Predicted functional domains for several of the selected transcript candidates. Functional domains annotation based on Pfam hidden Markov models. Legend box shows a classification of the domain hits based on its match to complete domain model; the boxes height is proportional to the E-value score provided for each match. Significant matches were considered for HMMER  E-value < 0.001; however, low-significance matches are also shown, as well as hits to Pfam-B models produced by automated alignment protocols. Further annotation over Smed454 transcripts is already available at the GBrowse2 URL planarian.bio.ub.edu/gbrowse/smed454_transcriptome; an example can also be found on Figure 4.