SubtiWiki - User contributions [en]

SR4

2014-04-02T15:23:30Z

134.76.38.147:

* '''Description:''' antitoxin RNA, inhibits'' [[bsrG]]'' translation and causes destabilization of the ''[[bsrG]]'' mRNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''SR4''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || antitoxin RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||inhibition of [[BsrG]] toxin expression
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 180 bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[bsrG]]'', ''[[yokL]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA sequence '''
|-
|colspan="2" | '''Genetic context''' [[Image:bsrG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[SPß prophage]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* cell lysis on agar plates {{PubMed|22229825}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=The RNA=
binds the ''[[bsrG]]'' mRNA and triggers its degradation {{PubMed|22229825}}, moreover SR4 inhibits ''[[bsrG]]'' translation {{PubMed|23969414}}

=Expression and regulation=

* '''Operon:''' ''[[SR4]]'' {{PubMed|22229825}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22229825}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** half-life of the mRNA: 3 min {{PubMed|22229825}}
** maturation of the RNA requires [[PnpA]] {{PubMed|22229825}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

[[Sabine Brantl]], Jena, Germany

=Your additional remarks=

=References=
<pubmed> 23969414 22229825</pubmed>

[[Category:Small RNA]]

SurC

2014-04-02T15:23:28Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''surC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dnaJ]]'', ''[[dnaK]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:SurC_context.jpeg]]
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sporulation/ other]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigK regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''surC'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Sigma factor:''' [[SigK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Regulation:''' expressed during sporulation in the mother cell ([[SigK]], [[GerE]])[http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Regulatory mechanism:''' [[GerE]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

=Your additional remarks=

=References=

<pubmed>16385044,,16385044, </pubmed>

[[Category:small RNA]]

SurA

2014-04-02T15:23:26Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''surA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 280 bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yndK]]'', ''[[yndL]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:SurA_context.jpg]]
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=S655_1915134_1915264_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:surA_expression.png|500px]]
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''surA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Regulation:''' induced at the beginning of sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Regulatory mechanism:''' [[Spo0A]]: unknown, indirect effect, probably via [[AbrB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16385044 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

=Your additional remarks=

=References=

<pubmed>16385044,20525796</pubmed>

[[Category:small RNA]]

BsrI

2014-04-02T15:23:24Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrI''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sufC]]'', ''[[yurZ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, </pubmed>

[[Category:small RNA]]

BsrH

2014-04-02T15:23:23Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ratA]]'', ''[[as-bsrH]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[Skin element]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[as-bsrH regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, 20525796</pubmed>

[[Category:small RNA]]

BsrG

2014-04-02T15:23:20Z

134.76.38.147:

* '''Description:''' hydrophobic toxin 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrG''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || toxin
|-
|style="background:#ABCDEF;" align="center"|'''Function''' ||unknown
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' ||
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 294 bp, 38 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yolA]]'', ''[[SR4]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein '''
|-
|colspan="2" | '''Genetic context''' [[Image:bsrG_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[SPß prophage]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

=== 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:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''
** membrane protein (based on the presence of a trans-membrane domain) {{PubMed|22229825}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure:'''

* '''UniProt:'''

* '''KEGG entry:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[bsrG]]'' {{PubMed|22229825}}

* '''Sigma factor:''' [[SigA]] {{PubMed|22229825}}

* '''Regulation:'''
** expression increases at the onset of the stationary phase {{PubMed|22229825}}
** the mRNA is destabilized upon interaction with the antitoxin RNA [[SR4]] {{PubMed|22229825}}
** the mRNA is degraded by [[Rnc]], [[Rny]] and [[Rnr]] {{PubMed|22229825}}

* '''Regulatory mechanism:'''
** the mRNA is degraded by [[Rnc]], [[Rny]] and [[Rnr]], degradation is enhanced at higher temperature {{PubMed|22229825}}

* '''Additional information:'''
** half-life of the mRNA: 15 min {{PubMed|22229825}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/protein=

[[Sabine Brantl]], Jena, Germany

=Your additional remarks=

=References=
<pubmed>18948176, 20525796 23969414 22229825</pubmed>

[[Category:Protein-coding genes]]

