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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />
<link REL="SHORTCUT ICON" HREF="http://tanto.bioe.uic.edu/bbtmst/favicon.ico">
<title>bbTM supporting material</title>
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<body>
<table width="675" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td colspan="2" class="style13"><a name="top" id="top"></a></td>
</tr>
<tr>
<td colspan="2" class="style13"><table width="98%" border="0" align="center" cellpadding="0" cellspacing="0">
<tr>
<td width="30%"><a href="http://www.uic.edu/uic/" target="_blank" class="style38">University of Illinos at Chicago </a></td>
<td width="41%"><div align="center"><a href="http://gila.bioe.uic.edu/lab/" target="_blank" class="style37">Jie Liang Lab</a></div></td>
<td width="30%"><div align="right"><a href="http://www.bioe.uic.edu/BIOE/WebHome" target="_blank" class="style37">Department of Bioengineering</a></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2" class="style13"> </td>
</tr>
<tr>
<td colspan="2" class="style13"><table width="100%" border="0" align="center" cellpadding="1" cellspacing="1" bgcolor="#000000">
<tr bgcolor="#000000">
<td width="28%"><div align="center"><img src="images/logobbtmblack.jpg" width="167" height="125" /></div></td>
<td width="72%"><span class="style15"><span class="style20"><span class="style40">Pattern of Amino Acid Substitution in Transmembrane Segments of </span></span></span><span class="style44"><span class="style20"><span class="style21">β-Barrel Membrane Proteins</span></span></span><span class="style15"><span class="style20"><br />
</span></span><span class="style45">David Jimenez-Morales and Jie Liang</span></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2" class="style13"><div align="center" class="style16">
<p class="style28">Supporting Material </p>
</div></td>
</tr>
<tr>
<td colspan="2" class="style13"><div align="center"><span class="style22"><a href="index.html">Main</a> · <a href="#subraes">Substitution Rate and Scoring Matrices</a> · <a href="#msa">Multiple Sequence Alignments</a> · <a href="#data">Data Set</a> · <a href="bbtmstool.php">BBTM-SearchTool</a></span></div></td>
</tr>
<tr>
<td colspan="2" class="style13"><div align="center" class="style22">.<a name="subraes" id="subraes"></a></div></td>
</tr>
<tr>
<td colspan="2"><table width="99%" border="1" align="center" cellpadding="0" cellspacing="0" bordercolor="#0066CC" bgcolor="#000000">
<tr>
<td><div align="center"><span class="style46">Substitution Rate and bbTM Scoring Matrices</span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center"><span class="style22">.</span></div></td>
</tr>
<tr>
<td colspan="2"><blockquote>
<p><span class="style4">A Bayesian Monte Carlo approach based on the technique of Markov chain Monte Carlo was used to estimate the posterior mean values of the instantaneous rates of residue substitution, using the selected set of sequences homologous to the template protein and its phylogenetic tree. The entries <em>q</em><sub>ij</sub> of the matrix <em>Q</em> are substitution rates of amino acid residues for the 20 amino acids at an infinitesimally small time interval. <em>Q</em> takes the form <em>Q</em> = <em>D/2*S + S*D/2</em>, where <em>D</em> is a diagonal matrix with values taken from the amino acid composition of the set of aligned sequences studied, and <em>S</em> is a symmetric matrix with 0 values in diagonal elements, and whose off-diagonal entries are estimated. Phylogenetic trees were obtained using a maximum likelihood method based on the entire length of the protein sequences. </span></p>
</blockquote></td>
</tr>
<tr>
<td colspan="2"><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td width="48%" align="left" valign="middle" class="style13"><div align="center"><img src="images/tmall-w.jpg" width="200" height="162" /></div> </td>
<td width="52%" align="left" valign="top"><p class="style18">TM-ALL region</p>
<p class="style13">The fragments embedded within the outer membrane region. </p>
<p class="style13">- <em><a href="supmat/qmatrices/subraes_TMall.qmat" target="_blank">Symmetric Q-all</a></em> matrix (S to A) - <a href="supmat/qmatrices/TMALL.jpg" target="_blank">bubble plot</a> <br />
- <span class="style21"><strong><a href="supmat/bbTMmatrices/bbTMall">bbTM-all</a></strong></span> scoring matrix<br />
<br />
<br />
<br />
</p></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"> </td>
</tr>
<tr>
<td colspan="2"><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td width="48%" align="center" valign="middle"><img src="images/tmout-w.jpg" width="200" height="162" /></td>
<td width="52%" align="left" valign="top"><p class="style23">TM-OUT region</p>
<p class="style13">Amino Acids facing the lipid interface, from the fragments embedded within the outer membrane region. </p>
<p class="style13">- <em><a href="supmat/qmatrices/subraes_TMout.qmat" target="_blank">Symmetric Q-out</a></em> matrix (S to A) - <a href="supmat/qmatrices/TMOUT.jpg" target="_blank">bubble plot</a><br />
- <span class="style21"><strong><a href="supmat/bbTMmatrices/bbTMout" target="_blank">bbTM-out</a></strong></span> scoring matrix</p></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"> </td>
</tr>
<tr>
<td colspan="2"><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td width="48%" align="center" valign="middle"><img src="images/tmin-w.jpg" alt="Residues facing the interior of the beta barrel pore" width="200" height="156" /></td>
