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Iron sulfur clusters - Revision history
2024-03-28T21:37:56Z
Revision history for this page on the wiki
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Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-27T17:34:23Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:34, 27 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l76">Line 76:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>FAM96B is remarkably conserved throughout eukaryotes. It duplicated in the earliest metazoan ancestor, giving rise to FAM96A after the divergence of choanflagellates but before those of sponge, trichoplax, ctenophore or cnidarian. Both FAM96B and FAM96A have been retained in all metazoan lineages. In vertebrates but not earlier diverging deuterostomes, FAM96A acquired an unmistakable signal peptide, meaning it was no longer targeted to the cytoplasm. The species with the signal peptide are exactly those with an extra pair of invariant cysteines, suggesting a disulfide suitable for an oxidizing subcellular compartment such as endoplasmic reticulum. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>FAM96B is remarkably conserved throughout eukaryotes. It duplicated in the earliest metazoan ancestor, giving rise to FAM96A after the divergence of choanflagellates but before those of sponge, trichoplax, ctenophore or cnidarian. Both FAM96B and FAM96A have been retained in all metazoan lineages. In vertebrates but not earlier diverging deuterostomes, FAM96A acquired an unmistakable signal peptide, meaning it was no longer targeted to the cytoplasm. The species with the signal peptide are exactly those with an extra pair of invariant cysteines, suggesting a disulfide suitable for an oxidizing subcellular compartment such as endoplasmic reticulum. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>However these new cysteines are not in proper crystallographic position to form a disulfide, though the new Cys99 and the long conserved near-terminal Cys155 are within range and may form a disulfide under certain conditions. <del style="font-weight: bold; text-decoration: none;">The positions of two Cys90</del>, <del style="font-weight: bold; text-decoration: none;">one </del>from <del style="font-weight: bold; text-decoration: none;">each monomer</del>, <del style="font-weight: bold; text-decoration: none;">may also be capable </del>of <del style="font-weight: bold; text-decoration: none;">forming </del>a <del style="font-weight: bold; text-decoration: none;">disulfide, 2Fe</del>-<del style="font-weight: bold; text-decoration: none;">2S, or zinc ligand provided the protein is purified anaerobically or reconstituted using some sort of activity assay. The phylogenetic conservation of cysteines is explored in the alignment below</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>However these new cysteines are not in proper crystallographic position to form a disulfide, though the new Cys99 and the long conserved near-terminal Cys155 are within range and may form a disulfide under certain conditions. <ins style="font-weight: bold; text-decoration: none;">A disulfide between Cys99 and Cys155</ins>, <ins style="font-weight: bold; text-decoration: none;">while physically plausible </ins>from <ins style="font-weight: bold; text-decoration: none;">3UX2 and signal peptide</ins>, <ins style="font-weight: bold; text-decoration: none;">is however not evolutionarily plausible because the counterpart </ins>of <ins style="font-weight: bold; text-decoration: none;">Cys155 in FAM96B is </ins>a <ins style="font-weight: bold; text-decoration: none;">long</ins>-<ins style="font-weight: bold; text-decoration: none;">conserved surface residue for another reason</ins>. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The two encoded proteins both bind CIA01. However they must have distinct functions in vivo to account for their <del style="font-weight: bold; text-decoration: none;">+</del>retention in so many lineages for so long. The usual explanations -- specialized time of expression during development or in differentiated populations of cells -- is not generally applicable from single-celled organisms to human. Since the signal peptide in FAM96A arose fairly late, it too cannot explain retention in earlier diverging species. (Note however tools that recognize signal peptides are not adequately trained on these species.) Since the duplication is restricted to metazoans (ie animals), it could possibly be associated with dietary, rather than diffusive, acquisition of iron. Secondary duplications of FAM96B occurred in various lineages (eg insects, slime molds).</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The positions of two Cys90, one from each monomer, may also be capable of forming a disulfide, 2Fe-2S, or zinc ligand provided the protein is purified anaerobically or reconstituted using some sort of activity assay. The phylogenetic conservation of cysteines is explored in the alignment below.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The two encoded proteins both bind CIA01. However they must have distinct functions in vivo to account for their retention in so many lineages for so long. The usual explanations -- specialized time of expression during development or in differentiated populations of cells -- is not generally applicable from single-celled organisms to human. Since the signal peptide in FAM96A arose fairly late, it too cannot explain retention in earlier diverging species. (Note however tools that recognize signal peptides are not adequately trained on these species.) Since the duplication is restricted to metazoans (ie animals), it could possibly be associated with dietary, rather than diffusive, acquisition of iron. Secondary duplications of FAM96B occurred in various lineages (eg insects, slime molds).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The placement and phase of introns in FAM96B and FAM96A -- largely conserved -- implies that FAM96B was largely intronated prior to gene duplication. Although the two genes did go their separate ways during the subsequent 600 million years (both gains and losses of introns occurred), the patterns remain very closely related today even comparing human to sponge. Most remarkably, the first intron was already present in early diverging stramenopiles (eg Phytophthora infestans) and the last exon in the last common ancestor of human and amoebozoa (eg Dictyostelium discoideum). Convergent evolution is implausible given 450 possibilities (three possible phases at 150 sites).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The placement and phase of introns in FAM96B and FAM96A -- largely conserved -- implies that FAM96B was largely intronated prior to gene duplication. Although the two genes did go their separate ways during the subsequent 600 million years (both gains and losses of introns occurred), the patterns remain very closely related today even comparing human to sponge. Most remarkably, the first intron was already present in early diverging stramenopiles (eg Phytophthora infestans) and the last exon in the last common ancestor of human and amoebozoa (eg Dictyostelium discoideum). Convergent evolution is implausible given 450 possibilities (three possible phases at 150 sites).</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l159">Line 159:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as none such exist, according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate C..C seen in prokaryotes and some early diverging eukaryotes, does not extend to plants. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as none such exist, according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate C..C seen in prokaryotes and some early diverging eukaryotes, does not extend to plants. