TransMembrane prediction using Hidden Markov Models for Rv2395B




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.026370.000000.97363
2 P0.026370.000000.97363
3 G0.026370.000000.97363
4 L0.026370.000000.97363
5 V0.026370.000000.97363
6 P0.026370.000000.97363
7 A0.026370.000000.97363
8 M0.026370.000000.97363
9 P0.026370.000000.97363
10 L0.026370.000000.97363
11 D0.026370.000000.97363
12 A0.026370.000000.97363
13 L0.026370.000000.97363
14 R0.026370.000000.97363
15 P0.026370.000000.97363
16 A0.026370.000000.97363
17 R0.026370.000000.97363
18 Q0.026370.000000.97363
19 P0.026370.000000.97363
20 T0.026370.000000.97363
21 S0.026370.000000.97363
22 G0.026370.000000.97363
23 L0.026370.000000.97363
24 G0.026370.000000.97363
25 E0.026370.000000.97363
26 C0.026370.000000.97363
27 A0.026370.000000.97363
28 T0.026370.000000.97363
29 M0.026370.000000.97363
30 R0.026370.000000.97363
31 R0.026370.000000.97363
32 P0.026370.000000.97363
33 E0.026370.000000.97363
34 A0.026370.000000.97363
35 G0.026370.000000.97363
36 N0.026370.000000.97363
37 E0.026370.000000.97363
38 K0.026370.000000.97363
39 V0.026370.000000.97363
40 A0.026370.000000.97363
41 V0.026370.000000.97363
42 I0.026370.000000.97363
43 W0.026370.000000.97363
44 E0.026370.000000.97363
45 S0.026370.000000.97363
46 L0.026370.000000.97363
47 D0.026370.000000.97363
48 V0.026370.000000.97363
49 V0.026370.000000.97363
50 P0.026370.000000.97363
51 P0.026370.000000.97363
52 E0.026370.000000.97363
53 S0.026370.000000.97363
54 L0.026370.000000.97363

General Statistics
Length: 54
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0
Exp number, first 60 AAs: 0
Total prob of N-in: 0.02637
outside: from residue 1 to 54
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