TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv2258c

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.12592	0.00000	0.87409
2 S	0.12592	0.00000	0.87409
3 G	0.12592	0.00000	0.87409
4 A	0.12592	0.00000	0.87409
5 L	0.12592	0.00000	0.87409
6 E	0.12592	0.00000	0.87409
7 T	0.12591	0.00001	0.87409
8 T	0.12591	0.00001	0.87409
9 E	0.12585	0.00007	0.87409
10 E	0.12584	0.00168	0.87249
11 F	0.11369	0.01438	0.87193
12 G	0.06680	0.06138	0.87183
13 N	0.01906	0.10949	0.87145
14 R	0.01903	0.10952	0.87145
15 F	0.01903	0.12902	0.85196
16 V	0.01769	0.13036	0.85196
17 A	0.01685	0.13121	0.85195
18 A	0.01683	0.13124	0.85193
19 I	0.01660	0.13148	0.85193
20 D	0.01634	0.13174	0.85192
21 S	0.01243	0.13566	0.85191
22 A	0.01225	0.13585	0.85189
23 G	0.01211	0.13600	0.85189
24 L	0.01202	0.13610	0.85188
25 A	0.01201	0.13611	0.85188
26 I	0.01200	0.13612	0.85188
27 L	0.01200	0.13611	0.85189
28 V	0.01201	0.13605	0.85194
29 S	0.01205	0.13549	0.85246
30 V	0.01216	0.13427	0.85358
31 G	0.01320	0.12152	0.86528
32 H	0.01515	0.10276	0.88209
33 Q	0.02378	0.08350	0.89272
34 T	0.02423	0.07305	0.90272
35 G	0.02454	0.04560	0.92987
36 L	0.02461	0.01711	0.95829
37 L	0.02494	0.01457	0.96049
38 D	0.03415	0.00451	0.96134
39 T	0.03415	0.00434	0.9615
40 M	0.03416	0.00408	0.96176
41 A	0.03416	0.00368	0.96215
42 G	0.03417	0.00328	0.96256
43 L	0.03417	0.00275	0.96308
44 P	0.03417	0.00023	0.9656
45 P	0.03419	0.00011	0.9657
46 A	0.03419	0.00007	0.96574
47 T	0.03420	0.00003	0.96578
48 S	0.03420	0.00002	0.96579
49 M	0.03420	0.00001	0.96579
50 E	0.03420	0.00001	0.96579
51 I	0.03420	0.00001	0.96579
52 A	0.03420	0.00001	0.96579
53 E	0.03420	0.00001	0.96579
54 A	0.03420	0.00001	0.96579
55 A	0.03420	0.00001	0.96579
56 G	0.03420	0.00001	0.96579
57 L	0.03420	0.00001	0.96579
58 E	0.03420	0.00000	0.9658
59 E	0.03420	0.00000	0.9658
60 R	0.03420	0.00000	0.9658
61 Y	0.03420	0.00000	0.9658
62 V	0.03420	0.00000	0.9658
63 R	0.03420	0.00000	0.9658
64 E	0.03420	0.00000	0.9658
65 W	0.03420	0.00001	0.9658
66 L	0.03420	0.00001	0.96579
67 G	0.03420	0.00001	0.96579
68 G	0.03420	0.00001	0.96579
69 M	0.03420	0.00002	0.96579
70 T	0.03419	0.00002	0.96579
71 T	0.03419	0.00002	0.96579
72 G	0.03419	0.00002	0.96579
73 Q	0.03419	0.00002	0.96579
74 I	0.03419	0.00002	0.96579
75 V	0.03419	0.00002	0.96579
76 E	0.03419	0.00002	0.96579
77 Y	0.03419	0.00002	0.96579
78 D	0.03419	0.00002	0.96579
79 A	0.03419	0.00002	0.96579
80 G	0.03419	0.00002	0.96579
81 S	0.03419	0.00002	0.96579
82 S	0.03419	0.00002	0.96579
83 T	0.03419	0.00002	0.96579
84 Y	0.03419	0.00002	0.96579
85 S	0.03419	0.00002	0.96579
86 L	0.03419	0.00001	0.96579
87 P	0.03420	0.00001	0.96579
88 A	0.03420	0.00001	0.96579
89 H	0.03420	0.00000	0.96579
90 R	0.03420	0.00000	0.96579
