TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0003

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 V	0.00869	0.00000	0.99131
2 Y	0.00869	0.00000	0.99131
3 V	0.00869	0.00000	0.99131
4 R	0.00869	0.00000	0.99131
5 H	0.00869	0.00000	0.99131
6 L	0.00869	0.00000	0.99131
7 G	0.00869	0.00000	0.99131
8 L	0.00869	0.00000	0.99131
9 R	0.00869	0.00000	0.99131
10 D	0.00869	0.00000	0.99131
11 F	0.00869	0.00000	0.99131
12 R	0.00869	0.00000	0.99131
13 S	0.00868	0.00001	0.99131
14 W	0.00868	0.00001	0.99131
15 A	0.00868	0.00001	0.99131
16 C	0.00868	0.00001	0.99131
17 V	0.00868	0.00001	0.99131
18 D	0.00868	0.00001	0.99131
19 L	0.00868	0.00001	0.99131
20 E	0.00868	0.00001	0.99131
21 L	0.00867	0.00001	0.99131
22 H	0.00867	0.00001	0.99131
23 P	0.00867	0.00001	0.99131
24 G	0.00867	0.00002	0.99131
25 R	0.00867	0.00002	0.99131
26 T	0.00867	0.00002	0.99131
27 V	0.00867	0.00002	0.99131
28 F	0.00866	0.00003	0.99131
29 V	0.00866	0.00003	0.99131
30 G	0.00866	0.00003	0.99131
31 P	0.00866	0.00002	0.99131
32 N	0.00866	0.00003	0.99131
33 G	0.00866	0.00003	0.99131
34 Y	0.00866	0.00003	0.99131
35 G	0.00866	0.00003	0.99131
36 K	0.00866	0.00002	0.99132
37 T	0.00866	0.00002	0.99132
38 N	0.00866	0.00003	0.99132
39 L	0.00865	0.00003	0.99132
40 I	0.00865	0.00003	0.99132
41 E	0.00865	0.00003	0.99132
42 A	0.00865	0.00003	0.99132
43 L	0.00865	0.00003	0.99132
44 W	0.00865	0.00003	0.99132
45 Y	0.00865	0.00003	0.99132
46 S	0.00865	0.00002	0.99132
47 T	0.00865	0.00002	0.99133
48 T	0.00865	0.00002	0.99133
49 L	0.00865	0.00002	0.99133
50 G	0.00865	0.00002	0.99133
51 S	0.00865	0.00002	0.99133
52 H	0.00865	0.00001	0.99133
53 R	0.00865	0.00001	0.99133
54 V	0.00865	0.00001	0.99133
55 S	0.00865	0.00001	0.99134
56 A	0.00865	0.00001	0.99134
57 D	0.00865	0.00001	0.99134
58 L	0.00865	0.00001	0.99134
59 P	0.00865	0.00001	0.99134
60 L	0.00865	0.00001	0.99134
61 I	0.00865	0.00001	0.99134
62 R	0.00865	0.00000	0.99134
63 V	0.00865	0.00000	0.99134
64 G	0.00865	0.00000	0.99135
65 T	0.00865	0.00000	0.99135
66 D	0.00865	0.00000	0.99135
67 R	0.00865	0.00000	0.99135
68 A	0.00865	0.00000	0.99135
69 V	0.00865	0.00000	0.99135
70 I	0.00865	0.00000	0.99135
71 S	0.00865	0.00000	0.99135
72 T	0.00865	0.00000	0.99135
73 I	0.00865	0.00000	0.99135
74 V	0.00865	0.00000	0.99135
75 V	0.00865	0.00000	0.99135
76 N	0.00865	0.00000	0.99135
77 D	0.00865	0.00000	0.99135
78 G	0.00865	0.00000	0.99135
79 R	0.00865	0.00000	0.99135
80 E	0.00865	0.00000	0.99135
81 C	0.00865	0.00000	0.99135
82 A	0.00865	0.00000	0.99135
83 V	0.00865	0.00000	0.99135
84 D	0.00865	0.00000	0.99135
85 L	0.00865	0.00000	0.99135
86 E	0.00865	0.00000	0.99135
87 I	0.00865	0.00000	0.99135
88 A	0.00865	0.00000	0.99135
89 T	0.00865	0.00000	0.99135
90 G	0.00865	0.00000	0.99135
91 R	0.00865	0.00000	0.99135
92 V	0.00865	0.00000	0.99135
93 N	0.00865	0.00000	0.99135
94 K	0.00865	0.00000	0.99135
95 A	0.00865	0.00000	0.99135
96 R	0.00865	0.00000	0.99135
97 L	0.00865	0.00000	0.99135
98 N	0.00865	0.00000	0.99135
