 </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=xynA_2054599_2055240_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:xynA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xynA_2054599_2055240_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:xynA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18840]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pps]]'', ''[[yozV]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18840 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18840 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18840 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18840 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:xynA_context.gif]]

@@ Line 37: / Line 37: @@
 <br/><br/><br/><br/>
 <br/><br/><br/><br/>
-<br/><br/><br/><br/>
+<br/><br/>
 = [[Categories]] containing this gene/protein =
@@ Line 110: / Line 106: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xynA_2054599_2055240_-1 xynA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|8628241}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8628241}}
 * '''Regulation:'''
@@ Line 143: / Line 139: @@
 ==Original publications==
 '''Additional publications:''' {{PubMed|21785938}}
-<pubmed>19531602 ,8012596, 18957862, 19422059  19994888 20096384 20188130 21466172 8628241 20525796 21966517 21964501</pubmed>
+<pubmed>19531602 ,8012596, 18957862, 19422059  19994888 20096384 20188130 21466172 8628241 20525796 21966517 21964501 23459129 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 639 bp, 213 aa
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pps]]'', ''[[yobD]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pps]]'', ''[[yozV]]''
 |-
 |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13776&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''