TransMembrane prediction using Hidden Markov Models for Rv2393




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.055250.000000.94475
2 T0.055250.000000.94475
3 A0.055250.000000.94475
4 P0.055250.000000.94475
5 A0.055250.000000.94475
6 T0.055250.000000.94475
7 M0.055250.000010.94475
8 Q0.055250.000010.94475
9 S0.055240.000010.94475
10 A0.055240.000020.94474
11 A0.055230.000020.94474
12 M0.055190.000070.94474
13 L0.055110.000150.94474
14 R0.055110.000150.94474
15 S0.055110.000150.94474
16 G0.055110.000150.94474
17 A0.055110.000150.94474
18 I0.055110.000150.94474
19 E0.055110.000150.94474
20 A0.055110.000150.94474
21 P0.055110.000150.94474
22 P0.055110.000150.94474
23 A0.055110.000150.94474
24 T0.055110.000150.94474
25 M0.055110.000150.94474
26 Q0.055110.000150.94474
27 S0.055110.000140.94474
28 A0.055110.000140.94474
29 A0.055110.000140.94475
30 M0.055110.000110.94478
31 R0.055110.000070.94482
32 W0.055100.000080.94482
33 G0.055100.000070.94483
34 H0.055100.000070.94483
35 L0.055100.000060.94485
36 P0.055100.000020.94488
37 L0.055100.000020.94488
38 A0.055100.000020.94488
39 E0.055100.000020.94488
40 E0.055100.000020.94488
41 S0.055100.000020.94488
42 G0.055100.000020.94488
43 T0.055100.000020.94488
44 I0.055100.000020.94488
45 A0.055100.000020.94488
46 P0.055100.000020.94488
47 Q0.055100.000020.94488
48 L0.055100.000020.94488
49 V0.055100.000020.94488
50 L0.055100.000020.94488
51 T0.055100.000020.94489
52 A0.055100.000010.94489
53 H0.055100.000010.94489
54 G0.055100.000010.94489
55 S0.055100.000000.9449
56 K0.055100.000000.9449
57 D0.055100.000000.9449
58 P0.055100.000000.9449
59 R0.055100.000000.9449
60 S0.055100.000000.9449
61 A0.055100.000000.9449
62 A0.055100.000000.9449
63 N0.055100.000000.9449
64 A0.055100.000000.9449
65 R0.055100.000000.9449
66 A0.055100.000000.9449
67 I0.055100.000000.9449
68 A0.055100.000000.9449
69 G0.055100.000000.9449
70 R0.055100.000000.9449
71 L0.055100.000000.9449
72 A0.055100.000000.9449
73 R0.055100.000000.9449
74 M0.055100.000000.9449
75 R0.055100.000000.9449
76 P0.055100.000000.9449
77 G0.055100.000000.9449
78 L0.055100.000000.9449
79 D0.055100.000000.9449
80 V0.055100.000000.9449
81 R0.055100.000000.9449
82 V0.055100.000000.9449
83 A0.055100.000000.9449
84 F0.055100.000000.9449
85 C0.055100.000000.9449
86 E0.055100.000000.9449
87 L0.055100.000000.9449
88 N0.055100.000000.9449
89 S0.055100.000000.9449
90 P0.055100.000000.9449
91 N0.055100.000000.9449
92 L0.055100.000000.9449
93 V0.055100.000000.9449
94 D0.055100.000000.9449
95 V0.055100.000000.9449
96 L0.055090.000010.9449
97 N0.055090.000020.9449
98 R0.055090.000020.9449
99 C0.055070.000030.9449
100 R0.055070.000040.9449
101 G0.055030.000080.94488
102 A0.055030.000080.94488
103 A0.055030.000090.94488
104 V0.055030.000090.94488
105 V0.055030.000090.94488
106 T0.055030.000090.94488
107 P0.055030.000090.94488
108 L0.055030.000090.94488
109 L0.055030.000090.94488
110 L0.055030.000090.94488
111 A0.055030.000090.94488
112 D0.055030.000090.94488
113 A0.055030.000090.94488
114 Y0.055030.000080.94489
115 H0.055030.000080.94489
116 A0.055030.000070.94489
117 R0.055030.000060.94491
118 V0.055030.000050.94491
119 D0.055040.000010.94494
120 I0.055040.000010.94495
121 P0.055040.000010.94495
122 A0.055040.000000.94495
123 Q0.055040.000000.94495
124 I0.055040.000000.94495
125 A0.055040.000000.94495
126 S0.055040.000000.94496
127 C0.055040.000000.94496
128 R0.055040.000000.94496
129 V0.055040.000000.94496
130 G0.055040.000000.94496
131 H0.055040.000000.94496
132 R0.055040.000000.94496
133 V0.055040.000000.94496
134 R0.055040.000000.94496
135 Q0.055040.000000.94496
136 A0.055040.000000.94496
137 S0.055040.000000.94496
138 V0.055040.000000.94496
139 L0.055040.000000.94496
140 G0.055040.000000.94496
141 E0.055040.000000.94496
142 D0.055040.000000.94496
143 I0.055040.000000.94496
144 R0.055040.000000.94496
145 L0.055040.000000.94496