91 A	0.03420	0.00003	0.96577
92 G	0.03417	0.00018	0.96565
93 M	0.03416	0.00024	0.96559
94 L	0.03415	0.00031	0.96553
95 T	0.03415	0.00033	0.96552
96 R	0.03415	0.00034	0.96552
97 A	0.03414	0.00042	0.96545
98 A	0.03413	0.00044	0.96543
99 G	0.03412	0.00046	0.96542
100 P	0.03412	0.00046	0.96542
101 D	0.03412	0.00046	0.96542
102 N	0.03412	0.00046	0.96542
103 L	0.03411	0.00047	0.96542
104 A	0.03411	0.00047	0.96542
105 V	0.03411	0.00047	0.96542
106 I	0.03411	0.00047	0.96542
107 A	0.03411	0.00047	0.96542
108 Q	0.03411	0.00047	0.96542
109 F	0.03411	0.00047	0.96542
110 V	0.03411	0.00047	0.96542
111 S	0.03412	0.00046	0.96542
112 L	0.03412	0.00046	0.96543
113 L	0.03413	0.00044	0.96544
114 G	0.03418	0.00038	0.96544
115 E	0.03435	0.00018	0.96547
116 V	0.03439	0.00013	0.96548
117 E	0.03449	0.00002	0.9655
118 Q	0.03449	0.00001	0.9655
119 K	0.03449	0.00001	0.9655
120 V	0.03449	0.00001	0.9655
121 I	0.03449	0.00001	0.9655
122 R	0.03449	0.00000	0.96551
123 C	0.03449	0.00000	0.96551
124 F	0.03449	0.00000	0.96551
125 R	0.03449	0.00000	0.96551
126 E	0.03449	0.00000	0.96551
127 G	0.03449	0.00000	0.96551
128 G	0.03449	0.00000	0.96551
129 G	0.03449	0.00000	0.96551
130 V	0.03449	0.00000	0.96551
131 P	0.03449	0.00000	0.96551
132 Y	0.03449	0.00000	0.96551
133 S	0.03449	0.00000	0.96551
134 E	0.03449	0.00000	0.96551
135 Y	0.03449	0.00000	0.96551
136 P	0.03449	0.00000	0.96551
137 R	0.03449	0.00000	0.96551
138 F	0.03447	0.00002	0.96551
139 H	0.03447	0.00003	0.9655
140 K	0.03442	0.00009	0.96548
141 L	0.03423	0.00040	0.96537
142 M	0.03414	0.00055	0.9653
143 A	0.03403	0.00075	0.96522
144 E	0.03400	0.00081	0.96519
145 M	0.03366	0.00131	0.96503
146 S	0.03348	0.00154	0.96498
147 G	0.03328	0.00185	0.96487
148 M	0.03325	0.00194	0.96481
149 V	0.03324	0.00196	0.9648
150 F	0.03324	0.00196	0.9648
151 D	0.03324	0.00196	0.9648
152 A	0.03324	0.00196	0.9648
153 A	0.03324	0.00196	0.9648
154 L	0.03324	0.00196	0.9648
155 I	0.03324	0.00196	0.9648
156 D	0.03324	0.00196	0.9648
157 V	0.03324	0.00196	0.9648
158 V	0.03324	0.00196	0.9648
159 L	0.03324	0.00195	0.96481
160 P	0.03325	0.00190	0.96486
161 L	0.03326	0.00179	0.96494
162 V	0.03333	0.00168	0.96499
163 D	0.03361	0.00099	0.9654
164 G	0.03365	0.00081	0.96554
165 L	0.03369	0.00059	0.96572
166 P	0.03385	0.00024	0.9659
167 D	0.03393	0.00005	0.96602
168 R	0.03394	0.00002	0.96604
169 L	0.03394	0.00002	0.96604
170 R	0.03394	0.00000	0.96605
171 S	0.03394	0.00000	0.96605
172 G	0.03394	0.00000	0.96605
173 A	0.03394	0.00000	0.96605
174 D	0.03394	0.00000	0.96605
175 V	0.03394	0.00000	0.96605
176 A	0.03394	0.00000	0.96605
177 D	0.03394	0.00000	0.96605
178 F	0.03394	0.00000	0.96605
179 G	0.03394	0.00000	0.96605
180 C	0.03394	0.00000	0.96605
181 G	0.03394	0.00000	0.96605
