YodU - Revision history

Jstuelk: /* Expression and regulation */

2015-04-06T14:28:02Z

‎Expression and regulation

Jstuelk at 16:28, 1 April 2015

2015-04-01T16:28:55Z

Jstuelk at 16:40, 14 November 2014

2014-11-14T16:40:32Z

Jstuelk: /* References */

2014-10-20T07:29:10Z

‎References

Jstuelk at 08:46, 10 October 2014

2014-10-10T08:46:26Z

Jstuelk at 08:37, 10 October 2014

2014-10-10T08:37:49Z

Jstuelk: /* Additional information */

2014-10-10T08:28:17Z

‎Additional information

Jstuelk at 08:17, 10 October 2014

2014-10-10T08:17:42Z

Jstuelk: /* References */

2014-10-10T07:59:23Z

‎References

Julian at 12:59, 24 April 2014

2014-04-24T12:59:46Z

← Older revision		Revision as of 14:28, 6 April 2015
Line 1:		Line 1:
−	* '''Description:''' N-terminal part of the split gene ''spsM'' (together with ''[[ypqP]]''), spore envelope polysaccharide biosynthesis, in ''B. subtilis'' 168 the gene is disrupted by the [[SP-beta prophage]] <br/><br/>	+	{{#bank: YodU}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''yodU''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ypqP, spsM''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| unknown~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| spore envelope polysaccharide biosynthesis~~
−	\|-
−	\|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=BSU19810 yodU]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 15 kDa, 9.819~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 423 bp, 141 aa (SpsM: 341 aa)~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[phy]]'', ''[[sprB]]''~~
−	\|-
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yodU_nucleotide.txt Gene sequence (+200bp) ]'''~~
−	~~\|style="background:#FAF8CC;" align="center"\|'''[http://subtiwiki.uni-goettingen.de/yodU_protein.txt Protein sequence]'''~~
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:yodU_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=ypqP_2151626_2152045_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:yodU_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19810]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[sporulation proteins]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[SigK regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[GerE regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU19810
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19810&redirect=T BSU19810]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13547]
−
−	~~=== Additional information===~~
−	* rearrangement (deletion of the [[SP-beta prophage]] and generation of the spsM gene) occurs during [[sporulation]] and in response to DNA damage to allow production of spore polysaccharide {{PubMed\|25299644}}
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):''' [[EpsC]] (for SpsM)
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:''' SpsM: Polysacc_synt_2 domain (Pfam accession number, PF02719) in the 18–296-aa region {{PubMed\|25299644}}
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−
−	* '''[[Localization]]:'''
−	** secreted (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19810&redirect=T BSU19810]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O34490 O34490]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19810]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:'''
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ypqP_2151626_2152045_1 yodU] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigK]] {{PubMed\|25299644,15383836}}
−
−	* '''Regulation:'''
−	** expressed late during [[sporulation]] in the mother cell ([[SigK]], [[GerE]]) {{PubMed\|25299644,15383836}}
−
−	* '''Regulatory mechanism:'''
−	** [[GerE]]: transcription activation {{PubMed\|25299644,15383836}}
−
−	* '''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> 25299644 15383836 25326298 </pubmed>~~
−	~~[[Category:Protein-coding genes]]~~

← Older revision		Revision as of 16:28, 1 April 2015
Line 1:		Line 1:
−	* '''Description:''' , N-terminal part of the split gene ''spsM'' (together with ''[[ypqP]]''), spore envelope polysaccharide biosynthesis, in ''B. subtilis'' 168 the gene is disrupted by the [[SP-beta prophage]] <br/><br/>	+	* '''Description:''' N-terminal part of the split gene ''spsM'' (together with ''[[ypqP]]''), spore envelope polysaccharide biosynthesis, in ''B. subtilis'' 168 the gene is disrupted by the [[SP-beta prophage]] <br/><br/>

	{\| align="right" border="1" cellpadding="2"		{\| align="right" border="1" cellpadding="2"

@@ Line 6: / Line 6: @@
 |''yodU''
 |-
-|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypqP''
+|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ypqP, spsM''
 |-
 |style="background:#ABCDEF;" align="center"| '''Essential''' || no

@@ Line 138: / Line 138: @@
 =References=
-<pubmed> 25299644 15383836 </pubmed>
+<pubmed> 25299644 15383836 25326298 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 20: / Line 20: @@
 |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 423 bp, 141 aa (SpsM: 341 aa)
 |-
-|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phy]]'', ''[[yotN]]''
+|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phy]]'', ''[[sprB]]''
 |-
 |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yodU_nucleotide.txt     Gene sequence      (+200bp)   ]'''

@@ Line 42: / Line 42: @@
 = This gene is a member of the following [[regulons]] =
+{{SubtiWiki regulon|[[SigK regulon]]}},
 =The gene=
@@ Line 108: / Line 109: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=ypqP_2151626_2152045_1 yodU] {{PubMed|22383849}}
-* '''[[Sigma factor]]:'''
+* '''[[Sigma factor]]:''' [[SigK]] {{PubMed|25299644,15383836}}
 * '''Regulation:'''
 * '''Regulatory mechanism:'''
 * '''Additional information:'''
@@ Line 135: / Line 138: @@
 =References=
-<pubmed> 25299644 </pubmed>
+<pubmed> 25299644 15383836 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 60: / Line 60: @@
 === Additional information===
-* rearrangement (deletion of the [[SP-beta prophage]] and generation of the spsM gene) occurs during [[sporulation]] to allow production of spore polysaccharide {{PubMed|25299644}}
+* rearrangement (deletion of the [[SP-beta prophage]] and generation of the spsM gene) occurs during [[sporulation]] and in response to DNA damage to allow production of spore polysaccharide {{PubMed|25299644}}
 =The protein=

@@ Line 1: / Line 1: @@
-* '''Description:''' similar to capsular polysaccharide biosynthesis <br/><br/>
+* '''Description:''' , N-terminal part of the split gene ''spsM'' (together with ''[[ypqP]]''), spore envelope polysaccharide biosynthesis, in ''B. subtilis'' 168 the gene is disrupted by the [[SP-beta prophage]] <br/><br/>
 {| align="right" border="1" cellpadding="2"
@@ Line 12: / Line 12: @@
 |style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 |-
-|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+|style="background:#ABCDEF;" align="center"|'''Function''' || spore envelope polysaccharide biosynthesis
 |-
 |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=BSU19810 yodU]
@@ Line 18: / Line 18: @@
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 15 kDa, 9.819
 |-
-|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 423 bp, 141 aa
+|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 423 bp, 141 aa (SpsM: 341 aa)
 |-
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phy]]'', ''[[yotN]]''
@@ Line 39: / Line 39: @@
 = [[Categories]] containing this gene/protein =
 {{SubtiWiki category|[[sporulation proteins]]}}
@@ Line 61: / Line 60: @@
 === Additional information===
+* rearrangement (deletion of the [[SP-beta prophage]] and generation of the spsM gene) occurs during [[sporulation]] to allow production of spore polysaccharide {{PubMed|25299644}}
 =The protein=
@@ Line 73: / Line 70: @@
 * '''Protein family:'''
-* '''Paralogous protein(s):'''
+* '''Paralogous protein(s):''' [[EpsC]] (for SpsM)
 === Extended information on the protein ===
@@ Line 79: / Line 76: @@
 * '''Kinetic information:'''
-* '''Domains:'''
+* '''Domains:''' SpsM: Polysacc_synt_2 domain (Pfam accession number, PF02719) in the 18–296-aa region {{PubMed|25299644}}
 * '''Modification:'''