SubtiWiki - User contributions [en]

Bacillus amyloliquefaciens

2009-06-17T16:51:03Z

Paola Bisicchia:

''B. amyloliquefaciens'' FZB42 was sequenced by Chen et al. (2007)

[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=genome&Cmd=ShowDetailView&TermToSearch=21282 access to the sequence]

<pubmed>17704766 </pubmed>

Bacillus amyloliquefaciens

2009-06-17T16:47:44Z

Paola Bisicchia:

''B. amyloliquefaciens'' FZB42 was sequenced by Chen et al. (2007)

<pubmed>17704766 </pubmed>

Bacillus amyloliquefaciens

2009-06-17T16:46:01Z

Paola Bisicchia: Created page with '''B. amyloliquefaciens'' FZB42 was sequenced by Chen et al. (2007)'

''B. amyloliquefaciens'' FZB42 was sequenced by Chen et al. (2007)

Additional genome projects for Bacillus subtilis and other Bacilli

2009-06-17T16:44:28Z

Paola Bisicchia: Created page with '==Genome projects for other B. subtilis strains== ==Genome projects for other Bacillus species== * ''Bacillus amyloliquefaciens'''

==Genome projects for other B. subtilis strains==

==Genome projects for other Bacillus species==

* ''[[Bacillus amyloliquefaciens]]''

Ressources on Bacillus

2009-06-17T16:42:30Z

Paola Bisicchia:

This is a partial list of ''Bacillus'' resources:

* [http://genolist.pasteur.fr/SubtiList/ SubtiList]: The genome database
* [https://www.genoscope.cns.fr/agc/mage/wwwpkgdb/Viewer/viewer.php?wwwpkgdb=4a62689b309780e25c57f662fadfddef&nocache=7c3dbfa86fa22feb09c74f80d006dacd&dir= BacilluScope]: Here you get access to a new genome sequence and the corresponding database (Barbe ''et al''., 2009)
* [http://dbtbs.hgc.jp/ DBTBS]: The transcription regulation database
* [http://www.bgsc.org BGSC]: The ''Bacillus'' Genetic Stock Center
* [http://www.bacell.eu/ BACELL]: The European ''Bacillus'' community homepage
* [http://www.proteopedia.org/wiki/index.php/Category:Bacillus_subtilis Proteopedia] a Wiki devoted to protein structures, see the list of structures for ''B. subtilis''
* [[additional genome projects for Bacillus subtilis and other Bacilli]]

Ressources on Bacillus

2009-06-17T16:41:41Z

Paola Bisicchia:

This is a partial list of ''Bacillus'' resources:

* [http://genolist.pasteur.fr/SubtiList/ SubtiList]: The genome database
* [https://www.genoscope.cns.fr/agc/mage/wwwpkgdb/Viewer/viewer.php?wwwpkgdb=4a62689b309780e25c57f662fadfddef&nocache=7c3dbfa86fa22feb09c74f80d006dacd&dir= BacilluScope]: Here you get access to a new genome sequence and the corresponding database (Barbe ''et al''., 2009)
* [http://dbtbs.hgc.jp/ DBTBS]: The transcription regulation database
* [http://www.bgsc.org BGSC]: The ''Bacillus'' Genetic Stock Center
* [http://www.bacell.eu/ BACELL]: The European ''Bacillus'' community homepage
* [http://www.proteopedia.org/wiki/index.php/Category:Bacillus_subtilis Proteopedia] a Wiki devoted to protein structures, see the list of structures for ''B. subtilis''
* [[addtional genome projects for ''Bacillus subtilis'' and other Bacilli]]

Spo0A

2009-06-17T16:38:33Z

Paola Bisicchia: /* References */

* '''Description:''' two-component response regulator, initiation of sporulation 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''spo0A''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0C, spo0G, spoIIL, sof-1 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/glutamate.html Ammonium/ glutamate], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism], [http://subtiwiki.uni-goettingen.de/pathways/carbohydrate_metabolic_pathways.html Sugar catabolism], [http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress], [http://subtiwiki.uni-goettingen.de/pathways/tRNA_charging.html tRNA charging]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.989
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 801 bp, 267 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqiG]]'', ''[[spoIVB]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB14353]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:spo0A_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU24220

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spo0A.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10765]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

* '''Protein family:'''

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

=== Genes controlled by Spo0A ===

* '''Activation by Spo0A:''' ''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[spoIIE]]'', ''[[spoIIGA]]-[[sigE]]-[[sigG]]''

* '''Repression by Spo0A:''' ''[[abrB]], [[kinA]], [[kinC]], [[spo0A]]'', ''[[metS]]''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:''' receives phosphorylation from [[Spo0B]], dephosphorylation by [[Spo0E]]

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

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

* '''Interactions:''' [[Spo0A]]-[[Spo0E]], [[Spo0A]]-[[SigA]]

* '''Localization:'''

