Difference between revisions of "Team:York/Parts"

 
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<div class="col-md-10 layer">
 
<div class="col-md-10 layer">
 
<!-- CONTENT GOES HERE :D -->
 
<!-- CONTENT GOES HERE :D -->
−
 
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<br>
  
  
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     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
−
  <tr>
+
<tr>
 
     <td><i><b>Escherichia coli</b></i></td>
 
     <td><i><b>Escherichia coli</b></i></td>
−
     <td>EcPPK</td>
+
     <td>EcPPX</td>
−
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807002">BBa_K1807002</a></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 class="width">Phosphate Kinase</td>
 
     <td></td>
 
     <td></td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
   </tr>
 
   </tr>
−
<tr>
+
  <tr>
 
     <td><i><b>Escherichia coli</b></i></td>
 
     <td><i><b>Escherichia coli</b></i></td>
−
     <td>EcPPX</td>
+
     <td>EcPPK</td>
−
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807001">BBa_K1807001</a></td>
+
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807002">BBa_K1807002</a></td>
−
     <td class="width">Phosphate Kinase</td>
+
     <td class="width">Phosphate Kinase</td>
 
     <td></td>
 
     <td></td>
 
     <td>✔</td>
 
     <td>✔</td>
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     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807006">BBa_K1807006</a></td>
 
     <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807006">BBa_K1807006</a></td>
 
     <td class="width">PolyPhosphate Kinase</td>
 
     <td class="width">PolyPhosphate Kinase</td>
−
     <td></td>
+
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
 
     <td>✔</td>
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<div class="col-md-1"></div>
 
<div class="col-md-1"></div>
  
 +
<div class="col-md-12">
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<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>
 +
<div class="col-md-1"></div>
 +
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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.