SkfA - Revision history

JGerwig: /* Biological materials */

2015-02-03T15:57:49Z

‎Biological materials

JGerwig: /* Biological materials */

2015-02-03T15:56:58Z

‎Biological materials

JGerwig: /* Biological materials */

2015-02-03T15:52:43Z

‎Biological materials

JGerwig: /* Biological materials */

2015-02-03T15:52:18Z

‎Biological materials

JGerwig: /* Biological materials */

2015-02-03T15:51:50Z

‎Biological materials

134.76.38.147 at 12:52, 2 April 2014

2014-04-02T12:52:36Z

134.76.70.252 at 14:12, 18 November 2013

2013-11-18T14:12:58Z

Jstuelk at 11:28, 11 September 2013

2013-09-11T11:28:25Z

134.76.70.252 at 12:25, 16 May 2013

2013-05-16T12:25:49Z

134.76.70.252 at 09:20, 14 May 2013

2013-05-14T09:20:27Z

← Older revision		Revision as of 15:57, 3 February 2015
Line 1:		Line 1:
−	* '''Description:~~''' spore killing factor <br/><br/>~~	+	{{#bank: SkfA}}

−	~~{\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''skfA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ybcO''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| spore killing factor~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| killing of sister cells~~
−	\|-
−	\|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=BSU01910 skfA]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 5 kDa, 10.648~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 165 bp, 55 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[ybcM]]'', ''[[skfB]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ybcO_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=skfA_213941_214108_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:skfA_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[toxins, antitoxins and immunity against toxins]]}},~~
−	~~{{SubtiWiki category\|[[prophage 1]]}}~~
−
−	~~= This gene is a member of the following [[regulons]] =~~
−	~~{{SubtiWiki regulon\|[[AbrB regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[PhoP regulon]]}},~~
−	~~{{SubtiWiki regulon\|[[Spo0A regulon]]}}~~
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU01910
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]
−
−	* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12713]
−
−	~~=== Additional information===~~
−
−
−
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:'''
−
−	* '''Protein family:'''
−
−	* '''Paralogous protein(s):'''
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:''' the mature SKF is cyclic 26-amino acid peptide that is posttranslationally modified with one disulfide and one cysteine thioether bridged to the alpha-position of a methionine {{PubMed\|20805502}}, the thioether bond is generated by [[SkfB]] {{PubMed\|23282011}}
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** [[SkfA]]-[[SkfB]] {{PubMed\|23282011}}
−
−	* '''[[Localization]]:''' secreted (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU01910&redirect=T BSU01910]
−
−	* '''Structure:'''
−
−	* '''UniProt:''' [http://www.uniprot.org/uniprot/O31422 O31422]
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU01910]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
−
−	* '''Regulation:'''
−	** repressed by glucose (33-fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
−	** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
−	** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
−	** induced by phosphate starvation ([[PhoP]]) [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
−	** induced by rhamnogalacturonan [http://www.ncbi.nlm.nih.gov/sites/entrez/17449691 PubMed]
−
−	* '''Regulatory mechanism:'''
−	** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647,15687200 PubMed]
−	** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15687200,17720793 PubMed]
−	** [[PhoP]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
−
−	* '''Additional information:'''
−	** Northern blotting during during phosphate limitation showed an intense 0.25 kb ''[[skfA]]''-specific transcript, and a weaker 6.5 kb ''[[skfA]]-[[skfB]]-[[skfC]]-[[skfE]]-[[skfF]]-[[skfG]]-[[skfH]]'' transcript.
−	** The ''[[skfA]]'' transcript is stabilized by a stem-loop structure in the ''[[skfA]]-[[skfB]]'' intergenic region. [http://www.ncbi.nlm.nih.gov/pubmed/16816204 PubMed]
−	** The mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
−
−	~~=Biological materials =~~
−
−	* '''Mutant:'''
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:'''
−
−	* '''GFP fusion:'''
−	** GP1645 ''[[ymdB]]''::''spc'' P''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
−
−	* '''two-hybrid system:'''
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20955377 </pubmed>~~
−	~~==Original Publications==~~
−	~~'''Additional publications:''' {{PubMed\|23282011,20805502}}~~
−	~~<pubmed>12884008,15812018,14651647,15687200, 17720793, 12850135,12817086,16816204,17449691,18840696 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 142: / Line 142: @@
 * '''GFP fusion:'''
-** GP1645 ''[[ymdB]]''::''spc'' ''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
+** GP1645 ''[[ymdB]]''::''spc'' P''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
 * '''two-hybrid system:'''

@@ Line 143: / Line 143: @@
 * '''GFP fusion:'''
 ** GP1645 ''[[ymdB]]''::''spc'' ''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
 * '''two-hybrid system:'''

← Older revision		Revision as of 15:52, 3 February 2015
Line 142:		Line 142:

	* '''GFP fusion:'''		* '''GFP fusion:'''
−	** GP1645 ''[[ymdB]]''::spc ''skf-gfp'' (spc) in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab	+	** GP1645 ''[[ymdB]]''::''spc'' ''skf-gfp'' (''spc'') in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab

← Older revision		Revision as of 15:51, 3 February 2015
Line 142:		Line 142:

	* '''GFP fusion:'''		* '''GFP fusion:'''
		+	** GP1645 ''[[ymdB]]''::spc ''skf-gfp'' (spc) in the NCIB3610 background, available in [[ Jörg Stülke]]'s lab
		+

	* '''two-hybrid system:'''		* '''two-hybrid system:'''

@@ Line 57: / Line 57: @@
 === Database entries ===
 * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/skf.html]
@@ Line 95: / Line 96: @@
 === Database entries ===
 * '''Structure:'''

@@ 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=BSU01910 skfA]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/SkfA SkfA]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SkfA SkfA]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.648

@@ Line 40: / Line 40: @@
 = [[Categories]] containing this gene/protein =
-{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}}
+{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
 = This gene is a member of the following [[regulons]] =
@@ Line 111: / Line 112: @@
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 skfA] {{PubMed|22383849}}
-* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
+* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/pubmed/16452424 PubMed]
 * '''Regulation:'''

@@ 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=skfA_213941_214108_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:skfA_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=skfA_213941_214108_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:skfA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU01910]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ybcM]]'', ''[[skfB]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU01910 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU01910 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU01910 DNA_with_flanks]
 |-
 |colspan="2" | '''Genetic context''' <br/> [[Image:ybcO_context.gif]]