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Crystallographic structures from the euryarchaeote Archaeoglobus fulgidus (3KB1 or 2PH1) can be used as </del>structural template for HCF101 <del style="font-weight: bold; text-decoration: none;">(and related sequences, notably </del>human NUBP1). Percent identity at <del style="font-weight: bold; text-decoration: none;">39</del>% <del style="font-weight: bold; text-decoration: none;">is low </del>but adequate for some purposes. <del style="font-weight: bold; text-decoration: none;">The biologically challenged Structural Genomics Consortium picked family representatives lacking Duf59 and </del>DUF971 <del style="font-weight: bold; text-decoration: none;">domains. No article or commentary accompanies the 2008 submissions</del>. The <del style="font-weight: bold; text-decoration: none;">dimer has a zinc ion at its top center held together by deeply conserved pair </del>of <del style="font-weight: bold; text-decoration: none;">C..C motifs that are lacking </del>plants. <del style="font-weight: bold; text-decoration: none;">This zinc could conceivably be occupied by a 4Fe</del>-<del style="font-weight: bold; text-decoration: none;">4S cluster </del>in <del style="font-weight: bold; text-decoration: none;">vivo</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The best </ins>structural template for <ins style="font-weight: bold; text-decoration: none;">the triple fusion protein DUF59-NBP35-DUF971 (Arabidopsis </ins>HCF101 <ins style="font-weight: bold; text-decoration: none;">or unfused </ins>human NUBP1) <ins style="font-weight: bold; text-decoration: none;">is the DUF59 structure 3KB1 of the euryarchaeote Archaeoglobus fulgidus</ins>. Percent identity <ins style="font-weight: bold; text-decoration: none;">is low </ins>at <ins style="font-weight: bold; text-decoration: none;">40</ins>% but adequate for some purposes. <ins style="font-weight: bold; text-decoration: none;">Note </ins>DUF971 <ins style="font-weight: bold; text-decoration: none;">is a free-standing protein of unknown function in bacteria</ins>. </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The <ins style="font-weight: bold; text-decoration: none;">triple fusion </ins>of <ins style="font-weight: bold; text-decoration: none;">HCF101 did not arise in </ins>plants <ins style="font-weight: bold; text-decoration: none;">-- it is already present in early diverging eukaryotes (stramenopiles and alveolata) which lack chloroplasts (the intra-cellular location of HCF101)</ins>. <ins style="font-weight: bold; text-decoration: none;">The double fusion DUF59</ins>-<ins style="font-weight: bold; text-decoration: none;">NUBPL too is older, occurring </ins>in <ins style="font-weight: bold; text-decoration: none;">both bacteria and archaea. Fungi and metazoans lack DUF59-NUBPL and NUBPL-DUF971 fusion proteins though Duf971 is not altogether lost (eg human Fe dioxygenases BBOX1 and TMLHE)</ins>. <ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Further, this pattern </del>is <del style="font-weight: bold; text-decoration: none;">present </del>in <del style="font-weight: bold; text-decoration: none;">all three paralogs of all three vertebrate proteins, as is </del>the <del style="font-weight: bold; text-decoration: none;">proline providing </del>the <del style="font-weight: bold; text-decoration: none;">sharp bend </del>and the <del style="font-weight: bold; text-decoration: none;">dimer</del>-<del style="font-weight: bold; text-decoration: none;">bridging phenylalanine, suggesting the dimer structure is phylogenetically invariant (with the exception of HCF101 in plants):</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">The Archaeoglobus protein </ins>is <ins style="font-weight: bold; text-decoration: none;">also a dimer with a central zinc ion held by a deeply conserved pair of CpnC motifs </ins>in the <ins style="font-weight: bold; text-decoration: none;">NUBPL that however are not available in Arabidopsis HCF101 which has one conserved cysteine taken up by </ins>the <ins style="font-weight: bold; text-decoration: none;">DUF59 active site </ins>and <ins style="font-weight: bold; text-decoration: none;">another by </ins>the <ins style="font-weight: bold; text-decoration: none;">ATP-binding P</ins>-<ins style="font-weight: bold; text-decoration: none;">loop and so lacks conserved cysteines or histidines at homologous position to CpnC. </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> NUBP2_homSap <del style="font-weight: bold; text-decoration: none;">ENMSGFt</del><font color=red>C</font><font color=<del style="font-weight: bold; text-decoration: none;">green</del>><del style="font-weight: bold; text-decoration: none;">P</del></font><del style="font-weight: bold; text-decoration: none;">H</del><font color=red>C</font><del style="font-weight: bold; text-decoration: none;">tECtsv</del><font color=BLUE>F</font></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">However alignment of archaeal protein with the triple paralog system in humans shows remarkable conservation in this region, so the dimer may well bind a 4Fe-4S cluster as that paper concluded. Plants including Arabidopsis do have a second standalone NUBPL counterpart with the CpnC motif so that is probably the proper comparison here, with HCF101 representing a loss in certain early diverging eukaryotes though not all (eg the Paramecium triple fusion).</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> NUBP1_homSap <del style="font-weight: bold; text-decoration: none;">ENMSGFi</del><font color=<del style="font-weight: bold; text-decoration: none;">red</del>><del style="font-weight: bold; text-decoration: none;">C</del></font><font color=<del style="font-weight: bold; text-decoration: none;">green</del>><del style="font-weight: bold; text-decoration: none;">P</del></font><del style="font-weight: bold; text-decoration: none;">K</del><font color=red>C</font>KKESQI<font color=BLUE>F</font></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"><BR clear=all></ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> NUBPL_homSap <del style="font-weight: bold; text-decoration: none;">QNMSVFQ</del><font color=<del style="font-weight: bold; text-decoration: none;">red</del>><del style="font-weight: bold; text-decoration: none;">C</del></font><font color=<del style="font-weight: bold; text-decoration: none;">green</del>><del style="font-weight: bold; text-decoration: none;">P</del></font><del style="font-weight: bold; text-decoration: none;">K</del><font color=red>C</font>KHKTHI<font color=BLUE>F</font></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> NUBP2_homSap <ins style="font-weight: bold; text-decoration: none;">E<font color=BLUE>NM</font>SGFt</ins><font color=red>C</font><ins style="font-weight: bold; text-decoration: none;">PH</ins><font color=<ins style="font-weight: bold; text-decoration: none;">red</ins>><ins style="font-weight: bold; text-decoration: none;">C</ins></font><ins style="font-weight: bold; text-decoration: none;">tE</ins><font color=red>C</font><ins style="font-weight: bold; text-decoration: none;">tsv</ins><font color=BLUE>F</font> <ins style="font-weight: bold; text-decoration: none;">(consensus of 46</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> archaeal 3KB1 <del style="font-weight: bold; text-decoration: none;">ENMAYFE</del><font color=red>C</font><font color=<del style="font-weight: bold; text-decoration: none;">green</del>><del style="font-weight: bold; text-decoration: none;">P</del></font><del style="font-weight: bold; text-decoration: none;">N</del><font color=red>C</font><del style="font-weight: bold; text-decoration: none;">GERTYL</del><font color=BLUE>F</font></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> NUBP1_homSap <ins style="font-weight: bold; text-decoration: none;">E</ins><font color=<ins style="font-weight: bold; text-decoration: none;">BLUE</ins>><ins style="font-weight: bold; text-decoration: none;">NM</ins></font><ins style="font-weight: bold; text-decoration: none;">SGFi</ins><font color=<ins style="font-weight: bold; text-decoration: none;">red</ins>><ins style="font-weight: bold; text-decoration: none;">C</ins></font><ins style="font-weight: bold; text-decoration: none;">PK</ins><font color=red>C</font>KKESQI<font color=BLUE>F</font></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> NUBPL_homSap <ins style="font-weight: bold; text-decoration: none;">Q</ins><font color=<ins style="font-weight: bold; text-decoration: none;">BLUE</ins>><ins style="font-weight: bold; text-decoration: none;">NM</ins></font><ins style="font-weight: bold; text-decoration: none;">SVFQ</ins><font color=<ins style="font-weight: bold; text-decoration: none;">red</ins>><ins style="font-weight: bold; text-decoration: none;">C</ins></font><ins style="font-weight: bold; text-decoration: none;">PK</ins><font color=red>C</font>KHKTHI<font color=BLUE>F</font></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> archaeal 3KB1 <ins style="font-weight: bold; text-decoration: none;">E<font color=BLUE>NM</font>AYFE<font color=red>C</font>PN<font color=red>C</font>GERTYL<font color=BLUE>F</font></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Arabidopsis E<font color=BLUE>NM</font><font color=red>C</font>HFDAD--GKRYYP<font color=BLUE>F</font> HCF101 </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Arabidopsis E<font color=BLUE>NM</font>S<font color=red>C</font>FV<font color=red>C</font>PH<font color=red>C</font>NEPSFI<font color=BLUE>F</font> NP_193689 chromosome partitioning</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>S<font color=red>C</font>FK<font color=red>C</font>SK<font color=red>C</font>GEKSYI<font color=BLUE>F</font> Zea mays NP_001150831</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>S</ins><font color=red>C</font><ins style="font-weight: bold; text-decoration: none;">FK</ins><font color=<ins style="font-weight: bold; text-decoration: none;">red</ins>><ins style="font-weight: bold; text-decoration: none;">C</ins></font><ins style="font-weight: bold; text-decoration: none;">PK</ins><font color=red>C</font><ins style="font-weight: bold; text-decoration: none;">GEKSYI<font color=BLUE>F</font> Oryza sativa EEC75781</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>SHHT<font color=red>C</font>SK<font color=red>C</font>GHVERI<font color=BLUE>F</font> Volvox carteri XP_002954172</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>SYFK<font color=red>C</font>PN<font color=red>C</font>GERSHI<font color=BLUE>F</font> Physcomitrella