99 R	0.00865	0.00000	0.99135
100 S	0.00865	0.00000	0.99135
101 S	0.00865	0.00000	0.99135
102 V	0.00865	0.00001	0.99135
103 R	0.00865	0.00001	0.99135
104 S	0.00864	0.00001	0.99135
105 T	0.00864	0.00001	0.99135
106 R	0.00864	0.00001	0.99135
107 D	0.00864	0.00001	0.99135
108 V	0.00859	0.00006	0.99135
109 V	0.00856	0.00009	0.99135
110 G	0.00856	0.00010	0.99135
111 V	0.00856	0.00010	0.99135
112 L	0.00856	0.00010	0.99135
113 R	0.00856	0.00010	0.99135
114 A	0.00856	0.00010	0.99135
115 V	0.00856	0.00010	0.99135
116 L	0.00856	0.00010	0.99135
117 F	0.00856	0.00010	0.99135
118 A	0.00856	0.00009	0.99135
119 P	0.00856	0.00009	0.99135
120 E	0.00856	0.00009	0.99135
121 D	0.00856	0.00009	0.99135
122 L	0.00856	0.00009	0.99135
123 G	0.00856	0.00009	0.99135
124 L	0.00856	0.00009	0.99135
125 V	0.00856	0.00008	0.99136
126 R	0.00856	0.00004	0.9914
127 G	0.00856	0.00002	0.99142
128 D	0.00856	0.00001	0.99143
129 P	0.00856	0.00001	0.99143
130 A	0.00856	0.00001	0.99143
131 D	0.00856	0.00000	0.99144
132 R	0.00856	0.00000	0.99144
133 R	0.00856	0.00000	0.99144
134 R	0.00856	0.00000	0.99144
135 Y	0.00856	0.00000	0.99144
136 L	0.00856	0.00000	0.99144
137 D	0.00856	0.00000	0.99144
138 D	0.00856	0.00000	0.99144
139 L	0.00856	0.00000	0.99144
140 A	0.00856	0.00000	0.99144
141 I	0.00856	0.00000	0.99144
142 V	0.00856	0.00000	0.99144
143 R	0.00856	0.00000	0.99144
144 R	0.00856	0.00000	0.99144
145 P	0.00856	0.00000	0.99144
146 A	0.00856	0.00000	0.99144
147 I	0.00856	0.00000	0.99144
148 A	0.00856	0.00000	0.99144
149 A	0.00856	0.00000	0.99144
150 V	0.00856	0.00000	0.99144
151 R	0.00856	0.00000	0.99144
152 A	0.00856	0.00000	0.99144
153 E	0.00856	0.00000	0.99144
154 Y	0.00856	0.00000	0.99144
155 E	0.00856	0.00000	0.99144
156 R	0.00856	0.00000	0.99144
157 V	0.00856	0.00000	0.99144
158 L	0.00856	0.00000	0.99144
159 R	0.00856	0.00000	0.99144
160 Q	0.00856	0.00000	0.99144
161 R	0.00856	0.00000	0.99144
162 T	0.00856	0.00000	0.99144
163 A	0.00856	0.00000	0.99144
164 L	0.00856	0.00000	0.99144
165 L	0.00856	0.00000	0.99144
166 K	0.00856	0.00000	0.99144
167 S	0.00856	0.00000	0.99144
168 V	0.00856	0.00000	0.99144
169 P	0.00856	0.00000	0.99144
170 G	0.00856	0.00000	0.99144
171 A	0.00856	0.00000	0.99144
172 R	0.00856	0.00000	0.99144
173 Y	0.00856	0.00000	0.99144
174 R	0.00856	0.00000	0.99144
175 G	0.00856	0.00000	0.99144
176 D	0.00856	0.00000	0.99144
177 R	0.00856	0.00000	0.99144
178 G	0.00856	0.00000	0.99144
179 V	0.00856	0.00000	0.99144
180 F	0.00856	0.00000	0.99144
181 D	0.00856	0.00000	0.99144
182 T	0.00856	0.00000	0.99144
183 L	0.00856	0.00000	0.99144
184 E	0.00856	0.00000	0.99144
185 V	0.00856	0.00000	0.99144
186 W	0.00856	0.00000	0.99144
187 D	0.00856	0.00000	0.99144
188 S	0.00856	0.00000	0.99144
189 R	0.00856	0.00000	0.99144
190 L	0.00856	0.00000	0.99144
191 A	0.00856	0.00000	0.99144
192 E	0.00856	0.00000	0.99144
193 H	0.00856	0.00000	0.99144
194 G	0.00856	0.00000	0.99144
195 A	0.00856	0.00000	0.99144
196 E	0.00856	0.00000	0.99144