<td width="52%" align="left" valign="top"><p class="style24">TM-IN region</p>
<p class="style13">Amino Acids facing the interior of the beta barrel pore, from the fragments embedded within the outer membrane region. </p>
<p class="style13">- <em><a href="supmat/qmatrices/subraes_TMin.qmat" target="_blank">Symmetric Q-in</a></em> matrix (S to A) - <a href="supmat/qmatrices/TMOUT.jpg" target="_blank">bubble plot</a> <br />
- <span class="style21"><strong><a href="supmat/bbTMmatrices/bbTMin">bbTM-in</a></strong></span> scoring matrix</p></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center" class="style4">
<div align="right">
<blockquote>
<p id="msa" name="msa"><a name="msa" id="msa"></a> <a href="#top">up</a></p>
</blockquote>
</div>
</div>
<div align="right"></div></td>
</tr>
<tr>
<td colspan="2"><table width="99%" border="1" align="center" cellpadding="0" cellspacing="0" bordercolor="#0066CC" bgcolor="#000000">
<tr>
<td><div align="center"><span class="style46">Multiple Sequence Alignments</span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center"><span class="style22">.</span></div></td>
</tr>
<tr>
<td colspan="2"><blockquote>
<p><span class="style13">Multiple sequence aligments of the beta barrel membrane proteins used in this study. </span></p>
</blockquote></td>
</tr>
<tr>
<td width="334"><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td><div align="center"><span class="style26">ScrY: Sucrose-Specific Porin (PDB:1A0S) </span></div></td>
</tr>
<tr>
<td><div align="center"><img src="images/a1a0small.jpg" width="126" height="100" /></div></td>
</tr>
<tr>
<td><div align="center" class="style26"><a href="supmat/msa/msa1A0S.zip">Download 1A0S-MSAs</a><br />
View msa: <a href="supmat/msa/out1A0S.pdf">1A0S-OUT</a>, <a href="supmat/msa/in1A0S.pdf">1A0S-IN</a> <br />
<a href="supmat/betatrees/1A0S.tree" target="_blank">Phylogenetic tree</a> </div></td>
</tr>
</table></td>
<td width="316"><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">OmpA: Protein A (PDB:1BXW)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/b1BXWs.jpg" width="56" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1BXW.zip">Download 1BXW-MSAs</a><br />
View msa: <a href="supmat/msa/out1BXW.pdf">1BXW-OUT</a>, <a href="supmat/msa/in1BXW.pdf">1BXW-IN</a></span><br />
<span class="style26"><a href="supmat/betatrees/1BXW.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center" class="style27">
<div align="center">~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ <span class="style27">~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ ~ _ </span></div>
</div> </td>
</tr>
<tr>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">Omp32: Anion-selective porin (PDB:1E54)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/c1E54s.jpg" width="88" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1E54.zip">Download 1E54-MSAs</a><br />
View msa: <a href="supmat/msa/out1E54.pdf">1E54-OUT</a>, <a href="supmat/msa/in1E54.pdf">1E54-IN</a></span><br />
<span class="style26"><a href="supmat/betatrees/1E54.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">FepA: Ferric enterobactin receptor (PDB:1FEP)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/d1FEPs.jpg" width="82" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1FEP.zip">Download 1FEP-MSAs</a><br />
View msa: <a href="supmat/msa/out1FEP.pdf">1FEP-OUT</a>, <a href="supmat/msa/in1FEP.pdf">1FEP-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1FEP.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center"><span class="style4"><span class="style22">- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -</span></span></div></td>
</tr>
<tr>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">OmpT: Protease (PDB:1I78)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/e1I78s.jpg" width="104" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1I78.zip">Download 1I78-MSAs</a><br />
View msa: <a href="supmat/msa/out1I78.pdf">1I78-OUT</a>, <a href="supmat/msa/in1I78.pdf">1I78-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1I78.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">FecA: Transporter (PDB:1KMO)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/f1KMOs.jpg" width="86" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1KMO.zip">Download 1KMO-MSAs</a><br />
View msa: <a href="supmat/msa/out1KMO.pdf">1KMO-OUT</a>, <a href="supmat/msa/in1KMO.pdf">1KMO-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1KMO.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center"><span class="style4"><span class="style22">- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -</span></span></div></td>
</tr>
<tr>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">BtuB: Cobalamin transporter (PDB:1NQE)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/g1NQEs.jpg" width="81" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1NQE.zip">Download 1NQE-MSAs</a><br />
View msa: <a href="supmat/msa/out1NQE.pdf">1NQE-OUT</a>, <a href="supmat/msa/in1NQE.pdf">1NQE-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1NQE.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">Phospholipase A (PDB: 1QD6)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/h1QD6s.jpg" width="129" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1QD6.zip">Download 1QD6-MSAs</a><br />
