TransMembrane prediction using Hidden Markov Models for Rv2234




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.037020.000000.96297
2 S0.037020.000000.96297
3 D0.037020.000000.96297
4 P0.037020.000390.96259
5 L0.036990.000520.96249
6 H0.036990.000520.96248
7 V0.036970.000540.96248
8 T0.036970.000540.96248
9 F0.036970.000540.96248
10 V0.036970.000540.96248
11 C0.036970.000540.96248
12 T0.036970.000540.96248
13 G0.036970.000540.96248
14 N0.036970.000540.96248
15 I0.036970.000540.96248
16 C0.036970.000540.96248
17 R0.036970.000540.96249
18 S0.036970.000540.96249
19 P0.036990.000530.96249
20 M0.037000.000520.96249
21 A0.037020.000490.96249
22 E0.037410.000070.96252
23 K0.037440.000030.96253
24 M0.037440.000030.96253
25 F0.037440.000030.96253
26 A0.037450.000020.96253
27 Q0.037460.000010.96253
28 Q0.037460.000000.96253
29 L0.037460.000000.96253
30 R0.037460.000000.96253
31 H0.037460.000000.96253
32 R0.037460.000000.96253
33 G0.037460.000010.96253
34 L0.037460.000010.96253
35 G0.037460.000010.96253
36 D0.037460.000010.96252
37 A0.037460.000010.96252
38 V0.037460.000010.96252
39 R0.037460.000010.96252
40 V0.037460.000010.96252
41 T0.037460.000010.96252
42 S0.037460.000010.96252
43 A0.037460.000010.96252
44 G0.037460.000010.96252
45 T0.037460.000010.96252
46 G0.037460.000010.96252
47 N0.037460.000010.96252
48 W0.037460.000010.96252
49 H0.037460.000010.96252
50 V0.037460.000010.96252
51 G0.037470.000010.96252
52 S0.037470.000010.96252
53 C0.037470.000000.96252
54 A0.037470.000000.96252
55 D0.037470.000000.96252
56 E0.037470.000000.96252
57 R0.037470.000000.96252
58 A0.037470.000000.96252
59 A0.037470.000000.96252
60 G0.037470.000000.96252
61 V0.037470.000000.96252
62 L0.037470.000000.96252
63 R0.037470.000000.96252
64 A0.037470.000000.96252
65 H0.037470.000000.96252
66 G0.037470.000000.96252
67 Y0.037470.000000.96252
68 P0.037470.000000.96252
69 T0.037470.000000.96252
70 D0.037470.000000.96252
71 H0.037470.000010.96252
72 R0.037470.000020.96251
73 A0.037470.000020.96251
74 A0.037470.000020.9625
75 Q0.037470.000020.9625
76 V0.037470.000020.9625
77 G0.037470.000020.9625
78 T0.037470.000020.9625
79 E0.037470.000020.9625
80 H0.037470.000020.9625
81 L0.037470.000020.9625
82 A0.037470.000020.9625
83 A0.037470.000020.9625
84 D0.037470.000020.9625
85 L0.037470.000020.9625
86 L0.037470.000020.9625
87 V0.037470.000020.9625
88 A0.037470.000020.9625
89 L0.037480.000020.9625
90 D0.037490.000000.9625
91 R0.037490.000000.9625
92 N0.037490.000000.9625
93 H0.037490.000000.9625
94 A0.037490.000000.9625
95 R0.037490.000000.9625
96 L0.037490.000000.9625
97 L0.037490.000000.9625
98 R0.037490.000000.9625
99 Q0.037490.000000.9625
100 L0.037490.000000.9625
101 G0.037490.000000.9625
102 V0.037490.000000.9625
103 E0.037490.000000.9625
104 A0.037490.000000.9625
105 A0.037490.000000.9625
106 R0.037490.000000.9625
107 V0.037490.000000.9625
108 R0.037490.000000.9625
109 M0.037490.000000.9625
110 L0.037490.000000.9625
111 R0.037490.000000.9625
112 S0.037490.000000.9625
113 F0.037490.000000.9625
114 D0.037490.000000.9625
115 P0.037490.000000.9625
116 R0.037490.000000.9625
117 S0.037490.000000.9625
118 G0.037490.000000.9625
119 T0.037490.000000.9625
120 H0.037490.000000.9625
121 A0.037490.000000.9625
122 L0.037490.000000.9625
123 D0.037490.000000.9625
124 V0.037490.000000.9625
125 E0.037490.000000.9625
126 D0.037490.000000.9625
127 P0.037490.000000.9625
128 Y0.037490.000000.9625
129 Y0.037490.000000.9625
130 G0.037490.000000.9625
131 D0.037490.000000.9625
132 H0.037490.000000.9625
133 S0.037490.000000.9625
134 D0.037490.000000.9625
135 F0.037490.000000.9625
136 E0.037490.000000.9625
137 E0.037490.000000.9625
138 V0.037490.000000.9625
139 F0.037490.000000.9625
140 A0.037490.000000.9625
141 V0.037490.000000.9625
142 I0.037490.000000.9625
143 E0.037490.000000.9625
144 S0.037490.000000.9625
145 A0.037490.000000.9625
146 L0.037490.000000.9625
147 P0.037490.000000.9625
148 G0.037490.000000.9625
149 L0.037490.000000.9625
150 H0.037490.000000.9625
151 D0.037490.000000.9625
152 W0.037490.000000.9625
153 V0.037490.000000.9625
154 D0.037490.000000.9625
155 E0.037490.000000.9625
156 R0.037490.000000.9625
157 L0.037490.000000.9625
158 A0.037490.000000.9625
159 R0.037490.000000.9625
160 N0.037490.000000.9625
161 G0.037490.000000.9625
162 P0.037490.000000.9625
163 S0.037490.000000.9625

General Statistics
Length: 163
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.01021
Exp number, first 60 AAs: 0.00983999999999999
Total prob of N-in: 0.03702
outside: from residue 1 to 163
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