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1QMP 1QMP] (with phosphorylated aspartate, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/explore.do?structureId=1FC3 1FC3] (trans-activation domain, ''Geobacillus stearothermophilus''), [http://www.rcsb.org/pdb/explore.do?structureId=1LQ1 1LQ1] (complex with DNA)

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P06534 P06534]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU24220]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/1391039 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

* [[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
* [[Imrich Barak]], Slovak Academy of Science, Bratislava, Slovakia [http://imb.savba.sk/~barak/ homepage]
* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]

=Your additional remarks=

=References=

<pubmed>19528067, 8730857,2106683,3157992,12067336,10869437,16385044,9287005,8127878,9287022,8231806,1905258,16452424,2118505,8207022,12176382,9733708,11069677,1391039,12730135,2437099,8288522,16166384,9495766,2118512,1556084,18296515,7768874,3145384,14651647,1537790,9658000,8509330,14762002,1846779,2981817,15687200,9477965,8600030,18840696,1391039, 14679239, 14976210, 19207565 </pubmed>

Talk:SubtiPathways

2009-06-17T16:34:11Z

Paola Bisicchia: /* Lysine, threonine */

<big>'''Discovered something unusual in the diagrams? Please leave a comment in the corresponding section!'''</big>

__NOTOC__

== General comments about all diagrams ==
* There seem to be some compatibility problems using Google Chrome. Nonetheless, Mozilla Firefox, Netscape, Microsoft Explorer, Safari, and Opera are working properly.
* Comments in brackets have been changed in the original files, but have not been uploaded yet.

 
== Carbon metabolism ==

=== Central carbon metabolism ===

*Please check whether the "y" genes in the diagrams have already new names. For example, yqjH is polY1. If you are on the PolY1 page in subtiwiki and you get the link to the pathway it is not obvious whtat to look for (PolY1) is not in the list. Jörg

=== Utilization of different carbon sources ===

*(sugar between gluconate and xylose = '''beta'''-xylosides)

 
== Cellwall ==

write comments here

 
== CoA synthesis ==

write comments here

 
== Folate biosynthesis ==

write comments here

 
== Menaquinone ==

write comments here

 
== Nitrogen and amino acid metabolism ==

=== Ammonium assimilation and glutamate metabolism (incl. glutamine and arginine) ===

write comments here

=== Alanine, glycine, serine ===

write comments here

=== Aspartate, asparagine ===

write comments here

=== Cysteine, methionine ===

write comments here

=== Histidine ===

*Description for HutU

=== Isoleucine, valine, leucine ===

write comments here

=== Lysine, threonine ===

* SpoVF hieß das früher, jetzt sind es zwei Proteine (SpoVFA und SpoVFB), die kommen ja auch im Regulationsteil vor und sind richtig zu SubtiWiki verlinkt. Man sollte da also oben auch den Komplex aus beiden reinmachen und dann das Popup-Fenster entspechend verändern. Ich kopiere diese Message auhc mal auf die SubtiPathways-Wishlist, dann könnte das in einer größeren Überarbeitungsaktion mal in Angriff genommen werden.

=== Phenylalanine, tyrosine, tryptophan ===

write comments here

=== Proline ===

write comments here

 
== Nucleotides ==

=== Gene regulation of nucleotides ===

write comments here

=== Nucleosides catabolism ===

write comments here

=== Purine metabolism ===

write comments here

=== Purines catabolism ===

write comments here

=== Purines salvage pathways ===

*(RelA muss groß geschrieben werden)

=== Pyrimidines metabolism ===

write comments here

 
== Stress response ==

* (PurP muss PurS sein)
* (SpoVt muss SpoVT sein)
* (sigB groß)
 

== Sulfate assimilation ==

write comments here

 
== tRNA charging ==

*Arne, wir hatten doch eine Extra-Diskussion über die Rolle von TilS. Das fehlt hier aber! Jörg

The people behind SubtiWiki, SubtiPathways and SubtInteract

2009-06-17T16:32:57Z

Paola Bisicchia:

[[File:Bild subtiwiki.jpg|600px|thumb|right|'''The Wiki Boys [[User:Lflorez| Lope]], [[aschmei | Arne ]], [[clammers | Repel]], [[ sroppel | Fips]], [[ Jörg Stülke| Jörg]] (We dance for money at your party, just [mailto:heilers@gwdg.de send a mail] to our [[user:heilers| manager]])''']]

* [http://wwwuser.gwdg.de/~genmibio/stuelke2.html Prof. Dr. Jörg Stülke]
* [http://wwwuser.gwdg.de/~genmibio/members/lflorez.htm Lope A. Florez]
* [[sroppel |Sebastian "Fips" Roppel]]
* [[clammers |Christoph "Repel" Lammers]]
* [[aschmei |Arne Schmeisky]]
 

Hallo Jörg,

anscheinend läuft die Werbekampagne ganz gut, bei den ganzen Neuanmeldungen.

