E residue at position 216 shown as spheres. Panels A and B depict an active web site with threonine at position 216, whereas C and D depict an active web-site with valine at position 216. Maltose (A and C) and isomaltose (B and D) are represented as sticks. This structural evaluation shows that threonine is in a position to form a hydrogen bond with a hydroxyl from the secondary glucose in maltose (A). The secondary glucose of isomaltose, however, is positioned in such a way that it causes unfavorable interactions (B). On the other hand, when residue 216 is usually a valine, it might kind hydrophobic interactions with isomaltose (D).The hydrophobic side chain of valine is incompatible with all the hydrophilic binding mode of maltose (C). (TIF) Figure S9 Strains lacking one of the MAL12/MAL32 paralogs possess a fitness defect on maltose compared to wild type. mal12 (KV1151) and mal32 (KV1153) strains show a significant fitness defect compared to the wild-type strain (KV1042) on maltose. A mal12 mal32 double deletion strain doesn’t grow on maltose. Asterisks indicate considerable differences in between mutant and wildtype strains (a = 0.05). Error bars represent 95 confidence intervals. (TIF) Table S1 Outcomes of ancestral sequence reconstruction assuming(ZIP)Dataset SMAFFT alignment from the 50 MalS sequences. AA sequences of resurrected enzymes.(TXT)Dataset S(TXT)Figure S1 Bayesian consensus topology of the 50 MALS genes.MrBayes consensus tree in the 50 MALS genes (AA-based, LG+I+G model with 4 rate categories). Posterior MedChemExpress (Z)-4-Hydroxytamoxifen probabilities are indicated on the branches. (TIF)Figure S2 Maximum likelihood phylogeny of your 50 MALS genes. Maximum likelihood phylogeny with the 50 MALS genes calculated with PhyML (AA-based, LG+I+G model with four price categories, 1,000 bootstraps). Bootstrap values are indicated around the branches. (TIF) Figure S3 Bayesian consensus topology from the 50 MALS geneswith speedy evolving websites removed. MrBayes consensus tree of your 50 MALS genes (AA-based, LG+I+G model with 4 rate categories). All AA websites with much more than three variable AAs within the outgroup had been stripped in the alignment. Posterior probabilities are indicated on the branches. (TIF)Figure S4 Bayesian consensus topology with the MALS geneswithout K. lactis. MrBayes consensus tree with the MALS genes (AAbased, LG+I+G model with 4 price categories). The K. lactis branch was not included in the tree reconstruction. Posterior probabilities are indicated around the branches. (TIF)Figure S5 Bayesian consensus topology with the MALS geneswithout the outgroup. MrBayes consensus tree of your MALS genes (AA-based, LG+I+G model with four rate categories). The outgroup branches had been not incorporated in the tree reconstruction. Posterior probabilities are indicated around the branches. (TIF)Figure SSchematic tree showing inferred orthology aralogy relationships involving unique MALS genes. A schematic version from the codon-based phylogenetic tree inferred with MrBayes (see Figure 4) is shown. Duplication events, D; speciation events, S. Asterisks denote nodes along a segment with ambiguous speciation/duplication history. (TIF)S7 Structural variations among K. lactis [GI: 50312678] and K. lactis [GI:5441460] can clarify lack ofFiguredifferent models of protein evolution. Except for the protein evolution models utilized, all reconstructions were performed utilizing the exact same PAML settings. The JTT reconstruction, which was used to synthesize the ancestral proteins, was performed using PAML v4.2a, although the WAG and LG reconstructions w.
