Table 6.

Predicted △G_app values (in kcal mol⁻¹) for membrane insertion of each of the four TMDs of the indicated metallophosphoesterase (YkuE) proteins. Sequences were analysed using the △G_app prediction server (http://dgpred.cbr.su.se/) that are based on hydrophobicity scales generated from (Hessa et al., 2005, 2007). This server uses the SCAMPI2/TOPCONS servers (Tsirigos et al., 2015, 2016) to predict the positions of the TMDs.

DOI: http://dx.doi.org/10.7554/eLife.26577.028

		Predicted △Gapp
Family/Species	Protein ID	TM1	TM2	Tm3†	TM4
Capnocytophaga canimorsus	F9YSF9	−1.595	−1.327	−1.266	0.957
Desulfitibacter alkalitolerans	WP_028307559.1	−1.409	−2.217	−2.075	1.087
Nitrospirae bacterium RBG_16_64_22	A0A1G1HRI1	−1.326	−0.017	0.628	1.579
Gemmatimonadetes bacterium 13_2_20 CM_69_27	A0A1Q6W294	−1.397	−0.016	−0.881	1.282

†Positive values for ΔG_app value noted internal TMD. This marginally hydrophobic TMD is, however, still likely to be integrated by the Sec pathway. Many individual TMD in multi-spanning membrane proteins have an unfavourable free energy of membrane insertion and are unable to stably integrate by themselves, requiring TMD sequence-extrinsic features for membrane insertion. It is, however, usual for the first and last TMD to be more hydrophobic as they lack these sequence-extrinsic features (Hedin et al., 2010; Virkki et al., 2014; Elofsson and von Heijne, 2007; White and von Heijne, 2008b).