[Bio] / FigWebPages / ProteinFamiliesExamples.html Repository:
ViewVC logotype

View of /FigWebPages/ProteinFamiliesExamples.html

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.3 - (download) (as text) (annotate)
Fri Jan 27 20:24:54 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, rast_rel_2008_09_30, caBIG-13Feb06-00, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, caBIG-05Apr06-00, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, rast_rel_2008_11_24, HEAD
Changes since 1.2: +132 -152 lines
RAE: Changes to Protein Families

<h1 style="text-align: center">Protein Families Examples</h1>
<h2 style="text-align: center">Updated January 27, 2006. Rob Edwards</h2>

<center><h2>Protein Families</h2></center>

<p><a href="ProteinFamilies.html">General</a> help and description about the protein families is also available. This is a series of working examples, to be extended.</p>


<p>These are some example protein families, mainly chosen because they are small and convenient to look at. They may change over time as the families are updated.</p>

<h3>Example 1</h3>

<p>This little example shows one protein that is misannotated in PIR and several that are wrong in PFAMs</p>
<ul>
<li>Start at <a href="../protein.cgi?prot=fig|83333.1.peg.1994" target="_blank">fig|83333.1.peg.1994</a>
<li>Click on the <a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1994&equivalence=1" target="_blank">explore protein families link</a></li>
<li>Choose PIR from the second pull down family menu</li>
<li>Click "Compare these families"</li>
<li>You will only see one protein, and it is clearly mis-annotated in PIR</li>
<li>This table is only showing those proteins that are in family 1 and not in family two AND could be a candidate for family 2</li>
<ul>
<li>Now, click the checkbox next to "Show all proteins in the two families"</li>
<li>Click "Compare these families"</li>
<li>This shows all the proteins that are in family 1 and not in family 2, regardless of whether there are candidates in other PIR families</li>
</ul>
<li>You should also look at the comparisons using family 2 not family 1, OR, and AND to see what is present in each family</li>
</ul>



<h3>Example 2</h3>

<p>This is a little example from Histidine Biosynthesis</p>
<ul>
<li>Start at <a href="../protein.cgi?prot=fig|103690.1.peg.4768" target="_blank">fig|103690.1.peg.4768</a></li>
<li>Click on the <a href="../proteinfamilies.cgi?prot=fig|103690.1.peg.4768&equivalence=1" target="_blank">explore protein families link</a></li>
<li>On the two pull down menu's choose PIR from the second menu</li>
<li>Click "Compare these families"</li>
<ul>
<li>There are no proteins that are in the FIGfam that are not in the PIR fam but are in another family</li>
<li>If you check the show all box and try again, it will show you all the proteins that are in the FIGfam, and the other families they are in</li>
</ul>
<li>Now click "In family two and NOT family one" and click submit again</li>
<li>This shows the proteins that are in the PIR family but not in the FIG family</li>
<li>The cells colored red do not have the same function as the column header. Mouse over to find roles of proteins</li>
</ul>



<h1>Other examples, not yet explored</h1>

<p>These examples are ones that are worth looking at and exploring. The comparisons were done with Family 1 NOT Family 2. The for and against are just as shown in the final tables, so you generally want a result with some "againsts" to look at. Also, the "Red" column is the number of cells that would be colored red (i.e. wrong).</p>

