Known peptide-binding sites for the human MH class II molecule [ 3] were annotated on the mouse model, along with sites under positive selection in the seahorse.
Identified A-to-I editing sites are annotated on the genome and are viewable in relation to gene model annotations on GBrowse.
We found 3253 sites that can be annotated on protein sequences assigned to the clade of coelomata, which is the common taxonomy node of human, mouse and fly.
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This leaves out 18 sites, of which 3 sites were annotated on sequence records as being observed in large-scale phosphoproteomics experiments based on mass spectrometry, similar to the data used in the current study.
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After the removal of data redundancy and inconsistency, as presented in Table 1, totally 66,301, 41,716 and 3754 experimentally confirmed phosphorylation sites are annotated on 10,257 human, 7306 mouse and 1203 rat phosphoproteins (substrates), respectively.
The strength of CDD's approach is that conserved sites can be annotated on large numbers of protein sequences with relatively little effort, as a single model may provide 'specific domain hits' to hundreds or thousands of protein sequences.
