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276    
277  </div>  </div>
278    
279  <p>Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. The downloading and installation of the data is run in the background because it takes a signficant amount of time and resources. You can monitor the progress in the <a href="/FIG/seed_ctl.cgi">SEED control panel</a>. While the data is being installed you should really not use the PIR superfamilies. Although they will show up they are being edited, added, and deleted, and are therefore unstable. Installation of the data should take about 10-15 minutes.</p>  <p>Clicking on the "Update Data" or "Update Anyway" buttons will start the download and reinitiate the comparison of the SEED data with the PIR data. The downloading and installation of the data is run in the background using the script 'load_pirsf'  because it takes a signficant amount of time and resources. You can monitor the progress in the <a href="/FIG/seed_ctl.cgi">SEED control panel</a>. While the data is being installed you should really not use the PIR superfamilies. Although they will show up they are being edited, added, and deleted, and are therefore unstable. Installation of the data should take about 10-15 minutes.</p>
280    
281  <p>Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete.</p>  <p>Once the update is run, you will see the front page again, however there will be a message telling you that the update is complete.</p>
282    
283    
284    <a name="spreadsheet"><h2>Subsystem Spreadsheets</h2></a>
285    
286    <p>The correspondence between PIR and SEED is highlighted in the spreadsheets. A sample of a few columns are shown below. <small>Note this table is for demonstration purposes only and the correspondence will likely change.</small>
287    
288    <div class="example">
289    <table border=1>
290    
291    <tr>
292                    <td><b>Genome ID</b></td>
293                    <td><b>Organism</b></td>
294                    <td><b>Variant Code</b></td>
295                    <td><b>cysB</b></td>
296                    <td><b>cysC</b></td>
297                    <td><b>cysD</b></td>
298                    <td><b>cysI</b></td>
299                    <td><b>cysJ</b></td>
300                    <td><b>cysN</b></td>
301                    <td><b>cysQ</b></td>
302                    <td><b>cysS</b></td>
303            </tr>
304            <tr>
305                    <td><input type="text" name="genome214092.1" value="214092.1" size="15" /></td>
306                    <td>Yersinia pestis CO92 [B]</td>
307                    <td><input type="text" name="vcode214092.1" value="0311" size="10" /></td>
308                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.2277&user=master:RobE>2277</a></td>
309                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3343&user=master:RobE>3343</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
310                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3345&user=master:RobE>3345</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
311                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3349&user=master:RobE>3349</a></td>
312                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3350&user=master:RobE>3350</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
313                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3344&user=master:RobE>3344</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
314                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3504&user=master:RobE>3504</a></td>
315                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|214092.1.peg.3079&user=master:RobE>3079</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
316            </tr>
317            <tr>
318                    <td><input type="text" name="genome223926.1" value="223926.1" size="15" /></td>
319                    <td>Vibrio parahaemolyticus RIMD 2210633 [B]</td>
320                    <td><input type="text" name="vcode223926.1" value="0200" size="10" /></td>
321                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.1101&user=master:RobE>1101</a></td>
322                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.296&user=master:RobE>296</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
323                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.292&user=master:RobE>292</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
324                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.2721&user=master:RobE>2721</a></td>
325                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.2722&user=master:RobE>2722</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
326                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.293&user=master:RobE>293</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
327                    <td bgcolor="#FFFFFF"></td>
328                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|223926.1.peg.1150&user=master:RobE>1150</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
329            </tr>
330            <tr>
331                    <td><input type="text" name="genome198214.1" value="198214.1" size="15" /></td>
332                    <td>Shigella flexneri 2a str. 301 [B]</td>
333                    <td><input type="text" name="vcode198214.1" value="1311" size="10" /></td>
334                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.1222&user=master:RobE>1222</a></td>
335                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2595&user=master:RobE>2595</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
336                    <td bgcolor="#C0C0C0"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2597&user=master:RobE>2597</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF002936">1</a>] </sup> </td>
337                    <td bgcolor="#C08080"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2601&user=master:RobE>2601</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000244">8</a>] </sup> </td>
338                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2602&user=master:RobE>2602</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
339                    <td bgcolor="#FF40C0"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.2596&user=master:RobE>2596</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF003010">2</a>] </sup> </td>
340                    <td bgcolor="#FFFFFF"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.4023&user=master:RobE>4023</a></td>
341                    <td bgcolor="#FF8040"><a href=/FIG/protein.cgi?prot=fig|198214.1.peg.444&user=master:RobE>444</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
342            </tr>
343    
344            <tr>
345                    <td><input type="text" name="genome272558.1" value="272558.1" size="15" /></td>
346                    <td>Bacillus halodurans C-125 [B]</td>
347                    <td><input type="text" name="vcode272558.1" value="2200" size="10" /></td>
348                    <td bgcolor="#FFFFFF"></td>
349                    <td bgcolor="#00FF80"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.1489&user=master:RobE>1489</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000544">10</a>] </sup> </td>
350                    <td bgcolor="#FFFFFF"></td>
351                    <td bgcolor="#C08080"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.610&user=master:RobE>610</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000244">8</a>] </sup> </td>
352                    <td bgcolor="#C0FF00"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.609&user=master:RobE>609</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF000207">9</a>] </sup> </td>
353                    <td bgcolor="#FFFFFF"></td>
354                    <td bgcolor="#FFFFFF"></td>
355                    <td bgcolor="#FFC040"><a href=/FIG/protein.cgi?prot=fig|272558.1.peg.111&user=master:RobE>111</a>, <a href=http://theseed.uchicago.edu/FIG/protein.cgi?prot=fig|272558.1.peg.112&user=master:RobE>112</a> &nbsp; <sup> [<a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF005520">5</a>, <a href="pir.cgi?&amp;user=master:RobE&amp;pirsf=PIRSF001536">3</a>] </sup> </td>
356            </tr>
357    </table>
358    </div>
359    
360    <p>The columns of the table are colored based on the superfamilies that the proteins are in, and in theory each column should be the same color and complete throughout.
361    <br />
362    Note that the small numbers that are slightly superscripted <span class="example"><sup style="margin: 1px"> [<a href="/FIG/pir.cgi?&user=master:RobE&pirsf=PIRSF005520">5</a>] </SUP></span> are linked to the PIR <a href="#correspondence">correspondence</a> table so you can click through and see proteins missing from either side as described above.</p>
363    
364    <p>This example demonstrates this different aspects of the PIR/SEED interactions:</p>
365    <ul>
366    <li>Protein in SEED subsystem but not in a PIR superfamily.</li>
367    <br>cysB is a conserved family in SEED but there is no corresponding PIR superfamily for these yet</br>
368    <li>Protein in SEED subsystem and in PIR superfamily.</li>
369    <br>cysC and cysJ are consistent across both PIR superfamilies and SEED subsystems.</br>
370    <li>Proteins in a PIR superfamily but not in a SEED subsystem</li>
371    <br>You can't actually see these from this table, you have to look at the <a href="#correspondence">correspondence</a> table.</br>
372    <li>Proteins in SEED subsystem but missing from the PIR superfamily.</li>
373    <br>For example, cysI is missing from the superfamily for the first two organisms</br>
374    <li>Duplicate proteins</li>
375    <br>Some proteins like cysS either have two proteins in one cell or may have one protein mapping to two superfamilies. These are shown as more than one entry in the superscript</br>
376    </ul>
377    
378    
379    

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