patens XP_001755735</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>S<font color=red>C</font>FK<font color=red>C</font>PN<font color=red>C</font>GHPSYI<font color=BLUE>F</font> Vitis vinifera XP_002282449</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>AYHR<font color=red>C</font>GK<font color=red>C</font>GHVEHI<font color=BLUE>F</font> Chlamydomonas reinhardtii XP_001702721</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> E<font color=BLUE>NM</font>SFFK<font color=red>C</font>PH<font color=red>C</font>GEPSFI</ins><font color=BLUE>F</font> <ins style="font-weight: bold; text-decoration: none;">Populus trichocarpa XP_002307635</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20448&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-26T23:03:29Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:03, 26 June 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Beginning with the Bacillus anthracis DUF59 domain with determined structure (3LNO Q81XF6), tBlastn against compete bacterial genomes may turn up instructive operon membership in at least some species. While the gene, often called YitW is adjacent to presumably related entitites yitV and yitU, these are ordinary hydrolases unrelated to iron sulfur complexes. In other Bacillus selenitireducens, it is adjacent to a P-loop NTPase helicase, mildly suggestive of an association. In Halobacillus halophilus, it is adjacent to and transcribed in the same direction as molybotperin biosynthetic proteins MobB moaE moaD, an association often observed with DUF59 domains and one that might make sense in terms of Fe-S clusters (moaD is the sulfur carrier protein).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Beginning with the Bacillus anthracis DUF59 domain with determined structure (3LNO Q81XF6), tBlastn against compete bacterial genomes may turn up instructive operon membership in at least some species. While the gene, often called YitW is adjacent to presumably related entitites yitV and yitU, these are ordinary hydrolases unrelated to iron sulfur complexes. In other Bacillus selenitireducens, it is adjacent to a P-loop NTPase helicase, mildly suggestive of an association. In Halobacillus halophilus, it is adjacent to and transcribed in the same direction as molybotperin biosynthetic proteins MobB moaE moaD, an association often observed with DUF59 domains and one that might make sense in terms of Fe-S clusters (moaD is the sulfur carrier protein).</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Crystallographic structures from the euryarchaeote Archaeoglobus fulgidus (3KB1 or 2PH1) can be used as structural template for HCF101 (and related sequences, notably human NUBP1). Percent identity at 39% is low but adequate for some purposes. The seemingly biologically illiterate Structural Genomics Consortium picked family representatives lacking Duf59 and DUF971 domains. No article or commentary accompanies the 2008 submissions. The dimer has a zinc ion at its center held together by deeply conserved pair of CPNC motifs that however are lacking in higher eukaryotes such as plants. </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Arabidopsis protein HCF101 is a triple fusion of a DUF59 domain, a P-loop ATpase resembling human NUBPL somewhat more than NUBP1 (NBP35) or NUBP2 (CFD1), and a DUF971 domain (a free-standing protein of unknown function in bacteria). The triple fusion did not arise in plants -- it is already found in early diverging eukaryotes (stramenopiles and alveolata). Since both bacteria and archaea (euryarchaeotes and thaumarchaeotes but not crenarchaeotes which have only standalone NUBP1 eg YP_004781840) have the DUF59-NUBPL fusion, the initial double fusion is ancient. Fungi and metazoans have no DUF59-NUBPL fusion proteins though Duf971 is not altogether lost (eg two Fe dioxygenases BBOX1 TMLHE in human). Frog and hydra have odd fusions accessions, possibly processed pseudogene fusions: XP_002945459, XP_002161498.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The Arabidopsis protein HCF101 is a triple fusion of a DUF59 domain, a P-loop ATpase resembling human NUBPL somewhat more than NUBP1 (NBP35) or NUBP2 (CFD1), and a DUF971 domain (a free-standing protein of unknown function in bacteria). The triple fusion did not arise in plants -- it is already found in early diverging eukaryotes (stramenopiles and alveolata). Since both bacteria and archaea (euryarchaeotes and thaumarchaeotes but not crenarchaeotes which have only standalone NUBP1 eg YP_004781840) have the DUF59-NUBPL fusion, the initial double fusion is ancient. Fungi and metazoans have no DUF59-NUBPL fusion proteins though Duf971 is not altogether lost (eg two Fe dioxygenases BBOX1 TMLHE in human). Frog and hydra have odd fusions accessions, possibly processed pseudogene fusions: XP_002945459, XP_002161498.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as none such exist, according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate <del style="font-weight: bold; text-decoration: none;">CPHC </del>seen in prokaryotes and some early diverging eukaryotes, does not extend to plants.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as none such exist, according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate <ins style="font-weight: bold; text-decoration: none;">C..C </ins>seen in prokaryotes and some early diverging eukaryotes, does not extend to plants. </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Crystallographic structures from the euryarchaeote Archaeoglobus fulgidus (3KB1 or 2PH1) can be used as structural template for HCF101 (and related sequences, notably human NUBP1). Percent identity at 39% is low but adequate for some purposes. The biologically challenged Structural Genomics Consortium picked family representatives lacking Duf59 and DUF971 domains. No article or commentary accompanies the 2008 submissions. The dimer has a zinc ion at its top center held together by deeply conserved pair of C..C motifs that are lacking plants. This zinc could conceivably be occupied by a 4Fe-4S cluster in vivo.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Further, this pattern is present in all three paralogs of all three vertebrate proteins, as is the proline providing the sharp bend and the dimer-bridging phenylalanine, suggesting the dimer structure is phylogenetically invariant (with the exception of HCF101 in plants):</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">Crystallographic structures from the euryarchaeote Archaeoglobus fulgidus (</del>3KB1 <del style="font-weight: bold; text-decoration: none;">or 2PH1) can be used as structural template for HCF101 (and related sequences, notably human NUBP1). Percent identity at 39% is low but adequate for some purposes. The seemingly biologically illiterate Structural Genomics Consortium picked family representatives lacking Duf59 and DUF971 domains. No article or commentary accompanies the 2008 submissions. The dimer has a zinc ion at its center held together by deeply conserved pair of CPNC motifs that however are lacking in higher eukaryotes such as plants. This zinc could conceivably be occupied by a 4Fe-4S cluster in vivo.</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> NUBP2_homSap ENMSGFt<font color=red>C</font><font color=green>P</font>H<font color=red>C</font>tECtsv<font color=BLUE>F</font></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> NUBP1_homSap ENMSGFi<font color=red>C</font><font color=green>P</font>K<font color=red>C</font>KKESQI<font color=BLUE>F</font></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> NUBPL_homSap QNMSVFQ<font color=red>C</font><font color=green>P</font>K<font color=red>C</font>KHKTHI<font color=BLUE>F</font></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> archaeal </ins>3KB1 <ins style="font-weight: bold; text-decoration: none;"> ENMAYFE<font color=red>C</font><font color=green>P</font>N<font color=red>C</font>GERTYL<font color=BLUE>F</font></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20447&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-26T22:11:42Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:11, 26 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l123">Line 123:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SufTalign.gif|400px|thumb|left|SufT alignment: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:SufTalign.gif|400px|thumb|left|SufT alignment: click to enlarge]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DufNUBPLduf.gif|400px|thumb|left|Triple fusion DUF59-NUBPL-Duf971 (HCF101): click to enlarge]] </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DufNUBPLduf.gif|400px|thumb|left|Triple fusion DUF59-NUBPL-Duf971 (HCF101): click to enlarge]] </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Image:NUBP1arcFul3KB1.gif|left|400px|thumb|Archaeal NUBP1 NBP35 dimer CxxC pair Zn: click to enlarge]]</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:PaaDalign.gif|400px|thumb|left|PaaD alignment: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:PaaDalign.gif|400px|thumb|left|PaaD alignment: click to enlarge]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59s.gif|400px|thumb|left|DUF59 structural comparison: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59s.gif|400px|thumb|left|DUF59 structural comparison: click to enlarge]]</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l152">Line 152:</td>
