TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv1726

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.10580	0.00000	0.8942
2 T	0.10580	0.00000	0.8942
3 A	0.10580	0.00000	0.8942
4 T	0.10580	0.00000	0.8942
5 L	0.10580	0.00000	0.8942
6 T	0.10580	0.00000	0.8942
7 K	0.10580	0.00000	0.8942
8 T	0.10580	0.00000	0.8942
9 L	0.10580	0.00000	0.8942
10 G	0.10580	0.00000	0.8942
11 S	0.10580	0.00000	0.8942
12 L	0.10580	0.00000	0.8942
13 D	0.10580	0.00000	0.8942
14 D	0.10580	0.00000	0.8942
15 F	0.10580	0.00000	0.8942
16 R	0.10580	0.00000	0.8942
17 G	0.10580	0.00000	0.8942
18 T	0.10580	0.00000	0.8942
19 L	0.10580	0.00000	0.8942
20 C	0.10580	0.00000	0.8942
21 V	0.10580	0.00000	0.8942
22 P	0.10580	0.00000	0.8942
23 G	0.10580	0.00000	0.8942
24 D	0.10580	0.00000	0.8942
25 P	0.10580	0.00000	0.8942
26 D	0.10580	0.00000	0.8942
27 Y	0.10580	0.00000	0.8942
28 P	0.10580	0.00000	0.8942
29 R	0.10580	0.00000	0.8942
30 V	0.10580	0.00000	0.8942
31 R	0.10580	0.00000	0.8942
32 A	0.10580	0.00000	0.8942
33 I	0.10580	0.00000	0.8942
34 W	0.10580	0.00000	0.8942
35 N	0.10580	0.00000	0.8942
36 G	0.10580	0.00000	0.8942
37 Q	0.10580	0.00000	0.8942
38 V	0.10580	0.00000	0.8942
39 A	0.10580	0.00000	0.8942
40 R	0.10580	0.00000	0.8942
41 E	0.10580	0.00000	0.89419
42 P	0.10580	0.00000	0.89419
43 A	0.10580	0.00000	0.89419
44 L	0.10580	0.00000	0.89419
45 I	0.10580	0.00000	0.89419
46 A	0.10580	0.00000	0.89419
47 T	0.10580	0.00000	0.89419
48 C	0.10580	0.00000	0.89419
49 H	0.10580	0.00000	0.89419
50 D	0.10580	0.00000	0.89419
51 A	0.10580	0.00000	0.89419
52 C	0.10580	0.00000	0.89419
53 D	0.10580	0.00000	0.89419
54 V	0.10580	0.00000	0.89419
55 R	0.10580	0.00000	0.89419
56 T	0.10579	0.00001	0.89419
57 V	0.10578	0.00002	0.89419
58 L	0.10578	0.00002	0.89419
59 R	0.10578	0.00002	0.89419
60 R	0.10578	0.00002	0.89419
61 A	0.10577	0.00003	0.89419
62 V	0.10577	0.00003	0.89419
63 D	0.10577	0.00004	0.89419
64 A	0.10575	0.00005	0.89419
65 G	0.10574	0.00007	0.89419
66 M	0.10571	0.00010	0.89419
67 V	0.10474	0.00113	0.89412
68 T	0.10468	0.00120	0.89412
69 A	0.10441	0.00147	0.89412
70 V	0.10433	0.00155	0.89412
71 R	0.10431	0.00158	0.89412
72 G	0.10360	0.00230	0.8941
73 G	0.10344	0.00246	0.89409
74 G	0.10328	0.00263	0.89409
75 H	0.10309	0.00283	0.89409
76 N	0.10289	0.00305	0.89407
77 V	0.10270	0.00348	0.89383
78 A	0.10267	0.00351	0.89381
79 G	0.10267	0.00352	0.89382
80 T	0.10266	0.00352	0.89382
81 A	0.10266	0.00353	0.89382
82 L	0.10266	0.00352	0.89382
83 C	0.10266	0.00351	0.89383
84 D	0.10266	0.00350	0.89384
85 G	0.10266	0.00350	0.89384
86 G	0.10266	0.00350	0.89384
87 V	0.10266	0.00349	0.89385
88 V	0.10266	0.00348	0.89386
89 I	0.10267	0.00334	0.894
90 D	0.10274	0.00211	0.89514
91 L	0.10275	0.00205	0.89521
92 S	0.10275	0.00180	0.89545
93 A	0.10275	0.00171	0.89553
94 M	0.10276	0.00157	0.89568
95 R	0.10277	0.00088	0.89635