<h2>Histidine Biosynthesis compared to PIR</h2>
<table border=1>
<tr><th>Genome</th><th>peg</th><th>Family 1</th><th>Family 2</th><th>For</th><th>Against</th><th>Red</th></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1994&equivalence=1" target="_blank">fig|83333.1.peg.1994</a></td><td>fig|PF000056</td><td>pir|PIRSF000486</td><td>18</td><td>-7</td><td>1</td></tr>
<tr><td>Symbiobacterium thermophilum IAM 14863</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|292459.1.peg.2713&equivalence=1" target="_blank">fig|292459.1.peg.2713</a></td><td>fig|PF000056</td><td>pir|PIRSF006650</td><td>66</td><td>0</td><td>0</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.573&equivalence=1" target="_blank">fig|272626.1.peg.573</a></td><td>fig|PF003447</td><td>pir|PIRSF006650</td><td>10</td><td>0</td><td>0</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.574&equivalence=1" target="_blank">fig|272626.1.peg.574</a></td><td>fig|PF000991</td><td>pir|PIRSF001549</td><td>19</td><td>-7</td><td>2</td></tr>
<tr><td>Thermotoga maritima MSB8</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|243274.1.peg.1033&equivalence=1" target="_blank">fig|243274.1.peg.1033</a></td><td>fig|PF000991</td><td>pir|PIRSF027379</td><td>0</td><td>-17</td><td>1</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF001505</td><td>pir|PIRSF001258</td><td>108</td><td>-147</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF002226</td><td>pir|PIRSF001258</td><td>111</td><td>-155</td><td>2</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.566&equivalence=1" target="_blank">fig|272626.1.peg.566</a></td><td>fig|PF001505</td><td>pir|PIRSF006833</td><td>120</td><td>0</td><td>0</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.567&equivalence=1" target="_blank">fig|272626.1.peg.567</a></td><td>fig|PF002226</td><td>pir|PIRSF029243</td><td>112</td><td>0</td><td>0</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1999&equivalence=1" target="_blank">fig|83333.1.peg.1999</a></td><td>fig|PF002424</td><td>pir|PIRSF001484</td><td>35</td><td>-5</td><td>3</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2000&equivalence=1" target="_blank">fig|83333.1.peg.2000</a></td><td>fig|PF001996</td><td>pir|PIRSF001454</td><td>15</td><td>0</td><td>0</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.2360&equivalence=1" target="_blank">fig|4896.1.peg.2360</a></td><td>fig|PF001996</td><td>pir|PIRSF036936</td><td>122</td><td>-344</td><td>3</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.2360&equivalence=1" target="_blank">fig|4896.1.peg.2360</a></td><td>fig|PF002743</td><td>pir|PIRSF036936</td><td>241</td><td>-339</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1998&equivalence=1" target="_blank">fig|83333.1.peg.1998</a></td><td>fig|PF002743</td><td>pir|PIRSF000495</td><td>7</td><td>-2</td><td>1</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1997&equivalence=1" target="_blank">fig|83333.1.peg.1997</a></td><td>fig|PF001687</td><td>pir|PIRSF001410</td><td>27</td><td>-81</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1997&equivalence=1" target="_blank">fig|83333.1.peg.1997</a></td><td>fig|PF003299</td><td>pir|PIRSF001410</td><td>290</td><td>-156</td><td>2</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.571&equivalence=1" target="_blank">fig|272626.1.peg.571</a></td><td>fig|PF003299</td><td>pir|PIRSF001409</td><td>115</td><td>-3</td><td>3</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1996&equivalence=1" target="_blank">fig|83333.1.peg.1996</a></td><td>fig|PF000244</td><td>pir|PIRSF000518</td><td>316</td><td>-5</td><td>2</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.2026&equivalence=1" target="_blank">fig|272626.1.peg.2026</a></td><td>fig|PF000244</td><td>pir|PIRSF006455</td><td>327</td><td>-3</td><td>1</td></tr>
<tr><td>Lactococcus lactis subsp. lactis Il1403</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272623.1.peg.1241&equivalence=1" target="_blank">fig|272623.1.peg.1241</a></td><td>fig|PF000244</td><td>pir|PIRSF005473</td><td>374</td><td>-5</td><td>2</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.575&equivalence=1" target="_blank">fig|272626.1.peg.575</a></td><td>fig|PF001687</td><td>pir|PIRSF019058</td><td>19</td><td>-35</td><td>3</td></tr>
<tr><td>Pseudomonas aeruginosa PAO1</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|208964.1.peg.6&equivalence=1" target="_blank">fig|208964.1.peg.6</a></td><td>fig|PF001687</td><td>pir|PIRSF004682</td><td>2</td><td>-69</td><td>3</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.210&equivalence=1" target="_blank">fig|4896.1.peg.210</a></td><td>fig|PF001687</td><td>pir|PIRSF017203</td><td>38</td><td>-37</td><td>4</td></tr>
<tr><td>Corynebacterium efficiens YS-314</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|196164.1.peg.1995&equivalence=1" target="_blank">fig|196164.1.peg.1995</a></td><td>fig|PF003597</td><td>pir|PIRSF004949</td><td>8</td><td>0</td><td>0</td></tr>
<tr><td>Corynebacterium efficiens YS-314</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|196164.1.peg.809&equivalence=1" target="_blank">fig|196164.1.peg.809</a></td><td>fig|PF003597</td><td>pir|PIRSF500194</td><td>20</td><td>0</td><td>0</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1995&equivalence=1" target="_blank">fig|83333.1.peg.1995</a></td><td>fig|PF002941</td><td>pir|PIRSF000099</td><td>11</td><td>0</td><td>0</td></tr>
</table>