<td colspan="2" class="diff-lineno">Line 153:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Beginning with the Bacillus anthracis DUF59 domain with determined structure (3LNO Q81XF6), tBlastn against compete bacterial genomes may turn up instructive operon membership in at least some species. While the gene, often called YitW is adjacent to presumably related entitites yitV and yitU, these are ordinary hydrolases unrelated to iron sulfur complexes. In other Bacillus selenitireducens, it is adjacent to a P-loop NTPase helicase, mildly suggestive of an association. In Halobacillus halophilus, it is adjacent to and transcribed in the same direction as molybotperin biosynthetic proteins MobB moaE moaD, an association often observed with DUF59 domains and one that might make sense in terms of Fe-S clusters (moaD is the sulfur carrier protein).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Beginning with the Bacillus anthracis DUF59 domain with determined structure (3LNO Q81XF6), tBlastn against compete bacterial genomes may turn up instructive operon membership in at least some species. While the gene, often called YitW is adjacent to presumably related entitites yitV and yitU, these are ordinary hydrolases unrelated to iron sulfur complexes. In other Bacillus selenitireducens, it is adjacent to a P-loop NTPase helicase, mildly suggestive of an association. In Halobacillus halophilus, it is adjacent to and transcribed in the same direction as molybotperin biosynthetic proteins MobB moaE moaD, an association often observed with DUF59 domains and one that might make sense in terms of Fe-S clusters (moaD is the sulfur carrier protein).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The Arabidopsis protein HCF101 is a triple fusion of a DUF59 domain, a P-loop ATpase resembling human NUBPL somewhat more than NUBP1 (NBP35) or NUBP2 (CFD1), and a <del style="font-weight: bold; text-decoration: none;">Duf971 </del>domain (a free-standing protein of unknown function in bacteria). The triple fusion did not arise in plants -- it is already found in early diverging eukaryotes (stramenopiles and alveolata). Since both bacteria and archaea (euryarchaeotes and thaumarchaeotes but not crenarchaeotes which have only standalone NUBP1 eg YP_004781840) have the DUF59-NUBPL fusion, the initial double fusion is ancient. Fungi and metazoans have no DUF59-NUBPL fusion proteins though Duf971 is not altogether lost (eg two Fe dioxygenases BBOX1 TMLHE in human). <del style="font-weight: bold; text-decoration: none;">(</del>Frog and hydra have odd fusions accessions, possibly processed pseudogene fusions: XP_002945459, XP_002161498<del style="font-weight: bold; text-decoration: none;">)</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The Arabidopsis protein HCF101 is a triple fusion of a DUF59 domain, a P-loop ATpase resembling human NUBPL somewhat more than NUBP1 (NBP35) or NUBP2 (CFD1), and a <ins style="font-weight: bold; text-decoration: none;">DUF971 </ins>domain (a free-standing protein of unknown function in bacteria). The triple fusion did not arise in plants -- it is already found in early diverging eukaryotes (stramenopiles and alveolata). Since both bacteria and archaea (euryarchaeotes and thaumarchaeotes but not crenarchaeotes which have only standalone NUBP1 eg YP_004781840) have the DUF59-NUBPL fusion, the initial double fusion is ancient. Fungi and metazoans have no DUF59-NUBPL fusion proteins though Duf971 is not altogether lost (eg two Fe dioxygenases BBOX1 TMLHE in human). Frog and hydra have odd fusions accessions, possibly processed pseudogene fusions: XP_002945459, XP_002161498.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as <del style="font-weight: bold; text-decoration: none;">these do not </del>exist according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate CPHC seen in prokaryotes and some early diverging eukaryotes, does not extend to plants. HCF101 <del style="font-weight: bold; text-decoration: none;">itself </del>is <del style="font-weight: bold; text-decoration: none;">completely unsuitable </del>for <del style="font-weight: bold; text-decoration: none;">passing </del>4Fe-4S cluster <del style="font-weight: bold; text-decoration: none;">to apo-proteins and must have some other non-scaffold role </del>in <del style="font-weight: bold; text-decoration: none;">cluster formation</del>.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Despite [http://www.ncbi.nlm.nih.gov/pubmed/19817716 some evidence] to the contrary, the [http://www.ncbi.nlm.nih.gov/pubmed/20522543,14690502,19817716 HCF101 gene family] cannot bind a 4Fe-4S cluster via four conserved cysteines as <ins style="font-weight: bold; text-decoration: none;">none such </ins>exist<ins style="font-weight: bold; text-decoration: none;">, </ins>according to the broader set of orthologs available today. One conserved cysteine is taken up by the DUF59 domain and another by the P-loop itself; the only other candidate CPHC seen in prokaryotes and some early diverging eukaryotes, does not extend to plants.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Crystallographic structures from the euryarchaeote Archaeoglobus fulgidus (3KB1 or 2PH1) can be used as structural template for </ins>HCF101 <ins style="font-weight: bold; text-decoration: none;">(and related sequences, notably human NUBP1). Percent identity at 39% </ins>is <ins style="font-weight: bold; text-decoration: none;">low but adequate </ins>for <ins style="font-weight: bold; text-decoration: none;">some purposes. The seemingly biologically illiterate Structural Genomics Consortium picked family representatives lacking Duf59 and DUF971 domains. No article or commentary accompanies the 2008 submissions. The dimer has a zinc ion at its center held together by deeply conserved pair of CPNC motifs that however are lacking in higher eukaryotes such as plants. This zinc could conceivably be occupied by a </ins>4Fe-4S cluster in <ins style="font-weight: bold; text-decoration: none;">vivo</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The metazoans DUF59 domains FAM96B and FAM96A do not particularly resemble the DUF59 domain found in these fusion proteins (whose consensus sequence matches unfused YitW type best, then SufT). FAM96B occurs separately from DUF59-NUBPL-Duf971 in early eukaryotes and plants. Thus FAM96B did not arise from a breakup of the fusion protein after plant divergence; however NUBPL may have. If so, the gene duplication FAM96A appeared about the same time that free-standing NUBPL first arose and conceivably compensated for loss of the fused DUF59 domain.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Finally the remaining DUF59 domain of interest for annotation transfer is Thermotoga maritima (Q9WYV7 1WCJ) which despite two published [http://www.ncbi.nlm.nih.gov/pubmed/16199668,15213465 articles] provides no gene association clues to its function or target <del style="font-weight: bold; text-decoration: none;">apoproteins</del>. However the [http://string-db.org/ String] association tool provides some interesting suggestions:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Finally the remaining DUF59 domain of interest for annotation transfer is Thermotoga maritima (Q9WYV7 1WCJ) which despite two published [http://www.ncbi.nlm.nih.gov/pubmed/16199668,15213465 articles] provides no gene association clues to its function or target <ins style="font-weight: bold; text-decoration: none;">apo-proteins</ins>. However the [http://string-db.org/ String] association tool provides some interesting suggestions:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59string.png|left]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59string.png|left]]</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l677">Line 677:</td>