96 A	0.10277	0.00082	0.89642
97 V	0.10277	0.00072	0.89651
98 S	0.10279	0.00053	0.89667
99 L	0.10281	0.00039	0.8968
100 D	0.10306	0.00000	0.89694
101 P	0.10306	0.00000	0.89694
102 A	0.10306	0.00000	0.89694
103 T	0.10306	0.00000	0.89694
104 G	0.10306	0.00000	0.89694
105 R	0.10306	0.00000	0.89694
106 V	0.10306	0.00000	0.89694
107 R	0.10306	0.00000	0.89694
108 V	0.10306	0.00000	0.89694
109 Q	0.10306	0.00000	0.89694
110 G	0.10306	0.00000	0.89694
111 G	0.10306	0.00000	0.89694
112 A	0.10306	0.00000	0.89694
113 T	0.10306	0.00000	0.89694
114 L	0.10306	0.00000	0.89694
115 A	0.10306	0.00000	0.89694
116 D	0.10306	0.00000	0.89694
117 L	0.10306	0.00001	0.89694
118 D	0.10306	0.00001	0.89694
119 H	0.10304	0.00003	0.89694
120 A	0.10300	0.00008	0.89692
121 T	0.10291	0.00021	0.89688
122 V	0.09731	0.00626	0.89642
123 P	0.09533	0.00844	0.89623
124 F	0.09003	0.01424	0.89573
125 A	0.08733	0.01788	0.89479
126 R	0.08572	0.02016	0.89411
127 V	0.04701	0.06971	0.88327
128 A	0.03468	0.08395	0.88137
129 P	0.01785	0.10142	0.88073
130 A	0.00907	0.11123	0.8797
131 G	0.00645	0.11432	0.87924
132 I	0.00528	0.11589	0.87882
133 V	0.00507	0.11618	0.87875
134 T	0.00498	0.11631	0.87872
135 T	0.00494	0.11634	0.87871
136 T	0.00492	0.11637	0.87871
137 G	0.00489	0.11640	0.87871
138 V	0.00489	0.11640	0.87871
139 G	0.00489	0.11640	0.87872
140 G	0.00489	0.11635	0.87876
141 L	0.00489	0.11632	0.8788
142 T	0.00490	0.11615	0.87895
143 L	0.00491	0.11598	0.87911
144 G	0.00502	0.11530	0.87967
145 G	0.00555	0.10930	0.88514
146 G	0.00583	0.10670	0.88747
147 V	0.00636	0.10025	0.89339
148 G	0.00776	0.09382	0.89842
149 W	0.00891	0.08927	0.90181
150 T	0.02025	0.03848	0.94127
151 T	0.02235	0.02280	0.95485
152 R	0.02295	0.00383	0.97322
153 R	0.02303	0.00045	0.97651
154 F	0.02272	0.00055	0.97673
155 G	0.02273	0.00049	0.97678
156 L	0.02270	0.00049	0.97681
157 S	0.02273	0.00039	0.97688
158 C	0.02273	0.00039	0.97688
159 D	0.02273	0.00039	0.97688
160 N	0.02272	0.00040	0.97687
161 L	0.02252	0.00060	0.97687
162 V	0.02248	0.00065	0.97687
163 A	0.02248	0.00065	0.97687
164 V	0.02248	0.00065	0.97687
165 R	0.02248	0.00065	0.97687
166 L	0.02248	0.00065	0.97687
167 V	0.02248	0.00065	0.97687
168 T	0.02248	0.00065	0.97687
169 A	0.02248	0.00064	0.97688
170 A	0.02248	0.00064	0.97688
171 G	0.02248	0.00064	0.97688
172 D	0.02248	0.00062	0.9769
173 Y	0.02248	0.00062	0.97691
174 L	0.02248	0.00061	0.97691
175 S	0.02248	0.00059	0.97693
176 V	0.02248	0.00052	0.977
177 D	0.02248	0.00006	0.97746
178 D	0.02248	0.00003	0.97749
179 E	0.02248	0.00001	0.97751
180 R	0.02248	0.00000	0.97752
181 D	0.02248	0.00000	0.97752
182 P	0.02248	0.00000	0.97752
183 E	0.02248	0.00000	0.97752
184 L	0.02247	0.00001	0.97752
185 M	0.02246	0.00002	0.97752
186 W	0.02244	0.00005	0.97751
187 G	0.02243	0.00006	0.97751
188 L	0.02242	0.00006	0.97751
189 R	0.02242	0.00006	0.97751