<h2>Histidine Biosynthesis compared to PFAM</h2>

<table border=1>
<tr><th>Genome</th><th>peg</th><th>Family 1</th><th>Family 2</th><th>For</th><th>Against</th><th>Red</th></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1994&equivalence=1" target="_blank">fig|83333.1.peg.1994</a></td><td>fig|PF000056</td><td>pfam|PF08029.1</td><td>17</td><td>-2</td><td>1</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.573&equivalence=1" target="_blank">fig|272626.1.peg.573</a></td><td>fig|PF003447</td><td>pfam|PF01634.8</td><td>2</td><td>0</td><td>0</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.574&equivalence=1" target="_blank">fig|272626.1.peg.574</a></td><td>fig|PF000991</td><td>pfam|PF00587.14</td><td>4</td><td>-4</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF001505</td><td>pfam|PF01502.8</td><td>93</td><td>-106</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF001505</td><td>pfam|PF01503.7</td><td>39</td><td>-35</td><td>1</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF002226</td><td>pfam|PF01502.8</td><td>39</td><td>-38</td><td>1</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.2001&equivalence=1" target="_blank">fig|83333.1.peg.2001</a></td><td>fig|PF002226</td><td>pfam|PF01503.7</td><td>96</td><td>-117</td><td>2</td></tr>
<tr><td>Neurospora crassa</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|5141.1.peg.8508&equivalence=1" target="_blank">fig|5141.1.peg.8508</a></td><td>fig|PF001505</td><td>pfam|PF00815.9</td><td>283</td><td>-347</td><td>3</td></tr>
<tr><td>Neurospora crassa</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|5141.1.peg.8508&equivalence=1" target="_blank">fig|5141.1.peg.8508</a></td><td>fig|PF002226</td><td>pfam|PF00815.9</td><td>286</td><td>-360</td><td>3</td></tr>
<tr><td>Neurospora crassa</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|5141.1.peg.8508&equivalence=1" target="_blank">fig|5141.1.peg.8508</a></td><td>fig|PF002941</td><td>pfam|PF00815.9</td><td>2</td><td>-194</td><td>2</td></tr>
<tr><td>Neurospora crassa</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|5141.1.peg.8508&equivalence=1" target="_blank">fig|5141.1.peg.8508</a></td><td>fig|PF002941</td><td>pfam|PF01502.8</td><td>122</td><td>-578</td><td>3</td></tr>
<tr><td>Neurospora crassa</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|5141.1.peg.8508&equivalence=1" target="_blank">fig|5141.1.peg.8508</a></td><td>fig|PF002941</td><td>pfam|PF01503.7</td><td>122</td><td>-578</td><td>3</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.2360&equivalence=1" target="_blank">fig|4896.1.peg.2360</a></td><td>fig|PF001996</td><td>pfam|PF00117.15</td><td>122</td><td>-336</td><td>3</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.2360&equivalence=1" target="_blank">fig|4896.1.peg.2360</a></td><td>fig|PF002743</td><td>pfam|PF00117.15</td><td>1</td><td>-78</td><td>1</td></tr>
<tr><td>Schizosaccharomyces pombe</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|4896.1.peg.2360&equivalence=1" target="_blank">fig|4896.1.peg.2360</a></td><td>fig|PF002743</td><td>pfam|PF00977.10</td><td>241</td><td>-340</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1997&equivalence=1" target="_blank">fig|83333.1.peg.1997</a></td><td>fig|PF001687</td><td>pfam|PF00475.8</td><td>27</td><td>-70</td><td>2</td></tr>
<tr><td>Escherichia coli K12</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|83333.1.peg.1997&equivalence=1" target="_blank">fig|83333.1.peg.1997</a></td><td>fig|PF003299</td><td>pfam|PF00475.8</td><td>27</td><td>-59</td><td>1</td></tr>
<tr><td>Nostoc sp. PCC 7120</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|103690.1.peg.384&equivalence=1" target="_blank">fig|103690.1.peg.384</a></td><td>fig|PF003299</td><td>pfam|PF00702.13</td><td>0</td><td>-62</td><td>2</td></tr>
<tr><td>Photorhabdus luminescens subsp. laumondii TTO1</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|243265.1.peg.1484&equivalence=1" target="_blank">fig|243265.1.peg.1484</a></td><td>fig|PF000244</td><td>pfam|PF00815.9</td><td>264</td><td>-399</td><td>3</td></tr>
<tr><td>Photorhabdus luminescens subsp. laumondii TTO1</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|243265.1.peg.1484&equivalence=1" target="_blank">fig|243265.1.peg.1484</a></td><td>fig|PF002941</td><td>pfam|PF00155.9</td><td>239</td><td>-347</td><td>2</td></tr>
<tr><td>Listeria innocua Clip11262</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272626.1.peg.575&equivalence=1" target="_blank">fig|272626.1.peg.575</a></td><td>fig|PF001687</td><td>pfam|PF02811.7</td><td>0</td><td>-35</td><td>3</td></tr>
</table>

