Based on full length protein sequence, pairs of orthologs were observed in closely related species, such as P. berghei and P.y.
To better understand the relationship between the NP-like proteins within Populus we constructed an evolutionary tree based on full-length protein sequences retrieved from the Populus trichocarpa genome through Phytozome (Table 1).
To remove redundancy, we first created datasets of unique sequences (based on full-length protein sequence string comparison) within each database and then merged them to create a non-redundant dataset of interacting protein sequences, each indexed with our internal identifier.
Based on full-length protein sequence analysis, the 12 intact OR genes were classified into two small subfamilies that were found to be specific to mouse [7].
Phylogenetic reconstruction was performed using neighbor-joining (NJ) approaches with JTT and P-distance models based on full-length protein sequences, which resulted in generally similar topologies.
In particular, smaller databases that are based on full-length protein sequences might require a homology extension before being used with UProC.
However, our phylogenetic reconstruction based on full-length proteins also divided group II genes into two distinct subgroups, rather than the seven subgroups found when domain sequences were analyzed (subgroup II a-g) [ 4].
We noted that IC50 values against AarA were 2-fold (L58) to 14-fold (L44) higher (Table 1) in the assay based on full-length proteins than in the fluorescent assay; in fact, L35 and L41 did not inhibit AarA at all in this assay, but they did in the fluorescent peptide assay.
This is a strong argument for an integrating tool like O2EM that utilizes established protein family inferences based on full sequence lengths.
From calculations based on full, annotated genome sequences, the proportion of a genome that is protein coding varies considerably among taxa.
