SubtiWiki - User contributions [en]

IspE

2011-10-06T06:16:26Z

Chkuo:

* '''Description:''' 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ispE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yabH '', ''ipk''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 6.349
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 867 bp, 289 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspF]]'', ''[[purR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB11822]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:ispE_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|[[biosynthesis of lipids]]}},
{{SubtiWiki category|[[essential genes]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU00460

===Phenotypes of a mutant ===

essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10109]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' ATP + 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol = ADP + 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (according to Swiss-Prot)

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:'''

=== Database entries ===

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37550 P37550]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00460]

* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.148 2.7.1.148]

=== 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=
<pubmed> 17458547 </pubmed>

[[Category:Protein-coding genes]]

YwpB

2011-10-06T06:12:38Z

Chkuo:

* '''Description:''' β-hydroxyacyl-(acyl carrier protein) dehydratase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''ywpB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fabZ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || β-hydroxyacyl-ACP dehydratase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid biosynthesis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 9.36
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 396 bp, 132 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mscL]]'', ''[[rapD]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15654]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:ywpB_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|[[biosynthesis of lipids]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU36370

===Phenotypes of a mutant ===

=== Database entries ===

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

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12496]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

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

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

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

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

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

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

* '''Interactions:'''

* '''Localization:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3D6X 3D6X] (from ''Campylobacter jejuni'', 45% identity, 67% similarity) {{PubMed|19280690}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/P94584 P94584]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36370]

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

=== 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=
<pubmed>17919287 19280690 </pubmed>
[[Category:Protein-coding genes]]

User:Chkuo

2011-09-26T03:57:22Z

Chkuo: Created page with "Chih-Horng Kuo [http://ipmb.sinica.edu.tw/chkuo/]"

Chih-Horng Kuo
[http://ipmb.sinica.edu.tw/chkuo/]

Dra

2011-09-26T03:43:13Z

Chkuo: add synonym

* '''Description:''' deoxyribose-phosphate aldolase 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''dra''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''deoC''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || deoxyribose-phosphate aldolase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of nucleotides as carbon source
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 4.926
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 633 bp, 211 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nupC]]'', ''[[deoR]]''
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB15978]+-newId sequences] (Barbe ''et al.'', 2009)'''
|-
|colspan="2" | '''Genetic context''' [[Image:dra_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|[[utilization of nucleotides]]}}

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

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU39420

===Phenotypes of a mutant ===

=== Database entries ===

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/deoR-dra-nupC-pdp.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10983]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:''' 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (according to Swiss-Prot)

* '''Protein family:''' DeoC type 1 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]]:''' cytoplasm (according to Swiss-Prot)

=== Database entries ===

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1MZH 1MZH] (from ''Aquifex aeolicus'', 42% identity, 62% similarity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39121 P39121]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39420]

* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.4 4.1.2.4]

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[dra]]-[[nupC]]-[[pdp]]'' {{PubMed|8550462}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8550462}}

* '''Regulation:'''
** repressed by glucose ([[CcpA]]) {{PubMed|10666464}}
** induced by deoxynucleotides ([[DeoR]]) {{PubMed|8550462}}

* '''Regulatory mechanism:'''
** [[CcpA]]: transcription repression {{PubMed|10666464}}
** [[DeoR]]: transcription repression {{PubMed|8550462}}

* '''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>10666464,11065368,8550462,10074062, </pubmed>
[[Category:Protein-coding genes]]