182 S	0.03394	0.00000	0.96605
183 G	0.03394	0.00000	0.96605
184 R	0.03394	0.00000	0.96605
185 A	0.03394	0.00000	0.96605
186 V	0.03394	0.00000	0.96605
187 K	0.03394	0.00000	0.96605
188 L	0.03394	0.00000	0.96605
189 M	0.03394	0.00000	0.96605
190 A	0.03394	0.00000	0.96605
191 Q	0.03394	0.00000	0.96605
192 A	0.03394	0.00000	0.96605
193 F	0.03394	0.00000	0.96605
194 G	0.03394	0.00000	0.96605
195 A	0.03394	0.00000	0.96605
196 S	0.03394	0.00000	0.96605
197 R	0.03394	0.00000	0.96605
198 F	0.03394	0.00000	0.96605
199 T	0.03394	0.00000	0.96605
200 G	0.03394	0.00000	0.96605
201 I	0.03394	0.00000	0.96605
202 D	0.03394	0.00000	0.96606
203 F	0.03394	0.00000	0.96606
204 S	0.03394	0.00000	0.96606
205 D	0.03394	0.00000	0.96606
206 E	0.03394	0.00000	0.96606
207 A	0.03394	0.00000	0.96606
208 V	0.03394	0.00000	0.96606
209 A	0.03394	0.00000	0.96606
210 A	0.03394	0.00000	0.96606
211 G	0.03394	0.00000	0.96606
212 T	0.03394	0.00000	0.96606
213 E	0.03394	0.00000	0.96606
214 E	0.03394	0.00000	0.96606
215 A	0.03394	0.00000	0.96606
216 A	0.03394	0.00000	0.96606
217 R	0.03394	0.00000	0.96606
218 L	0.03394	0.00000	0.96606
219 G	0.03394	0.00000	0.96606
220 L	0.03394	0.00000	0.96606
221 A	0.03394	0.00000	0.96606
222 N	0.03394	0.00000	0.96606
223 A	0.03394	0.00000	0.96606
224 T	0.03394	0.00000	0.96606
225 F	0.03394	0.00000	0.96606
226 E	0.03394	0.00000	0.96606
227 R	0.03394	0.00000	0.96606
228 H	0.03394	0.00000	0.96606
229 D	0.03394	0.00000	0.96606
230 L	0.03394	0.00000	0.96606
231 A	0.03394	0.00000	0.96606
232 E	0.03394	0.00000	0.96606
233 L	0.03394	0.00000	0.96606
234 D	0.03394	0.00000	0.96606
235 K	0.03394	0.00000	0.96606
236 V	0.03394	0.00000	0.96606
237 G	0.03394	0.00000	0.96606
238 A	0.03394	0.00000	0.96606
239 Y	0.03394	0.00000	0.96606
240 D	0.03394	0.00000	0.96606
241 V	0.03394	0.00000	0.96606
242 I	0.03394	0.00000	0.96606
243 T	0.03394	0.00000	0.96606
244 V	0.03394	0.00000	0.96606
245 F	0.03394	0.00000	0.96606
246 D	0.03394	0.00000	0.96606
247 A	0.03394	0.00000	0.96606
248 I	0.03394	0.00000	0.96606
249 H	0.03394	0.00000	0.96606
250 D	0.03394	0.00000	0.96606
251 Q	0.03394	0.00000	0.96606
252 A	0.03394	0.00000	0.96606
253 Q	0.03394	0.00000	0.96606
254 P	0.03394	0.00000	0.96606
255 A	0.03394	0.00000	0.96606
256 R	0.03394	0.00000	0.96606
257 V	0.03394	0.00000	0.96606
258 L	0.03394	0.00000	0.96606
259 Q	0.03394	0.00000	0.96606
260 N	0.03393	0.00001	0.96606
261 I	0.03393	0.00001	0.96606
262 Y	0.03393	0.00002	0.96606
263 R	0.03392	0.00002	0.96606
264 A	0.03392	0.00002	0.96606
265 L	0.03391	0.00003	0.96606
266 R	0.03391	0.00003	0.96606
267 P	0.03391	0.00003	0.96606
268 G	0.03391	0.00003	0.96606
269 G	0.03391	0.00003	0.96606
270 V	0.03391	0.00003	0.96606
271 L	0.03391	0.00003	0.96606
