XylA - Revision history

134.76.38.147 at 13:49, 2 April 2014

2014-04-02T13:49:14Z

134.76.70.252 at 10:52, 7 January 2014

2014-01-07T10:52:19Z

134.76.70.252 at 13:27, 16 May 2013

2013-05-16T13:27:49Z

134.76.70.252 at 10:19, 14 May 2013

2013-05-14T10:19:44Z

134.76.70.252 at 12:55, 13 May 2013

2013-05-13T12:55:24Z

134.76.70.252 at 10:40, 20 September 2012

2012-09-20T10:40:43Z

Jstuelk: /* References */

2012-08-23T16:44:57Z

‎References

134.76.70.252 at 10:05, 7 August 2012

2012-08-07T10:05:33Z

134.76.70.252 at 10:17, 19 April 2012

2012-04-19T10:17:07Z

134.76.70.252 at 09:40, 13 April 2012

2012-04-13T09:40:13Z

← Older revision		Revision as of 13:49, 2 April 2014
Line 1:		Line 1:
−	* '''Description:~~''' xylose isomerase <br/><br/>~~	+	{{#bank: XylA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''xylA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| xylose isomerase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| utilization of xylan and xylose~~
−	\|-
−	\|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=BSU17600 xylA]
−	\|-
−	\|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=xylA xylA]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 50 kDa, 5.635~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1335 bp, 445 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[xylR]]'', ''[[xylB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU17600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU17600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU17600 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:xylA_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=xylA_1891908_1893245_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:xylA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU17600]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<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]] =~~
−	~~{{SubtiWiki regulon\|[[CcpA regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[XylR regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU17600
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xylAB.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10806]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' D-xylose = D-xylulose (according to Swiss-Prot)
−
−	* '''Protein family:''' xylose isomerase 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]]:'''
−	** cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1A0D 1A0D] (Geobacillus stearothermophilus)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P04788 P04788]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU17600]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/5.3.1.5 5.3.1.5]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[xylA]]-[[xylB]]'' {{PubMed\|1921970}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xylA_1891908_1893245_1 xylA] {{PubMed\|22383849}}
−
−	* '''Sigma factor:''' [[SigA]] {{PubMed\|2454911}}
−
−	* '''Regulation:'''
−	** carbon catabolite repression ([[CcpA]]) {{PubMed\|8132469}}
−	** induction by xylose ([[XylR]]) {{PubMed\|2454911}}
−
−	* '''Regulatory mechanism:'''
−	** [[CcpA]]: transcription repression {{PubMed\|8132469}}
−	** [[XylR]]: transcription repression {{PubMed\|2454911}}
−
−	* '''Additional information:'''
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1151 (del aphA3) available in [[Stülke]] lab
−	** 1A719 (no resistance), {{PubMed\|1719948}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A719&Search=1A719 BGSC]
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−
−	~~<pubmed>7966270,,1921970 8132469 2454911 1588910, 22900538 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ 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=BSU17600 xylA]
 |-
-|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=xylA xylA]'''
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 5.635

@@ Line 31: / Line 31: @@
   <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=xylA_1891908_1893245_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:xylA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xylA_1891908_1893245_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:xylA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU17600]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU17600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU17600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU17600 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU17600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU17600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU17600 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || utilization of xylan and xylose
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU17600 xylA]
+|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=BSU17600 xylA]
 |-
 |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]'''
@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xylR]]'', ''[[xylB]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13644&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU17600 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU17600 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU17600 Advanced_DNA]
 |-
 |-

← Older revision		Revision as of 10:40, 20 September 2012
Line 131:		Line 131:

	* '''Mutant:''' GP1151 (del aphA3) available in [[Stülke]] lab		* '''Mutant:''' GP1151 (del aphA3) available in [[Stülke]] lab
		+	** 1A719 (no resistance), {{PubMed\|1719948}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A719&Search=1A719 BGSC]

	* '''Expression vector:'''		* '''Expression vector:'''

@@ Line 150: / Line 150: @@
 =References=
-<pubmed>7966270,,1921970 8132469 2454911 1588910, </pubmed>
+<pubmed>7966270,,1921970 8132469 2454911 1588910, 22900538 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 28: / Line 28: @@
 |colspan="2" | '''Genetic context''' <br/> [[Image:xylA_context.gif]]
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
 |}
 __TOC__
 <br/><br/><br/><br/><br/><br/>

@@ Line 104: / Line 104: @@
 * '''Operon:''' ''[[xylA]]-[[xylB]]'' {{PubMed|1921970}}
-* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|2454911}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=xylA_1891908_1893245_1 xylA] {{PubMed|22383849}}
 * '''Regulation:'''