http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&feed=atom&action=historyATP binding domain 4 Evolution - Revision history2024-03-28T21:31:49ZRevision history for this page on the wikiMediaWiki 1.39.6http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=14283&oldid=prevNabilahAhmadKamal2: /* Discussion */2009-06-14T09:01:14Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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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" 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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which <del style="font-weight: bold; text-decoration: none;">indicates </del>the sequence similarity between bacteria species and ''Pyrococcus furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which <ins style="font-weight: bold; text-decoration: none;">indicate </ins>the sequence similarity between bacteria species and ''Pyrococcus furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. It was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. It was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=14201&oldid=prevNabilahAhmadKamal2: /* Discussion */2009-06-13T05:18:47Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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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>'''Multiple sequence alignment'''</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>'''Multiple sequence alignment'''</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>From the multiple sequence alignment, there are seven conserved regions found in all species from Domain Eukarya and Archaea (based on BlastP search) but only five conserved residues which are significant to the function and structure of the protein since these residues are identified to be conserved amino acid sequence motif for P-loop of nucleotide binding domains which might be important in phosphate binding (Bork and Koonin<del style="font-weight: bold; text-decoration: none;">. </del>1994). These conserved residues are Serine-12, Glysine-13 and Glysine-14, Lysine-15 and Aspartic acid-16 . Since this motif presence in uncharacterized ATP pyrophosphatase domain, the motif is called PP motif and can be written as S-G(2)-K-D-[GS]. PP-loop motif is a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding (Bork and Koonin,1994). However, based on the multiple sequence alignment, the amino acids for PP-loop that are conserved across all species in Eukarya and Archaea are Glysine-12 and Glysine-14. Substitution of Serine with Threonine in ''Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Thermoproteus neutrophilis, Pyrobaculum islandicum'' and ''Staphlothermus marinus'', are conserved since both amino acids are polar uncharged amino acid, suggesting that this residue is also important. However, this residue is not conserved in ATP Binding Domain 4 in ''Homo sapiens'' which is only encoded by 259 amino acid sequences and the sequence started from Glysine-13. Moreover, amino acid in residue 17 is also one of the important residues in PP motif. This residue is conserved across all species except for ''Theileria parva'' and ''Theileria annulata'' where Serine is substituted with Glysine. </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>From the multiple sequence alignment, there are seven conserved regions found in all species from Domain Eukarya and Archaea (based on BlastP search) but only five conserved residues which are significant to the function and structure of the protein since these residues are identified to be conserved amino acid sequence motif for P-loop of nucleotide binding domains which might be important in phosphate binding (Bork and Koonin<ins style="font-weight: bold; text-decoration: none;">, </ins>1994). These conserved residues are Serine-12, Glysine-13 and Glysine-14, Lysine-15 and Aspartic acid-16 . Since this motif presence in uncharacterized ATP pyrophosphatase domain, the motif is called PP motif and can be written as S-G(2)-K-D-[GS]. PP-loop motif is a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding (Bork and Koonin,1994). However, based on the multiple sequence alignment, the amino acids for PP-loop that are conserved across all species in Eukarya and Archaea are Glysine-12 and Glysine-14. Substitution of Serine with Threonine in ''Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Thermoproteus neutrophilis, Pyrobaculum islandicum'' and ''Staphlothermus marinus'', are conserved since both amino acids are polar uncharged amino acid, suggesting that this residue is also important. However, this residue is not conserved in ATP Binding Domain 4 in ''Homo sapiens'' which is only encoded by 259 amino acid sequences and the sequence started from Glysine-13. Moreover, amino acid in residue 17 is also one of the important residues in PP motif. This residue is conserved across all species except for ''Theileria parva'' and ''Theileria annulata'' where Serine is substituted with Glysine. </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>BlastP search revealed the very low E value from many sequences from different species. These sequences appear to be encoding different group of proteins such as ATP pyrophosphatase, ATP-binding protein, ATPase and endoribonuclease. Although these proteins are responsible for different functions, the similarities of sequence between the proteins across species are very high (as indicated by E value) and the sequences which are conserved are a part of PP motif, suggesting that these proteins descend from a common ancestral sequence and therefore are paralogs. Such phenomenon could be as the result of duplication of genes within a genome.