SndA - Revision history

Jstuelk at 13:32, 5 January 2014

2014-01-05T13:32:44Z

Jstuelk at 11:46, 18 August 2013

2013-08-18T11:46:00Z

Jstuelk: /* Basic information/ Evolution */

2013-08-18T11:34:23Z

‎Basic information/ Evolution

Jstuelk at 11:30, 18 August 2013

2013-08-18T11:30:51Z

Jstuelk: Jstuelk moved page YtnL to SndA: 23944997

2013-08-18T09:45:04Z

Jstuelk moved page YtnL to SndA: 23944997

134.76.70.252 at 14:17, 16 May 2013

2013-05-16T14:17:21Z

134.76.70.252 at 10:59, 14 May 2013

2013-05-14T10:59:56Z

134.76.70.252 at 13:35, 13 May 2013

2013-05-13T13:35:27Z

Jstuelk at 19:51, 29 April 2013

2013-04-29T19:51:09Z

134.76.70.252 at 14:52, 7 August 2012

2012-08-07T14:52:56Z

← Older revision		Revision as of 13:32, 5 January 2014
Line 1:		Line 1:
−	* '''Description:~~''' sulphur compound N-deacetylase, required for the conversion of S-methyl-cysteine to cysteine<br/><br/>~~	+	{{#bank: SndA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''sndA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''hipO, ytnL ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| sulphur compound N-deacetylase~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| utilization of S-methyl-cysteine~~
−	\|-
−	\|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=BSU29290 sndA]
−	\|-
−	\|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/riboflavin.html Riboflavin / FAD]'''
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 45 kDa, 5.545~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1248 bp, 416 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ytnM]]'', ''[[ribR]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29290 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ytnL_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=ytnL_2999717_3000967_-1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:ytnL_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29290]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[sulfur metabolism]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[CymR regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[AscR regulon]]}},~~
−	~~[[Efp-dependent proteins]]~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU29290
−
−	~~===Phenotypes of a mutant ===~~
−	* a ''[[sndA]] [[sndB]] [[sndC]]'' triple mutant does not grow with N-acetyl cysteine {{PubMed\|23944997}}
−
−	~~=== Database entries ===~~
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ytmIJKLMNO-ytnIJ-ribR-ytnLM.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12596]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:''' peptidase M20 family (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[SndB]], [[SndC]], [[YkuR]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−
−	~~=== Database entries ===~~
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34980 O34980]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29290]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−	The gene was annotated in KEGG and MetaCyc as hippurate hydrolase EC 3.5.1.32. In Swiss-Prot it is marked as “uncharacterized hydrolase”. No literature/experimental evidence supporting ththeannotation was removed as of November 2009. {{PubMed\|19935659}}
−
−	~~=Expression and regulation=~~
−	* '''Operon:''' ''[[snaA]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[cmoO]]-[[cmoI]]-[[cmoJ]]-[[ribR]]-[[sndA]]-[[ytnM]]'' {{PubMed\|15668000}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytnL_2999717_3000967_-1 sndA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|15272571}}
−
−	* '''Regulation:'''
−	** repressed in the presence of cysteine ([[CymR]]) {{PubMed\|16109943}}
−	** induced in the presence of S-methyl-cysteine ([[AscR]]) {{PubMed\|23944997}}
−
−	* '''Regulatory mechanism:'''
−	** [[CymR]]: transcription repression {{PubMed\|16109943}}
−	** [[AscR]]: transcription activation {{PubMed\|16109943}}
−
−	* '''Additional information:'''
−	** [[translation]] is likely to require [[Efp]] due to the presence of several consecutive proline residues {{PubMed\|23239624,23239623}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~<pubmed>16109943,15668000,15272571 23944997</pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 11:46, 18 August 2013
Line 54:		Line 54:

	===Phenotypes of a mutant ===		===Phenotypes of a mutant ===
		+	* a ''[[sndA]] [[sndB]] [[sndC]]'' triple mutant does not grow with N-acetyl cysteine {{PubMed\|23944997}}