View msa: <a href="supmat/msa/out1QD6.pdf">1QD6-OUT</a>, <a href="supmat/msa/in1QD6.pdf">1QD6-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1QD6.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
</tr>
<tr>
<td colspan="2"><div align="center"><span class="style4"><span class="style22">- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -</span></span></div></td>
</tr>
<tr>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td class="style26"><div align="center">OMPX: Protein X (PDB: 1QJ8)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/i1QJ8s.jpg" width="59" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa1QJ8.zip">Download 1QJ8-MSAs</a><br />
View msa: <a href="supmat/msa/out1QJ8.pdf">1QJ8-OUT</a>, <a href="supmat/msa/in1QJ8.pdf">1QJ8-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/1QJ8.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
</tr>
</table></td>
<td><table width="95%" border="0" align="center" cellpadding="1" cellspacing="1">
<tr>
<td><div align="center" class="style26">lamB: Maltoporin (PDB:2MPR)</div></td>
</tr>
<tr>
<td><div align="center"><img src="images/j2mprs.jpg" width="101" height="100" /></div></td>
</tr>
<tr>
<td><div align="center"><span class="style26"><a href="supmat/msa/msa2MPR.zip">Download 2MPR-MSAs</a><br />
View msa: <a href="supmat/msa/out2MPR.pdf">2MPR-OUT</a>, <a href="supmat/msa/in2MPR.pdf">2MPR-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/2MPR.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
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<td colspan="2"><div align="center"><span class="style4"><span class="style22">- ~ = ~ = ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ - ~ -</span></span></div></td>
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<td><div align="center" class="style26">OmpF: Porin (PDB:2OMF) </div></td>
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<td><div align="center"><img src="images/k2OMFss.jpg" width="77" height="100" /></div></td>
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<td><div align="center"><span class="style26"><a href="supmat/msa/msa2OMF.zip">Download 2OMF-MSAs</a><br />
View msa: <a href="supmat/msa/out2OMF.pdf">2OMF-OUT</a>, <a href="supmat/msa/in2OMF.pdf">2OMF-IN</a></span><span class="style26"><a href="supmat/msa/in1BXW.pdf"></a></span><br />
<span class="style26"><a href="supmat/betatrees/2OMF.tree" target="_parent">Phylogenetic tree</a> </span></div></td>
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<p id="data" name="data"><span class="style4"><a href="#top">up</a></span></p>
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<td><div align="center"><span class="style32">Data Set </span></div></td>
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<td colspan="2"><div align="center"><span class="style22">.</span></div></td>
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<td colspan="2"><blockquote>
<p class="style4">Set of sequences used in this study </p>
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<td colspan="2"><blockquote>> <span class="style19"><span class="style33"><a href="supmat/ddbb/dataset_nrbigswiss.fasta" target="_blank">dataset nrbigswiss.fasta</a></span></span><em>:</em> <span class="style4">non-rendudant dat set containing known and predicted beta barrel membrane from <a href="http://www.igb.uci.edu/~baldig/tmb.html" target="_blank">TMBprof</a> and <a href="http://www.expasy.ch/sprot/" target="_blank">Swiss-Prot</a> database </span></blockquote></td>
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<td colspan="2"><blockquote> > <span class="style21"><em><strong><a href="supmat/ddbb/dataset_chalmemrandom.fasta" target="_blank">dataset chalmemrandom.fasta</a></strong></em></span>: <span class="style4">random sequences obtained from fully shuffled sequences of 385 α- helical and β-barrel membrane proteins from different organisms. These random sequences preserve the same amino acid composition as membrane proteins</span> </blockquote></td>
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<td colspan="2"><blockquote>> <em><strong><a href="supmat/ddbb/oMBp.fasta" target="_blank" class="style21">oMBp.fasta</a></strong></em>: <span class="style4">(for other MemBrane proteins) consists of membrane proteins with a different architecture (non-β-barrel). These were selected based on annotations of “SUBCELLULAR LOCATION: Cell membrane” from Eukaryota and Archaea. In total, 10,951 protein sequences (1,061 from Archaea and 9,890 from Eukaryota).</span></blockquote></td>
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<td colspan="2"><blockquote>
<p>> <em><strong><a href="supmat/ddbb/Globular.fasta" target="_blank" class="style21">Globular.fasta</a></strong></em>: <span class="style4">127,485 globular protein sequences from Uniprot with annotations that lack the word “membrane” (16,814 Archaea and 110,671 Eukaryota).</span></p>
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<p class="style4"><a href="#top">up</a></p>
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<p> </p>
<p><strong>
<a href="http://biodavidjm.github.io/" target="_blank">David Jimenez-Morales</a> and Jie Liang
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<td colspan="2"><p align="center" class="style4">Dept of Bioengineering/ Bioinformatics Program<br />
<span class="style3">University of Illinois at Chicago</span><br />
<span class="style6">Chicago, Illinois, United States of America</span></p> </td>
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