The Pfam database for this family, UPF0157, shows that it is present in 174 species across all kingdoms of life, ranging from archaea, cyanobacteria, viruses, S. cerevisiae, C. elegans, the nematodes, fruit flies, mice and even humans, in 5 different domain architectures and in 244 different sequences (Fig. 2A and B).
Instead of scanning a large number of weak BLAST hits by eye for remote homologues, a profile HMM can be calculated from the alignment and can be used to search a database for remote family members.
For this, we built on the gene clustering associations captured as described above, using these to construct a corresponding experimental subsystem in the SEED database for each family (see Methods).
For this reason we have built subsystems in the public SEED database for 78 families and made available the raw comparative genomic data for all gene families shared between Arabidopsis and prokaryotes (Additional file 1A, 1B, and 1C) so that other experts can bring their insight to our analysis in order to make and test their own predictions.
For this reason we have built subsystems in the public SEED database for 78 families (Additional file 2) so that readers can produce and test their own predictions for gene families that fall in their area of expertise.
We used InterPro, a database for protein families, domains, and functional sites, to understand domain structure [ 45].
We have searched the available databases for S100 family members in cartilaginous fish (Callorhinchus milii and Squalus acanthias) and a jawless fish, Petromyzon marinus.
We therefore searched the Ensembl and NCBI databases for dact family members in the two cyclostome genomes available (Petromyzon marinus and Lethenteron japonicum).
We also conducted a TBLASTN search in the NCBI/EMBL/DDBJ gymnosperm EST databases for CLEL family members using the A. thaliana CLEL motif sequences.
