Topography Prediction of Helical Transmembrane Proteins by a New Modification of the Sliding Window Method

Table 5

Prediction of hydrophobic regions and TMDs calculated upon processing of hydrophobicity functions 𝑓_𝑛(𝑘) at 𝑛=4,5 on 𝐻_𝑁(𝑖) (𝑁=3,4,5) scales for 𝛼-helical membrane proteins.

Protein name, code, length	Data source	Number and boundaries of hydrophobic regions, including TMDs
	Scale level	1	2	3	4	5	6	7
SP2Q_; BACSU P71044; 283 aa	[21], potential	22–42
	𝐻5(𝑖),𝑛=5; ⟨𝑢⟩=−0.127	20–47	70–94	107–124	130–175	207–229
	𝐻4(𝑖),𝑛=5; ⟨𝑢⟩=0.696	16–48	70–94	109–121	132–174	197–225
SP3AH_; BACSU P49785; 218 aa	[21], potential	7–26
	𝐻5(𝑖),𝑛=5; ⟨𝑢⟩=−0.137	3–31	92–106	146–179	193–211
	𝐻4(𝑖),𝑛=5; ⟨𝑢⟩=0.692	3–30	95–113	146–179	193–211
Q8TMG0_METAC; Q8TMG0; 194 aa	𝐻5(𝑖),𝑛=5; ⟨𝑢⟩=0.232	7–20	49–67	76–93	130–162
	𝐻3(𝑖),𝑛=5; ⟨𝑢⟩=0.041	0–22	45–62	77–91	127–163
HLYE_; ECOLI P77335; 303 aa	[21], potential					183–203
	𝐻3(𝑖),𝑛=5; ⟨𝑢⟩=−0.248	0–17	24–38	82–103	114–123	180–209	242–247	264–280
	𝐻5(𝑖),𝑛=4; ⟨𝑢⟩=0.029	5–26	32–40	81–102	115–123	179–208	242–253	267–275