BsrF

2014-04-02T15:23:18Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''SR2 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yobO]]'', ''[[csaA]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''bsrF'' [http://www.ncbi.nlm.nih.gov/sites/entrez/19542274 PubMed]

* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19542274 PubMed]

* '''Regulation:''' weakly activated by [[CodY]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19542274 PubMed]

* '''Regulatory mechanism:''' [[CodY]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/19542274 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutants:''' DB104::Delta bsrF::cat, DB104::Delta bsrF::ery, 168::Delta bsrF::cat, 168::Delta bsrF::ery available in the [[Sabine Brantl]] lab

* '''Expression vectors:'''
** pWSR2, multi-copy vector for tetracycline-inducible expression of ''bsrF'' (kanamycin resistance gene), available in the [[Sabine Brantl]] lab
** pUCB2SR2, multi-copy vector for constitutive expression of ''bsrF'' under its own promoter (kanamycin resistance gene), available in the [[Sabine Brantl]] lab

* '''lacZ fusions:''' pACG1 to pACG19 containing regions of different size upstream of the ''bsrF'' promoter available in the [[Sabine Brantl]] lab

=Labs working on this gene/RNA=

* [[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
* Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, 19542274 </pubmed>

[[Category:small RNA]]

BsrE

2014-04-02T15:23:16Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoyA]]'', ''[[yobJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, 20525796</pubmed>

[[Category:small RNA]]

BsrD

2014-04-02T15:23:14Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yddM]]'', ''[[yddN]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''bsrD'' {{PubMed|18948176}}

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, </pubmed>

[[Category:small RNA]]

BsrC

2014-04-02T15:23:11Z

134.76.38.147:

* '''Description:''' small RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''bsrC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydaG]]'', ''[[ydaH]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''bsrC''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

Kouji Nakamura, Tsukuba, University, Japan

=Your additional remarks=

=References=

<pubmed>18948176, </pubmed>

FbpC

2014-04-02T15:23:09Z

134.76.38.147:

* '''Description:''' small protein, acts as RNA chaperone for ''[[fsrA]]'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbpC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mrgC ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || write here
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || small protein, acts as RNA chaperone for ''[[fsrA]]''
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, 9.1
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 87 bp, 29 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dynA]]'', ''[[bpsB]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:FbpC_context.jpg]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[acquisition of iron]]}},
{{SubtiWiki category|[[iron metabolism]]}},
{{SubtiWiki category|[[RNA chaperones]]}},
{{SubtiWiki category|[[short peptides]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[Fur regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* transcription profile of a ''[[fbpC]]'' mutant strain: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

=== 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:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:''' no entry

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** induced upon iron starvation ([[Fur]]) {{PubMed|18697947}}

* '''Regulatory mechanism:'''
** [[Fur]]: transcription repression {{PubMed|18697947}}

* '''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>18697947 22389480 </pubmed>

[[Category:short peptide]]

RatA

2014-04-02T15:23:07Z

134.76.38.147:

* '''Description:''' regulatory RNA, [[small RNAs|ncRNA]], antisense for ''[[txpA]]'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ratA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ''[[txpA]]'' [[small RNAs|antisense RNA]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of ''[[txpA]]'' expression
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 222 bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[txpA]]'', ''[[bsrH]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=S976_2678362_2678577_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:ratA_expression.png|500px]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[Skin element]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The [[ratA regulon]]: ''[[txpA]]'' =
=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

* '''Structure:'''

=== Additional information===

=The RNA=

binds the ''[[txpA]]'' mRNA and triggers its degradation [http://www.ncbi.nlm.nih.gov/sites/entrez/16166525 PubMed]

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** the ''[[txpA]]'' mRNA-''[[RatA]]'' RNA duplex is degraded by [[rnc|RNase III]] {{PubMed|23300471}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard University, Cambridge, USA [http://www.mcb.harvard.edu/Losick/ Homepage]

