Difference between revisions of "Team:York/Parts"

 
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<br>
  
  
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<div class="col-md-1"></div>
 
<div class="col-md-1"></div>
−
<div class="col-md-7">
+
<div class="col-md-10">
−
<table >
+
<table width="100%">
 +
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  <col style="width:10%">
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  <col style="width:10%">
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 +
  <col style="width:5%">
 
   <tr>
 
   <tr>
−
     <td>Source Organism</td>
+
     <td><b>Source Organism</b></td>
−
     <td>Gene</td>
+
     <td><b>Gene</b></td>
−
     <td>Part Name</td>
+
     <td><b>Part Name</b></td>
−
     <td>Function</td>
+
     <td class="width"><b>Function</b></td>
−
     <td>Characterised?</td>
+
     <td><b>Characterised</b></td>
−
     <td>Sequenced?</td>
+
     <td><b>Sequenced</b></td>
−
     <td>Submitted?</td>
+
     <td><b>Submitted</b></td>
 
   </tr>
 
   </tr>
−
   <tr>
+
<tr>
−
     <td><i>Escherichia coli</i></td>
+
    <td><b>Expression vector “pAdapt” in pSB1C3</b></td>
−
     <td>EcPPK</td>
+
    <td>lacZalpha</td>
−
     <td></td>
+
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807000">BBa_K1807000</a></td>
−
     <td>Phosphate Kinase</td>
+
    <td class="width">Used as cloning vector</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
   </tr>
 +
<tr>
 +
     <td><i><b>Escherichia coli</b></i></td>
 +
     <td>EcPPX</td>
 +
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807001">BBa_K1807001</a></td>
 +
     <td class="width">Phosphate Kinase</td>
 
     <td></td>
 
     <td></td>
 
     <td>✔</td>
 
     <td>✔</td>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td></td>
+
     <td><i><b>Escherichia coli</b></i></td>
−
     <td>EcPhoE</td>
+
     <td>EcPPK</td>
−
     <td></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807002">BBa_K1807002</a></td>
−
     <td>Phosphoporin</td>
+
     <td class="width">Phosphate Kinase</td>
 
     <td></td>
 
     <td></td>
 
     <td>✔</td>
 
     <td>✔</td>
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   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td></td>
+
     <td><i><b>Escherichia coli</b></i></td>
 
     <td>EcPstSCAB</td>
 
     <td>EcPstSCAB</td>
 
     <td></td>
 
     <td></td>
−
     <td>Phosphate specific transporter</td>
+
     <td class="width">Phosphate specific transporter</td>
 
     <td></td>
 
     <td></td>
 
     <td>✔</td>
 
     <td>✔</td>
−
     <td>✔</td>
+
     <td></td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td><i>Kingella oralis</i></td>
+
     <td><i><b>Kingella oralis</b></i></td>
 
     <td>KoPPK</td>
 
     <td>KoPPK</td>
−
     <td></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807006">BBa_K1807006</a></td>
−
     <td>PolyPhosphate Kinase</td>
+
     <td class="width">PolyPhosphate Kinase</td>
−
     <td></td>
+
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td><i>Sinorhizobium meliloti</i></td>
+
     <td><i><b>Sinorhizobium meliloti</b></i></td>
 
     <td>SmPstSCAB</td>
 
     <td>SmPstSCAB</td>
 
     <td></td>
 
     <td></td>
−
     <td>Phosphate specific transporter</td>
+
     <td class="width">Phosphate specific transporter</td>
−
    <td></td>
+
 
     <td>✔</td>
 
     <td>✔</td>
−
    <td>✔</td>
 
−
  </tr>
 
−
  <tr>
 
−
    <td><i>Candidatus accumulibacter phosphatis</i></td>
 
−
    <td>ApPstSCAB</td>
 
−
    <td></td>
 
−
    <td>Phosphate specific transporter</td>
 
−
    <td></td>
 
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td></td>
+
     <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 
     <td>ApPPK BA-91</td>
 
     <td>ApPPK BA-91</td>
−
     <td></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807003">BBa_K1807003</a></td>
−
     <td>PolyPhosphate kinase</td>
+
     <td class="width">PolyPhosphate kinase</td>
−
     <td></td>
+
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td></td>
+
     <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 
     <td>ApPPK SK-12</td>
 
     <td>ApPPK SK-12</td>
−
     <td></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807004">BBa_K1807004</a></td>
−
     <td>PolyPhosphate kinase</td>
+
     <td class="width">PolyPhosphate kinase</td>
−
     <td></td>
+
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
 