<h2>Leucine Degradation compared to PIR</h2>

<table border=1>
<tr><th>Genome</th><th>peg</th><th>Family 1</th><th>Family 2</th><th>For</th><th>Against</th><th>Red</th></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3860&equivalence=1" target="_blank">fig|224308.1.peg.3860</a></td><td>fig|PF002066</td><td>pir|PIRSF006468</td><td>188</td><td>-4</td><td>1</td></tr>
<tr><td>Bacillus anthracis str. Ames</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|198094.1.peg.1301&equivalence=1" target="_blank">fig|198094.1.peg.1301</a></td><td>fig|PF002066</td><td>pir|PIRSF000523</td><td>123</td><td>0</td><td>0</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2409&equivalence=1" target="_blank">fig|224308.1.peg.2409</a></td><td>fig|PF001207</td><td>pir|PIRSF000152</td><td>26</td><td>-14</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2409&equivalence=1" target="_blank">fig|224308.1.peg.2409</a></td><td>fig|PF002751</td><td>pir|PIRSF000152</td><td>23</td><td>-3</td><td>1</td></tr>
<tr><td>Bacillus halodurans C-125</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272558.1.peg.213&equivalence=1" target="_blank">fig|272558.1.peg.213</a></td><td>fig|PF001158</td><td>pir|PIRSF000152</td><td>31</td><td>-147</td><td>5</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF000067</td><td>pir|PIRSF000155</td><td>37</td><td>-2</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF001487</td><td>pir|PIRSF000155</td><td>41</td><td>-29</td><td>1</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF000067</td><td>pir|PIRSF036563</td><td>149</td><td>-110</td><td>3</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF001487</td><td>pir|PIRSF036563</td><td>195</td><td>-236</td><td>3</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF002666</td><td>pir|PIRSF036563</td><td>137</td><td>-279</td><td>3</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2407&equivalence=1" target="_blank">fig|224308.1.peg.2407</a></td><td>fig|PF001388</td><td>pir|PIRSF000432</td><td>31</td><td>-1</td><td>1</td></tr>
<tr><td>Shewanella oneidensis MR-1</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|211586.1.peg.2120&equivalence=1" target="_blank">fig|211586.1.peg.2120</a></td><td>fig|PF001388</td><td>pir|PIRSF000433</td><td>132</td><td>0</td><td>0</td></tr>
<tr><td>Streptomyces avermitilis MA-4680</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227882.1.peg.4367&equivalence=1" target="_blank">fig|227882.1.peg.4367</a></td><td>fig|PF001864</td><td>pir|PIRSF000432</td><td>197</td><td>-176</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1463&equivalence=1" target="_blank">fig|224308.1.peg.1463</a></td><td>fig|PF003391</td><td>pir|PIRSF000210</td><td>164</td><td>-10</td><td>4</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.145&equivalence=1" target="_blank">fig|224914.1.peg.145</a></td><td>fig|PF000100</td><td>pir|PIRSF000210</td><td>22</td><td>0</td><td>0</td></tr>
<tr><td>Bordetella bronchiseptica RB50</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|257310.1.peg.2524&equivalence=1" target="_blank">fig|257310.1.peg.2524</a></td><td>fig|PF003391</td><td>pir|PIRSF000212</td><td>769</td><td>-263</td><td>4</td></tr>
