YcbD - Revision history

134.76.38.147 at 12:54, 2 April 2014

2014-04-02T12:54:21Z

134.76.70.252 at 12:27, 16 May 2013

2013-05-16T12:27:51Z

134.76.70.252 at 09:23, 14 May 2013

2013-05-14T09:23:17Z

134.76.70.252 at 12:03, 13 May 2013

2013-05-13T12:03:04Z

134.76.70.252 at 09:23, 8 August 2012

2012-08-08T09:23:49Z

134.76.70.252 at 08:26, 8 August 2012

2012-08-08T08:26:54Z

134.76.70.252 at 15:11, 7 August 2012

2012-08-07T15:11:47Z

Jstuelk: Reverted edits by 134.76.70.252 (talk) to last revision by Jstuelk

2012-08-07T10:37:19Z

Reverted edits by 134.76.70.252 (talk) to last revision by Jstuelk

134.76.70.252 at 14:44, 6 August 2012

2012-08-06T14:44:00Z

134.76.70.252 at 13:34, 18 April 2012

2012-04-18T13:34:32Z

← Older revision		Revision as of 12:54, 2 April 2014
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−	* '''Description:~~''' NADP(+)-dependent alpha-ketoglutaric semialdehyde dehydrogenase <br/><br/>~~	+	{{#bank: YcbD}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''ycbD''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| '' ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| NADP(+)-dependent alpha-ketoglutaric semialdehyde dehydrogenase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| utilization of D-glucarate/galactarate~~
−	\|-
−	\|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=BSU02470 ycbD]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 52 kDa, 4.787~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1464 bp, 488 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ycbC]]'', ''[[ycbE]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02470 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ycbD_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=ycbD_268846_270312_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ycbD_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02470]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<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\|[[YcbG regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU02470
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ycbCDEFGHJ.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11159]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' an aldehyde + NAD<sup>+</sup> + H<sub>2</sub>O = an acid + NADH (according to Swiss-Prot)
−
−	* '''Protein family:''' aldehyde dehydrogenase family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[YfmT]], [[AldY]], [[GabD]], [[GbsA]], [[DhaS]], [[IolA]], [[PutC]], [[RocA]], [[AldX]], [[YwdH]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:''' [http://www.pdb.org/pdb/explore/explore.do?structureId=3RHH 3RHH] (from from ''Bacillus halodurans'' C-125 complexed with NADP, 36% identity, 69% similarity)
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/P42236 P42236]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU02470]
−
−	* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.1.3 1.2.1.3]
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon''' ''[[ycbC]]-[[ycbD]]-[[ycbE]]-[[ycbF]]-[[ycbG]]-[[ycbH]]-[[ycbJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycbD_268846_270312_1 ycbD] {{PubMed\|22383849}}
−
−	* '''Sigma factor:'''
−
−	* '''Regulation:''' induced by D-glucarate/galactarate ([[YcbG]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
−
−	* '''Regulatory mechanism:''' [[YcbG]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
−
−	* '''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>12044674,17202142 , , </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=ycbD_268846_270312_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ycbD_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycbD_268846_270312_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ycbD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU02470]]
 |-
 |}

@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycbC]]'', ''[[ycbE]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02470 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02470 DNA_with_flanks]
 |-
 |-

@@ Line 14: / Line 14: @@
 |style="background:#ABCDEF;" align="center"|'''Function''' || utilization of D-glucarate/galactarate
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://cellpublisher.gobics.de/subtiexpress/ ''Subti''Express]''': [http://cellpublisher.gobics.de/subtiexpress/bsu/BSU02470 ycbD]
+|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=BSU02470 ycbD]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.787
@@ Line 22: / Line 22: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ycbC]]'', ''[[ycbE]]''
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12041&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU02470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU02470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU02470 Advanced_DNA]
 |-
 |-

@@ Line 13: / Line 13: @@
 |-
 |style="background:#ABCDEF;" align="center"|'''Function''' || utilization of D-glucarate/galactarate
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 4.787

@@ Line 26: / Line 26: @@
 |colspan="2" | '''Genetic context''' <br/> [[Image:ycbD_context.gif]]
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
 |}
 __TOC__
 <br/><br/>

@@ Line 100: / Line 100: @@
 * '''Operon''' ''[[ycbC]]-[[ycbD]]-[[ycbE]]-[[ycbF]]-[[ycbG]]-[[ycbH]]-[[ycbJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]
-* '''[[Sigma factor]]:'''
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ycbD_268846_270312_1 ycbD] {{PubMed|22383849}}
 * '''Regulation:''' induced by D-glucarate/galactarate ([[YcbG]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12044674 PubMed]