TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0025

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.16903	0.00000	0.83097
2 S	0.16903	0.00000	0.83097
3 E	0.16903	0.00000	0.83097
4 Q	0.16903	0.00000	0.83097
5 A	0.16903	0.00000	0.83097
6 G	0.16903	0.00000	0.83097
7 S	0.16903	0.00000	0.83097
8 S	0.16903	0.00000	0.83097
9 V	0.16903	0.00000	0.83097
10 A	0.16903	0.00000	0.83097
11 V	0.16903	0.00000	0.83097
12 I	0.16903	0.00000	0.83097
13 Q	0.16903	0.00000	0.83097
14 E	0.16903	0.00000	0.83097
15 R	0.16903	0.00000	0.83097
16 Q	0.16903	0.00000	0.83097
17 A	0.16903	0.00000	0.83097
18 L	0.16903	0.00000	0.83097
19 L	0.16903	0.00000	0.83097
20 A	0.16903	0.00000	0.83097
21 R	0.16903	0.00000	0.83097
22 Q	0.16903	0.00000	0.83097
23 H	0.16903	0.00000	0.83097
24 D	0.16903	0.00000	0.83097
25 A	0.16903	0.00000	0.83097
26 V	0.16903	0.00000	0.83097
27 A	0.16903	0.00000	0.83097
28 E	0.16903	0.00000	0.83097
29 A	0.16903	0.00000	0.83097
30 D	0.16903	0.00000	0.83097
31 R	0.16903	0.00000	0.83097
32 E	0.16903	0.00000	0.83097
33 L	0.16903	0.00000	0.83097
34 A	0.16903	0.00000	0.83097
35 D	0.16903	0.00000	0.83097
36 V	0.16903	0.00000	0.83097
37 L	0.16903	0.00000	0.83097
38 A	0.16903	0.00000	0.83097
39 S	0.16903	0.00000	0.83097
40 A	0.16903	0.00000	0.83097
41 H	0.16903	0.00000	0.83097
42 A	0.16903	0.00000	0.83097
43 A	0.16903	0.00000	0.83097
44 M	0.16903	0.00000	0.83097
45 R	0.16903	0.00000	0.83097
46 E	0.16903	0.00000	0.83097
47 S	0.16903	0.00000	0.83097
48 V	0.16903	0.00000	0.83097
49 R	0.16903	0.00000	0.83097
50 R	0.16903	0.00000	0.83097
51 L	0.16903	0.00000	0.83097
52 D	0.16903	0.00000	0.83097
53 A	0.16903	0.00000	0.83097
54 I	0.16903	0.00000	0.83097
55 A	0.16903	0.00000	0.83097
56 A	0.16903	0.00000	0.83097
57 E	0.16903	0.00000	0.83097
58 L	0.16903	0.00000	0.83097
59 D	0.16903	0.00000	0.83097
60 R	0.16903	0.00000	0.83097
61 A	0.16903	0.00000	0.83097
62 V	0.16903	0.00000	0.83097
63 P	0.16903	0.00000	0.83097
64 D	0.16903	0.00000	0.83097
65 Q	0.16903	0.00000	0.83097
66 D	0.16903	0.00000	0.83097
67 Q	0.16903	0.00000	0.83097
68 L	0.16903	0.00000	0.83097
69 A	0.16903	0.00000	0.83097
70 V	0.16903	0.00000	0.83097
71 D	0.16903	0.00000	0.83097
72 T	0.16903	0.00000	0.83097
73 P	0.16903	0.00000	0.83097
74 M	0.16903	0.00000	0.83097
75 G	0.16903	0.00000	0.83097
76 A	0.16903	0.00000	0.83097
77 R	0.16903	0.00000	0.83097
78 E	0.16903	0.00000	0.83097
79 F	0.16903	0.00000	0.83096
80 Q	0.16903	0.00001	0.83096
81 T	0.16903	0.00001	0.83096
82 F	0.16903	0.00001	0.83095
83 L	0.16903	0.00001	0.83095
84 V	0.16903	0.00001	0.83095
85 A	0.16903	0.00001	0.83095
86 K	0.16903	0.00001	0.83095
87 Q	0.16903	0.00001	0.83095
88 R	0.16903	0.00001	0.83095
89 E	0.16903	0.00001	0.83095
90 I	0.16903	0.00001	0.83095
91 V	0.16903	0.00001	0.83095
92 A	0.16903	0.00001	0.83095
93 V	0.16903	0.00001	0.83095
94 V	0.16903	0.00001	0.83095
95 A	0.16903	0.00001	0.83095
96 A	0.16903	0.00001	0.83095
97 A	0.16903	0.00001	0.83095
98 H	0.16903	0.00001	0.83095
99 E	0.16903	0.00001	0.83095
100 L	0.16903	0.00001	0.83095
101 D	0.16904	0.00000	0.83096
102 R	0.16904	0.00000	0.83096
103 A	0.16904	0.00000	0.83096
104 K	0.16904	0.00000	0.83096
105 S	0.16904	0.00000	0.83096
106 A	0.16904	0.00000	0.83096
107 V	0.16904	0.00000	0.83096
108 L	0.16904	0.00000	0.83096
109 K	0.16904	0.00000	0.83096
110 R	0.16904	0.00000	0.83096
111 L	0.16904	0.00000	0.83096
112 R	0.16904	0.00000	0.83096
113 A	0.16904	0.00000	0.83096
114 Q	0.16904	0.00000	0.83096
115 Y	0.16904	0.00000	0.83096
116 T	0.16904	0.00000	0.83096
117 E	0.16904	0.00000	0.83096
118 P	0.16904	0.00000	0.83096
119 A	0.16904	0.00000	0.83096
120 R	0.16904	0.00000	0.83096

General Statistics

Length: 120

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.00021

Exp number, first 60 AAs: 0

Total prob of N-in: 0.16903

outside: from residue 1 to 120

TMHMM predicts transmembrane helices and the location of the intervening loop regions.

If the whole sequence is labeled as inside or outside, the prediction is that it contains no membrane helices. It is probably not wise to interpret it as a prediction of location. The prediction gives the most probable location and orientation of transmembrane helices in the sequence.

Plot of probabilities

The plot shows the probabilities of inside/outside/TM helix. Possible weak TM helices are sometimes not predicted, and one can get an idea of the certainty of each segment in the prediction.

At the top of the plot (between 1 and 1.2) the best prediction is shown.

The plot is obtained by calculating the total probability that a residue sits in helix, inside, or outside summed over all possible paths through the model. Sometimes it seems like the plot and the prediction are contradictory, but that is because the plot shows probabilities for each residue, whereas the prediction is the over-all most probable structure. Therefore the plot should be seen as a complementary source of information.

Remarks

Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.

One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment.

The program does not predict whether a non-membrane protein is cytoplasmic or not.

This prediction has been generated using TMHMM Server v. 2.0