<tr><td>Ralstonia metallidurans CH34</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|119219.1.peg.4104&equivalence=1" target="_blank">fig|119219.1.peg.4104</a></td><td>fig|PF003391</td><td>pir|PIRSF000350</td><td>840</td><td>-288</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF000094</td><td>pir|PIRSF000182</td><td>518</td><td>-427</td><td>5</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF002044</td><td>pir|PIRSF000182</td><td>183</td><td>-27</td><td>2</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.1924&equivalence=1" target="_blank">fig|224914.1.peg.1924</a></td><td>fig|PF001705</td><td>pir|PIRSF001591</td><td>102</td><td>0</td><td>0</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1824&equivalence=1" target="_blank">fig|224308.1.peg.1824</a></td><td>fig|PF003427</td><td>pir|PIRSF001593</td><td>36</td><td>0</td><td>0</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1825&equivalence=1" target="_blank">fig|224308.1.peg.1825</a></td><td>fig|PF000095</td><td>pir|PIRSF001406</td><td>5</td><td>-1</td><td>0</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1826&equivalence=1" target="_blank">fig|224308.1.peg.1826</a></td><td>fig|PF000193</td><td>pir|PIRSF001367</td><td>13</td><td>-7</td><td>3</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.2310&equivalence=1" target="_blank">fig|262316.1.peg.2310</a></td><td>fig|PF000193</td><td>pir|PIRSF015582</td><td>0</td><td>-42</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1829&equivalence=1" target="_blank">fig|224308.1.peg.1829</a></td><td>fig|PF000104</td><td>pir|PIRSF001552</td><td>291</td><td>-584</td><td>3</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1829&equivalence=1" target="_blank">fig|224308.1.peg.1829</a></td><td>fig|PF001188</td><td>pir|PIRSF001552</td><td>29</td><td>-41</td><td>3</td></tr>
<tr><td>Bacillus halodurans C-125</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272558.1.peg.1137&equivalence=1" target="_blank">fig|272558.1.peg.1137</a></td><td>fig|PF001188</td><td>pir|PIRSF001550</td><td>30</td><td>-11</td><td>2</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3904&equivalence=1" target="_blank">fig|224308.1.peg.3904</a></td><td>fig|PF000160</td><td>pir|PIRSF000859</td><td>15</td><td>-13</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3904&equivalence=1" target="_blank">fig|224308.1.peg.3904</a></td><td>fig|PF000359</td><td>pir|PIRSF000859</td><td>13</td><td>-25</td><td>1</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.3861&equivalence=1" target="_blank">fig|262316.1.peg.3861</a></td><td>fig|PF000359</td><td>pir|PIRSF000858</td><td>28</td><td>-99</td><td>2</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.3861&equivalence=1" target="_blank">fig|262316.1.peg.3861</a></td><td>fig|PF000530</td><td>pir|PIRSF000858</td><td>57</td><td>-74</td><td>2</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.3861&equivalence=1" target="_blank">fig|262316.1.peg.3861</a></td><td>fig|PF003527</td><td>pir|PIRSF000858</td><td>57</td><td>-64</td><td>2</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3903&equivalence=1" target="_blank">fig|224308.1.peg.3903</a></td><td>fig|PF000530</td><td>pir|PIRSF012663</td><td>16</td><td>-21</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3903&equivalence=1" target="_blank">fig|224308.1.peg.3903</a></td><td>fig|PF003527</td><td>pir|PIRSF012663</td><td>13</td><td>-7</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1717&equivalence=1" target="_blank">fig|224308.1.peg.1717</a></td><td>fig|PF001265</td><td>pir|PIRSF500082</td><td>6</td><td>0</td><td>0</td></tr>
</table>

