Additional and not yet published material concerning the PRED-TMR algorithm





Annexe I :Propensity values for the 20 amino acid residue types to belong to transmembrane segments and a hydrophobicity scale , calculated from the entire SwissProt database, release 35.

Residue  Pi    Hi  
Phenylalanine (F)2.2350.804
Isoleucine (I)2.0830.734
Leucine (L)1.8450.612
Tryptophan (W)1.7900.582
Valine (V)1.7560.563
Methionine (M)1.5020.407
Alanine (A)1.3830.324
Cysteine (C)1.2020.184
Glycine (G)1.1580.147
Tyrosine (Y)1.0750.073
Threonine (T)0.879-0.129
Serine (S)0.806-0.216
Proline (P)0.597-0.516
Histidine (H)0.395-0.930
Asparagine (N)0.389-0.944
Glutamine (Q)0.273-1.300
Aspartic acid (D)0.153-1.877
Glutamic acid (E)0.131-2.033
Arginine (R)0.124-2.085
Lysine (K)0.108-2.230

Pi = propensity value of residue type i
Hi = measurement of the "hydrophobicity" of a residue of type i



Annexe II :Positional propensities for the 20 amino acid residue types in the relevant nominal positions of decapeptides (0-9; see also Figure 1 and Methods) at the N and C-terminal ends of transmembrane segments, derived from a statistical analysis of the entire SwissProt database, release 35.

 
 0     1     2     3     4     5     6     7     8     9

 A 

 C 

 D 

 E 

 F 

 G 

 H 

 I 

 K 

 L 

 M 

 N 

 P 

 Q 

 R 

 S 

 T 

 V 

 W 

 Y 

1.07  0.99  1.04  0.92  0.79  1.31  1.43  1.36  1.49  1.52

0.62  0.66  0.70  0.79  0.74  0.64  0.79  0.81  0.87  1.05

0.75  0.66  0.63  0.80  1.15  0.10  0.14  0.22  0.17  0.15

0.70  0.64  0.61  0.64  0.93  0.10  0.15  0.19  0.13  0.14

1.21  1.35  1.24  0.99  0.40  2.59  2.33  2.17  2.21  2.06

1.04  1.03  0.98  1.05  0.87  0.94  1.11  1.14  1.22  1.14

0.99  1.00  0.99  1.10  1.43  0.30  0.38  0.63  0.56  0.44

1.00  1.06  1.05  0.83  0.30  2.72  2.19  2.11  2.11  2.19

1.00  0.97  0.94  1.11  1.60  0.09  0.12  0.17  0.12  0.12

1.01  1.07  1.10  0.89  0.53  2.02  1.90  1.77  1.67  1.91

1.42  1.08  1.09  1.13  0.73  1.64  1.59  1.81  1.54  1.49

0.94  0.99  1.00  1.12  1.44  0.28  0.37  0.43  0.35  0.42

0.93  0.90  0.91  0.91  0.94  0.51  0.51  0.60  0.60  0.56

0.90  0.90  0.88  0.89  1.21  0.18  0.26  0.36  0.27  0.32

1.32  1.29  1.30  1.70  2.38  0.15  0.13  0.17  0.16  0.16

0.99  0.99  0.97  1.01  1.20  0.41  0.70  0.72  0.78  0.72

1.00  1.10  1.08  1.15  1.23  0.65  0.80  0.86  0.94  1.01

0.93  0.93  0.96  0.79  0.42  1.99  1.76  1.66  1.75  1.78

1.66  1.85  1.77  1.83  1.04  2.87  2.51  2.10  2.09  1.45

1.15  1.18  1.47  1.34  1.14  1.37  1.42  1.38  1.46  1.03


Annexe III :Distribution of the agreement factor Q , produced after applying the PRED-TMR algorithm on all transmembrane proteins of the SwissProt database, release 35 (9392 sequences).




Claude Pasquier