TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0007

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 V	0.82335	0.00000	0.17666
2 T	0.82335	0.00000	0.17666
3 A	0.82335	0.00000	0.17666
4 P	0.82335	0.00000	0.17666
5 N	0.82335	0.00000	0.17666
6 E	0.82335	0.00000	0.17666
7 P	0.82335	0.00000	0.17666
8 G	0.82335	0.00000	0.17666
9 A	0.82335	0.00000	0.17666
10 L	0.82335	0.00000	0.17666
11 S	0.82335	0.00000	0.17666
12 K	0.82335	0.00000	0.17666
13 G	0.82335	0.00000	0.17666
14 D	0.82335	0.00000	0.17666
15 G	0.82335	0.00000	0.17666
16 P	0.82335	0.00000	0.17666
17 N	0.82335	0.00000	0.17666
18 A	0.82335	0.00000	0.17666
19 D	0.82335	0.00000	0.17666
20 G	0.82335	0.00000	0.17666
21 L	0.82335	0.00000	0.17666
22 V	0.82335	0.00000	0.17666
23 D	0.82335	0.00000	0.17666
24 R	0.82335	0.00000	0.17666
25 G	0.82335	0.00000	0.17666
26 G	0.82335	0.00000	0.17666
27 A	0.82335	0.00000	0.17666
28 H	0.82335	0.00000	0.17666
29 R	0.82335	0.00000	0.17666
30 A	0.82335	0.00000	0.17666
31 A	0.82335	0.00000	0.17666
32 T	0.82335	0.00000	0.17666
33 G	0.82335	0.00000	0.17666
34 P	0.82335	0.00000	0.17666
35 G	0.82335	0.00000	0.17666
36 R	0.82335	0.00000	0.17666
37 I	0.82335	0.00000	0.17666
38 P	0.82335	0.00000	0.17666
39 D	0.82335	0.00000	0.17666
40 A	0.82335	0.00000	0.17666
41 G	0.82335	0.00000	0.17666
42 D	0.82335	0.00000	0.17666
43 P	0.82335	0.00000	0.17666
44 P	0.82335	0.00000	0.17666
45 P	0.82335	0.00000	0.17666
46 W	0.82335	0.00000	0.17666
47 Q	0.82335	0.00000	0.17666
48 R	0.82335	0.00000	0.17666
49 A	0.82335	0.00000	0.17666
50 A	0.82335	0.00000	0.17666
51 T	0.82335	0.00000	0.17666
52 R	0.82335	0.00000	0.17666
53 Q	0.82335	0.00000	0.17666
54 S	0.82335	0.00000	0.17666
55 Q	0.82335	0.00000	0.17666
56 A	0.82335	0.00000	0.17666
57 G	0.82335	0.00000	0.17666
58 H	0.82335	0.00000	0.17666
59 R	0.82335	0.00000	0.17666
60 Q	0.82335	0.00000	0.17666
61 P	0.82335	0.00000	0.17666
62 P	0.82335	0.00000	0.17666
63 P	0.82335	0.00000	0.17666
64 V	0.82335	0.00000	0.17666
65 S	0.82335	0.00000	0.17666
66 H	0.82335	0.00000	0.17666
67 P	0.82335	0.00000	0.17666
68 E	0.82335	0.00000	0.17666
69 G	0.82335	0.00000	0.17666
70 R	0.82335	0.00000	0.17666
71 P	0.82335	0.00000	0.17666
72 T	0.82335	0.00000	0.17666
73 N	0.82335	0.00000	0.17666
74 P	0.82335	0.00000	0.17666
75 P	0.82335	0.00000	0.17666
76 A	0.82335	0.00000	0.17665
77 A	0.82335	0.00000	0.17665
78 A	0.82335	0.00000	0.17665
79 D	0.82335	0.00000	0.17665
80 A	0.82334	0.00003	0.17663
81 R	0.82334	0.00005	0.17661