<h2>Leucine Degradation compared to PFAM</h2>
 
<table border=1>
<tr><th>Genome</th><th>peg</th><th>Family 1</th><th>Family 2</th><th>For</th><th>Against</th><th>Red</th></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3860&equivalence=1" target="_blank">fig|224308.1.peg.3860</a></td><td>fig|PF002066</td><td>pfam|PF01063.8</td><td>3</td><td>-1</td><td>0</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2409&equivalence=1" target="_blank">fig|224308.1.peg.2409</a></td><td>fig|PF001207</td><td>pfam|PF00676.9</td><td>16</td><td>-11</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2409&equivalence=1" target="_blank">fig|224308.1.peg.2409</a></td><td>fig|PF002751</td><td>pfam|PF00676.9</td><td>16</td><td>-3</td><td>1</td></tr>
<tr><td>Bacillus halodurans C-125</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|272558.1.peg.213&equivalence=1" target="_blank">fig|272558.1.peg.213</a></td><td>fig|PF001158</td><td>pfam|PF00676.9</td><td>11</td><td>-122</td><td>5</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF000067</td><td>pfam|PF02779.12</td><td>17</td><td>-1</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF000067</td><td>pfam|PF02780.9</td><td>17</td><td>-1</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF001487</td><td>pfam|PF02779.12</td><td>17</td><td>-26</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.2408&equivalence=1" target="_blank">fig|224308.1.peg.2408</a></td><td>fig|PF001487</td><td>pfam|PF02780.9</td><td>17</td><td>-26</td><td>1</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.2120&equivalence=1" target="_blank">fig|224914.1.peg.2120</a></td><td>fig|PF000067</td><td>pfam|PF00676.9</td><td>145</td><td>-3</td><td>1</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.2120&equivalence=1" target="_blank">fig|224914.1.peg.2120</a></td><td>fig|PF001487</td><td>pfam|PF00676.9</td><td>190</td><td>-56</td><td>1</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF000067</td><td>pfam|PF00364.11</td><td>149</td><td>-106</td><td>3</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF001487</td><td>pfam|PF00364.11</td><td>195</td><td>-233</td><td>3</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF002666</td><td>pfam|PF00364.11</td><td>137</td><td>-279</td><td>3</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF002666</td><td>pfam|PF02779.12</td><td>1</td><td>-67</td><td>2</td></tr>
<tr><td>Rhodopseudomonas palustris CGA009</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|258594.1.peg.2850&equivalence=1" target="_blank">fig|258594.1.peg.2850</a></td><td>fig|PF002666</td><td>pfam|PF02780.9</td><td>1</td><td>-67</td><td>2</td></tr>
<tr><td>Coxiella burnetii RSA 493</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227377.1.peg.612&equivalence=1" target="_blank">fig|227377.1.peg.612</a></td><td>fig|PF001864</td><td>pfam|PF00198.12</td><td>9</td><td>-94</td><td>1</td></tr>
<tr><td>Coxiella burnetii RSA 493</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227377.1.peg.612&equivalence=1" target="_blank">fig|227377.1.peg.612</a></td><td>fig|PF001864</td><td>pfam|PF00364.11</td><td>11</td><td>-98</td><td>2</td></tr>
<tr><td>Coxiella burnetii RSA 493</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227377.1.peg.612&equivalence=1" target="_blank">fig|227377.1.peg.612</a></td><td>fig|PF001864</td><td>pfam|PF02817.6</td><td>11</td><td>-99</td><td>2</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1463&equivalence=1" target="_blank">fig|224308.1.peg.1463</a></td><td>fig|PF003391</td><td>pfam|PF00070.16</td><td>4</td><td>-3</td><td>2</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1463&equivalence=1" target="_blank">fig|224308.1.peg.1463</a></td><td>fig|PF003391</td><td>pfam|PF07992.2</td><td>4</td><td>-3</td><td>2</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1463&equivalence=1" target="_blank">fig|224308.1.peg.1463</a></td><td>fig|PF003391</td><td>pfam|PF02852.11</td><td>19</td><td>-2</td><td>1</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.145&equivalence=1" target="_blank">fig|224914.1.peg.145</a></td><td>fig|PF000100</td><td>pfam|PF00070.16</td><td>22</td><td>0</td><td>0</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.145&equivalence=1" target="_blank">fig|224914.1.peg.145</a></td><td>fig|PF000100</td><td>pfam|PF07992.2</td><td>22</td><td>0</td><td>0</td></tr>