<td colspan="2" class="diff-lineno">Line 680:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> TNWSDLDYLIVDLPPGTGDIPLTLAQTIPITGILVVTTPQDVASNVAVKAVSMFEKLNVPIIGVVENMSHFICPNCNEKHYIFGEGGAKKISEQFNMPFL</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> TNWSDLDYLIVDLPPGTGDIPLTLAQTIPITGILVVTTPQDVASNVAVKAVSMFEKLNVPIIGVVENMSHFICPNCNEKHYIFGEGGAKKISEQFNMPFL</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> GEIPLNSGIMAGSDLGKPIMITNPDSPSAVAFRKSAKNIAAQCSILAAKLQDEMAAESSEPTPEPTN</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> GEIPLNSGIMAGSDLGKPIMITNPDSPSAVAFRKSAKNIAAQCSILAAKLQDEMAAESSEPTPEPTN</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> >NBP35_pyrFum Pyrolobus fumarii YP_004781840 no Duf59_NUBPL in crenarchaeotes, most like NUBP1</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> >NBP35_pyrFum Pyrolobus fumarii YP_004781840 no Duf59_NUBPL in crenarchaeotes, most like NUBP1</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> MRVLVVSDALVKQRAEIMKKVIEQQRMIAEKMKKVRYKLVILSGKGGVGKSFVTASLAMALAMKGRRVAVFDADVHGPSIPKMLGVHGKRMYALPDGRLLPVEGPLGVKVVSIDFLLESEEQAVIWRGPLKTAAIRELLA</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> MRVLVVSDALVKQRAEIMKKVIEQQRMIAEKMKKVRYKLVILSGKGGVGKSFVTASLAMALAMKGRRVAVFDADVHGPSIPKMLGVHGKRMYALPDGRLLPVEGPLGVKVVSIDFLLESEEQAVIWRGPLKTAAIRELLA</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> YTDWGELDYLLVDLPPGTGDEQLTIAQLIPGLSGTIIVTIPSDVARIVVKKAITFAKRLNIPIVGVIENMSYFECPDGSRHYIFGKGAGRRIAEEMGVPFLGEIPIDPRISKANDEGKPFFVEYPDSSAAKAFLEIAERVIERVEGKGEGRSESQAKE</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> YTDWGELDYLLVDLPPGTGDEQLTIAQLIPGLSGTIIVTIPSDVARIVVKKAITFAKRLNIPIVGVIENMSYFECPDGSRHYIFGKGAGRRIAEEMGVPFLGEIPIDPRISKANDEGKPFFVEYPDSSAAKAFLEIAERVIERVEGKGEGRSESQAKE</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> >NUBPa_arcFul Archaeoglobus fulgidus NP_071094 3KB1</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> MQKRVTDEDIKERLDKIGFRIAVMSGKGGVGKSTVTALLAVHYAKQGKKVGILDADFLGPSIPHLFGLEKGKVAVSDEGLEPVLTQRLGIKVMSIQFLLP</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> KRETPVIWRGPLIAGMIREFLGRVAWGELDYLLIDLPPGTGDAPLTVMQDAKPNGAVIVSTPQELTAAVVEKAITMAEQTKTAVLGIVENMAYFECPNCG</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> ERTYLFGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWFEFFPY</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> >NUBPb_arcFul Archaeoglobus fulgidus NP_071205 2PH1</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> MQKRVTDEEIKERLGKIKSRIAVMSGKGGVGKSTVTALLAVHYARQGKKVGILDADFLGPSIPILFGLRNARIAVSAEGLEPVLTQKYGIKVMSMQFLLP</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> KENTPVIWRGPLIAGMIREFLGRVAWGELDHLLIDLPPGTGDAPLTVMQDAKPTGVVVVSTPQELTAVIVEKAINMAEETNTSVLGLVENMSYFVCPNCG</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> HKSYIFGEGKGESLAKKYNIGFFTSIPIEEELIKLADSGRIEEYEKDWFESAPF</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== NARFL (IOP1) ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== NARFL (IOP1) ===</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20445&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-26T18:40:50Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<a href="https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20445&oldid=20441">Show changes</a>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20441&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-25T18:04:32Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<a href="https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20441&oldid=20438">Show changes</a>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20438&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-25T12:54:33Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:54, 25 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l109">Line 109:</td>
<td colspan="2" class="diff-lineno">Line 109:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A 3UX2 Q9H5X1 22683786,2261886 Homo sapiens cytosolic 4Fe-4S cluster formation</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A 3UX2 Q9H5X1 22683786,2261886 Homo sapiens cytosolic 4Fe-4S cluster formation</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B '3UX2' Q9Y3D0 22678362,22678361 Homo sapiens from FAM96A utilizing >50% sequence identity</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B '3UX2' Q9Y3D0 22678362,22678361 Homo sapiens from FAM96A utilizing >50% sequence identity</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> DUF59 1WCJ TM0487 16199668,15213465 Thermotogo maritima 216 homologs<del style="font-weight: bold; text-decoration: none;">. </del>1UWD</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> DUF59 1WCJ TM0487 16199668,15213465 Thermotogo maritima 216 homologs 1UWD</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> DUF59 3LNO Q81XF6 -------- Bacillus anthracis article never published</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> DUF59 3LNO Q81XF6 -------- Bacillus anthracis article never published</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> DUF59 3CQ1 Q53W28 -------- Thermus thermophilus <del style="font-weight: bold; text-decoration: none;">assigned to </del>dDTP-4-Keto-L-Rhamnose <del style="font-weight: bold; text-decoration: none;">Reductase </del>TTHB138<del style="font-weight: bold; text-decoration: none;">, aka </del>2CU6</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> DUF59 3CQ1 Q53W28 -------- Thermus thermophilus dDTP-4-Keto-L-Rhamnose <ins style="font-weight: bold; text-decoration: none;">reductase-retlated </ins>TTHB138 2CU6</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> SufT ---- <del style="font-weight: bold; text-decoration: none;">Q0K120 </del>-------- Ralstonia eutropha iron sulfur cluster assembly protein</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> SufT ---- <ins style="font-weight: bold; text-decoration: none;">AM260480 </ins>-------- Ralstonia eutropha iron sulfur cluster assembly protein</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> PaaD '3CQ1' G8RCQ5 16199668 Staphylococcus aureus aromatic ring hydroxylating enzyme Fe-S assembly</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> PaaD '3CQ1' G8RCQ5 16199668 Staphylococcus aureus aromatic ring hydroxylating enzyme Fe-S assembly</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> HCF101 ---- Q6STH5 14690502,19817716 Arabidopsis thaliana chloroplast 4Fe-4S cluster formation</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> HCF101 ---- Q6STH5 14690502,19817716 Arabidopsis thaliana chloroplast 4Fe-4S cluster formation</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l138">Line 138:</td>
<td colspan="2" class="diff-lineno">Line 138:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The PaaD protein contains an N-terminal DUF95 domain, at best 38% identical and 55% similar to FAM96B, sharing the single universally conserved central cysteine and a few but not all additional motifs. Following a non-conserved spacer, a strongly conserved C-terminal region of 41 residues containing 6 invariant cysteines emerges. While not a known domain and not found outside bacteria, it suggests an iron-sulfur carrier functionality. Outside of bacteria, PaaD has weak blast matches to assorted DUF59 domains. Thus since its divergence from a common ancestral protein with FAM96B billions of years ago, PaaD has become restricted and highly adapted to the bacterial aromatic catabolic pathway.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The PaaD protein contains an N-terminal DUF95 domain, at best 38% identical and 55% similar to FAM96B, sharing the single universally conserved central cysteine and a few but not all additional motifs. Following a non-conserved spacer, a strongly conserved C-terminal region of 41 residues containing 6 invariant cysteines emerges. While not a known domain and not found outside bacteria, it suggests an iron-sulfur carrier functionality. Outside of bacteria, PaaD has weak blast matches to assorted DUF59 domains. Thus since its divergence from a common ancestral protein with FAM96B billions of years ago, PaaD has become restricted and highly adapted to the bacterial aromatic catabolic pathway.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The DUF59 domain appears in still other annotational contexts in bacteria, notably YITW<del style="font-weight: bold; text-decoration: none;">, MIP18 </del>and rhamnose reductase-related protein. While partly attributable to unsatisfactory computer annotation and nomenclatural multiplicities, other specific targeting systems may occur in these homologs. Alternatively, the DUF59 domain has duplicated into functionally diverged proteins with a shared fold but no value in annotation transfer to FAM96B<del style="font-weight: bold; text-decoration: none;">. However this would accommodate </del>multiple DUF59 domains within a single prokaryotic genome<del style="font-weight: bold; text-decoration: none;">, so far </del>not observed.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The DUF59 domain appears in still other annotational contexts in bacteria, notably YITW <ins style="font-weight: bold; text-decoration: none;">(N-6 adenine-specific DNA methylase) </ins>and rhamnose reductase-related protein. <ins style="font-weight: bold; text-decoration: none;">A peculiar practise in structural genomics programs -- selecting targets at random, posting structures to PDB, never bothering with an article -- results in orphaned uncharacterized entries, 3LNO Bacillus anthracis and 3CQ1 Thermus thermophilus in the case of DUF59.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While partly attributable to unsatisfactory computer annotation and nomenclatural multiplicities, other specific targeting systems may occur in these homologs. Alternatively, the DUF59 domain has duplicated into functionally diverged proteins with a shared fold but no value in annotation transfer to FAM96B<ins style="font-weight: bold; text-decoration: none;">; to date, </ins>multiple DUF59 domains within a single prokaryotic genome <ins style="font-weight: bold; text-decoration: none;">have </ins>not <ins style="font-weight: bold; text-decoration: none;">been </ins>observed.