82 L	0.82332	0.00010	0.17658
83 N	0.82332	0.00011	0.17657
84 R	0.82332	0.00013	0.17656
85 F	0.82330	0.00017	0.17653
86 I	0.82330	0.00017	0.17653
87 S	0.82330	0.00017	0.17653
88 G	0.82330	0.00017	0.17653
89 A	0.82330	0.00017	0.17653
90 S	0.82330	0.00017	0.17653
91 A	0.82330	0.00017	0.17653
92 P	0.82330	0.00017	0.17653
93 V	0.82330	0.00017	0.17653
94 T	0.82330	0.00017	0.17653
95 G	0.82330	0.00017	0.17653
96 P	0.82330	0.00017	0.17653
97 A	0.82330	0.00017	0.17653
98 A	0.82330	0.00017	0.17653
99 A	0.82330	0.00017	0.17653
100 V	0.82332	0.00015	0.17653
101 R	0.82338	0.00008	0.17655
102 T	0.82339	0.00006	0.17655
103 P	0.82341	0.00002	0.17657
104 Q	0.82342	0.00001	0.17657
105 P	0.82343	0.00000	0.17657
106 D	0.82343	0.00000	0.17658
107 P	0.82343	0.00000	0.17658
108 D	0.82343	0.00000	0.17658
109 A	0.82343	0.00000	0.17658
110 S	0.82343	0.00000	0.17658
111 L	0.82343	0.00000	0.17658
112 G	0.82343	0.00000	0.17658
113 C	0.82343	0.00000	0.17658
114 G	0.82343	0.00000	0.17658
115 D	0.82343	0.00000	0.17658
116 G	0.82343	0.00000	0.17658
117 S	0.82343	0.00000	0.17658
118 P	0.82343	0.00000	0.17658
119 A	0.82343	0.00000	0.17658
120 E	0.82343	0.00000	0.17658
121 A	0.82343	0.00000	0.17658
122 Y	0.82343	0.00000	0.17658
123 A	0.82343	0.00000	0.17658
124 S	0.82343	0.00000	0.17658
125 E	0.82343	0.00000	0.17658
126 L	0.82343	0.00000	0.17658
127 P	0.82343	0.00000	0.17658
128 D	0.82343	0.00000	0.17658
129 L	0.82343	0.00000	0.17658
130 S	0.82343	0.00000	0.17658
131 G	0.82343	0.00000	0.17658
132 P	0.82343	0.00000	0.17658
133 T	0.82343	0.00000	0.17658
134 P	0.82343	0.00000	0.17658
135 R	0.82343	0.00000	0.17658
136 A	0.82343	0.00000	0.17658
137 P	0.82343	0.00000	0.17658
138 Q	0.82343	0.00000	0.17658
139 R	0.82343	0.00000	0.17658
140 N	0.82343	0.00000	0.17658
141 P	0.82343	0.00000	0.17658
142 A	0.82343	0.00000	0.17658
143 P	0.82343	0.00000	0.17658
144 A	0.82343	0.00000	0.17658
145 R	0.82343	0.00000	0.17658
146 P	0.82343	0.00000	0.17658
147 A	0.82343	0.00000	0.17658
148 E	0.82343	0.00000	0.17658
149 G	0.82343	0.00000	0.17658
150 G	0.82343	0.00000	0.17658
151 A	0.82343	0.00000	0.17658
152 G	0.82343	0.00000	0.17658
153 S	0.82343	0.00000	0.17658
154 R	0.82343	0.00000	0.17658
155 G	0.82343	0.00000	0.17658
156 D	0.82343	0.00000	0.17658
157 S	0.82343	0.00000	0.17658
158 A	0.82343	0.00000	0.17658
159 A	0.82343	0.00000	0.17658
160 G	0.82343	0.00000	0.17658
161 S	0.82343	0.00000	0.17658
162 S	0.82343	0.00000	0.17658
163 G	0.82343	0.00000	0.17658
164 G	0.82343	0.00000	0.17658
