Distribution of putative genes involved in starch degradation in 85 fungal genomes.

Taxonomy information of above fungi is extracted from Taxonomy Browser in NCBI (http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi). Overall protein sequences of Rhizopus oryzae and Ustilago maydis were downloaded from the Broad Institute (http://www.broadinstitute.org/scientific-community/data), Monascus ruber was from our lab and others were from genome resource of NCBI (http://www.ncbi.nlm.nih.gov/genome/browse/). Putative amylolytic enzymes from the GH13, GH15 and GH31 families in each species were inferred by searching its overall proteins with the corresponding profile hidden Markov models from Pfam (http://pfam.sanger.ac.uk/) and their annotations followed by BlastP comparisons against the database of non-redundant protein sequences (http://blast.ncbi.nlm.nih.gov/Blast.cgi). Accession numbers of putative proteins were shown in the corresponding phylogenetic trees later. Some proteins from the family GH13 with equivocal assignment between α-amylases and α-glucosidases were assigned to the group of α-glucosidase (GH13).