190 G	0.02238	0.00011	0.97751
191 G	0.02236	0.00014	0.97751
192 G	0.02233	0.00017	0.9775
193 G	0.02230	0.00020	0.9775
194 N	0.02224	0.00028	0.97748
195 F	0.02204	0.00063	0.97733
196 G	0.02193	0.00089	0.97717
197 I	0.02164	0.00186	0.97649
198 V	0.02160	0.00196	0.97644
199 T	0.02157	0.00204	0.97638
200 E	0.02156	0.00209	0.97636
201 F	0.02150	0.00224	0.97627
202 E	0.02144	0.00246	0.9761
203 F	0.02129	0.00309	0.97562
204 A	0.02125	0.00332	0.97543
205 T	0.02124	0.00334	0.97542
206 H	0.02124	0.00334	0.97541
207 P	0.02123	0.00335	0.97542
208 F	0.02123	0.00335	0.97543
209 G	0.02123	0.00334	0.97544
210 P	0.02123	0.00332	0.97545
211 V	0.02123	0.00332	0.97546
212 A	0.02123	0.00331	0.97546
213 V	0.02123	0.00328	0.97549
214 A	0.02124	0.00326	0.97551
215 G	0.02124	0.00321	0.97555
216 F	0.02125	0.00319	0.97557
217 V	0.02126	0.00312	0.97562
218 V	0.02139	0.00283	0.97578
219 Y	0.02156	0.00251	0.97593
220 R	0.02250	0.00116	0.97634
221 L	0.02264	0.00094	0.97643
222 D	0.02323	0.00021	0.97656
223 D	0.02334	0.00005	0.97661
224 G	0.02335	0.00003	0.97662
225 P	0.02335	0.00002	0.97663
226 A	0.02335	0.00002	0.97663
227 V	0.02335	0.00002	0.97663
228 L	0.02335	0.00001	0.97664
229 R	0.02336	0.00001	0.97664
230 G	0.02336	0.00001	0.97664
231 Y	0.02336	0.00000	0.97664
232 R	0.02336	0.00000	0.97664
233 Q	0.02336	0.00000	0.97664
234 F	0.02336	0.00001	0.97664
235 A	0.02336	0.00001	0.97664
236 A	0.02336	0.00001	0.97664
237 A	0.02336	0.00001	0.97664
238 A	0.02336	0.00001	0.97664
239 P	0.02336	0.00001	0.97664
240 E	0.02336	0.00001	0.97664
241 E	0.02336	0.00001	0.97664
242 V	0.02335	0.00001	0.97664
243 T	0.02335	0.00001	0.97664
244 T	0.02335	0.00001	0.97664
245 I	0.02335	0.00001	0.97664
246 V	0.02335	0.00001	0.97664
247 V	0.02335	0.00001	0.97664
248 L	0.02335	0.00001	0.97664
249 R	0.02335	0.00001	0.97664
250 H	0.02335	0.00001	0.97664
251 A	0.02335	0.00001	0.97664
252 P	0.02335	0.00001	0.97664
253 P	0.02336	0.00000	0.97664
254 A	0.02336	0.00000	0.97664
255 P	0.02336	0.00000	0.97664
256 W	0.02336	0.00000	0.97664
257 I	0.02336	0.00000	0.97664
258 P	0.02336	0.00000	0.97664
259 V	0.02336	0.00000	0.97665
260 D	0.02336	0.00000	0.97665
261 Q	0.02336	0.00000	0.97665
262 R	0.02335	0.00000	0.97665
263 G	0.02335	0.00000	0.97665
264 K	0.02335	0.00001	0.97665
265 P	0.02334	0.00003	0.97664
266 V	0.02332	0.00005	0.97663
267 V	0.02331	0.00005	0.97663
268 M	0.02331	0.00005	0.97663
269 I	0.02331	0.00006	0.97663
270 G	0.02331	0.00006	0.97663
271 A	0.02331	0.00006	0.97663
272 V	0.02331	0.00006	0.97663
273 H	0.02331	0.00006	0.97663
274 T	0.02331	0.00006	0.97663
275 G	0.02331	0.00006	0.97663
276 S	0.02331	0.00006	0.97663
277 I	0.02331	0.00006	0.97663
278 Q	0.02331	0.00006	0.97663
279 T	0.02331	0.00006	0.97663
280 G	0.02331	0.00006	0.97663
281 I	0.02331	0.00005	0.97663
282 E	0.02331	0.00005	0.97663