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>These alternatives may be difficult to resolve because potential Fe-S apo-protein targets associated to DUF59 modification may not be annotated as such, having proven notoriously difficult to detect in the case of DNA helicases, polymerases and primases. The problem arises from loss during aerobic protein purification (perhaps with replacement by Zn) and lack of reliable bioinformatic signature for iron-sulfur clusters, notably an 'insufficient' number of conserved liganding cysteines (due to cooperating dimeric sites or [http://www.ncbi.nlm.nih.gov/pubmed/22687047,12011041, 19290777 glutathione] contributing unsuspected cysteines), a lack of consistent pattern spacing in the cysteines, and ambiguity relative dedicated zinc binding sites.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>These alternatives may be difficult to resolve because potential Fe-S apo-protein targets associated to DUF59 modification may not be annotated as such, having proven notoriously difficult to detect in the case of DNA helicases, polymerases and primases. The problem arises from loss during aerobic protein purification (perhaps with replacement by Zn) and lack of reliable bioinformatic signature for iron-sulfur clusters, notably an 'insufficient' number of conserved liganding cysteines (due to cooperating dimeric sites or [http://www.ncbi.nlm.nih.gov/pubmed/22687047,12011041, 19290777 glutathione] contributing unsuspected cysteines), a lack of consistent pattern spacing in the cysteines, and ambiguity relative dedicated zinc binding sites.</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20436&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-24T18:49:51Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 18:49, 24 June 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_nemVec PSFGASRIDNDVNSQSNRNLALDV<font color=red>YD</font>LIKDI<font color=blue>KD</font>PEKPQTLEDLKVVYESCVEVQKVAGQDHITIT FTPTVPHCSLATL<font color=red>IG</font>LCIRVKLEKSLPEKF<font color=blue>KL</font>DIYLKKGTHSTEN<font color=red>EI</font>NKQINDKERIAAAMENPNLRKIVENCIDEDN</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_nemVec PSFGASRIDNDVNSQSNRNLALDV<font color=red>YD</font>LIKDI<font color=blue>KD</font>PEKPQTLEDLKVVYESCVEVQKVAGQDHITIT FTPTVPHCSLATL<font color=red>IG</font>LCIRVKLEKSLPEKF<font color=blue>KL</font>DIYLKKGTHSTEN<font color=red>EI</font>NKQINDKERIAAAMENPNLRKIVENCIDEDN</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_acrPal MSENKILSTAADSSFDNLVLVQEV<font color=red>FD</font>IVKDI<font color=blue>RD</font>PELPQTLEELHVIEEEFIKIDKIENDEYIIKIEFTPTVPHCSLATL<font color=red>IG</font>LCLRVKLERSLPYKF<font color=blue>KL</font>DIFLSRGTHSTEN<font color=red>EI</font>NKQINDKERIAAAMENPNLKKIVEECILDAN</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_acrPal MSENKILSTAADSSFDNLVLVQEV<font color=red>FD</font>IVKDI<font color=blue>RD</font>PELPQTLEELHVIEEEFIKIDKIENDEYIIKIEFTPTVPHCSLATL<font color=red>IG</font>LCLRVKLERSLPYKF<font color=blue>KL</font>DIFLSRGTHSTEN<font color=red>EI</font>NKQINDKERIAAAMENPNLKKIVEECILDAN</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_triAdh <font color=red>E</font>LIRDI<font color=blue>KD</font>PELPQTLEELNVVTEDEIFVRNMKQGEACIRINFTPTVPHCSLATL<font color=red>IG</font>LCIRVKLQRCLDQDY<font color=blue>KL</font>DIYVTKGSHDTED<font color=red>GV</font>NKQINDKERVAAAIENPNVKKLVEECLQEVQ</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> FAM96A_triAdh <ins style="font-weight: bold; text-decoration: none;"> </ins><font color=red>E</font>LIRDI<font color=blue>KD</font>PELPQTLEELNVVTEDEIFVRNMKQGEACIRINFTPTVPHCSLATL<font color=red>IG</font>LCIRVKLQRCLDQDY<font color=blue>KL</font>DIYVTKGSHDTED<font color=red>GV</font>NKQINDKERVAAAIENPNVKKLVEECLQEVQ</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B_homSap SGERPVTAGEEDEQVPDSIDAREI<font color=red>FD</font>LIRSINDPEHPLTLEELNVVEQVRV<font color=blue>QV</font>SDPESTVAVAFTPTIPHCSMATLIGLSIKVKLLRSLPQRF<font color=blue>KM</font>DVHITPGTHASEH<font color=red>AV</font>NKQLADKERVAAALENTHLLEVVNQCLSARS</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B_homSap SGERPVTAGEEDEQVPDSIDAREI<font color=red>FD</font>LIRSINDPEHPLTLEELNVVEQVRV<font color=blue>QV</font>SDPESTVAVAFTPTIPHCSMATLIGLSIKVKLLRSLPQRF<font color=blue>KM</font>DVHITPGTHASEH<font color=red>AV</font>NKQLADKERVAAALENTHLLEVVNQCLSARS</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l120">Line 120:</td>
<td colspan="2" class="diff-lineno">Line 120:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Phenyl.png|400px|thumb|left|Phenylacetate catabolism: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Phenyl.png|400px|thumb|left|Phenylacetate catabolism: click to enlarge]]</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Image:SufTalign.gif|400px|thumb|left|SufT alignment: click to enlarge]]</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:PaaDalign.gif|400px|thumb|left|PaaD alignment: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:PaaDalign.gif|400px|thumb|left|PaaD alignment: click to enlarge]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59s.gif|400px|thumb|left|DUF59 structural comparison: click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DUF59s.gif|400px|thumb|left|DUF59 structural comparison: click to enlarge]]</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l236">Line 236:</td>
<td colspan="2" class="diff-lineno">Line 237:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B_leiInf DPIDAWEVFEIIRRIRDPEHPNSLEQLKVVEPSLITV---DWKKRHIRVLFTPTVPH<font color = red>C</font>SLTTLIGLSIRLQLERSLPEYTKVDIYVTPGTHEQEAQVNKQLNDKERVAAALEN<font color = red>C</font>NLLNVVES<font color = red>C</font>INEFD</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> FAM96B_leiInf DPIDAWEVFEIIRRIRDPEHPNSLEQLKVVEPSLITV---DWKKRHIRVLFTPTVPH<font color = red>C</font>SLTTLIGLSIRLQLERSLPEYTKVDIYVTPGTHEQEAQVNKQLNDKERVAAALEN<font color = red>C</font>NLLNVVES<font color = red>C</font>INEFD</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Alignment of bacterial SufT proteins:</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> *</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_ralEut -EPDSLEGRVIAALRTVYDPEIPVNIYDLGLIYQLSVDEASGKVGIRMTLTAPG<font color=red>C</font>PVAQTFPGVVESAVMEASGVDAVEVELVWDPPWSRERMSEAARLELGLL Ralstonia eutropha</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_burTer -TTERLEVRVIDALRTVFDPEIPVNIYDLGLVYGLDVDQAEGRVEIRMTLTAPG<font color=red>C</font>PVAQTFPATVEDAVF<font color=red>C</font>V<font color=red>C</font>GVNEVHVELVWDPPWSRERMSDAARLQLGML Burkholderia terrae </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_azoSpp -EGEGLRDEVVAVLRLIYDPEIPVNIYDLGLIYGLDIDEAKGKVDIRMTLTAPA<font color=red>C</font>PVAESLVSSVKEAVASVDGVEDAAVELVWDPPWTQDRMSEAARLDLGLL Azoarcus spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_pseFer -PVSELQQRVIEALRTVYDPEIPVNIYDLGLVYALDVDDAEGKVRIDLTLTAPG<font color=red>C</font>PVAQTFPALVAEAVERVDGVHEAEVELVWEPPWSQDMMSEAARLELGLL Pseudogulbenkiania ferrooxidans </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_polSpp -PVTGLQARVIEALRGVFDPEIPVNIYDLGLVYGLDVDEALGKVHIRLTLTAPG<font color=red>C</font>PVAQTFPEVVGSTVDGVPGVNEVEVELVWQPPWSKGMMSEAARLQLGLL Polaromonas spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_legLon -DSELLKEAIINALRGVYDPEIPVNIYDLGLIYDVSIDD-NAHVLIQMTLTTPG<font color=red>C</font>PVAQTFPGTVEQAVNQVEGVSD<font color=red>C</font>TVELVWEPPWSQERMTEAARLELGIF Legionella longbeachae </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_metSpp -TAEDLKEDVIEMLKTIYDPEIPVNIYELGLIYQIDVSD-SGNVVIQMTLTAPG<font color=red>C</font>PVAQTFPGDVENKIRSIDGVNKVHVELVWDPPWTRDQMSEAAQLQLGMF Methylophaga spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_fluDum -DAELLKEAIVNALREIYDPEIPVNIYDLGLIYDISIDD-ESHVTIQMTLTTPG<font color=red>C</font>PVAQTFPGTVEQAVNKVEGV<font color=red>C</font>D<font color=red>C</font>TVELVWEPPWSQERMTEAARLELGMF Fluoribacter dumoffii </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_ricGry -NEATLKNSIVNTLKHIYDPEIPVNIYDLGLIYHIFIDV-PGHVTIQMTLTTPG<font color=red>C</font>PVAQTFPSMVENAVNAIDGVHETQVELVWDPPWTSAKMSEAAKLQLGML Rickettsiella grylli </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_metMob -SREALLVRVKEMLQTIYDPELPVNIYDLGLVYKLEATE-SGQVSIEMTLTTPN<font color=red>C</font>PVAQTFPDTVREKLL<font color=red>C</font>VPGVSSVGVTLVWDPPWGRDSMSEAAKLQLGML Methylotenera mobilis </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_pedHep -DKEALKQKVID<font color=red>C</font>LQTIYDPEIPVNIYELGLIYETEILPPLNNVQIVMTLTAPG<font color=red>C</font>PAAQSIPLEVEQKVKEIDGINEVTVEVTWDPPWNRDMMSETARLELGMM Pedobacter heparinus </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_allVin MDPEELREPIIASLRGVHDPEIPVNIYDLGLIYRIDIAG-NGDVSVDMTLTAPG<font color=red>C</font>PVAGMMPLMVKSAVERVEGVGQVSVQLVWDPPWSADNMSDEARLQLGLM Allochromatium vinosum </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_marPur VDVEALRESIVTALRGVHDPEIPVNIYDLGLIYTIDIAA-DGTVAVEMTLTAPG<font color=red>C</font>PVAGMMPLMVKQAVARVEGVGEVDVALVWDPPWTQERMSDEARLQLGLM Marichromatium purpuratum </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_nitMob VGGERLREAVVEALQ<font color=red>C</font>VYDPEIPINIYALGLIYELDVND-EGFVDVVMTLTSPS<font color=red>C</font>PVAGQMPGMVKSAVEQVAGVRAAEVELTWDPPWSSDRVSEAGKLQLGLI Nitrococcus mobilis </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_tisMob DDPGDLEAAVIDVLRS<font color=red>C</font>YDPEIPVNIYDLGLIYEVRIDA-GDQAYIRMTLTSPM<font