http://subtiwiki.uni-goettingen.de/wiki//api.php?action=feedcontributions&user=Chkuo&feedformat=atom
SubtiWiki - User contributions [en]
2024-03-28T21:05:40Z
User contributions
MediaWiki 1.30.0
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=IspE&diff=146153
IspE
2011-10-06T06:16:26Z
<p>Chkuo: </p>
<hr />
<div>* '''Description:''' 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ispE''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yabH '', ''ipk''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed] <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || isoprenoid biosynthesis <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 6.349 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 867 bp, 289 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspF]]'', ''[[purR]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11822&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ispE_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis of lipids]]}},<br />
{{SubtiWiki category|[[essential genes]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU00460<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10109]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''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) <br />
<br />
* '''Protein family:''' IspE subfamily (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:'''<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37550 P37550]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00460]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.1.148 2.7.1.148]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed> 17458547 </pubmed><br />
<br />
[[Category:Protein-coding genes]]</div>
Chkuo
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=YwpB&diff=146152
YwpB
2011-10-06T06:12:38Z
<p>Chkuo: </p>
<hr />
<div>* '''Description:''' β-hydroxyacyl-(acyl carrier protein) dehydratase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''ywpB''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''fabZ''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || β-hydroxyacyl-ACP dehydratase <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || fatty acid biosynthesis<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/fatty_acid_synthesis.html Lipid synthesis]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 14 kDa, 9.36 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 396 bp, 132 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[mscL]]'', ''[[rapD]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15654&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|-<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:ywpB_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[biosynthesis of lipids]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU36370<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' no entry<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12496]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' <br />
<br />
* '''Protein family:''' FabZ subfamily (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):''' [[YcsD]]<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''Interactions:'''<br />
<br />
* '''Localization:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?pdbId=3D6X 3D6X] (from ''Campylobacter jejuni'', 45% identity, 67% similarity) {{PubMed|19280690}}<br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P94584 P94584]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU36370]<br />
<br />
* '''E.C. number:'''<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
<br />
* '''Operon:''' <br />
<br />
* '''[[Sigma factor]]:''' <br />
<br />
* '''Regulation:''' <br />
<br />
* '''Regulatory mechanism:''' <br />
<br />
* '''Additional information:''' <br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>17919287 19280690 </pubmed><br />
[[Category:Protein-coding genes]]</div>
Chkuo
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=User:Chkuo&diff=146086
User:Chkuo
2011-09-26T03:57:22Z
<p>Chkuo: Created page with "Chih-Horng Kuo [http://ipmb.sinica.edu.tw/chkuo/]"</p>
<hr />
<div>Chih-Horng Kuo<br />
[http://ipmb.sinica.edu.tw/chkuo/]</div>
Chkuo
http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Dra&diff=146085
Dra
2011-09-26T03:43:13Z
<p>Chkuo: add synonym</p>
<hr />
<div>* '''Description:''' deoxyribose-phosphate aldolase <br/><br/><br />
<br />
{| align="right" border="1" cellpadding="2" <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Gene name'''<br />
|''dra''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''deoC''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Essential''' || no <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Product''' || deoxyribose-phosphate aldolase<br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Function''' || utilization of nucleotides as carbon source <br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)]'''<br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 4.926 <br />
|-<br />
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 633 bp, 211 aa <br />
|-<br />
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nupC]]'', ''[[deoR]]''<br />
|-<br />
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15978&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''<br />
|-<br />
|colspan="2" | '''Genetic context''' <br/> [[Image:dra_context.gif]]<br />
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div><br />
|-<br />
|}<br />
<br />
__TOC__<br />
<br />
<br/><br/><br/><br/><br/><br/><br />
<br />
= [[Categories]] containing this gene/protein =<br />
{{SubtiWiki category|[[utilization of nucleotides]]}}<br />
<br />
= This gene is a member of the following [[regulons]] =<br />
{{SubtiWiki regulon|[[CcpA regulon]]}},<br />
{{SubtiWiki regulon|[[DeoR regulon]]}}<br />
<br />
=The gene=<br />
<br />
=== Basic information ===<br />
<br />
* '''Locus tag:''' BSU39420<br />
<br />
===Phenotypes of a mutant ===<br />
<br />
=== Database entries ===<br />
<br />
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/deoR-dra-nupC-pdp.html]<br />
<br />
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10983]<br />
<br />
=== Additional information===<br />
<br />
<br />
<br />
<br />
=The protein=<br />
<br />
=== Basic information/ Evolution ===<br />
<br />
* '''Catalyzed reaction/ biological activity:''' 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde (according to Swiss-Prot) <br />
<br />
* '''Protein family:''' DeoC type 1 subfamily (according to Swiss-Prot)<br />
<br />
* '''Paralogous protein(s):'''<br />
<br />
=== Extended information on the protein ===<br />
<br />
* '''Kinetic information:''' <br />
<br />
* '''Domains:''' <br />
<br />
* '''Modification:'''<br />
<br />
* '''Cofactor(s):'''<br />
<br />
* '''Effectors of protein activity:'''<br />
<br />
* '''[[SubtInteract|Interactions]]:'''<br />
<br />
* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)<br />
<br />
=== Database entries ===<br />
<br />
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1MZH 1MZH] (from ''Aquifex aeolicus'', 42% identity, 62% similarity) <br />
<br />
* '''UniProt:''' [http://www.uniprot.org/uniprot/P39121 P39121]<br />
<br />
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU39420]<br />
<br />
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.1.2.4 4.1.2.4]<br />
<br />
=== Additional information===<br />
<br />
=Expression and regulation=<br />
* '''Operon:''' ''[[dra]]-[[nupC]]-[[pdp]]'' {{PubMed|8550462}} <br />
<br />
* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8550462}}<br />
<br />
* '''Regulation:''' <br />
** repressed by glucose ([[CcpA]]) {{PubMed|10666464}} <br />
** induced by deoxynucleotides ([[DeoR]]) {{PubMed|8550462}}<br />
<br />
* '''Regulatory mechanism:''' <br />
** [[CcpA]]: transcription repression {{PubMed|10666464}} <br />
** [[DeoR]]: transcription repression {{PubMed|8550462}}<br />
<br />
* '''Additional information:'''<br />
<br />
=Biological materials =<br />
<br />
* '''Mutant:'''<br />
<br />
* '''Expression vector:'''<br />
<br />
* '''lacZ fusion:'''<br />
<br />
* '''GFP fusion:'''<br />
<br />
* '''two-hybrid system:''' <br />
<br />
* '''Antibody:'''<br />
<br />
=Labs working on this gene/protein=<br />
<br />
=Your additional remarks=<br />
<br />
=References=<br />
<pubmed>10666464,11065368,8550462,10074062, </pubmed><br />
[[Category:Protein-coding genes]]</div>
Chkuo