283 A	0.02331	0.00004	0.97664
284 L	0.02331	0.00003	0.97665
285 R	0.02332	0.00001	0.97666
286 P	0.02332	0.00001	0.97667
287 V	0.02332	0.00001	0.97667
288 K	0.02332	0.00000	0.97667
289 S	0.02332	0.00000	0.97667
290 L	0.02332	0.00000	0.97667
291 A	0.02332	0.00000	0.97667
292 R	0.02332	0.00000	0.97667
293 P	0.02332	0.00000	0.97667
294 V	0.02332	0.00000	0.97667
295 A	0.02332	0.00000	0.97667
296 D	0.02332	0.00000	0.97667
297 T	0.02332	0.00000	0.97667
298 V	0.02332	0.00000	0.97667
299 W	0.02332	0.00000	0.97667
300 P	0.02332	0.00000	0.97667
301 T	0.02332	0.00000	0.97667
302 P	0.02332	0.00000	0.97667
303 F	0.02332	0.00000	0.97667
304 L	0.02332	0.00000	0.97667
305 A	0.02332	0.00000	0.97667
306 H	0.02332	0.00000	0.97667
307 Q	0.02332	0.00000	0.97667
308 A	0.02332	0.00000	0.97667
309 V	0.02332	0.00000	0.97667
310 L	0.02332	0.00000	0.97667
311 D	0.02332	0.00000	0.97667
312 A	0.02332	0.00000	0.97667
313 S	0.02332	0.00000	0.97667
314 N	0.02332	0.00000	0.97667
315 P	0.02332	0.00000	0.97667
316 A	0.02332	0.00000	0.97667
317 G	0.02332	0.00000	0.97667
318 H	0.02332	0.00000	0.97667
319 R	0.02332	0.00000	0.97667
320 Y	0.02332	0.00000	0.97667
321 Y	0.02332	0.00000	0.97667
322 W	0.02332	0.00000	0.97667
323 K	0.02332	0.00000	0.97667
324 S	0.02332	0.00000	0.97667
325 D	0.02332	0.00000	0.97667
326 H	0.02332	0.00000	0.97667
327 L	0.02332	0.00000	0.97667
328 A	0.02332	0.00000	0.97667
329 E	0.02332	0.00000	0.97667
330 L	0.02332	0.00000	0.97667
331 N	0.02332	0.00000	0.97667
332 D	0.02332	0.00000	0.97667
333 E	0.02332	0.00000	0.97667
334 A	0.02332	0.00000	0.97667
335 I	0.02332	0.00000	0.97667
336 D	0.02332	0.00000	0.97667
337 L	0.02332	0.00000	0.97667
338 L	0.02332	0.00000	0.97667
339 V	0.02332	0.00000	0.97667
340 E	0.02332	0.00000	0.97667
341 Q	0.02332	0.00000	0.97667
342 T	0.02332	0.00000	0.97667
343 A	0.02332	0.00000	0.97667
344 Q	0.02332	0.00000	0.97667
345 L	0.02332	0.00000	0.97667
346 S	0.02332	0.00000	0.97667
347 S	0.02332	0.00001	0.97667
348 P	0.02332	0.00001	0.97667
349 D	0.02332	0.00001	0.97667
350 S	0.02332	0.00001	0.97667
351 L	0.02332	0.00001	0.97666
352 I	0.02332	0.00001	0.97666
353 G	0.02332	0.00001	0.97666
354 I	0.02332	0.00001	0.97666
355 F	0.02332	0.00001	0.97666
356 Q	0.02332	0.00001	0.97666
357 L	0.02332	0.00001	0.97666
358 G	0.02332	0.00001	0.97666
359 G	0.02332	0.00001	0.97666
360 A	0.02332	0.00001	0.97666
361 A	0.02332	0.00001	0.97666
362 A	0.02332	0.00001	0.97666
363 R	0.02332	0.00001	0.97666
364 G	0.02333	0.00001	0.97666
365 G	0.02333	0.00001	0.97666
366 E	0.02333	0.00001	0.97666
367 R	0.02333	0.00000	0.97666
368 S	0.02333	0.00000	0.97666
369 C	0.02333	0.00000	0.97666
370 F	0.02333	0.00000	0.97666
371 P	0.02333	0.00000	0.97666
372 S	0.02333	0.00000	0.97666
373 R	0.02333	0.00000	0.97666
374 H	0.02333	0.00000	0.97666
375 A	0.02333	0.00000	0.97666
376 R	0.02333	0.00000	0.97666