197 L	0.00856	0.00000	0.99144
198 V	0.00856	0.00000	0.99144
199 A	0.00856	0.00000	0.99144
200 A	0.00856	0.00000	0.99144
201 R	0.00856	0.00000	0.99144
202 I	0.00856	0.00000	0.99144
203 D	0.00856	0.00000	0.99144
204 L	0.00856	0.00000	0.99144
205 V	0.00856	0.00000	0.99144
206 N	0.00856	0.00000	0.99144
207 Q	0.00856	0.00000	0.99144
208 L	0.00856	0.00000	0.99144
209 A	0.00856	0.00000	0.99144
210 P	0.00856	0.00000	0.99144
211 E	0.00856	0.00000	0.99144
212 V	0.00856	0.00000	0.99144
213 K	0.00856	0.00000	0.99144
214 K	0.00856	0.00000	0.99144
215 A	0.00856	0.00000	0.99144
216 Y	0.00856	0.00000	0.99144
217 Q	0.00856	0.00000	0.99144
218 L	0.00856	0.00000	0.99144
219 L	0.00856	0.00000	0.99144
220 A	0.00856	0.00000	0.99144
221 P	0.00856	0.00000	0.99144
222 E	0.00856	0.00000	0.99144
223 S	0.00856	0.00000	0.99144
224 R	0.00856	0.00000	0.99144
225 S	0.00856	0.00000	0.99144
226 A	0.00856	0.00000	0.99144
227 S	0.00856	0.00000	0.99144
228 I	0.00856	0.00000	0.99144
229 G	0.00856	0.00000	0.99144
230 Y	0.00856	0.00000	0.99144
231 R	0.00856	0.00000	0.99144
232 A	0.00856	0.00000	0.99144
233 S	0.00856	0.00000	0.99144
234 M	0.00856	0.00000	0.99144
235 D	0.00856	0.00000	0.99144
236 V	0.00856	0.00000	0.99144
237 T	0.00856	0.00000	0.99144
238 G	0.00856	0.00000	0.99144
239 P	0.00856	0.00000	0.99144
240 S	0.00856	0.00000	0.99144
241 E	0.00856	0.00000	0.99144
242 Q	0.00856	0.00000	0.99144
243 S	0.00856	0.00000	0.99144
244 D	0.00856	0.00000	0.99144
245 I	0.00856	0.00000	0.99144
246 D	0.00856	0.00000	0.99144
247 R	0.00856	0.00000	0.99144
248 Q	0.00856	0.00000	0.99144
249 L	0.00856	0.00000	0.99144
250 L	0.00856	0.00000	0.99144
251 A	0.00856	0.00000	0.99144
252 A	0.00856	0.00000	0.99144
253 R	0.00856	0.00000	0.99144
254 L	0.00856	0.00000	0.99144
255 L	0.00856	0.00000	0.99144
256 A	0.00856	0.00000	0.99144
257 A	0.00856	0.00000	0.99144
258 L	0.00856	0.00000	0.99144
259 A	0.00856	0.00000	0.99144
260 A	0.00856	0.00000	0.99144
261 R	0.00856	0.00000	0.99144
262 R	0.00856	0.00000	0.99144
263 D	0.00856	0.00000	0.99144
264 A	0.00856	0.00000	0.99144
265 E	0.00856	0.00000	0.99144
266 L	0.00856	0.00000	0.99144
267 E	0.00856	0.00000	0.99144
268 R	0.00856	0.00000	0.99144
269 G	0.00856	0.00000	0.99144
270 V	0.00856	0.00000	0.99144
271 C	0.00856	0.00000	0.99144
272 L	0.00856	0.00000	0.99144
273 V	0.00856	0.00000	0.99144
274 G	0.00856	0.00000	0.99144
275 P	0.00856	0.00000	0.99144
276 H	0.00856	0.00000	0.99144
277 R	0.00856	0.00000	0.99144
278 D	0.00856	0.00000	0.99144
279 D	0.00856	0.00000	0.99144
280 L	0.00856	0.00000	0.99144
281 I	0.00856	0.00000	0.99144
282 L	0.00856	0.00000	0.99144
283 R	0.00856	0.00000	0.99144
284 L	0.00856	0.00000	0.99144
285 G	0.00856	0.00000	0.99144
286 D	0.00856	0.00000	0.99144
287 Q	0.00856	0.00000	0.99144
288 P	0.00856	0.00000	0.99144
289 A	0.00856	0.00000	0.99144
290 K	0.00856	0.00000	0.99144
291 G	0.00855	0.00005	0.99141
292 F	0.00854	0.00006	0.9914
293 A	0.00854	0.00006	0.99139
294 S	0.00854	0.00007	0.99139