   <tr>
 
   <tr>
−
     <td></td>
+
     <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 
     <td>ApPPK UW-1</td>
 
     <td>ApPPK UW-1</td>
−
     <td></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807005">BBa_K1807005</a></td>
−
     <td>PolyPhosphate kinase</td>
+
     <td class="width">PolyPhosphate kinase</td>
−
     <td></td>
+
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
−
<tr>
+
  <tr>
−
     <td>Expression vector “pAdapt” in pSB1C3</td>
+
     <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 +
    <td>ApPstSCAB</td>
 +
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807007">BBa_K1807007</a></td>
 +
    <td class="width">Phosphate specific transporter</td>
 
     <td></td>
 
     <td></td>
−
    <td>BBa_K1807000</td>
 
−
    <td>Used as cloning vector</td>
 
−
    <td>✔</td>
 
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
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<div class="col-md-4"></div>
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<div class="col-md-1"></div>
 +
 
 +
<div class="col-md-12">
 +
<h1>So what do all of these parts do?</h1>
 +
 
 +
<div class="col-md-3">
 +
  <div class="navbar">
 +
      <ul>
 +
<li style="display:block;">Click to view:</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807000')">BBa_K1807000</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807001')">BBa_K1807001</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807002')">BBa_K1807002</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807003')">BBa_K1807003</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807004')">BBa_K1807004</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807005')">BBa_K1807005</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807006')">BBa_K1807006</li>
 +
<li style="display:block;" onclick="toggleSection('BBa_K1807007')">BBa_K1807007</li>
 +
      </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807000">
 +
    <h3>BBa_K1807000</h3>
 +
    <ul>
 +
    <li>This device allows for the IPTG-inducible expression of lacZα peptide which in the presence of Xgal in the medium and chromosomal lacZΔM15 produces blue-coloured colonies. The device was used as an expression vector. SmaI restriction sites flank the lacZ alpha coding sequence. Cutting the part with this enzyme allows for the in-frame insertion of any desired protein coding sequence that contains the splice-in flanking sequences (they can be found in the design section). </li>
 +
  <li>BBa_K1807000 was designed as a blue-white screening device that would also be easily used in Gibson Assembly. Surrounding the lacZ alpha coding sequence are two SmaI restriction sites (CCC/GGG). SmaI is a blunt-end endonuclease- we used it to simulatenously linearize our vector and remove the lacZ alpha coding sequence. Our BioBricks contained overhangs that make them compatible with the SmaI-digested BBa_K1807000.
 +
The overhang sequences used to make this part are as follows:
 +
<br>- BBa_K1807000 Assembly 5'end Overhang (complementary to pSB1C3): cgctaaggatgatttctgGAATTCGCGGCCGCTTCTAGAG
 +
<br>- BBa_K1807000 Assembly 3'end Overhang (complementary to pSB1C3): TACTAGTAGCGGCCGCTGCAGtccggcaaaaaagggcaag
 +
The subparts of the device are as follows: BBa_R0011, BBa_B0034, BBa_E0038, BBa_B0015.</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807001">
 +
    <h3>BBa_K1807001</h3>
 +
    <ul>
 +
    <li>This part codes for the exopolyphosphatase (PPX) enzyme of <i>Escherichia coli</i>. PPX is able to release phosphate residues from the ends of a polyphosphate chain.</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807002">
 +
    <h3>BBa_K1807002</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from <i>Escherichia coli</i>. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain (Akiyama et al., 1992). This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807003">
 +
    <h3>BBa_K1807003</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from <i>Candidatus Accumulibacter phosphatis</i> strain BA-91. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807004">
 +
    <h3>BBa_K1807004</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from <i>Candidatus Accumulibacter phosphatis</i> strain Sk-12. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807005">
 +
    <h3>BBa_K1807005</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from <i>Candidatus Accumulibacter phosphatis</i> strain UW-1. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807006">
 +
    <h3>BBa_K1807006</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from <i>Kingella oralis</i>. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).</li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
<div class="col-md-9">
 +
  <div class="section" id="BBa_K1807007">
 +
    <h3>BBa_K1807007</h3>
 +
    <ul>
 +
    <li>This part is a protein coding device containing the Phosphate Specific Transporter (Pst) gene from <i>Candidatus Accumulibacter phosphatis</i>SCAB. This transporter consists of 4 individual genes- pstA, pstC, pstB and pstS. PstA and pstC are phosphate transporter permeases, pstB is a phosphate transporter ATPase and pstS is a phosphate transporter periplasmic binding protein. </li>
 +
    </ul>
 +
  </div>
 +
</div>
 +
 
