Difference between revisions of "Team:York/Parts"

 
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<h2> Part Documentation</h2>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<h4>Note</h4>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<h4>Adding parts to the registry</h4>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<br>
  
  
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<h4>What information do I need to start putting my parts on the Registry?</h4>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<ul>
 
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<li>Part Name</li>
 
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<li>Part type</li>
 
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<li>Creator</li>
 
−
<li>Sequence</li>
 
−
<li>Short Description (60 characters on what the DNA does)</li>
 
−
<li>Long Description (Longer description of what the DNA does)</li>
 
−
<li>Design considerations</li>
 
−
</ul>
 
  
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<p>
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<h2>Part Table </h2>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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  <col style="width:5%">
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  <col style="width:5%">
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  <col style="width:5%">
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  <tr>
 +
    <td><b>Source Organism</b></td>
 +
    <td><b>Gene</b></td>
 +
    <td><b>Part Name</b></td>
 +
    <td class="width"><b>Function</b></td>
 +
    <td><b>Characterised</b></td>
 +
    <td><b>Sequenced</b></td>
 +
    <td><b>Submitted</b></td>
 +
  </tr>
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<tr>
 +
    <td><b>Expression vector “pAdapt” in pSB1C3</b></td>
 +
    <td>lacZalpha</td>
 +
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807000">BBa_K1807000</a></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>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Escherichia coli</b></i></td>
 +
    <td>EcPPK</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></td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Escherichia coli</b></i></td>
 +
    <td>EcPstSCAB</td>
 +
    <td></td>
 +
    <td class="width">Phosphate specific transporter</td>
 +
    <td></td>
 +
    <td>✔</td>
 +
    <td></td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Kingella oralis</b></i></td>
 +
    <td>KoPPK</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>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Sinorhizobium meliloti</b></i></td>
 +
    <td>SmPstSCAB</td>
 +
    <td></td>
 +
    <td class="width">Phosphate specific transporter</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 +
    <td>ApPPK BA-91</td>
 +
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807003">BBa_K1807003</a></td>
 +
    <td class="width">PolyPhosphate kinase</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 +
    <td>ApPPK SK-12</td>
 +
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807004">BBa_K1807004</a></td>
 +
    <td class="width">PolyPhosphate kinase</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <td><i><b>Candidatus Accumulibacter phosphatis</b></i></td>
 +
    <td>ApPPK UW-1</td>
 +
    <td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1807005">BBa_K1807005</a></td>
 +
    <td class="width">PolyPhosphate kinase</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
    <td>✔</td>
 +
  </tr>
 +
  <tr>
 +
    <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>✔</td>
 +
  </tr>
 +
</table>
 +
</div>
 +
<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>
  
−
<h4>Inspiration</h4>
+
<div class="col-md-9">
−
<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
+
  <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>
  
−
<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
+
<div class="col-md-9">
−
<ul>
+
  <div class="section" id="BBa_K1807003">
−
<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
+
    <h3>BBa_K1807003</h3>
−
<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
+
    <ul>
−
<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
+
    <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>
+
    </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>
  
−
<h4>Part Table </h4>
+
<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>
  
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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.