Repel ist aufgefallen, dass es im AS-Diagramm ein Protein SpoVF gibt, das gibt es auch in der Literatur (PMID: 10986255) , nur leider im Subtiwiki nicht, weißt du vielleicht, ob es sich dabei um ein Synonym handelt?

viel Spaß noch im golden state und noch eine erfolgreiche Tagung weiterhin.

Gruß Arne

Hallo Arne,

SpoVF hieß das früher, jetzt sind es zwei Proteine (SpoVFA und SpoVFB), die kommen ja auch im Regulationsteil vor und sind richtig zu SubtiWiki verlinkt. Man sollte da also oben auch den Komplex aus beiden reinmachen und dann das Popup-Fenster entspechend verändern. Ich kopiere diese Message auhc mal auf die SubtiPathways-Wishlist, dann könnte das in einer größeren Überarbeitungsaktion mal in Angriff genommen werden.

Viele Grüße

Jörg

The people behind SubtiWiki, SubtiPathways and SubtInteract

2009-06-17T16:27:28Z

Paola Bisicchia:

The people behind SubtiWiki, SubtiPathways and SubtInteract

2009-06-17T14:47:55Z

Paola Bisicchia:

[[File:Bild subtiwiki.jpg|600px|thumb|right|'''The Wiki Boys [[User:Lflorez| Lope]], [[aschmei | Arne ]], [[clammers | Repel]], [[ sroppel | Fips]], [[ Jörg Stülke| Jörg]] (We dance for money at your party, just [mailto:heilers@gwdg.de send a mail] to our [[user:heilers| manager]])''']]

* [http://wwwuser.gwdg.de/~genmibio/stuelke2.html Prof. Dr. Jörg Stülke]
* [http://wwwuser.gwdg.de/~genmibio/members/lflorez.htm Lope A. Florez]
* [[sroppel |Sebastian "Fips" Roppel]]
* [[clammers |Christoph "Repel" Lammers]]
* [[aschmei |Arne Schmeisky]]
 

Hi Wikiboys,

guten Morgen! Hier ist es gerade 7 Uhr. Wir sind vorhin aufgestanden und waren erst mal im Ozean, der direkt vor unserer Unterkunft ist, baden. Nachher geht es dann wieder los.
Inzwischen waren auch die beiden Postersessions und SubtiWiki ist extrem gut angekommen. Die Leute sind echt begeistert.

Heute Abend ist dann das Dinner. Das Früchtchen ist übrigens auch hier.

Viele Grüße an Euch und alle anderen,

Jörg

Hi Jörg,

klingt super! Dann müssen sich die Leute nun nur noch fleißig anmelden und editieren!
Hab mich schon gewundert, was Paola hier wohl schreiben könnte :)!

Schwimmen würd ich auch gern, aber das Wetter ist bis auf heute nicht so prickelnd, vor allem am Dies nicht. Da kam genug Wasser von oben. Aber wir waren vergleichsweise erfolgreich (keine Eigentore und ein Tor von Pavel :))!

Wie du bestimmt gesehen hast, sind auch eine Menge neuer Marker hinzugekommen. Aminosäuren sollten heute noch fertig werden, denk ich!
Dann fehlen nur noch die für die Nucleotide!

Gruß
Repel

Hi Repel,

ja, ich hab mich uach gewundert, was die Paola auf dieser Seite sucht. Bis ich bemerkt habe, dass sie sich gestern abend hier eingeloggt hat und noch eingeloggt ist. Ist ja auch nicht so schlimm!

Ich hab schon gesehen, dass Du gut vorangekommen bist!

Bis bald,

Jörg

The people behind SubtiWiki, SubtiPathways and SubtInteract

2009-06-17T14:26:17Z

Paola Bisicchia:

YocH

2009-06-17T01:43:32Z

Paola Bisicchia: /* References */

* '''Description:''' probable peptidoglycan hydrolase (amidase) 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''yocH''
|-
|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
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 30 kDa, 8.371
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 861 bp, 287 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[desR]]'', ''[[yocI]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13813]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:yocH_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|}

__TOC__

 

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU19210

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13521]

=== 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:'''

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot), extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]

=== Database entries ===

* '''Structure:'''

* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34669 O34669]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19210]

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

=== Additional information===

=Expression and regulation=

* '''Operon:'''

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

* '''Regulation:'''
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
** repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
** [[AbrB]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/15101989 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:''' AH024 knock-out mutant (kan) available in the lab of [[Kevin Devine]]

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

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

* '''Antibody:'''

=Labs working on this gene/protein=

[[Kevin Devine]]

=Your additional remarks=

=References=

<pubmed>14651647,15101989,18957862,12950927, </pubmed>

YocH

2009-06-17T01:41:41Z

Paola Bisicchia: /* Labs working on this gene/protein */