Difference between revisions of "Sandbox"

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* '''Description:''' transporter for citrate and malate (proton symport) <br/><br/>
+
* '''Description:''' cytochrome bd ubiquinol oxidase (subunit I), high affinity terminal oxidase <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''cimH''
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|''cydA''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxkJ ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxkK ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || transporter for citrate and malate (proton symport)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cytochrome bd ubiquinol oxidase (subunit I), high affinity terminal oxidase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || citrate and malate uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || respiration
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 6.554  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 8.935  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1350 bp, 450 aa  
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1404 bp, 468 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cydA]]'', ''[[yxkI]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cydB]]'', ''[[cimH]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:yxkJ_context.gif]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:cydA_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Database entries ===
 
=== Database entries ===
  
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* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cydABCD.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12546]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11925]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' uptake of citrate and malate (symport with protons) [http://www.ncbi.nlm.nih.gov/sites/entrez/11566984 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' 2-hydroxycarboxylate transporter family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[MaeN]]
+
* '''Paralogous protein(s):''' [[YthA]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38770]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU38760]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[cydA]]-[[cydB]]-[[cydC]]-[[cydD]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by glucose ([[CcpA]]), induced under anaerobic conditions ([[Rex]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression, [[Rex]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/16207915 PubMed]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
# Krom et al. (2001) ''Bacillus subtilis'' YxkJ is a secondary transporter of the 2-hydroxycarboxylate transporter family that transports L-malate and citrate. ''J. Bacteriol.'' '''183:''' 5862-5869. [http://www.ncbi.nlm.nih.gov/sites/entrez/11566984 PubMed]
+
 
 +
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 17:02, 15 April 2009

  • Description: cytochrome bd ubiquinol oxidase (subunit I), high affinity terminal oxidase

Gene name cydA
Synonyms yxkK
Essential no
Product cytochrome bd ubiquinol oxidase (subunit I), high affinity terminal oxidase
Function respiration
MW, pI 52 kDa, 8.935
Gene length, protein length 1404 bp, 468 aa
Immediate neighbours cydB, cimH
Hier soll was neues rein
Genetic context
CydA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): YthA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulation: repressed by glucose (CcpA), induced under anaerobic conditions (Rex) PubMed
  • Regulatory mechanism: CcpA: transcription repression, Rex: transcription repression 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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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