=Your additional remarks=

=References=
==Reviews==
<pubmed> 23300472 </pubmed>

==Original publications==
<big>''Durand S, Gilet L, Condon C'' </big>
<big>'''The essential function of ''B. subtilis'' RNase III is to silence foreign toxin genes.''' </big>
<big>PLoS Genet. 2012 8(12): e1003181.</big>
[http://www.ncbi.nlm.nih.gov/pubmed/23300471 PubMed:23300471]
<pubmed>16166525, </pubmed>

[[Category:small RNA]]

FsrA

2014-04-02T15:23:04Z

134.76.38.147:

* '''Description:''' regulatory RNA 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fsrA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || sRNA FsrA
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibition of ''[[sdhC]]'' translation
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || aaa bp
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykuI]]'', ''[[ykuJ]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:FsrA_context.jpg]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[carbon core metabolism]]}},
{{SubtiWiki category|[[acquisition of iron]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[Fur regulon]]}}
=The [[FsrA regulon]]''=

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* transcription profile of a ''[[fsrA]]'' mutant strain: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

* '''Structure:'''

=== Additional information===

* '''Swiss prot entry:'''

* '''KEGG entry:''' no entry

* '''E.C. number:'''

=== Additional information===

=The RNA=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' hybridizes to ''[[sdhC]], [[citB]], [[lutB]], [[gltA]]-[[gltB]]'', and ''[[leuC]]-[[leuD]]'' mRNAs and inhibits their translation. {{PubMed|18697947,22389480}}

=== Extended information on the RNA===

* '''Kinetic information'''

* '''[[SubtInteract|Interactions]]:'''
** Binds ''[[sdhC]], [[citB]], [[lutB]], [[gltA]]-[[gltB]]'', and ''[[leuC]]-[[leuD]]'' mRNAs {{PubMed|18697947,22389480}}

* '''[[Localization]]'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure''':

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:''' induced by iron starvation ([[Fur]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]

* '''Regulatory mechanism:''' [[Fur]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

=Labs working on this gene/RNA=

[[John Helmann]], Cornell University, USA [http://www.micro.cornell.edu/research/labs/helmann-lab/index.cfm Homepage]

=Your additional remarks=

=References=

<pubmed>22427629,18697947,22389480</pubmed>

[[Category:small RNA]]

FbpA

2014-04-02T15:23:02Z

134.76.38.147:

* '''Description:''' Fur-regulated basic protein, acts as RNA chaperone for ''[[fsrA]]'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fbpA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ydbN''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || Fur-regulated basic protein, acts as RNA chaperone for ''[[fsrA]]''
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA chaperone
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || xx,x kDa, 9.50
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 159 bp, 53 amino acids
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fbpB]]'', ''[[ydbO]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:FbpA_fbpB_context.jpeg]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[acquisition of iron]]}},
{{SubtiWiki category|[[iron metabolism]]}},
{{SubtiWiki category|[[RNA chaperones]]}},
{{SubtiWiki category|[[short peptides]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[Fur regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===
* transcription profile of a ''[[fbpA]] [[fbpB]]'' double mutant strain: [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12081]

* '''GEO entry:''' [http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27416 GEO] {{PubMed|22389480}}

=== Additional information===

The sequence of the former ydbN gene was corrected, and does now contain two genes, [[fbpA]] and [[fbpB]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/18697947 PubMed]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:''' no entry

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[fbpA]]-[[fbpB]]'' {{PubMed|18697947}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** induced upon iron starvation ([[Fur]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12354229 PubMed]

* '''Regulatory mechanism:'''
** [[Fur]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12354229 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>18697947, 22389480 </pubmed>

[[Category:short peptide]]

MciZ

2014-04-02T15:23:00Z

134.76.38.147:

* '''Description:''' [[FtsZ]] inhibition peptide 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mciZ''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[FtsZ]] inhibition peptide
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || inhibits GTPase activity of [[FtsZ]] and Z ring formation during sporulation
|-
|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=MciZ MciZ]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 4.8 kDa, y.yy
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 120 bp, 40 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nudF]]'', ''[[yqkF]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_protein.txt Protein sequence]'''
|-
|colspan="2" | '''Genetic context''' [[Image:nudF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[cell division]]}},
{{SubtiWiki category|[[short peptides]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