<tr><td>Brucella melitensis 16M</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224914.1.peg.145&equivalence=1" target="_blank">fig|224914.1.peg.145</a></td><td>fig|PF000100</td><td>pfam|PF02852.11</td><td>22</td><td>0</td><td>0</td></tr>
<tr><td>Bordetella bronchiseptica RB50</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|257310.1.peg.2524&equivalence=1" target="_blank">fig|257310.1.peg.2524</a></td><td>fig|PF003391</td><td>pfam|PF00364.11</td><td>765</td><td>-255</td><td>4</td></tr>
<tr><td>Ralstonia metallidurans CH34</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|119219.1.peg.4104&equivalence=1" target="_blank">fig|119219.1.peg.4104</a></td><td>fig|PF003391</td><td>pfam|PF00403.14</td><td>840</td><td>-281</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF000094</td><td>pfam|PF00441.13</td><td>37</td><td>-219</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF000094</td><td>pfam|PF02770.8</td><td>82</td><td>-247</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF000094</td><td>pfam|PF02771.6</td><td>104</td><td>-250</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF002044</td><td>pfam|PF00441.13</td><td>17</td><td>-11</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF002044</td><td>pfam|PF02770.8</td><td>17</td><td>-11</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1830&equivalence=1" target="_blank">fig|224308.1.peg.1830</a></td><td>fig|PF002044</td><td>pfam|PF02771.6</td><td>19</td><td>-12</td><td>1</td></tr>
<tr><td>Streptomyces avermitilis MA-4680</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227882.1.peg.5280&equivalence=1" target="_blank">fig|227882.1.peg.5280</a></td><td>fig|PF003232</td><td>pfam|PF02785.8</td><td>2</td><td>-30</td><td>4</td></tr>
<tr><td>Streptomyces avermitilis MA-4680</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227882.1.peg.5280&equivalence=1" target="_blank">fig|227882.1.peg.5280</a></td><td>fig|PF003232</td><td>pfam|PF00364.11</td><td>0</td><td>-21</td><td>4</td></tr>
<tr><td>Streptomyces avermitilis MA-4680</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227882.1.peg.5280&equivalence=1" target="_blank">fig|227882.1.peg.5280</a></td><td>fig|PF003232</td><td>pfam|PF00289.11</td><td>2</td><td>-30</td><td>4</td></tr>
<tr><td>Streptomyces avermitilis MA-4680</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|227882.1.peg.5280&equivalence=1" target="_blank">fig|227882.1.peg.5280</a></td><td>fig|PF003232</td><td>pfam|PF02786.6</td><td>2</td><td>-30</td><td>4</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1826&equivalence=1" target="_blank">fig|224308.1.peg.1826</a></td><td>fig|PF000193</td><td>pfam|PF00682.8</td><td>0</td><td>-7</td><td>3</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.2310&equivalence=1" target="_blank">fig|262316.1.peg.2310</a></td><td>fig|PF000193</td><td>pfam|PF03328.4</td><td>0</td><td>-34</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1829&equivalence=1" target="_blank">fig|224308.1.peg.1829</a></td><td>fig|PF000104</td><td>pfam|PF00501.15</td><td>4</td><td>-280</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.1829&equivalence=1" target="_blank">fig|224308.1.peg.1829</a></td><td>fig|PF001188</td><td>pfam|PF00501.15</td><td>5</td><td>-11</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3904&equivalence=1" target="_blank">fig|224308.1.peg.3904</a></td><td>fig|PF000160</td><td>pfam|PF01144.12</td><td>9</td><td>-11</td><td>1</td></tr>
<tr><td>Bacillus subtilis subsp. subtilis str. 168</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|224308.1.peg.3904&equivalence=1" target="_blank">fig|224308.1.peg.3904</a></td><td>fig|PF000359</td><td>pfam|PF01144.12</td><td>7</td><td>-19</td><td>1</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.3861&equivalence=1" target="_blank">fig|262316.1.peg.3861</a></td><td>fig|PF000530</td><td>pfam|PF01144.12</td><td>12</td><td>-38</td><td>2</td></tr>
<tr><td>Mycobacterium avium subsp. paratuberculosis str. k10</td><td><a href="../proteinfamilies.cgi?user=&prot=fig|262316.1.peg.3861&equivalence=1" target="_blank">fig|262316.1.peg.3861</a></td><td>fig|PF003527</td><td>pfam|PF01144.12</td><td>9</td><td>-23</td><td>2</td></tr>
</table>


MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3