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<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>
<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>
<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>
<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>

<h3>Example 2</h3>

<p>This is a little example from Histidine Biosynthesis</p>
<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>
<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>
<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>

<h3>Example </h3>

<p>Polymyxin resistance protein PmrJ, predicted deacetylase</p>
<p>A nice small family that you can compare to PFAM. There are two different views. The family centric view shows the whole family. The table that shows the other families that are also represented shows <em>all</em> families that are also related to the proteins in the table.</p>

<p>On the other hand, the protein centric view comes in from a single protein (e.g. if you have clicked a link from the protein page, and only shows you those other families that are related to this particular protein</p>.

        <li><a href="../proteinfamilies.cgi?family=fig|PF003364">family centric</a></li>
        <li><a href="../proteinfamilies.cgi?user=$user&prot=fig|119912.1.peg.2301&equivalence=1">gene centric</a></li>

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