=== Additional information===

This gene was only recently identified. [http://www.ncbi.nlm.nih.gov/sites/entrez/18284588 PubMed]

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' inhibits GTPase activity of [[FtsZ]] and Z ring formation during sporulation {{PubMed|18284588}}

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[MciZ]]-[[FtsZ]] {{PubMed|18284588}}

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure:'''

* '''Swiss prot entry:'''

* '''KEGG entry:''' no entry

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:''' [[SigE]] {{PubMed|18284588}}

* '''Regulation:'''
** expressed early during sporulation in the mother cell ([[SigE]]) {{PubMed|18284588}}

* '''Regulatory mechanism:'''

* '''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=

==Reviews==
<pubmed> 19680248 </pubmed>

==Original Publications==
<pubmed>,18284588, </pubmed>

[[Category:short peptide]]

TetL

2014-04-02T15:22:57Z

134.76.38.147:

YtrG

2014-04-02T15:22:55Z

134.76.38.147:

YszA

2014-04-02T15:22:54Z

134.76.38.147:

YokH

2014-04-02T15:22:53Z

134.76.38.147:

YolD

2014-04-02T15:22:51Z

134.76.38.147:

YouB

2014-04-02T15:22:50Z

134.76.38.147:

YomL

2014-04-02T15:22:48Z

134.76.38.147:

As-yonT

2014-04-02T15:22:45Z

134.76.38.147:

* '''Description:''' regulatory RNA, [[small RNAs|ncRNA]], antisense for ''[[yonT]]'' 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''as-yonT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || ''[[as-yonT]]'' [[small RNAs|antisense RNA]]
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of ''[[yonT]]'' expression
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' ||
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoyJ]]'', ''[[yonT]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE_nucleotide.txt Gene sequence (+200bp) ]'''
|-
|colspan="2" | '''Genetic context''' [[Image:genE_context.gif]]
|-
|}

__TOC__

 

= [[Categories]] containing this gene/RNA =
{{SubtiWiki category|[[toxins, antitoxins and immunity against toxins]]}},
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[ncRNA]]}}

= This gene is a member of the following [[regulons]] =

=The [[as-yonT regulon]]: ''[[yonT]]'' =
=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:'''

* '''Structure:'''

=== Additional information===

=The RNA=

binds the ''[[yonT]]'' mRNA and triggers its degradation {{PubMed|23300471}}

=Expression and regulation=

* '''Operon:'''

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** the ''[[yonT]]'' mRNA-''[[as-yonT]]'' RNA duplex is degraded by [[rnc|RNase III]] {{PubMed|23300471}}

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Richard Losick]], Harvard University, Cambridge, USA [http://www.mcb.harvard.edu/Losick/ Homepage]

=Your additional remarks=

=References=
<pubmed></pubmed>
<big>''Durand S, Gilet L, Condon C'' </big>
<big>'''The essential function of ''B. subtilis'' RNase III is to silence foreign toxin genes.''' </big>
<big>PLoS Genet. 2012 8(12): e1003181.</big>
[http://www.ncbi.nlm.nih.gov/pubmed/23300471 PubMed:23300471]

[[Category:small RNA]]

YoqW

2014-04-02T15:22:43Z

134.76.38.147:

* '''Description:''' similar to general secretion pathway protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yoqW''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|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=BSU20490 yoqW]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 4.937
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 672 bp, 224 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yoqX]]'', ''[[ligB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU20490 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU20490 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU20490 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yoqW_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU20490 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yoqW_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU20490]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[protein secretion]]}},
{{SubtiWiki category|[[SP-beta prophage]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU20490

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU20490&redirect=T BSU20490]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13681]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' XPT subfamily (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]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU20490&redirect=T BSU20490]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31916 O31916]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU20490]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU20490 yoqW] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

[[Category:Protein-coding genes]]

YotF

2014-04-02T15:22:41Z

134.76.38.147:

