Analysis of the Vaccinia Virus protein VP39 (CATH:126.96.36.199) dataset
There are 3 entries in this dataset.
EC Class Composition
CATH Domain Composition
There are an average of 3 number of steps in this dataset. The median number of steps is 4. The maximum number of steps in this dataset is 4 and the minimum is 2. The following graph shows the frequency of MACiE entries in this dataset with a given number of steps.
Amino Acid Residues
There are an average of 2.66 number of catalytic amino acid residues in a MACiE reaction for this dataset. The maximum number of amino acid residues in this dataset is 4 and the minimum is 1. The following barchart shows the frequency of the different catalytic amino acid residues in this dataset.
For the purposes of the following graph, amino acid residues are split into three generaic categories: polar (neutral), polar (charged) and hydrophobic. The neutral residues are: Ser, Thr, Cys, Asn, Gln, Tyr as well as the main chain portions of the amide and carbonyl groups. The charged residues are: Lys, Arg, His, Asp, Glu as well as the main chain portions of the N and C termini. The hydrophobic residues are: Ala, Val, Leu, Ile, Met, Phe, Trp, Pro, Gly. The following pie charts show the distribution of amino acid residue type by dataset (left) to the complete MACiE dataset (right)
Functional Profiles of the catalytic amino acids in Vaccinia Virus protein VP39 (CATH:188.8.131.52) Entries
The number below the residue name is the normalisation factor, and is calculated as the number of reactions in which that residue type occurs, divided by the total number of reactions in the dataset. The top number (emboldened) is the raw profile of that residue type and is calculated as the total number of unique residues of a given type performing a given function divided by the total number of that residue type in the dataset. The lower number is the normalised profile, which is calculated as the raw profile multiplied by the normalisation factor. Thus, if the residue is only ever seen in the dataset acting as a stabiliser, the raw profile will be 1, however, if that residue is only present in half the reactions, then the normailsation factor will be 0.5 and the normalised profile will also be 0.5.
Catalytic Machinery Similarities
This is calculated as a combination of the complement of catalytic amino acid residues present in each entry and the superimposition of the active site as calculated using IsoCleft.
CATH:184.108.40.206 dataset has no cofactors associated with it.
The following graphs show the distribution of mechanism class by dataset (left) to the complete MACiE dataset (right)
The following graphs show the distribution of mechanism type by dataset (left) to the complete MACiE dataset (right)
Overall Reaction Overview
Overall Reaction (Bond only) Similarities
Step Centric Overview
Composite Reaction (Bond only) Similarities
This measure of similarity is based off the sum of all the bond changes in all the steps involved in the reaction mechanism.
This measure of similarity is based off the overall reaction bond change (10%), the sum of all the bond changes in all the steps involved in the reaction mechanism (65%) plus the complement of catalytic residues (25%) to give an estimate of the total similarity between two reactions.