TransMembrane prediction using Hidden Markov Models for Rv2392




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.058570.000000.94143
2 S0.058570.000000.94143
3 G0.058570.000000.94143
4 E0.058570.000000.94143
5 T0.058570.000000.94143
6 T0.058570.000000.94143
7 R0.058570.000000.94143
8 L0.058570.000000.94143
9 T0.058570.000000.94143
10 E0.058570.000000.94143
11 P0.058570.000000.94143
12 Q0.058570.000000.94143
13 L0.058570.000000.94143
14 R0.058570.000000.94143
15 E0.058570.000000.94143
16 L0.058570.000000.94143
17 A0.058570.000000.94143
18 A0.058570.000000.94143
19 R0.058570.000000.94143
20 G0.058570.000000.94143
21 A0.058570.000000.94143
22 A0.058570.000000.94143
23 E0.058570.000000.94143
24 L0.058570.000000.94143
25 D0.058570.000000.94143
26 G0.058570.000000.94143
27 A0.058570.000000.94143
28 T0.058570.000000.94143
29 A0.058570.000000.94143
30 T0.058570.000000.94143
31 D0.058570.000000.94143
32 M0.058570.000000.94143
33 L0.058570.000000.94143
34 R0.058570.000000.94143
35 W0.058570.000000.94143
36 T0.058570.000000.94143
37 D0.058570.000000.94143
38 E0.058570.000010.94143
39 T0.058570.000020.94142
40 F0.058560.000030.94141
41 G0.058560.000030.94141
42 D0.058560.000030.94141
43 I0.058560.000040.94141
44 G0.058560.000040.94141
45 G0.058560.000040.94141
46 A0.058560.000040.94141
47 G0.058560.000040.94141
48 G0.058560.000040.94141
49 G0.058560.000040.94141
50 V0.058560.000040.9414
51 S0.058560.000050.9414
52 G0.058550.000050.9414
53 H0.058550.000050.9414
54 R0.058550.000050.9414
55 G0.058540.000070.94139
56 W0.058530.000080.94139
57 T0.058530.000080.9414
58 T0.058520.000090.9414
59 C0.058500.000110.9414
60 N0.058460.000140.9414
61 Y0.058440.000160.9414
62 V0.058410.000190.9414
63 V0.058410.000190.9414
64 A0.058410.000190.9414
65 S0.058420.000180.9414
66 N0.058420.000180.94141
67 M0.058420.000180.9414
68 A0.058420.000180.9414
69 D0.058420.000180.9414
70 A0.058410.000190.9414
71 V0.058400.000200.9414
72 L0.058400.000200.9414
73 V0.058400.000200.9414
74 D0.058410.000180.94141
75 L0.058400.000190.94141
76 A0.058400.000190.94141
77 A0.058400.000180.94142
78 K0.058400.000100.9415
79 V0.058400.000100.94151
80 R0.058400.000080.94152
81 P0.058400.000080.94152
82 G0.058390.000090.94153
83 V0.058390.000090.94153
84 P0.058390.000080.94154
85 V0.058390.000060.94155
86 I0.058390.000060.94155
87 F0.058390.000060.94156
88 L0.058390.000060.94156
89 D0.058390.000050.94156
90 T0.058390.000050.94156
91 G0.058390.000050.94156
92 Y0.058390.000050.94156
93 H0.058390.000040.94157
94 F0.058390.000030.94158
95 V0.058390.000030.94158
96 E0.058400.000020.94158
97 T0.058400.000020.94159
98 I0.058400.000020.94159
99 G0.058400.000010.94159
100 T0.058400.000010.94159
101 R0.058400.000000.9416
102 D0.058400.000000.9416
103 A0.058400.000000.9416
104 I0.058400.000000.9416
105 E0.058400.000000.9416
106 S0.058400.000000.9416
107 V0.058400.000000.9416
108 Y0.058400.000000.9416
109 D0.058400.000000.9416
110 V0.058400.000000.9416
111 R0.058400.000000.9416
112 V0.058400.000000.9416
113 L0.058400.000000.9416
114 N0.058400.000000.9416
115 V0.058400.000000.9416
116 T0.058400.000000.9416
117 P0.058400.000000.9416
118 E0.058400.000000.9416
119 H0.058400.000000.9416
120 T0.058400.000000.9416
121 V0.058400.000000.9416
122 A0.058400.000000.9416
123 E0.058400.000000.9416
124 Q0.058400.000000.9416
125 D0.058400.000000.9416
126 E0.058400.000000.9416
127 L0.058400.000000.9416
128 L0.058400.000000.9416
129 G0.058400.000000.9416
130 K0.058400.000000.9416