295 H	0.00854	0.00007	0.99139
296 G	0.00854	0.00007	0.99139
297 E	0.00854	0.00007	0.99139
298 A	0.00854	0.00007	0.99139
299 W	0.00854	0.00007	0.99139
300 S	0.00854	0.00007	0.99139
301 L	0.00854	0.00007	0.99139
302 A	0.00854	0.00007	0.99139
303 V	0.00854	0.00007	0.99139
304 A	0.00854	0.00007	0.99139
305 L	0.00854	0.00007	0.99139
306 R	0.00854	0.00007	0.99139
307 L	0.00854	0.00007	0.99139
308 A	0.00854	0.00007	0.99139
309 A	0.00855	0.00006	0.99139
310 Y	0.00856	0.00005	0.99139
311 Q	0.00858	0.00003	0.99139
312 L	0.00858	0.00003	0.99139
313 L	0.00858	0.00002	0.99139
314 R	0.00859	0.00001	0.99141
315 V	0.00859	0.00001	0.99141
316 D	0.00859	0.00000	0.99141
317 G	0.00859	0.00000	0.99141
318 G	0.00859	0.00000	0.99141
319 E	0.00859	0.00000	0.99141
320 P	0.00859	0.00000	0.99141
321 V	0.00859	0.00000	0.99141
322 L	0.00859	0.00000	0.99141
323 L	0.00859	0.00000	0.99141
324 L	0.00859	0.00000	0.99141
325 D	0.00859	0.00000	0.99141
326 D	0.00859	0.00000	0.99141
327 V	0.00859	0.00000	0.99141
328 F	0.00859	0.00000	0.99141
329 A	0.00859	0.00000	0.99141
330 E	0.00859	0.00000	0.99141
331 L	0.00859	0.00000	0.99141
332 D	0.00859	0.00000	0.99141
333 V	0.00859	0.00000	0.99141
334 M	0.00859	0.00000	0.99141
335 R	0.00859	0.00000	0.99141
336 R	0.00859	0.00000	0.99141
337 R	0.00859	0.00000	0.99141
338 A	0.00859	0.00001	0.99141
339 L	0.00859	0.00001	0.99141
340 A	0.00859	0.00001	0.99141
341 T	0.00859	0.00001	0.9914
342 A	0.00859	0.00001	0.9914
343 A	0.00859	0.00001	0.9914
344 E	0.00859	0.00001	0.9914
345 S	0.00859	0.00001	0.9914
346 A	0.00859	0.00001	0.9914
347 E	0.00859	0.00001	0.9914
348 Q	0.00859	0.00001	0.9914
349 V	0.00859	0.00001	0.9914
350 L	0.00859	0.00001	0.9914
351 V	0.00859	0.00001	0.9914
352 T	0.00859	0.00001	0.9914
353 A	0.00859	0.00001	0.9914
354 A	0.00859	0.00001	0.9914
355 V	0.00859	0.00001	0.9914
356 L	0.00859	0.00001	0.9914
357 E	0.00859	0.00001	0.9914
358 D	0.00859	0.00001	0.9914
359 I	0.00859	0.00001	0.9914
360 P	0.00859	0.00001	0.9914
361 A	0.00859	0.00001	0.9914
362 G	0.00859	0.00000	0.9914
363 W	0.00859	0.00000	0.9914
364 D	0.00860	0.00000	0.9914
365 A	0.00860	0.00000	0.9914
366 R	0.00860	0.00000	0.9914
367 R	0.00860	0.00000	0.9914
368 V	0.00860	0.00000	0.9914
369 H	0.00860	0.00000	0.9914
370 I	0.00860	0.00000	0.9914
371 D	0.00860	0.00000	0.9914
372 V	0.00860	0.00000	0.9914
373 R	0.00860	0.00000	0.9914
374 A	0.00860	0.00000	0.9914
375 D	0.00860	0.00000	0.9914
376 D	0.00860	0.00000	0.9914
377 T	0.00860	0.00000	0.9914
378 G	0.00860	0.00000	0.9914
379 S	0.00860	0.00000	0.9914
380 M	0.00860	0.00000	0.9914
381 S	0.00860	0.00000	0.9914
382 V	0.00860	0.00000	0.9914
383 V	0.00860	0.00000	0.9914
384 L	0.00860	0.00000	0.9914
385 P	0.00860	0.00000	0.9914

General Statistics

Length: 385

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.00439999999999999

Exp number, first 60 AAs: 0.00091

Total prob of N-in: 0.00869

outside: from residue 1 to 385

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