</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>BlastP search revealed the very low E value from many sequences from different species. These sequences appear to be encoding different group of proteins such as ATP pyrophosphatase, ATP-binding protein, ATPase and endoribonuclease. Although these proteins are responsible for different functions, the similarities of sequence between the proteins across species are very high (as indicated by E value) and the sequences which are conserved are a part of PP motif, suggesting that these proteins descend from a common ancestral sequence and therefore are paralogs. Such phenomenon could be as the result of duplication of genes within a genome.</div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=14200&oldid=prevNabilahAhmadKamal2: /* Results */2009-06-13T05:08:53Z<p><span dir="auto"><span class="autocomment">Results</span></span></p>
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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:Blastp search-1ru8.png |left|thumb|1200px|'''Figure 1.0'''. The result of BlastP search which used N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' as query sequence (1RU8A)]] </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:Blastp search-1ru8.png |left|thumb|1200px|'''Figure 1.0'''. The result of BlastP search which used N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' as query sequence (1RU8A)]] </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>[[Image:Blastp-Macaca mulatta.png |left|thumb|1200px|'''Figure 1.1'''. The result of BlastP search which used protein sequence that is predicted to be similar <del style="font-weight: bold; text-decoration: none;">ro </del>ATP binding domain 4 from ''Macaca mulatta'']] <BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR></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>[[Image:Blastp-Macaca mulatta.png |left|thumb|1200px|'''Figure 1.1'''. The result of BlastP search which used protein sequence that is predicted to be similar <ins style="font-weight: bold; text-decoration: none;">to </ins>ATP binding domain 4 from ''Macaca mulatta'']] <BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR></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>'''[[Multiple sequence alignment-ClustalX]]'''</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>'''[[Multiple sequence alignment-ClustalX]]'''</div></td></tr>
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</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13563&oldid=prevNabilahAhmadKamal2: /* Discussion */2009-06-09T08:08:39Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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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" 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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which indicates the sequence similarity between bacteria species and ''<del style="font-weight: bold; text-decoration: none;">Pyroccoccuus </del>furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which indicates the sequence similarity between bacteria species and ''<ins style="font-weight: bold; text-decoration: none;">Pyrococcus </ins>furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. It was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. It was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13560&oldid=prevNabilahAhmadKamal2: /* Discussion */2009-06-09T08:05:20Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<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 08:05, 9 June 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l67">Line 67:</td>
<td colspan="2" class="diff-lineno">Line 67:</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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which indicates the sequence similarity between bacteria species and ''Pyroccoccuus furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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 phylogenetic tree and bootstrap revealed that PP-loop motif from ATP binding domain 4 (belongs to N-type ATP pyrophosphatase/ATPases) and other related proteins are found in species of Archaea and Eukarya suggesting that this motif is highly conserved throughout evolution. However, Bacteria found to be lacking of this conserved sequences since none of the species belongs to Domain Bacteria. Nevertheless, based on STRING: functional protein association networks, some bacteria species still have protein sequences which belong to N-type ATP pyrophosphatase superfamily. BlastP was conducted to compare the protein sequences