146 V0.055040.000000.94496
147 S0.055040.000000.94496
148 A0.055040.000000.94496
149 L0.055040.000000.94496
150 H0.055040.000000.94496
151 E0.055040.000000.94495
152 R0.055040.000010.94495
153 L0.055020.000070.94491
154 T0.055010.000090.9449
155 E0.055010.000100.94489
156 L0.054980.000170.94485
157 G0.054970.000230.94479
158 V0.054970.000290.94474
159 S0.054970.000330.9447
160 P0.054960.000370.94467
161 F0.054960.000420.94462
162 D0.054960.000450.94459
163 H0.054960.000490.94455
164 T0.054950.000530.94452
165 L0.054950.000540.94451
166 G0.054950.000540.94451
167 V0.054950.000540.94451
168 V0.054950.000540.94451
169 V0.054950.000540.94451
170 L0.054950.000540.94451
171 A0.054950.000540.94451
172 I0.054950.000540.94451
173 G0.054960.000520.94452
174 S0.054980.000490.94452
175 S0.055010.000460.94454
176 H0.055060.000380.94455
177 P0.055080.000360.94456
178 A0.055090.000350.94456
179 A0.055130.000300.94457
180 N0.055240.000170.94459
181 A0.055320.000090.94459
182 R0.055370.000030.9446
183 T0.055380.000020.9446
184 S0.055390.000020.9446
185 T0.055390.000020.9446
186 V0.055380.000020.9446
187 A0.055390.000010.9446
188 S0.055390.000010.9446
189 R0.055390.000010.9446
190 L0.055390.000020.9446
191 A0.055380.000020.9446
192 E0.055380.000020.9446
193 G0.055380.000020.9446
194 T0.055380.000020.94459
195 Q0.055380.000020.94459
196 W0.055380.000030.94459
197 A0.055380.000030.94459
198 A0.055380.000030.94459
199 V0.055380.000030.94459
200 T0.055380.000030.94459
201 T0.055380.000030.94459
202 A0.055380.000030.94459
203 F0.055380.000030.94459
204 I0.055380.000030.94459
205 T0.055380.000020.9446
206 R0.055380.000020.9446
207 P0.055380.000020.9446
208 E0.055380.000010.9446
209 A0.055380.000010.9446
210 S0.055390.000010.9446
211 L0.055390.000010.9446
212 A0.055390.000010.9446
213 D0.055390.000000.9446
214 A0.055390.000000.9446
215 T0.055390.000000.9446
216 D0.055390.000000.9446
217 R0.055390.000000.9446
218 L0.055390.000000.9446
219 R0.055390.000000.9446
220 R0.055390.000010.9446
221 H0.055080.000520.94439
222 G0.054790.000990.94422
223 A0.054730.001110.94417
224 R0.054710.001140.94416
225 R0.054620.001280.9441
226 M0.054420.001980.9436
227 V0.053840.003390.94277
228 I0.053800.003630.94257
229 A0.053790.003640.94256
230 P0.053790.003640.94256
231 W0.053790.003640.94256
232 L0.053790.003640.94256
233 L0.053790.003640.94256
234 A0.053790.003640.94256
235 P0.053790.003640.94256
236 G0.053790.003640.94257
237 I0.053790.003640.94257
238 L0.053800.003610.94258
239 S0.053930.003260.94281
240 D0.054170.002680.94315
241 R0.054190.002620.94319
242 V0.054200.002600.9432
243 R0.054260.002480.94326
244 G0.054300.002410.94328
245 Y0.054550.001890.94356
246 A0.055610.000630.94377
247 R0.055720.000400.94388
248 E0.055700.000450.94385
249 A0.055350.001380.94326
250 G0.055240.001620.94314
251 I0.055120.002260.94262
252 A0.055120.002290.94259
253 M0.055120.002300.94258
254 A0.055120.002310.94258
255 Q0.055120.002310.94258
256 P0.055120.002310.94258
257 L0.055120.002310.94257
258 G0.055120.002310.94257
259 A0.055120.002310.94257
260 H0.055120.002310.94257
261 P0.055120.002310.94257
262 M0.055120.002310.94257
263 V0.055130.002300.94257
264 A0.055150.002270.94259
265 A0.055210.002200.9426
266 T0.055250.002140.94261
267 M0.055350.001990.94265
268 W0.055450.001820.94273
269 D0.056530.000270.94319
270 R0.056590.000190.94322
271 Y0.056600.000160.94323
272 R0.056700.000020.94328
273 Q0.056720.000010.94328
274 A0.056720.000000.94328
275 V0.056720.000000.94328
276 A0.056720.000000.94328
277 G0.056720.000000.94328
278 R0.056720.000000.94328
279 I0.056720.000000.94328
280 A0.056720.000000.94328
281 A0.056720.000000.94328

General Statistics
Length: 281
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.13059
Exp number, first 60 AAs: 0.00347
Total prob of N-in: 0.05525
outside: from residue 1 to 281
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