"
Team:UPO-Sevilla/Foundational Advances/MiniTn7/Bioinformatics/Tn7 organisms
From 2011.igem.org
| Line 22: | Line 22: | ||
<p><strong>Figure 3. A</strong>. glmS gene multialignment of several organisms in which the Tn7 family transposon has been found. The blue box represents the terminal part of this gene which corresponds to attTn7 site. <strong>B</strong>. Obtained logo for the attTn7 site by introducing the last 38 bases of all the showed sequences. The translation of the obtained logo nucleotide sequence is shown below</p> | <p><strong>Figure 3. A</strong>. glmS gene multialignment of several organisms in which the Tn7 family transposon has been found. The blue box represents the terminal part of this gene which corresponds to attTn7 site. <strong>B</strong>. Obtained logo for the attTn7 site by introducing the last 38 bases of all the showed sequences. The translation of the obtained logo nucleotide sequence is shown below</p> | ||
| - | <p></p> | + | <p>From the performed multi sequence alignment (figure 3.A) arises that the last part of the glmS gene is highly conserved.</p> |
| - | <p></p> | + | |
| - | <p></p> | + | <p>The obtained logo (figure 3.B) showed a nucleotide sequence in which, as reported by Rupak (figure 2) (<a href="http://www.mobilednajournal.com/content/1/1/18" target="_blank">Rupak et al, 2010</a>) the first two positions at each codon were highly conserved, and variation was seen only at the third ‘wobble’ position. However, the obtained nucleotide logo sequence was similar to that reported by Rupak but it also differed in many positions.</p> |
| - | <p></p> | + | |
| + | <p>By contrast, when translating the obtained logo nucleotide sequence, the resulting amino acidic sequence was the same as obtained by Rupak and colleagues (<a href="http://www.mobilednajournal.com/content/1/1/18" target="_blank">Rupak et al, 2010</a>). As in Rupak paper is not totally explained which organisms have been used to obtain the shown logo, we cannot completely explain the found logo differences.</p> | ||
| + | |||
| + | <img class="center" width="300px" src="https://static.igem.org/mediawiki/2011/7/70/UPOSevilla-BioInfo-Fig4.jpg" alt="Phylogenetic trees for organisms with Tn7 transposon"/> | ||
| + | |||
| + | <p><strong>Figure 4</strong>. <strong>A</strong>. Squared phylogenetic tree obtained for the figure 3 multi sequence alignment. <strong>B</strong>. Circular phylogenetic tree for the same sequences as in A.</p> | ||
| + | |||
<p></p> | <p></p> | ||
</div> | </div> | ||
Revision as of 16:27, 19 September 2011
Results. Organisms with Tn7 transposon
Figure 3. A. glmS gene multialignment of several organisms in which the Tn7 family transposon has been found. The blue box represents the terminal part of this gene which corresponds to attTn7 site. B. Obtained logo for the attTn7 site by introducing the last 38 bases of all the showed sequences. The translation of the obtained logo nucleotide sequence is shown below
From the performed multi sequence alignment (figure 3.A) arises that the last part of the glmS gene is highly conserved.
The obtained logo (figure 3.B) showed a nucleotide sequence in which, as reported by Rupak (figure 2) (Rupak et al, 2010) the first two positions at each codon were highly conserved, and variation was seen only at the third ‘wobble’ position. However, the obtained nucleotide logo sequence was similar to that reported by Rupak but it also differed in many positions.
By contrast, when translating the obtained logo nucleotide sequence, the resulting amino acidic sequence was the same as obtained by Rupak and colleagues (Rupak et al, 2010). As in Rupak paper is not totally explained which organisms have been used to obtain the shown logo, we cannot completely explain the found logo differences.
Figure 4. A. Squared phylogenetic tree obtained for the figure 3 multi sequence alignment. B. Circular phylogenetic tree for the same sequences as in A.
Sponsors