color=red>C</font>PVAESLPVEIETKIRDIAGISDVTVEVVWDPPWTPEMMSEDARLELNMF Tistrella mobilis </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_thiVio MEAEELREPIIAALRGVHDPEIPVNIYDLGLIYSVDIAP-NGDVAIDMTLTAPA<font color=red>C</font>PVAGMMPIMVKDAVSRVDGVGEVRVELVWDPPWGQENMSDEARLQLGLM Thiocystis violascens </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_ignAlb ISKQELEEKIIQALKT<font color=red>C</font>YDPEIPVDIFELGLIYEVAI-DDNNNVKIKMTLTSPM<font color=red>C</font>PAAQSLPLEVEGKVKSIPQVNDVKVEVVWNPPWNKDMMSEVAKLELGFL Ignavibacterium album </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_anaThe KEFLNIESDIVKVLKTVYDPEIPVNIYDLGLIYEIEVRDE-GKVKIVMTLTSPN<font color=red>C</font>PVAESLPEEVYEKVLAVDGVNDVELHLTFDPPWSKDMLSEEAMLELGLL Anaerophaga thermohalophila </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_zymMob PDKEKLKAEIIETLRDIYDPEIPVNIYDLGLIYDIEIGD-DNHVVIKMTLTTPN<font color=red>C</font>PVAGSMPAEIELRVGQIKGVGAVEVELVWDPPWGMDRISDEAKLELGLL Zymomonas mobilis </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_thiDre VDAEALREPIIAALRMVHDPEIPINIYDLGLIYRIDIAG-DGDVKVDMTLTAPA<font color=red>C</font>PVAGMMPLMVRDAVARVEGVGEVQVELVWDPPWNQNNMSDEARLQLGLM Thiorhodococcus drewsii </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_erySpp GAGSDLQQAVIDALKEIYDPEIPVNIYDLGLIYGVEVDD-EADATITMTLTTPH<font color=red>C</font>PVAETMPGEVELRAASVPGIRDAEVELVWDPPWSPEKMSDEARLELGML Erythrobacter spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_rosNub STDHPLYDGVVEA<font color=red>C</font>RTVYDPEIPVNIYDLGLIYTIDIDD-ESAVKIIMTLTAPG<font color=red>C</font>PVAGEMPGWVAEAIEPMAGVKQVDVELTWEPPWGMEMMSDEARLELGFM Roseovarius nubinhibens </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_rosSpp STDHPLYDQLVEA<font color=red>C</font>RTVYDPEIPVNIYDLGLIYTIEIDA-ENAVRVIMTLTAPG<font color=red>C</font>PVAGEMPGWVAEAIEPVAGVKQVDVELVWDPPWGMDMMSDEARLELGFM Roseobacter spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_sphAla AVGGDLYEAVIAALKDIYDPEIPVNIYDLGLIYNVEID--EGHVMVTMTLTTPH<font color=red>C</font>PVAESMPGEVELRVGAVPGVGDAEVNLVWDPPWSPANMSDEARLELGML Sphingopyxis alaskensis </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_braSpp ADKDALVTEIVAALRTVHDPEIPVNIYDLGLIYRIEPKD-DGQVDIDMTLTAPG<font color=red>C</font>PVAGEILTWVETAVRAIDGIAGVEVRLVFDPPWDSSRMSDDVKLELGLL Bradyrhizobium spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_pheZuc AELDRLTDQLIEKLKTVYDPEIPVDIYELGLIYKVDVSD-DKDVAIDMTLTAPG<font color=red>C</font>PVAGEMPGWVEDAVMEIDDIKS<font color=red>C</font>KVELVFDPPWDPSRMSDEAKLQLNMF Phenylobacterium zucineum </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_thiSpp MDAEELREPIIAALRRVHDPEIPVNIYDLGLIYKIDIAS-NGNVDVDMTLTAAA<font color=red>C</font>PVAGMMPLMVKDAVQKVEGVGQVEVELVWDPPWSQDNMSEEALLQLGMM Thiorhodovibrio spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_rhoBac TTDHPLYENVVEA<font color=red>C</font>RSVYDPEIPVNIYDLGLIYTIEIDA-ESDVAIKMSLTAPG<font color=red>C</font>PVAGEMPGWVAEAVEPLPGVKTVAVELVWEPPWGMEMMSDEARLELGFM Rhodobacterales bacterium </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_salRub TPDDDLYQRVVESLREIYDPEIPVNIYDLGLIYHLDVGE-DSHVDVLMTLTAPN<font color=red>C</font>PAAGVLPGQAEDAVRETEGVESVNLEMTFEPPFSPQMMSEEARLELGFM Salinibacter ruber </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_azoAma DGDPALMAAVFEALRTVRDPEIPVNLVDLGLIYRVRVHR-DGLVHIDMTLTTPA<font color=red>C</font>PVATTLPGQVQNLVSLVPGVSVVLVDMVWDPPWTRDRMTESARLELGLV Azospirillum amazonense </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_cycMar DDQEALKGKVINAIKDVYDPEIPVDVYELGLIYEITVYPV-NNVYILMTLTSPN<font color=red>C</font>PAAESIPSEVKESVGNIEGVNNVEVELTFDPPYSQDMMSEVAKLELGFL Cyclobacterium marinum </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_rhoMar LGDKELEQAIIEALKSVYDPEIPVNIYDLGLIYEIRIFE-DRTVYVKMTLTAPG<font color=red>C</font>PVAGTLPGQVEMRLQEVPGVKDARVELTFDPPYTIERMSDEARLALGWM Rhodothermus marinus </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_niaSol MEPDTIEEKVIKELQTVFDPELPVNIYELGLIYKVEVLND-NYVKILMTLTAPS<font color=red>C</font>PAAQSLPVEVDQKIRAIEGVSDVDVTITWDPAWNKSMMSEAAQLELGFL Niabella soli </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_xanAut EDEAALMEAIIAGLRTVTDPEIPVNIYDLGLIYRIELKD-DGVVEIDMTLTAPG<font color=red>C</font>PVAGQMLGWVQQAVGVVEGVSDVKMKLVFDPPWDKSRMSDEVQLELGLI Xanthobacter autotrophicus </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_cauCre DELNRLTDQLIEKLKTVYDPEIPVDIYELGLIYKVDVSD-SKDVAIDMTLTAPG<font color=red>C</font>PVAGEMPGWVKDAVMEIPGLKS<font color=red>C</font>TVELTFDPPWDASRMSDEAKLQLNMF Caulobacter crescentus </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_cytHut IDQAELKNKALEAIQTVYDPEIPVNIFELGLIYEVSVFPV-NNIFVQMTLTSPN<font color=red>C</font>PAAQSMPAEVENKIKAIEGVNEVTVEITFDPTWSQEMMSDAAKLELGFM Cytophaga hutchinsonii </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_ruePom SVDHDLYEPVVEA<font color=red>C</font>RTVYDPEIPVNIFELGLIYTVEISD-ENEVRVIMTLTAPG<font color=red>C</font>PVAGEMPGWVAAAVESVPGVKSVEVEMTWDPPWGMEMMSDEARLELGFM Ruegeria pomeroyi </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_jooMar IDTTALGEKIVTVLKTIYDPEIPVDIYELGLIYDVFVNED-SEVKILMTLTTPN<font color=red>C</font>PVAETLPVEVEEKIKTIDDVKDAEVEITFDPPWSQDLMSEEAKLELGLL Joostella marina </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_flaBac SKDVALGEQIVGVIKTIYDPEIPVDIYELGLIYDVLVNED-NEVKILMTLTSPN<font color=red>C</font>PVAETLPVEVEEKVKSIDAVKDAEVEITFDPPWTQELMSEAAKLELGML Flavobacteria bacterium </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_citSpp STGHPLHEALVEA<font color=red>C</font>RTVYDPEIPVNIYDLGLIYTIAIDD-ENAVKVIMTLTAPG<font color=red>C</font>PVAGEMPGWVQEATSTVPGVRDVDVEMVFDPPWGMDMMSDEARLELGFM Citreicella spp. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_celAlg IDTAELGEKIVGVLKTIYDPEIPVDIYELGLIYDVFVNED-NEVKILMTLTSPN<font color=red>C</font>PVAESLPAEVEEKVKSLDAVKDAEVEITFDPPWTQELMSEEAKLELGML Cellulophaga algicola </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_gluMor EGTVPDQDAIIASIATVYDPEIPVNIYELGLIYAIDLHD-DGRVKIEMTLTAPN<font color=red>C</font>PSAQELPEMVKDAVSHVPHVKNVEVEIVWDPPWDMSRMSDDARLALNMF Gluconobacter morbifer </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_dyaFer MSEEDLKEEVIRAIKTVYDPEIPVDVYELGLIYDLKVFPI-NNVFVSMTLTSPS<font color=red>C</font>PSAGTLPGEVEQKIREVEGVNDVSVELTFDPPYSTEMMSEEAKLELGFM Dyadobacter fermentans </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Consensus L !! al t!yDPEIPV#I%#LGL!Y V ! MTLTaP <font color=red>C</font>PvA P V v ! g! v Velvw#PPw MS# ArL#Lg </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Prim.cons. sDDEALKEAVIEALRTVYDPEIPVNIYDLGLIYEIDIDDDEGhVKIDMTLTAPG<font color=red>C</font>PVAGTMPGEVEEAVESVeGVKDVEVELVWDPPWSQDMMSEEARLELGML </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> FAM96_conSeq LIRSINDPEHPLTLEELNVVEESCVEVQEIDDDESLVIVRFTPTIPH<font color=red>C</font>SMATLIGLCIRVKLLRSLPFRFKVDIYITPGTHSSEEAVNKQLNDKER 88 sequences</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> SufT_conSeq ALRTVYDPEIPV-----NIYDLGLIYEIDIDDDEGHVKIDMTLTAPG<font color=red>C</font>PVAGTMPGEVEEAVESVEGVK-DVEVELVWDPPWSQDMMSEEARLELG 42 sequences</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> PaaD_conSeq LLSQVPDPEVPV----LSITDLGMVRDVEWEGD-GWVVVTFTPTYSG<font color=red>C</font>PATELILGDIRQALTEA-GFT-PVHVEVQLSPAWTTDWMSEEGREKLR 21 sequences</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Consensus llr ! DPE Pv ln! #lg ! #i#dDeg V ! fTpT pg<font color=red>C</font>p a li g !r al gf V !e p ws # mse# r klr </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> Alignment of bacterial PaaD proteins:</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> <-----------------------------------------DUF59---------------------------------------------> <--------- unknown 6-Cys domain -------></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> <-----------------------------------------DUF59---------------------------------------------> <--------- unknown 6-Cys domain -------></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> * - * * * * * * conserved cysteines</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> * - * * * * * * conserved cysteines</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20434&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-24T16:55:12Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<a href="https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20434&oldid=20432">Show changes</a>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20432&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-24T03:53:20Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:53, 24 June 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l120">Line 120:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><br clear=all></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Phenyl.png|left]][[Image:DUF59s.gif|430px|thumb|left|Click to enlarge]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Phenyl.png|left]][[Image:DUF59s.gif|430px|thumb|left|Click to enlarge]]</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Another important clue to FAM98B/SufT function may come from additional insights into the steps of the phenylacetic acid degradation pathway<del style="font-weight: bold; text-decoration: none;">] </del>-- an esoteric topic but [http://www.ncbi.nlm.nih.gov/pubmed/22398448,21296885,20660314,12846838,9748275,17259607,9600981,19208251 exceedingly well-studied]. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Another important clue to FAM98B/SufT function may come from additional insights into the steps of the phenylacetic acid degradation pathway -- an esoteric topic but [http://www.ncbi.nlm.nih.gov/pubmed/22398448,21296885,20660314,12846838,9748275,17259607,9600981,19208251 exceedingly well-studied]. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>An epic annotation error has propagated to thousands of GenBank and UniProt entries: the DUF59 domain of the phenylacetate catabolic pathway lies in PaaD, not PaaJ (which has only thiolase domains). Some entries state -- nonsensically -- that the PaaD protein is the product of the PaaJ gene; overall 85% of PaaD homologs are incorrectly named PaaJ (<del style="font-weight: bold; text-decoration: none;">with the </del>E.coli [http://www.uniprot.org/uniprot/P76080 accession P76080 <del style="font-weight: bold; text-decoration: none;">for </del>ydbQ] as correct starting point for PaaD): </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>An epic annotation error has propagated to thousands of GenBank and UniProt entries: the DUF59 domain of the phenylacetate catabolic pathway lies in PaaD, not PaaJ (which has only thiolase domains). Some entries state -- nonsensically -- that the PaaD protein is the product of the PaaJ gene; overall 85% of PaaD homologs are incorrectly named PaaJ (<ins style="font-weight: bold; text-decoration: none;">utilizing </ins>E.coli [http://www.uniprot.org/uniprot/P76080 accession P76080 <ins style="font-weight: bold; text-decoration: none;">or </ins>ydbQ] as correct starting point for PaaD): </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> >PaaD_escCol Escherichia coli <font color=red>8 conserved cysteines</font> P76080 PaaJ ydbQ DUF59 unacceptable synonym: PaaJ </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> >PaaD_escCol Escherichia coli <font color=red>8 conserved cysteines</font> P76080 PaaJ ydbQ DUF59 unacceptable synonym: PaaJ </div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l128">Line 128:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> VLQLDPAWTTDWMTPDARERLREYGISPPAGHS<font color=red>C</font>HAHLPPEVR<font color=red>C</font>PR<font color=red>C</font>ASVHTTLISEFGSTA<font color=red>C</font>KALYR<font color=red>C</font>DS<font color=red>C</font>REPFDYFK<font color=red>C</font>I*</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> VLQLDPAWTTDWMTPDARERLREYGISPPAGHS<font color=red>C</font>HAHLPPEVR<font color=red>C</font>PR<font color=red>C</font>ASVHTTLISEFGSTA<font color=red>C</font>KALYR<font color=red>C</font>DS<font color=red>C</font>REPFDYFK<font color=red>C</font>I*</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The initial aromatic ring oxygenation (using O2) utilizes a multisubunit complex requiring PaaA, PaaB, PaaC<del style="font-weight: bold; text-decoration: none;">, </del>and PaaE for in vitro reconstitution of catalytic activity. PaaD has no place in the complex but an [http://www.ncbi.nlm.nih.gov/pubmed/16997993 essential role in vivo] as established by mutation and supported by position within the Paa operon in many species.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The initial aromatic ring oxygenation (using O2) utilizes a multisubunit complex requiring PaaA, PaaB, PaaC and PaaE for in vitro reconstitution of catalytic activity. PaaD has no place in the complex but an [http://www.ncbi.nlm.nih.gov/pubmed/16997993 essential role in vivo] as established by mutation and supported by position within the Paa operon in many species.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Together, this suggests the DUF59 domain of PaaD establishes and/or repairs the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060524<del style="font-weight: bold; text-decoration: none;">/?tool=pubmed </del>2Fe-2S cluster of PaaE reductase] (which might be especially vulnerable to reactive oxygen species in the oligomer). Such a role for PaaD would not be a great departure from what its <del style="font-weight: bold; text-decoration: none;">homolog does </del>in eukaryotes. Note PaaA itself has a di-iron center though its regulatory paralog PaaC does not. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Together, this suggests the DUF59 domain of PaaD establishes and/or repairs the [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060524 2Fe-2S cluster of PaaE reductase] (which might be especially vulnerable to reactive oxygen species in the oligomer). Such a role for PaaD would not be a great departure from what its <ins style="font-weight: bold; text-decoration: none;">homologs FAM96A and FAM96B seem to do </ins>in eukaryotes. Note PaaA itself has a <ins style="font-weight: bold; text-decoration: none;">possibly relevant </ins>di-iron center though its regulatory paralog PaaC does not. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The DUF59 domain appears in multiple contexts in bacteria -- SufT, PaaD, YITW, MIP18 and rhamnose reductase-related protein. Some of this is attributable to poor quality computer annotation and nomenclatural confusion across species, but DUF59 does reside in at least two distinct operons, the iron sulfur cluster system Suf and the phenylacetic acid catabolism pathway Paa, the difference being that the DUF59 acts on a broader class of iron-sulfur <del style="font-weight: bold; text-decoration: none;">apoproteins </del>in bacterial species with a SufT-containing operon.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The DUF59 domain appears in multiple contexts in bacteria -- SufT, PaaD, YITW, MIP18 and rhamnose reductase-related protein. Some of this is attributable to poor quality computer annotation and nomenclatural confusion across species, but DUF59 does reside in at least two distinct operons, the iron sulfur cluster system Suf and the phenylacetic acid catabolism pathway Paa, the difference being that the DUF59 acts on a broader class of iron-sulfur <ins style="font-weight: bold; text-decoration: none;">apo-proteins </ins>in bacterial species with a SufT-containing operon.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The question here is whether all remaining DUF59 homologs assist in iron sulfur complex assembly, either specialized to a one <del style="font-weight: bold; text-decoration: none;">apoenzyme </del>or as part of a general system maturating numerous unrelated apoenzymes (like eukaryotic FAM96B). Alternatively -- consistent with poor percentage identity -- the DUF59 domain duplicated and diverged into dimly related functions with little in common apart from a shared fold. However this would allow multiple DUF59 domains within a single prokaryotic genome, so far not observed.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The question here is whether all remaining DUF59 homologs assist in iron sulfur complex assembly, either specialized to a one <ins style="font-weight: bold; text-decoration: none;">apo-enzyme </ins>or as part of a general system maturating numerous unrelated apoenzymes (like eukaryotic FAM96B). Alternatively -- consistent with poor percentage identity -- the DUF59 domain duplicated and diverged into dimly related functions with little in common apart from a shared fold. However this would allow multiple DUF59 domains within a single prokaryotic genome, so far not observed.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The first alternative implies that each enzyme closely associated to a DUF59 contains a Fe-S cluster. However these have proven notoriously difficult to detect in the case of DNA helicases, polymerases and primases. The problem arises from loss during aerobic protein purification (perhaps with replacement by Zn) and lack of reliable bioinformatic signature for iron-sulfur clusters, notably an 'insufficient' number of conserved liganding cysteines (due to composite dimeric sites or glutathione contributing unsuspected cysteines), a lack of consistent pattern spacing in the cysteines, and ambiguity relative dedicated zinc binding sites.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The first alternative implies that each enzyme closely associated to a DUF59 contains a Fe-S cluster. However these have proven notoriously difficult to detect in the case of DNA helicases, polymerases and primases. The problem arises from loss during aerobic protein purification (perhaps with replacement by Zn) and lack of reliable bioinformatic signature for iron-sulfur clusters, notably an 'insufficient' number of conserved liganding cysteines (due to composite dimeric sites or glutathione contributing unsuspected cysteines), a lack of consistent pattern spacing in the cysteines, and ambiguity relative dedicated zinc binding sites.</div></td></tr>
</table>
Tomemerald
https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20431&oldid=prev
Tomemerald: /* FAM98B is homologous to bacterial SufT */
2012-06-24T03:46:55Z
<p><span dir="auto"><span class="autocomment">FAM98B is homologous to bacterial SufT</span></span></p>
<a href="https://genomewiki.ucsc.edu/index.php?title=Iron_sulfur_clusters&diff=20431&oldid=20429">Show changes</a>
Tomemerald