131 D0.058400.000000.9416
132 L0.058400.000000.9416
133 F0.058400.000000.9416
134 A0.058400.000000.9416
135 R0.058400.000000.9416
136 N0.058400.000000.9416
137 P0.058400.000000.9416
138 H0.058400.000000.9416
139 E0.058400.000000.9416
140 C0.058400.000000.9416
141 C0.058400.000000.9416
142 R0.058400.000000.9416
143 L0.058400.000000.9416
144 R0.058400.000000.9416
145 K0.058400.000000.9416
146 V0.058400.000000.9416
147 V0.058400.000000.9416
148 P0.058400.000000.9416
149 L0.058400.000000.9416
150 G0.058400.000000.9416
151 K0.058400.000010.9416
152 T0.058400.000010.9416
153 L0.058400.000010.9416
154 R0.058400.000010.9416
155 G0.058400.000010.9416
156 Y0.058400.000010.9416
157 S0.058400.000010.9416
158 A0.058400.000010.9416
159 W0.058400.000010.9416
160 V0.058400.000010.9416
161 T0.058400.000010.9416
162 G0.058400.000000.9416
163 L0.058400.000000.9416
164 R0.058400.000000.9416
165 R0.058400.000000.9416
166 V0.058400.000000.9416
167 D0.058400.000000.9416
168 A0.058400.000000.9416
169 P0.058400.000000.9416
170 T0.058400.000000.9416
171 R0.058400.000000.9416
172 A0.058400.000000.9416
173 N0.058400.000000.9416
174 A0.058400.000000.9416
175 P0.058400.000000.9416
176 L0.058400.000000.9416
177 V0.058400.000000.9416
178 S0.058400.000000.9416
179 F0.058400.000000.9416
180 D0.058400.000000.9416
181 E0.058400.000000.9416
182 T0.058400.000000.9416
183 F0.058400.000000.9416
184 K0.058400.000000.9416
185 L0.058400.000000.9416
186 V0.058400.000000.9416
187 K0.058400.000000.9416
188 V0.058400.000000.9416
189 N0.058400.000000.9416
190 P0.058400.000000.9416
191 L0.058400.000000.9416
192 A0.058400.000000.9416
193 A0.058400.000000.9416
194 W0.058400.000000.9416
195 T0.058400.000000.9416
196 D0.058400.000000.9416
197 Q0.058400.000000.9416
198 D0.058400.000000.9416
199 V0.058400.000000.9416
200 Q0.058400.000000.9416
201 E0.058400.000000.9416
202 Y0.058400.000000.9416
203 I0.058400.000000.9416
204 A0.058400.000000.9416
205 D0.058400.000000.9416
206 N0.058400.000000.9416
207 D0.058400.000000.9416
208 V0.058400.000000.9416
209 L0.058400.000000.9416
210 V0.058400.000000.9416
211 N0.058400.000000.9416
212 P0.058400.000000.9416
213 L0.058400.000000.9416
214 V0.058400.000000.9416
215 R0.058400.000000.9416
216 E0.058400.000000.9416
217 G0.058400.000000.9416
218 Y0.058400.000000.9416
219 P0.058400.000000.9416
220 S0.058400.000000.9416
221 I0.058400.000000.9416
222 G0.058400.000000.9416
223 C0.058400.000000.9416
224 A0.058400.000000.9416
225 P0.058400.000000.9416
226 C0.058400.000000.9416
227 T0.058400.000000.9416
228 A0.058400.000000.9416
229 K0.058400.000000.9416
230 P0.058400.000000.9416
231 A0.058400.000000.9416
232 E0.058400.000000.9416
233 G0.058400.000000.9416
234 A0.058400.000000.9416
235 D0.058400.000000.9416
236 P0.058400.000000.9416
237 R0.058400.000000.9416
238 S0.058400.000000.9416
239 G0.058400.000000.9416
240 R0.058400.000000.9416
241 W0.058400.000000.9416
242 Q0.058400.000000.9416
243 G0.058400.000000.9416
244 L0.058400.000000.9416
245 A0.058400.000000.9416
246 K0.058400.000000.9416
247 T0.058400.000000.9416
248 E0.058400.000000.9416
249 C0.058400.000000.9416
250 G0.058400.000000.9416
251 L0.058400.000000.9416
252 H0.058400.000000.9416
253 A0.058400.000000.9416
254 S0.058400.000000.9416

General Statistics
Length: 254
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.00571999999999999
Exp number, first 60 AAs: 0.00121
Total prob of N-in: 0.05857
outside: from residue 1 to 254
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