377 F	0.02333	0.00000	0.97666
378 M	0.02333	0.00000	0.97666
379 V	0.02333	0.00000	0.97666
380 N	0.02333	0.00000	0.97666
381 Y	0.02333	0.00000	0.97666
382 A	0.02333	0.00000	0.97666
383 T	0.02333	0.00000	0.97666
384 H	0.02333	0.00000	0.97666
385 W	0.02333	0.00000	0.97666
386 T	0.02333	0.00000	0.97666
387 E	0.02333	0.00000	0.97666
388 A	0.02333	0.00000	0.97666
389 R	0.02333	0.00000	0.97666
390 E	0.02333	0.00000	0.97666
391 D	0.02333	0.00000	0.97666
392 D	0.02333	0.00000	0.97666
393 L	0.02333	0.00000	0.97666
394 H	0.02333	0.00000	0.97666
395 R	0.02333	0.00000	0.97666
396 Q	0.02333	0.00000	0.97666
397 W	0.02333	0.00002	0.97665
398 T	0.02333	0.00002	0.97665
399 R	0.02333	0.00002	0.97665
400 D	0.02332	0.00003	0.97664
401 A	0.02325	0.00015	0.9766
402 I	0.02321	0.00019	0.97659
403 E	0.02321	0.00020	0.97659
404 A	0.02318	0.00023	0.97658
405 L	0.02317	0.00024	0.97658
406 A	0.02317	0.00025	0.97658
407 P	0.02317	0.00025	0.97658
408 Y	0.02317	0.00025	0.97658
409 G	0.02317	0.00025	0.97658
410 L	0.02317	0.00025	0.97658
411 G	0.02317	0.00025	0.97658
412 T	0.02317	0.00025	0.97658
413 A	0.02317	0.00025	0.97658
414 Y	0.02317	0.00025	0.97658
415 V	0.02317	0.00025	0.97658
416 N	0.02317	0.00024	0.97659
417 F	0.02317	0.00024	0.97659
418 T	0.02318	0.00023	0.97659
419 A	0.02322	0.00015	0.97663
420 D	0.02325	0.00006	0.97669
421 D	0.02325	0.00004	0.97671
422 A	0.02325	0.00004	0.97671
423 P	0.02325	0.00003	0.97672
424 M	0.02325	0.00002	0.97673
425 H	0.02325	0.00001	0.97674
426 V	0.02325	0.00001	0.97674
427 E	0.02325	0.00000	0.97674
428 T	0.02325	0.00000	0.97675
429 L	0.02325	0.00000	0.97675
430 Y	0.02325	0.00000	0.97675
431 S	0.02325	0.00000	0.97675
432 T	0.02325	0.00000	0.97675
433 T	0.02325	0.00000	0.97675
434 E	0.02325	0.00000	0.97675
435 F	0.02325	0.00000	0.97675
436 S	0.02325	0.00000	0.97675
437 R	0.02325	0.00000	0.97675
438 L	0.02325	0.00000	0.97675
439 V	0.02325	0.00000	0.97675
440 T	0.02325	0.00000	0.97675
441 L	0.02325	0.00000	0.97675
442 K	0.02325	0.00000	0.97675
443 N	0.02325	0.00000	0.97675
444 R	0.02325	0.00000	0.97675
445 L	0.02325	0.00000	0.97675
446 D	0.02325	0.00000	0.97675
447 P	0.02325	0.00000	0.97675
448 D	0.02325	0.00000	0.97675
449 N	0.02325	0.00000	0.97675
450 V	0.02325	0.00000	0.97675
451 F	0.02325	0.00000	0.97675
452 R	0.02325	0.00000	0.97675
453 N	0.02325	0.00000	0.97675
454 N	0.02325	0.00000	0.97675
455 H	0.02325	0.00000	0.97675
456 N	0.02325	0.00000	0.97675
457 I	0.02325	0.00000	0.97675
458 R	0.02325	0.00000	0.97675
459 P	0.02325	0.00000	0.97675
460 S	0.02325	0.00000	0.97675
461 A	0.02325	0.00000	0.97675

General Statistics

Length: 461

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 2.79352

Exp number, first 60 AAs: 9e-05

Total prob of N-in: 0.10580

outside: from residue 1 to 461

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