 +
</div>
 
</div>
 
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<div class="col-md-1"></div>
 
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 +
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 +
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Latest revision as of 23:16, 18 September 2015


Part Table

Source Organism Gene Part Name Function Characterised Sequenced Submitted
Expression vector “pAdapt” in pSB1C3 lacZalpha BBa_K1807000 Used as cloning vector ✔ ✔ ✔
Escherichia coli EcPPX BBa_K1807001 Phosphate Kinase ✔ ✔
Escherichia coli EcPPK BBa_K1807002 Phosphate Kinase ✔ ✔
Escherichia coli EcPstSCAB Phosphate specific transporter ✔
Kingella oralis KoPPK BBa_K1807006 PolyPhosphate Kinase ✔ ✔ ✔
Sinorhizobium meliloti SmPstSCAB Phosphate specific transporter ✔ ✔ ✔
Candidatus Accumulibacter phosphatis ApPPK BA-91 BBa_K1807003 PolyPhosphate kinase ✔ ✔ ✔
Candidatus Accumulibacter phosphatis ApPPK SK-12 BBa_K1807004 PolyPhosphate kinase ✔ ✔ ✔
Candidatus Accumulibacter phosphatis ApPPK UW-1 BBa_K1807005 PolyPhosphate kinase ✔ ✔ ✔
Candidatus Accumulibacter phosphatis ApPstSCAB BBa_K1807007 Phosphate specific transporter ✔ ✔

So what do all of these parts do?

  • Click to view:
  • BBa_K1807000
  • BBa_K1807001
  • BBa_K1807002
  • BBa_K1807003
  • BBa_K1807004
  • BBa_K1807005
  • BBa_K1807006
  • BBa_K1807007

BBa_K1807000

  • This device allows for the IPTG-inducible expression of lacZα peptide which in the presence of Xgal in the medium and chromosomal lacZΔM15 produces blue-coloured colonies. The device was used as an expression vector. SmaI restriction sites flank the lacZ alpha coding sequence. Cutting the part with this enzyme allows for the in-frame insertion of any desired protein coding sequence that contains the splice-in flanking sequences (they can be found in the design section).
  • BBa_K1807000 was designed as a blue-white screening device that would also be easily used in Gibson Assembly. Surrounding the lacZ alpha coding sequence are two SmaI restriction sites (CCC/GGG). SmaI is a blunt-end endonuclease- we used it to simulatenously linearize our vector and remove the lacZ alpha coding sequence. Our BioBricks contained overhangs that make them compatible with the SmaI-digested BBa_K1807000. The overhang sequences used to make this part are as follows:
    - BBa_K1807000 Assembly 5'end Overhang (complementary to pSB1C3): cgctaaggatgatttctgGAATTCGCGGCCGCTTCTAGAG
    - BBa_K1807000 Assembly 3'end Overhang (complementary to pSB1C3): TACTAGTAGCGGCCGCTGCAGtccggcaaaaaagggcaag The subparts of the device are as follows: BBa_R0011, BBa_B0034, BBa_E0038, BBa_B0015.

BBa_K1807001

  • This part codes for the exopolyphosphatase (PPX) enzyme of Escherichia coli. PPX is able to release phosphate residues from the ends of a polyphosphate chain.

BBa_K1807002

  • This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from Escherichia coli. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain (Akiyama et al., 1992). This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).

BBa_K1807003

  • This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from Candidatus Accumulibacter phosphatis strain BA-91. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).

BBa_K1807004

  • This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from Candidatus Accumulibacter phosphatis strain Sk-12. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).

BBa_K1807005

  • This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from Candidatus Accumulibacter phosphatis strain UW-1. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).

BBa_K1807006

  • This part is a protein coding device containing the Polyphosphate Kinase (PPK) gene from Kingella oralis. PPK produces polyphosphate, more specifically PPK catalyzes the reversible conversion of the γ-phosphate of ATP to the end of the polyphosphate chain. This enzyme is responsible for the formation of long chain polyphosphate molecules (up to a thousand orthophosphate residues long).

BBa_K1807007

  • This part is a protein coding device containing the Phosphate Specific Transporter (Pst) gene from Candidatus Accumulibacter phosphatisSCAB. This transporter consists of 4 individual genes- pstA, pstC, pstB and pstS. PstA and pstC are phosphate transporter permeases, pstB is a phosphate transporter ATPase and pstS is a phosphate transporter periplasmic binding protein.