Additional file 16: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Table S3 Information of all the fungal genome sequences used in this study. (XLSX 38 kb

Additional file 3: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Table S2 The binding cavity analysis of all the predicted structures of newly found UPOs. The binding pockets are shown in surface and the aromatic residues are shown in sticks. (DOCX 13720 kb

Additional file 17: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Table S4 CPO sequences and MroUPO used in this study. (DOCX 14 kb

Representation of a genome, a PG and a CPG.

<p>(A) A rearranged duplicated genome with duplicated size of 3 is represented as a sequence of signed integers, where a positive (negative) sign is represented by the direction of the colored arrow. (B) The same genome is represented as a sequence of extremities (i.e., heads, tails or cap genes). (C) PG of the above genome. Each non-cap gene is cut into head and tail, which becomes two vertices in the partial graph. (D) The vertex reposition of the PG in (C). (E) The contracted PG that is converted from the PG showed in (C) and (D). Each vertex corresponds to an extremity family. Numbers on each edge indicate the copy IDs (i.e., subscripts) of the two extremities connected by the corresponding adjacency. Note that the edge (1^h, 2^t) in (E) corresponds to 2 adjacencies (or edges) in (C), so its multiplicity is 2.</p

Additional file 5: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Selection analyses data for UPOs. (XLSX 119 kb

Additional file 6: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Selection analyses data for CPOs. (XLSX 109 kb

Additional file 13: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Figure S9 An MSA of the clusters formed for the functional divergence analysis showing the Type-I functional divergent sites highlighted with black color. (TIF 7611 kb

Additional file 9: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Figure S5 Selection analysis on UPOs using aBSREL, a branch-site model. Thicker branches have a p-value < 0.05 showing evidence of undergoing positive diversifying selection. (TIF 1225 kb

Additional file 1: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Table S1 Number of putative sequences obtained in 35 different fungal species using the pipeline. (DOCX 13 kb

Additional file 15: of New insights on unspecific peroxygenases: superfamily reclassification and evolution

Figure S10 Structural representation of the newly found motifs adhering near the binding pockets (shown as surface) are shown in one species from each subfamily of UPOs; a) experimentally resolved structure of AaeUPO and modeled structures of b) Mixia osmundae iam14324, c) Jaapia argillacea mucl33604, d) Kalmanozyma brasiliensis ghg001, e) Glarea lozoyensis atcc20868, and f) Phialocephala scopiformis. (TIF 2498 kb