of ATPases from ''Pyrococcus furiosus'' and the bacteria species which under the clan of N-type ATP pyrophosphatase. The E value obtained from the result are below the E-value that is used as the cut-off-score. The bacteria species are ''Fusobacteruim nucleatum'' (1e-22), ''Caldicellulosiruptor saccharolyticus'' (1e-13),''Campylobacter jejuni'' (4e-19),''Chromobacterium violaceum'' (1e-21)and ''Polynucleobacter sp.'' (1e-24). These E value fall below the lowest E value based on BlastP from ''Pyrococcus furiosus'' and ''Macacca mulatta'' i.e: 5e-50 and 2e-25 respectively. These bacteria species can not be found in BlastP on the first place because the E value are quite high which indicates the sequence similarity between bacteria species and ''Pyroccoccuus furiosus'' and ''Macaca mulatta'' are very low. These suggested that although some bacteria species still have protein sequences which belong to N-type ATP pyrophosphtase superfamily, they are distantly related to both archaea and eukarya. Based on the high protein sequence similarity between Archaea and Eukarya, it can be suggested that Archaea and Eukarya are closely related compared to that for Bacteria.</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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. <del style="font-weight: bold; text-decoration: none;">From figure5, it </del>was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </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>Based on unrooted tree, the relatedness of the taxa and their relationship can be illustrated but the last common ancestor and how the species evolved cannot be observed. <ins style="font-weight: bold; text-decoration: none;">It </ins>was found that the taxa are clearly grouped into Domain Archaea and Eukarya. Moreover, in Eukarya, the taxa are nicely clustered according to parasites, vertebrates and invertebrates. Domain Bacteria is missing in this tree suggesting that Bacteria are distantly related to Archaea and Eukarya based on the sequence of ATP Binding Domain 4. </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>Phylogram (figure 3.0) is another way to illustrate the evolution of the taxa where the relationships between the taxa and the time or rate of evolution can be observed. </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>Phylogram (figure 3.0) is another way to illustrate the evolution of the taxa where the relationships between the taxa and the time or rate of evolution can be 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" 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>Bootstrap was conducted to test the reliability of the branching order of the phylogenetic tree. Based on the bootstrap value, we can be confident with the order of the phylogenetic tree thus allowing us to determine where speciation events occur. Bootstrap worked by performing 'pseudoreplicates' of multiple sequence alignments and in this project, 100 replicates was performed. The bootstrap tree can then be generated thus comparing the branching orders and distances of <del style="font-weight: bold; text-decoration: none;">phylogeny </del>tree. The bootstrap value for each branch are obtained in percentage which indicate the confidence of the branch being correct. If the value of bootstrap is less than 75%, the branching order is not very reliable and meaningless. If the value is between 90% and above, we can be confident that the branching orders are correct. Based on the bootstrap result, it was found that most of the value are lower than 75% suggesting that the branching patterns and distances are not reliable. Therefore, another phylogenetic tree need to be built in order to increase the reliability of the branching pattern and distances of the tree. </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>Bootstrap was conducted to test the reliability of the branching order of the phylogenetic tree. Based on the bootstrap value, we can be confident with the order of the phylogenetic tree thus allowing us to determine where speciation events occur. Bootstrap worked by performing 'pseudoreplicates' of multiple sequence alignments and in this project, 100 replicates was performed. The bootstrap tree can then be generated thus comparing the branching orders and distances of <ins style="font-weight: bold; text-decoration: none;">phylogenetic </ins>tree. The bootstrap value for each branch are obtained in percentage which indicate the confidence of the branch being correct. If the value of bootstrap is less than 75%, the branching order is not very reliable and meaningless. If the value is between 90% and above, we can be confident that the branching orders are correct. Based on the bootstrap result, it was found that most of the value are lower than 75% suggesting that the branching patterns and distances are not reliable. Therefore, another phylogenetic tree need to be built in order to increase the reliability of the branching pattern and distances of the tree. </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>Based on unrooted tree, it was found members of Domain Eukarya are nicely cluster at one side without any presence of other species from different domain i.e: members from different domains are well-seperated. Therefore, it can be suggested that the evolutionary model for the PP-loop motif is hold since there is no evidence of the occurrence of lateral gene transfer.