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Distribution plots of TMD length show clearly distinguishable profiles for Golgi versus plasma membrane proteins (Figures 3C and 3D), with mean values that are highly significantly different (Figure?3E).?As described above, the definition of TMD ends and the analyses of hydrophobic lengths were also performed using the Wimley-White and Biological hydrophobicity scales to avoid bias arising from using one particular hydrophobicity scale (Hessa et?al., 2007?and?Wimley GNAT2 and White, 1996). The plots of TMD hydropathy and TMD length distribution determined using these differently derived scales show very similar trends to those obtained with the GES scale (Figures S2D�CS2G). We also examined the distribution of TMD lengths predicted for the proteins by TMD prediction program Zpred2 (Papaloukas et?al., 2008) and again found similar trends (Figure?S2H). Overall, plasma membrane TMDs have a greater hydrophobic length than those TMDs that span Golgi membranes, and this difference is conserved between fungi and vertebrates. However, the plots also reveal some differences between fungi and vertebrates. SNS-032 order In fungi, the TGN/endosomal TMDs have a mean hydrophobic length intermediate between those of the Golgi and plasma membrane TMDs. However, in vertebrates, the TGN/endosomal TMDs appear to be of similar lengths to those of the plasma membrane. Indeed, the mean hydrophobicity values of the two sets of vertebrate proteins http://www.selleckchem.com/CDK.html are not very significantly different in the region where the TMDs come to their end (residues 16�C24), whereas for the fungal proteins there is a highly significant difference between the plasma membrane and TGN/endosomal TMDs at positions 21�C24 (p