272 L	0.03391	0.00003	0.96606
273 M	0.03391	0.00003	0.96606
274 V	0.03391	0.00003	0.96606
275 D	0.03391	0.00003	0.96606
276 I	0.03391	0.00003	0.96606
277 K	0.03391	0.00003	0.96606
278 A	0.03391	0.00003	0.96606
279 S	0.03391	0.00003	0.96606
280 S	0.03391	0.00003	0.96606
281 Q	0.03391	0.00003	0.96607
282 L	0.03391	0.00003	0.96607
283 E	0.03391	0.00001	0.96608
284 D	0.03391	0.00001	0.96609
285 N	0.03380	0.00014	0.96606
286 V	0.03329	0.00083	0.96588
287 G	0.03297	0.00136	0.96566
288 V	0.03295	0.00142	0.96562
289 P	0.03294	0.00147	0.96559
290 L	0.03287	0.00165	0.96549
291 S	0.03283	0.00179	0.96538
292 T	0.03279	0.00240	0.96482
293 Y	0.03275	0.00301	0.96425
294 L	0.03269	0.00356	0.96376
295 Y	0.03263	0.00453	0.96284
296 T	0.03259	0.00633	0.96108
297 T	0.03231	0.01272	0.95497
298 S	0.03210	0.01328	0.95462
299 L	0.03189	0.01428	0.95383
300 M	0.03180	0.01494	0.95326
301 H	0.03169	0.01525	0.95307
302 C	0.03135	0.01579	0.95286
303 M	0.03123	0.01607	0.95269
304 T	0.03116	0.01621	0.95263
305 V	0.03092	0.01647	0.95261
306 S	0.03091	0.01645	0.95263
307 L	0.03090	0.01646	0.95264
308 A	0.03093	0.01631	0.95275
309 L	0.03109	0.01571	0.95321
310 D	0.03144	0.01501	0.95356
311 G	0.03147	0.01496	0.95357
312 A	0.03151	0.01491	0.95358
313 G	0.03156	0.01482	0.95362
314 L	0.03164	0.01471	0.95365
315 G	0.03217	0.01413	0.9537
316 T	0.03274	0.01353	0.95372
317 V	0.03329	0.01293	0.95378
318 W	0.03444	0.01168	0.95388
319 G	0.03739	0.00849	0.95412
320 R	0.04369	0.00170	0.95461
321 Q	0.04398	0.00126	0.95476
322 L	0.04404	0.00113	0.95484
323 A	0.04424	0.00070	0.95507
324 T	0.04433	0.00047	0.9552
325 S	0.04438	0.00011	0.95552
326 M	0.04438	0.00009	0.95553
327 L	0.04438	0.00009	0.95553
328 A	0.04439	0.00006	0.95555
329 D	0.04439	0.00005	0.95556
330 A	0.04439	0.00006	0.95555
331 G	0.04439	0.00007	0.95554
332 F	0.04439	0.00007	0.95554
333 T	0.04439	0.00007	0.95553
334 D	0.04440	0.00007	0.95554
335 V	0.04440	0.00007	0.95554
336 T	0.04440	0.00007	0.95554
337 V	0.04440	0.00007	0.95554
338 A	0.04440	0.00007	0.95554
339 E	0.04440	0.00006	0.95554
340 I	0.04441	0.00006	0.95554
341 E	0.04441	0.00005	0.95554
342 S	0.04441	0.00005	0.95554
343 D	0.04441	0.00005	0.95554
344 V	0.04441	0.00005	0.95554
345 L	0.04441	0.00005	0.95554
346 N	0.04442	0.00005	0.95554
347 N	0.04442	0.00004	0.95554
348 Y	0.04442	0.00004	0.95554
349 Y	0.04442	0.00004	0.95554
350 I	0.04443	0.00003	0.95554
351 A	0.04445	0.00001	0.95554
352 R	0.04446	0.00000	0.95554
353 K	0.04446	0.00000	0.95554

General Statistics

Length: 353

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 3.34109

Exp number, first 60 AAs: 2.92065

Total prob of N-in: 0.12592

outside: from residue 1 to 353

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