Difference between revisions of "Team:Aalto-Helsinki/Future"
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<p>Our built phylogenetic trees are shown in Figure 1 and Figure 2. They are very similar with each other, despite that they were calculated with different algorithms. One major difference is that the oxidoreductase from <i>Sciscionella marina</i> is considered to be evolutionarily closer to our CAR than the enzyme from <i>Rhodococcus wratislaviensis</i> in the Bayesian MCMC tree, but the closer enzymes to CAR are grouped alike in the both trees. In the both figures the branch length to the thioester reductase-like protein of <i>Cryptosporangium arvum</i> is quite big. Therefore, we should consider the enzymes, which are closer to our CAR from the enzyme of <i>Cryptosporangium arvum</i>, as potential homologs which can replace CAR in the propane pathway as they have higher chance of having the same function. However, done research on found enzymes are low, especially the kinetic research. BRENDA, an enzyme database, only had kinetic values for a CAR homolog from <i>Nocardia iowensis</i>, so we really cannot tell if their performance is better. Nonetheless, if it is found in the future that one homolog has better kinetic values than CAR, it can be used to produce more propane.</p> | <p>Our built phylogenetic trees are shown in Figure 1 and Figure 2. They are very similar with each other, despite that they were calculated with different algorithms. One major difference is that the oxidoreductase from <i>Sciscionella marina</i> is considered to be evolutionarily closer to our CAR than the enzyme from <i>Rhodococcus wratislaviensis</i> in the Bayesian MCMC tree, but the closer enzymes to CAR are grouped alike in the both trees. In the both figures the branch length to the thioester reductase-like protein of <i>Cryptosporangium arvum</i> is quite big. Therefore, we should consider the enzymes, which are closer to our CAR from the enzyme of <i>Cryptosporangium arvum</i>, as potential homologs which can replace CAR in the propane pathway as they have higher chance of having the same function. However, done research on found enzymes are low, especially the kinetic research. BRENDA, an enzyme database, only had kinetic values for a CAR homolog from <i>Nocardia iowensis</i>, so we really cannot tell if their performance is better. Nonetheless, if it is found in the future that one homolog has better kinetic values than CAR, it can be used to produce more propane.</p> | ||
− | <figure style="margin-bottom:2%;margin-top:2%;"> | + | <figure > |
− | <a href="https://static.igem.org/mediawiki/2015/8/84/Aalto-Helsinki_BMCMC.jpeg"><img src="https://static.igem.org/mediawiki/2015/8/84/Aalto-Helsinki_BMCMC.jpeg" style="max-width:800px;" /></a> | + | <a href="https://static.igem.org/mediawiki/2015/e/ee/Aalto-Helsinki_upgma.png"><img src="https://static.igem.org/mediawiki/2015/e/ee/Aalto-Helsinki_upgma.png" style="max-width:800px;margin-top:2%;" /></a> |
− | <figcaption><p><b>Figure 2:</b> The Bayesian MCMC phylogenetic tree. The node labels are posterior values, which describe how accurate a branch point is. Because almost all values are over 0.9, we can believe its accuracy depending on initial values. Used Blosum62 as substitution model. ESS (effective sample size) was 6404.1033 for posterior. Click the image to enlarge it.</p></figcaption> | + | <figcaption style="margin-bottom:2%;margin-top:2%;"><p><b>Figure 1:</b> The UPGMA phylogenetis tree and sources for the proteins. The node labels describe how evolutionarily distant the proteins are: the higher a value is the more distant they are. The search method tells how we found the proteins and the ID its respective identification code. The enzyme from the human is picked to be an outsider group for calculations. The human enzyme actually functions to the opposite direction than our CAR; it oxidases butyraldehyde to butyric acid. Underlined enzyme is our CAR. The used substitution model for UPGMA was Jukes-Cantor. Click the image to enlarge it.</p></figcaption> |
+ | </figure> | ||
+ | |||
+ | <figure > | ||
+ | <a href="https://static.igem.org/mediawiki/2015/8/84/Aalto-Helsinki_BMCMC.jpeg"><img src="https://static.igem.org/mediawiki/2015/8/84/Aalto-Helsinki_BMCMC.jpeg" style="max-width:800px;margin-top:2%;" /></a> | ||
+ | <figcaption style="margin-bottom:2%;margin-top:2%;"><p><b>Figure 2:</b> The Bayesian MCMC phylogenetic tree. The node labels are posterior values, which describe how accurate a branch point is. Because almost all values are over 0.9, we can believe its accuracy depending on initial values. Used Blosum62 as substitution model. ESS (effective sample size) was 6404.1033 for posterior. Click the image to enlarge it.</p></figcaption> | ||
</figure> | </figure> | ||
Revision as of 17:40, 17 September 2015