</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>Based on unrooted tree, it was found members of Domain Eukarya are nicely cluster at one side without any presence of other species from different domain i.e: members from different domains are well-seperated. Therefore, it can be suggested that the evolutionary model for the PP-loop motif is hold since there is no evidence of the occurrence of lateral gene transfer.</div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13557&oldid=prevNabilahAhmadKamal2: /* Discussion */2009-06-09T08:03:15Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<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 08:03, 9 June 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l57">Line 57:</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>'''Multiple sequence alignment'''</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>'''Multiple sequence alignment'''</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>From the multiple sequence alignment, there are seven conserved regions found in all species from Domain Eukarya and Archaea (based on BlastP search) but only five conserved residues which are significant to the function and structure of the protein since these residues are identified to be conserved amino acid sequence motif for P-loop of nucleotide binding domains which might be important in phosphate binding (Bork and Koonin. 1994). These conserved residues are Serine-12, Glysine-13 and Glysine-14, Lysine-15 and Aspartic acid-16 . Since this motif presence in uncharacterized ATP pyrophosphatase domain, the motif is called PP motif and can be written as S-G(2)-K-D-[GS]. PP-loop motif is a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding (Bork and Koonin,1994). However, based on the multiple sequence alignment, the amino acids for PP-loop that are conserved across all species in Eukarya and Archaea are Glysine-12 and Glysine-14. Substitution of Serine with Threonine in ''Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Thermoproteus neutrophilis, Pyrobaculum islandicum'' and ''Staphlothermus marinus'', are conserved since both amino acids are polar uncharged amino acid, suggesting that this residue is also important. However, this residue is not conserved in <del style="font-weight: bold; text-decoration: none;">ATPBD4 </del>in ''Homo sapiens'' which is only encoded by 259 amino acid sequences and the sequence started from Glysine-13. Moreover, amino acid in residue 17 is also one of the important residues in PP motif. This residue is conserved across all species except for ''Theileria parva'' and ''Theileria annulata'' where Serine is substituted with Glysine. </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>From the multiple sequence alignment, there are seven conserved regions found in all species from Domain Eukarya and Archaea (based on BlastP search) but only five conserved residues which are significant to the function and structure of the protein since these residues are identified to be conserved amino acid sequence motif for P-loop of nucleotide binding domains which might be important in phosphate binding (Bork and Koonin. 1994). These conserved residues are Serine-12, Glysine-13 and Glysine-14, Lysine-15 and Aspartic acid-16 . Since this motif presence in uncharacterized ATP pyrophosphatase domain, the motif is called PP motif and can be written as S-G(2)-K-D-[GS]. PP-loop motif is a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding (Bork and Koonin,1994). However, based on the multiple sequence alignment, the amino acids for PP-loop that are conserved across all species in Eukarya and Archaea are Glysine-12 and Glysine-14. Substitution of Serine with Threonine in ''Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Thermoproteus neutrophilis, Pyrobaculum islandicum'' and ''Staphlothermus marinus'', are conserved since both amino acids are polar uncharged amino acid, suggesting that this residue is also important. However, this residue is not conserved in <ins style="font-weight: bold; text-decoration: none;">ATP Binding Domain 4 </ins>in ''Homo sapiens'' which is only encoded by 259 amino acid sequences and the sequence started from Glysine-13. Moreover, amino acid in residue 17 is also one of the important residues in PP motif. This residue is conserved across all species except for ''Theileria parva'' and ''Theileria annulata'' where Serine is substituted with Glysine. </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>BlastP search revealed the very low E value from many sequences from different species. These sequences appear to be encoding different group of proteins such as ATP pyrophosphatase, ATP-binding protein, ATPase and endoribonuclease. Although these proteins are responsible for different functions, the similarities of sequence between the proteins across species are very high (as indicated by E value) and the sequences which are conserved are a part of PP motif, suggesting that these proteins descend from a common ancestral sequence and therefore are paralogs. Such phenomenon could be as the result of duplication of genes within a genome.