	=== Database entries ===		=== Database entries ===

@@ Line 74: / Line 74: @@
 * '''Protein family:''' peptidase M20 family (according to Swiss-Prot)
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[SndB]], [[SndC]], [[YkuR]]
 === Extended information on the protein ===

@@ Line 1: / Line 1: @@
-* '''Description:''' unknown <br/><br/>
+* '''Description:''' sulphur compound N-deacetylase, required for the conversion of S-methyl-cysteine to cysteine<br/><br/>
 {| align="right" border="1" cellpadding="2"
 |-
 |style="background:#ABCDEF;" align="center"|'''Gene name'''
-|''ytnL''
+|''sndA''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hipO ''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hipO, ytnL ''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no
 |-
-|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+|style="background:#ABCDEF;" align="center"| '''Product''' || sulphur compound N-deacetylase
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of S-methyl-cysteine
 |-
-|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=BSU29290 ytnL]
+|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=BSU29290 sndA]
 |-
 |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/riboflavin.html Riboflavin / FAD]'''
@@ Line 40: / Line 40: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[proteins of unknown function]]}}
+{{SubtiWiki category|[[sulfur metabolism]]}}
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CymR regulon]]}},
-{{SubtiWiki regulon|[[YtlI regulon]]}},
+{{SubtiWiki regulon|[[AscR regulon]]}},
 [[Efp-dependent proteins]]
@@ Line 106: / Line 106: @@
 =Expression and regulation=
-* '''Operon:''' ''[[ytmI]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[ytmO]]-[[ytnI]]-[[ytnJ]]-[[ribR]]-[[ytnL]]-[[ytnM]]'' {{PubMed|15668000}}
+* '''Operon:''' ''[[snaA]]-[[tcyJ]]-[[tcyK]]-[[tcyL]]-[[tcyM]]-[[tcyN]]-[[cmoO]]-[[cmoI]]-[[cmoJ]]-[[ribR]]-[[sndA]]-[[ytnM]]'' {{PubMed|15668000}}
-* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytnL_2999717_3000967_-1 ytnL] {{PubMed|22383849}}
+* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytnL_2999717_3000967_-1 sndA] {{PubMed|22383849}}
 * '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15272571}}
@@ Line 114: / Line 114: @@
 * '''Regulation:'''
 ** repressed in the presence of cysteine ([[CymR]]) {{PubMed|16109943}}
 * '''Regulatory mechanism:'''
 ** [[CymR]]: transcription repression {{PubMed|16109943}}
-** [[YtlI]]: transcription activation {{PubMed|16109943}}
+** [[AscR]]: transcription activation {{PubMed|16109943}}
 * '''Additional information:'''
@@ Line 141: / Line 142: @@
 =References=
-'''Additional publications:''' {{PubMed|15272571}}
+<pubmed>16109943,15668000,15272571 23944997</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=ytnL_2999717_3000967_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ytnL_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytnL_2999717_3000967_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:ytnL_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU29290]]
 |-
 |}

← Older revision	Revision as of 09:45, 18 August 2013
(No difference)

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ytnM]]'', ''[[ribR]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29290 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU29290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU29290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU29290 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ytnL_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 48: / Line 44: @@
 = This gene is a member of the following [[regulons]] =
 {{SubtiWiki regulon|[[CymR regulon]]}},
-{{SubtiWiki regulon|[[YtlI regulon]]}}
+{{SubtiWiki regulon|[[YtlI regulon]]}},
 =The gene=
@@ Line 91: / Line 88: @@
 * '''Effectors of protein activity:'''
-* '''Interactions:'''
+* '''[[SubtInteract|Interactions]]:'''
-* '''Localization:'''
+* '''[[Localization]]:'''
 === Database entries ===
@@ Line 113: / Line 110: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ytnL_2999717_3000967_-1 ytnL] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] {{PubMed|15272571}}
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|15272571}}
 * '''Regulation:'''
@@ Line 123: / Line 120: @@
 * '''Additional information:'''
 =Biological materials =