* '''Description:''' similar to 3-hydroxy-3-methylglutaryl-CoA lyase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yotF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|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=BSU19900 yotF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 2 kDa, 3.874
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 75 bp, 25 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yotG]]'', ''[[yotE]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19900 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19900 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19900 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yotF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[SP-beta prophage]]}},
{{SubtiWiki category|[[poorly characterized/ putative enzymes]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19900

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19900&redirect=T BSU19900]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13739]

=== 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:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19900&redirect=T BSU19900]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O31869 O31869]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19900]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU19900 yotF] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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>,9387222, </pubmed>

[[Category:Protein-coding genes]]

YobM

2014-04-02T15:22:39Z

134.76.38.147:

* '''Description:''' unknown 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yobM''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|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=BSU19010 yobM]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 19 kDa, 4.074
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 486 bp, 162 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yobL]]'', ''[[yobN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU19010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU19010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU19010 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yobM_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU19010 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yobM_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU19010]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19010

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19010&redirect=T BSU19010]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13505]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' UPF0720 family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[YokH]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU19010&redirect=T BSU19010]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/O34377 O34377]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU19010]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU19010 yobM] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

[[Category:Protein-coding genes]]

YozK

2014-04-02T15:22:38Z

134.76.38.147:

YobH

2014-04-02T15:22:36Z

134.76.38.147:

* '''Description:''' C-terminal fragment of the Y family DNA polymerase [[YozK]]-[[YobH]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yobH''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|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=BSU18930 yobH]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23 kDa, 10.003
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 609 bp, 203 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[phrK]]'', ''[[yozK]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU18930 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU18930 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU18930 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yobH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU18930 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yobH_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU18930]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[DNA repair/ recombination]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[LexA regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU18930

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18930&redirect=T BSU18930]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yozLK-yobH.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13500]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' DNA polymerase type-Y family

* '''Paralogous protein(s):''' [[PolY1]], [[PolY2]], [[UvrX]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU18930&redirect=T BSU18930]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/C0SPA8 C0SPA8]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18930]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[yozL]]-[[yozK]]-[[yobH]]'' {{PubMed|16267290}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU18930 yobH] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''
** induced by DNA damage ([[LexA]]) {{PubMed|16267290}}

* '''Regulatory mechanism:'''
** [[LexA]]: transcription repression {{PubMed|16267290}}

* '''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>16267290, </pubmed>

[[Category:Protein-coding genes]]

YobE

2014-04-02T15:22:34Z

134.76.38.147:

YmzE/1

2014-04-02T15:22:33Z

134.76.38.147:

YddT

2014-04-02T15:22:31Z

134.76.38.147:

* '''Description:''' unknown 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yddT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no {{PubMed|24178028}}
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
|-
|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=BSU05100 yddT]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 25 kDa, 9.546
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 684 bp, 228 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydzM]]'', ''[[ydzN]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU05100 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU05100 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU05100 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:yddT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU05100 Expression at a glance]'''   {{PubMed|22383849}} [[Image:yddT_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU05100]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[proteins of unknown function]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[AbrB regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU05100

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU05100&redirect=T BSU05100]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12127]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' almost identical to the protein [[YomL]] encoded by the prophage SPß (the two proteins differ in only 4 out of 228 amino acids)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU05100&redirect=T BSU05100]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P96657 P96657]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU05100]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''''' [[yddT]]'' {{PubMed|20817675}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=BSU05100 yddT] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''
** [[AbrB]]: transcription repression {{PubMed|20817675}}

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
**BP116 (yddT::spc), available in [[Fabian Commichau]]'s lab {{PubMed|24178028}}

* '''Expression vector:'''
** IPTG inducible expression of Strep-''yddT'' in ''E. coli'': pGP2581 (in [[pGP172]]), available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed>17114254 23420519 20817675 24178028 </pubmed>
[[Category:Protein-coding genes]]

YdzM

2014-04-02T15:22:29Z

134.76.38.147:

CmpA

2014-04-02T15:22:28Z

134.76.38.147:

