Results

=**MEGA7 - Alignment Analysis - Topology Analysis**=


 * Medium-chain acyl-CoA Dehydrogenase enzyme Sequences**

MEGA7 protein sequence alignment
 * All positions containing gaps and missing data were eliminated. There were a total of 373 positions in the final data set. 386 total.


 * Protein Phylogeny Trees**

Protein Maximum Likelihood Protein Neighbor Joining Protein Minimum Likelihood __ Protein Phylogeny Trees (MCAD enzyme) __ -The MCAD enzyme phylogeny trees have strong bootstrap values and makes sense since they're all mammals and within the same class // Mammalia //, a clade of endothermic aminotes.
 * Values over 80 = strong topology


 * ACADM Gene Sequences**

MEGA7 nucleotide sequence alignment
 * All positions containing gaps and missing data were eliminated. There were a total of 1149 positions in the final data set. There were 1400 positions total and the //Homo sapien// was sequence was mostly altered.


 * Nucleotide Phylogeny Trees**

Nucleotide Maximum Likelihood Nucleotide Neighbor Joining __ Nucleotide Phylogeny Trees (ACADM gene) __ -The ACADM gene phylogeny trees did not show the same bootstrap values that suggested strong topology as the protein sequences showed.

=**Protein Model Portal - Structure Analysis**=

When searched for MCAD, a reviewed hit (Starred) and upon clicking the entry leads to available variants of the MCAD enzyme. Listed in the options are both the wildtype MCAD, the most prevalent mutant K304E, and //Mus musculus// MCAD for structure analysis



When comparing the structures of wildtype MCAD and the most common variant K304E, we know it is a single base pair and the structure would not be much different. The %ID of the mutant is 99%



=STRING - Protein Interaction Analysis=

Protein interaction maps were constructed for both //Homo sapiens & Mus musculus// ACADM Upon clicking the //Homo sapiens// ACADM (red circle) protein reference point you are able to wide search homologs among STRING organisms (2031 organisms total in database*)

Network stats for comparison Upon clicking any of the pathway ID's such as "fatty acid beta-oxidation" in Biological Process (GO), the gene sets that assist in fatty acid beta-oxidation will be highlighted red. Both // Homo sapiens & Mus musculus // have the same 5 gene sets that aid in fatty acid-beta oxidation except PCCD ( Propionyl CoA carboxylase, beta polypeptide) for // Homo sapiens // and ACSBG2 (acyl-CoA synthetase bubblegum family member 2) or // Mus musculus // - although both enzymes are in both // Homo sapiens & Mus musculus //.
 * each pathway can be selected and the corresponding proteins will be highlighted (Red)

After identifying which proteins are specifically involved in fatty acid beta-oxidation, the interaction paths may be selected and an info-panel will display with evidence suggesting a functional link - whether strong or weak. Higher scores suggest higher correlation.

Reviewing the protein homologs list for // Homo sapiens // and comparing it with the species lists that was used here, half the list were found along the range of 780.0 - 840.0 bitscore indicting strong similarity / topology as the phylogenic trees had demonstrated earlier in MEGA7.



MCADD homepage @Primary Research Materials and Methods Discussion References