</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>BlastP search revealed the very low E value from many sequences from different species. These sequences appear to be encoding different group of proteins such as ATP pyrophosphatase, ATP-binding protein, ATPase and endoribonuclease. Although these proteins are responsible for different functions, the similarities of sequence between the proteins across species are very high (as indicated by E value) and the sequences which are conserved are a part of PP motif, suggesting that these proteins descend from a common ancestral sequence and therefore are paralogs. Such phenomenon could be as the result of duplication of genes within a genome.</div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13555&oldid=prevNabilahAhmadKamal2: /* Results */2009-06-09T08:00:40Z<p><span dir="auto"><span class="autocomment">Results</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<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 08:00, 9 June 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l27">Line 27:</td>
<td colspan="2" class="diff-lineno">Line 27:</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>'''[[Multiple sequence alignment-ClustalX]]'''</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>'''[[Multiple sequence alignment-ClustalX]]'''</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>[[Image:Clustalx taken from residue 98-350.png |left|thumb|1200px|'''Figure 2.0'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed <del style="font-weight: bold; text-decoration: none;">three </del>important residue which are conserved across species in archaea and eukarya.]] </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>[[Image:Clustalx taken from residue 98-350.png |left|thumb|1200px|'''Figure 2.0'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed <ins style="font-weight: bold; text-decoration: none;">five </ins>important residue which are conserved across species in archaea and eukarya.]] </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;"><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>[[Image:Clustalx taken from residue 98-350 Part2.png |left|thumb|1200px|'''Figure 2.1'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed <del style="font-weight: bold; text-decoration: none;">three </del>important residue which are conserved across species in archaea and eukarya. gi:40889720 denotes N-type ATP pyrophosphatase in ''Pyrococcus furiosus.'' ]]</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>[[Image:Clustalx taken from residue 98-350 Part2.png |left|thumb|1200px|'''Figure 2.1'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed <ins style="font-weight: bold; text-decoration: none;">five </ins>important residue which are conserved across species in archaea and eukarya. gi:40889720 denotes N-type ATP pyrophosphatase in ''Pyrococcus furiosus.'' ]]</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>'''[[Phylogenetic tree]]'''</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>'''[[Phylogenetic tree]]'''</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l51">Line 51:</td>
<td colspan="2" class="diff-lineno">Line 51:</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:String_ATP_pyrophosphatase.png |left|thumb|1200px|'''Figure 5.0''': Result from STRING database illustrates that some Bacteria species still have protein which belong to N-type ATP pyrophosphatase superfamily.]]</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:String_ATP_pyrophosphatase.png |left|thumb|1200px|'''Figure 5.0''': Result from STRING database illustrates that some Bacteria species still have protein which belong to N-type ATP pyrophosphatase superfamily.]]</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><del style="font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2" class="diff-side-added"></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>== Discussion ==</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>== Discussion ==</div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13554&oldid=prevNabilahAhmadKamal2 at 07:59, 9 June 20092009-06-09T07:59:49Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<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 07:59, 9 June 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l32">Line 32:</td>
<td colspan="2" class="diff-lineno">Line 32:</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:Clustalx taken from residue 98-350 Part2.png |left|thumb|1200px|'''Figure 2.1'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed three important residue which are conserved across species in archaea and eukarya. gi:40889720 denotes N-type ATP pyrophosphatase in ''Pyrococcus furiosus.'' ]]</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:Clustalx taken from residue 98-350 Part2.png |left|thumb|1200px|'''Figure 2.1'''. Multiple sequence alignment obtained from ClustalX. Section of msa revealed three important residue which are conserved across species in archaea and eukarya. gi:40889720 denotes N-type ATP pyrophosphatase in ''Pyrococcus furiosus.'' ]]</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;">Phylogeny </del>tree]]'''</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;">Phylogenetic </ins>tree]]'''</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;"><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-lineno" id="mw-diff-left-l50">Line 50:</td>
