TransMembrane prediction using Hidden Markov Models for Rv2395A




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 L0.582870.000000.41713
2 T0.582870.000000.41713
3 M0.582870.000000.41713
4 T0.582870.000000.41713
5 A0.582870.000010.41712
6 S0.582870.000010.41712
7 V0.582870.000010.41712
8 A0.582870.000010.41712
9 K0.582870.000010.41712
10 V0.582870.000010.41712
11 T0.582870.000010.41712
12 A0.582870.000010.41712
13 A0.582870.000010.41712
14 R0.582870.000010.41712
15 P0.582870.000010.41712
16 E0.582870.000010.41712
17 P0.582870.000010.41712
18 S0.582870.000010.41712
19 A0.582870.000010.41712
20 A0.582870.000010.41712
21 W0.582870.000010.41712
22 A0.582870.000010.41712
23 E0.582870.000000.41712
24 A0.582880.000000.41712
25 R0.582880.000000.41712
26 R0.582880.000000.41712
27 R0.582880.000000.41712
28 V0.582880.000000.41712
29 R0.582880.000000.41712
30 Q0.582880.000000.41712
31 R0.582880.000000.41712
32 R0.582880.000000.41712
33 E0.582880.000000.41712
34 D0.582880.000000.41712
35 M0.582880.000000.41712
36 L0.582880.000000.41712
37 R0.582880.000000.41712
38 H0.582880.000000.41712
39 P0.582880.000000.41712
40 A0.582880.000000.41712
41 F0.582880.000000.41712
42 L0.582880.000000.41712
43 S0.582880.000000.41712
44 K0.582880.000000.41712
45 Q0.582880.000000.41712
46 L0.582880.000000.41712
47 P0.582880.000000.41712
48 A0.582880.000000.41712
49 E0.582880.000000.41712
50 P0.582880.000000.41712
51 A0.582880.000000.41712
52 D0.582880.000000.41712
53 D0.582880.000000.41712
54 D0.582880.000000.41712
55 G0.582880.000000.41712
56 V0.582880.000000.41712
57 A0.582880.000000.41712
58 A0.582880.000000.41712
59 V0.582880.000000.41712
60 Y0.582880.000000.41712
61 D0.582880.000000.41712
62 I0.582880.000000.41712
63 A0.582880.000000.41712
64 I0.582880.000000.41712
65 A0.582880.000000.41712
66 R0.582880.000000.41712
67 R0.582880.000000.41712
68 R0.582880.000000.41712
69 R0.582880.000000.41712
70 P0.582880.000000.41712
71 A0.582880.000000.41712

General Statistics
Length: 71
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.00018
Exp number, first 60 AAs: 0.00018
Total prob of N-in: 0.58287
inside: from residue 1 to 71
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