Each ribosomal protein has an associated MSA. First, an MSA reference was generated with MATRAS from multiple structure superimpositions. Then, amino acid sequences of species from the SEREB database were added to the reference alignment using MAFFT.
Alignment associated data (Fold, Phase)
DESIRE holds annotations of domain architecture from ECOD (Cheng; 10.1371/journal.pcbi.1003926) and ribosomal phase definitions (Kovacs; 10.1093/molbev/msx086) at residue level for one representative species (E. coli). Using the alignments, ProteoVision retrieves these annotations for each column of an alignment and displays them as a hovering pop-up next to each residue.
Available attributes for calculated mapping data:
Amino Acid frequencies
Amino acid frequencies in each column of an MSA were adjusted for presence of gaps. Thus, the gap frequencies were prorated and were treated as a uniform distribution among all possible amino acid characters, such that a single character in a gap counts as 0.05, as described by Bernier et al..
The Shannon entropy (as well as all properties listed below) was computed from the gap adjusted probabilities as:
Two group comparison (TwinCons)
In case of two groups selected in the phylogeny browser, ProteoVision provides an additional option to compute an in house developed score, TwinCons. TwinCons is computed for a single position of the MSA that compares two pre-defined groups (represented by vectors of the gap adjusted amino acid frequencies) based on their similarity defined by the pre-computed substitution matrix. TwinCons represents the transformation price between the two vector columns related by the substitution matrix.
Charge, hydropathy, hydrophobicity, polarity, mutability
The physico-chemical properties for each position within an MSA are computed as average properties for a given distribution of the amino acid frequencies. The tabulated values for each property were obtained from the available literature: - charges - hydropathy - hydrophobicity - polarity - mutability