<td colspan="2" class="diff-lineno">Line 50:</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>'''[[STRING]]'''</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>'''[[STRING]]'''</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>[[Image:String_ATP_pyrophosphatase.png |left|thumb|1200px|'''Figure 5.0''': Result from STRING database illustrates that some Bacteria species still have protein which belong to N-type ATP pyrophosphatase superfamily.]]<del style="font-weight: bold; text-decoration: none;"><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR></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>[[Image:String_ATP_pyrophosphatase.png |left|thumb|1200px|'''Figure 5.0''': Result from STRING database illustrates that some Bacteria species still have protein which belong to N-type ATP pyrophosphatase superfamily.]]</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><del style="font-weight: bold; text-decoration: none;"><BR><BR></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> </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>== Discussion ==</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>== Discussion ==</div></td></tr>
</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13553&oldid=prevNabilahAhmadKamal2: /* Results */2009-06-09T07:58:07Z<p><span dir="auto"><span class="autocomment">Results</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<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 07:58, 9 June 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l24">Line 24:</td>
<td colspan="2" class="diff-lineno">Line 24:</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:Blastp search-1ru8.png |left|thumb|1200px|'''Figure 1.0'''. The result of BlastP search which used N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' as query sequence (1RU8A)]] </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:Blastp search-1ru8.png |left|thumb|1200px|'''Figure 1.0'''. The result of BlastP search which used N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' as query sequence (1RU8A)]] </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>[[Image:Blastp-Macaca mulatta.png |<del style="font-weight: bold; text-decoration: none;">center</del>|thumb|1200px|'''Figure 1.1'''. The result of BlastP search which used protein sequence that is predicted to be similar ro ATP binding domain 4 from ''Macaca mulatta'']] <BR><BR></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>[[Image:Blastp-Macaca mulatta.png |<ins style="font-weight: bold; text-decoration: none;">left</ins>|thumb|1200px|'''Figure 1.1'''. The result of BlastP search which used protein sequence that is predicted to be similar ro ATP binding domain 4 from ''Macaca mulatta'']] <ins style="font-weight: bold; text-decoration: none;"><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR></ins><BR><BR></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>'''[[Multiple sequence alignment-ClustalX]]'''</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>'''[[Multiple sequence alignment-ClustalX]]'''</div></td></tr>
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</table>NabilahAhmadKamal2http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=ATP_binding_domain_4_Evolution&diff=13550&oldid=prevNabilahAhmadKamal2: /* Results */2009-06-09T07:52:55Z<p><span dir="auto"><span class="autocomment">Results</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 07:52, 9 June 2009</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> </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;"><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>From the BlastP search, it was found that the E value for both query sequence i.e; N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' and ATP Binding Domain 4 from ''Macaca mulatta'', are very low (Figure 1 .0 and Figure 1.1). The sequences with highest E-value for ''Pyrococcus furiosus'' and the ''Macaca mulatta'' are 2e-25 and 1e-49 respectively which are very low. Therefore, all 200 sequences were aligned by using ClustalX. From the multiple sequence alignment, it was found that only one conserved <del style="font-weight: bold; text-decoration: none;">region </del>presence in the <del style="font-weight: bold; text-decoration: none;">sequences</del>. Therefore, only extremely low E values were re-selected and unrelated sequences were ignored and deleted. Sequences were deleted in order to acheive the best multiple alignment. Based on these new re-selected sequences (88 sequences), it was found that there are seven conserved residues but only <del style="font-weight: bold; text-decoration: none;">three </del>conserved residues are significant since these residues are a part of PP-loop motif (Figure 2.0 and Figure 2.1).