* '''Description:''' spore coat protein, inhibits sporulation, required for proper spore coat assembly 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cmpA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || cortex morphogenetic protein A
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of spore cortex assembly
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' ||
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 111 bp, 37 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ydcI]]'', ''[[ydcK]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2012.08052.x/pdf sequences] (Ebmeier ''et al.'', 2012)'''
|-
|colspan="2" | '''Genetic context''' 
<div align="right"> 
|-
|}

__TOC__

 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[sporulation proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigE regulon]]}},
{{SubtiWiki regulon|[[SpoIIID regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' not available

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' no entry

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** orchestrates spore coat and cortex assembly {{PubMed|22463703}}
** represses cortex assembly until spore coat assembly successfully initiates {{PubMed|22463703}}
* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:'''
** surface of the developing forespore {{PubMed|22463703}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=?&redirect=T ?]

* '''Structure:'''

* '''UniProt:'''

* '''KEGG entry:'''

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cmpA]]'' {{PubMed|22463703}}

* '''[[Sigma factor]]:''' [[SigE]] {{PubMed|22463703}}

* '''Regulation:'''
** expressed early during sporulation in the mother cell ([[SigE]]) {{PubMed|22463703}}

* '''Regulatory mechanism:'''
** [[SpoIIID]]: transcription activation {{PubMed|22463703}}

* '''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=
'''Additional publications:''' {{PubMed|22463703,20709900}}
<pubmed></pubmed>

[[Category:Protein-coding genes]]

TrnA-Ala

2014-04-02T15:22:27Z

134.76.38.147:

TrnSL-Ala1

2014-04-02T15:22:25Z

134.76.38.147:

TrnSL-Arg1

2014-04-02T15:22:24Z

134.76.38.147:

TrnSL-Gly1

2014-04-02T15:22:23Z

134.76.38.147:

* '''Description:''' tRNA-Gly

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''trnSL-Gly1''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Gly
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 74 bp
|-|-

|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ygzD]]'', ''[[yhzB]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnSL-Gly1_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|''' '''
|-
|colspan="2" | '''Genetic context''' [[Image:trnSL-Gly1_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[translation]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU_TRNA_82&redirect=T BSU_tRNA_82]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00117]

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

[[Category:Transfer RNA]]

TrnE-Gly

2014-04-02T15:22:22Z

134.76.38.147:

* '''Description:''' tRNA-Gly

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''trnE-Gly''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || transfer RNA-Gly
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
|-
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 74 bp
|-|-

|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnE-Arg]]'', ''[[rrnE-16S]]''
|-
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/trnE-Gly_nucleotide.txt Gene sequence (+200bp) ]'''
|style="background:#FAF8CC;" align="center"|''' '''
|-
|colspan="2" | '''Genetic context''' [[Image:trnE-Gly_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

 
= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[translation]]}}

= This gene is a member of the following [[regulons]] =

=The gene=

=== Basic information ===

* '''Locus tag:'''

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU_TRNA_80&redirect=T BSU_tRNA_80]

* '''DBTBS entry:''' no entry

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00115]

* '''Structure:'''

=== Additional information===

=Expression and regulation=

* '''Operon:'''

* '''Sigma factor:'''

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''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=

[[Category:Transfer RNA]]

TrnA-Ile

2014-04-02T15:22:21Z

134.76.38.147:

TrnE-Arg

2014-04-02T15:22:19Z

134.76.38.147:

TrnSL-Val1

2014-04-02T15:22:17Z

134.76.38.147:

TrnSL-Tyr1

2014-04-02T15:22:16Z

134.76.38.147:

TrnSL-Glu2

2014-04-02T15:22:14Z

134.76.38.147:

TrnSL-Thr1

2014-04-02T15:22:14Z

134.76.38.147:

TrnSL-Gln2

2014-04-02T15:22:13Z

134.76.38.147:

TrnSL-Gln1

2014-04-02T15:22:11Z

134.76.38.147:

TrnB-Glu

2014-04-02T15:22:10Z

134.76.38.147:

TrnB-Ser2

2014-04-02T15:22:08Z

134.76.38.147:

TrnB-Asn

2014-04-02T15:22:06Z

134.76.38.147:

TrnSL-Ser1

2014-04-02T15:22:05Z

134.76.38.147: