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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqUtils-module.html">Package SeqUtils</a> ::
Module IsoelectricPoint
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<h1 class="epydoc">Module IsoelectricPoint</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SeqUtils.IsoelectricPoint-pysrc.html">source code</a></span></p>
<p>Calculate isoelectric points of polypeptides using methods of
Bjellqvist.</p>
<p>pK values and the methos are taken from:</p>
<p>* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F.,
Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing
positions of polypeptides in immobilized pH gradients can be predicted
from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.</p>
<p>* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference
points for comparisons of two-dimensional maps of proteins from different
human cell types defined in a pH scale where isoelectric points correlate
with polypeptide compositions. Electrophoresis 1994, 15, 529-539.</p>
<p>I designed the algorithm according to a note by David L. Tabb,
available at:
http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf</p>
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<a href="Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html" class="summary-name">IsoelectricPoint</a>
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<a name="positive_pKs"></a><span class="summary-name">positive_pKs</span> = <code title="{'H': 5.98, 'K': 10.0, 'Nterm': 7.5, 'R': 12.0}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">: </code>5.98<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">K</code><code class="variable-quote">'</code><code class="variable-op">: </code>10.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">Nterm</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.5<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">: </code>12.0<code class="variable-group">}</code></code>
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<a href="Bio.SeqUtils.IsoelectricPoint-module.html#negative_pKs" class="summary-name">negative_pKs</a> = <code title="{'C': 9.0, 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'Y': 10.0}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">C</code><code class="variable-quote">'</code><code class="variable-op">: </code>9.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">Cterm</code><code class="variable-quote">'</code><code class="variable-op">: </code>3.55<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.05<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.45<code class="variable-op">,</code><code class="variable-ellipsis">...</code></code>
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<a name="pKcterminal"></a><span class="summary-name">pKcterminal</span> = <code title="{'D': 4.55, 'E': 4.75}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.55<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.75<code class="variable-group">}</code></code>
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<a href="Bio.SeqUtils.IsoelectricPoint-module.html#pKnterminal" class="summary-name">pKnterminal</a> = <code title="{'A': 7.59,
'E': 7.7,
'M': 7.0,
'P': 8.36,
'S': 6.93,
'T': 6.82,
'V': 7.44}"><code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.59<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.7<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">M</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">P</code><code class="variable-quote">'</code><code class="variable-op">: </code>8.36<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">S</code><code class="variable-quote">'</code><code class="variable-op">: </code><code class="variable-ellipsis">...</code></code>
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<a name="charged_aas"></a><span class="summary-name">charged_aas</span> = <code title="('K', 'R', 'H', 'D', 'E', 'C', 'Y')"><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">K</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">R</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">H</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">C</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">Y</code><code class="variable-quote">'</code><code class="variable-group">)</code></code>
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<h3 class="epydoc">negative_pKs</h3>
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<dt>Value:</dt>
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<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">C</code><code class="variable-quote">'</code><code class="variable-op">: </code>9.0<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">Cterm</code><code class="variable-quote">'</code><code class="variable-op">: </code>3.55<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.05<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">: </code>4.45<code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">Y</code><code class="variable-quote">'</code><code class="variable-op">: </code>10.0<code class="variable-group">}</code>
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<h3 class="epydoc">pKnterminal</h3>
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<dt>Value:</dt>
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<code class="variable-group">{</code><code class="variable-quote">'</code><code class="variable-string">A</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.59<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">E</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.7<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">M</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.0<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">P</code><code class="variable-quote">'</code><code class="variable-op">: </code>8.36<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">S</code><code class="variable-quote">'</code><code class="variable-op">: </code>6.93<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">T</code><code class="variable-quote">'</code><code class="variable-op">: </code>6.82<code class="variable-op">,</code>
<code class="variable-quote">'</code><code class="variable-string">V</code><code class="variable-quote">'</code><code class="variable-op">: </code>7.44<code class="variable-group">}</code>
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