</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>From the BlastP search, it was found that the E value for both query sequence i.e; N-type ATP pyrophosphatase from ''Pyrococcus furiosus'' and ATP Binding Domain 4 from ''Macaca mulatta'', are very low (Figure 1 .0 and Figure 1.1). The sequences with highest E-value for ''Pyrococcus furiosus'' and the ''Macaca mulatta'' are 2e-25 and 1e-49 respectively which are very low. Therefore, all 200 sequences were aligned by using ClustalX. From the multiple sequence alignment, it was found that only one conserved <ins style="font-weight: bold; text-decoration: none;">residue </ins>presence in the <ins style="font-weight: bold; text-decoration: none;">alignment</ins>. Therefore, only extremely low E values were re-selected and unrelated sequences were ignored and deleted. Sequences were deleted in order to acheive the best multiple alignment. Based on these new re-selected sequences (88 sequences), it was found that there are seven conserved residues but only <ins style="font-weight: bold; text-decoration: none;">five </ins>conserved residues are significant since these residues are a part of PP-loop motif (Figure 2.0 and Figure 2.1).</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>Phylogram was constructed from Treeview software which indicates the relationship between the taxa (Figure 3.0). ''Macaca mulatta'' is closely related to ''Homo sapiens'' based on their high similarity of sequences of ATP binding domain 4. Therefore, ''Macaca mulatta'' <del style="font-weight: bold; text-decoration: none;">are </del>homologues to ''Homo sapiens''.</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>Phylogram was constructed from Treeview software which indicates the relationship between the taxa (Figure 3.0). ''Macaca mulatta'' is closely related to ''Homo sapiens'' based on their high similarity of sequences of ATP binding domain 4. Therefore, ''Macaca mulatta'' <ins style="font-weight: bold; text-decoration: none;">is </ins>homologues to ''Homo sapiens''.</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>Unrooted or radial tree was constructed from Treeview software (Figure 3.1). The tree showed the evolutionary relationship between taxa and it was found that the members of archaea and eukarya <del style="font-weight: bold; text-decoration: none;">are </del>clearly separated. Domain bacteria was absence in this tree. </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>Unrooted or radial tree was constructed from Treeview software (Figure 3.1). The tree showed the evolutionary relationship between taxa and it was found that the members of archaea and eukarya <ins style="font-weight: bold; text-decoration: none;">were </ins>clearly separated. Domain bacteria was absence in this tree. </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>Bootstrap was performed to see the reliability of branching order and distance i.e: a measure of the quality of phylogenetic tree. Bootstrap value indicates the confidence level of the branching order and distance. Value which is less than 50% are meaningless. In this project, some species from the phylogenetic tree were deleted when constructing Bootstrap tree since most of the Bootstrap value are 100%. Based on bootstrap tree (Figure 4.0), most of the value are lesser than 75%.</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>Bootstrap was performed to see the reliability of branching order and distance i.e: a measure of the quality of phylogenetic tree. Bootstrap value indicates the confidence level of the branching order and distance. Value which is less than 50% are meaningless. In this project, some species from the phylogenetic tree were deleted when constructing Bootstrap tree since most of the Bootstrap value are 100%. Based on bootstrap tree (Figure 4.0), most of the value are lesser than 75%.</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>Since domain bacteria was not found in the phylogenetic tree, STRING search of N-type ATP pyrophosphatase was performed and it was found that some bacteria species actually belong to N-type ATP pyrophosphatase (Figure 5.0). However, when the sequences <del style="font-weight: bold; text-decoration: none;">are </del>aligned with that for ''Pyrococcus furiosus'' and ''Macaca mulatta'', the sequences similarity are low and the E-values are quite high. </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>Since domain bacteria was not found in the phylogenetic tree, STRING search of N-type ATP pyrophosphatase was performed and it was found that some bacteria species actually belong to N-type ATP pyrophosphatase (Figure 5.0). However, when the sequences <ins style="font-weight: bold; text-decoration: none;">were </ins>aligned with that for ''Pyrococcus furiosus'' and ''Macaca mulatta'', the sequences similarity are low and the E-values are quite high. </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>'''[[BlastP]]'''</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>'''[[BlastP]]'''</div></td></tr>
</table>NabilahAhmadKamal2