165 R	0.82343	0.00000	0.17658
166 S	0.82343	0.00000	0.17658
167 I	0.82343	0.00000	0.17658
168 T	0.82343	0.00000	0.17658
169 A	0.82343	0.00000	0.17658
170 E	0.82343	0.00000	0.17658
171 S	0.82343	0.00000	0.17658
172 R	0.82343	0.00000	0.17658
173 D	0.82343	0.00000	0.17658
174 A	0.82343	0.00000	0.17658
175 R	0.82343	0.00000	0.17658
176 V	0.82343	0.00000	0.17658
177 Q	0.82343	0.00000	0.17658
178 L	0.82343	0.00000	0.17658
179 S	0.82343	0.00000	0.17658
180 A	0.82343	0.00000	0.17658
181 R	0.82343	0.00000	0.17658
182 R	0.82343	0.00000	0.17658
183 S	0.82343	0.00000	0.17658
184 R	0.82343	0.00000	0.17658
185 G	0.82343	0.00000	0.17658
186 P	0.82343	0.00000	0.17658
187 V	0.82343	0.00000	0.17658
188 R	0.82343	0.00000	0.17658
189 A	0.82343	0.00000	0.17658
190 S	0.82343	0.00000	0.17658
191 M	0.82343	0.00001	0.17657
192 Q	0.82343	0.00001	0.17657
193 I	0.82343	0.00001	0.17656
194 R	0.82343	0.00001	0.17656
195 R	0.82342	0.00003	0.17655
196 I	0.82337	0.00016	0.17646
197 D	0.82335	0.00021	0.17644
198 P	0.82149	0.00225	0.17625
199 W	0.81708	0.00690	0.17602
200 S	0.81385	0.01020	0.17595
201 T	0.80287	0.02141	0.17572
202 L	0.78516	0.03931	0.17553
203 K	0.77525	0.04962	0.17513
204 V	0.36920	0.48012	0.15068
205 S	0.25516	0.61632	0.12852
206 L	0.18004	0.71485	0.10511
207 L	0.16796	0.73702	0.09503
208 L	0.16111	0.74911	0.08978
209 S	0.15600	0.75805	0.08596
210 V	0.13077	0.79711	0.07212
211 A	0.10574	0.83852	0.05574
212 L	0.00378	0.98528	0.01094
213 F	0.00061	0.99316	0.00623
214 F	0.00015	0.99754	0.00231
215 V	0.00004	0.99951	0.00045
216 W	0.00006	0.99984	0.0001
219 T	0.00011	0.99968	0.00021
220 V	0.00005	0.99963	0.00032
221 A	0.00007	0.99789	0.00204
222 F	0.00004	0.99606	0.0039
223 L	0.00005	0.99426	0.00569
224 Y	0.00016	0.98368	0.01616
225 L	0.00035	0.97154	0.0281
226 V	0.00168	0.95274	0.04559
227 L	0.02417	0.59140	0.38443
228 G	0.05115	0.44859	0.50026
229 G	0.07608	0.34730	0.57661
230 M	0.08726	0.32253	0.59021
231 G	0.09078	0.31065	0.59857
232 V	0.09369	0.30124	0.60507
233 W	0.10480	0.26076	0.63443
234 A	0.12599	0.18854	0.68547
235 K	0.17093	0.01031	0.81876
236 L	0.17251	0.00650	0.82099
237 N	0.17531	0.00175	0.82294
238 S	0.17615	0.00041	0.82344
239 N	0.17623	0.00028	0.82349
240 V	0.17618	0.00033	0.82349
241 G	0.17615	0.00036	0.82348
242 D	0.17618	0.00033	0.82349
243 L	0.17579	0.00096	0.82324
244 L	0.17569	0.00116	0.82315
245 N	0.17554	0.00131	0.82314
246 N	0.17488	0.00231	0.8228
247 A	0.17275	0.00606	0.82118
248 S	0.17220	0.00872	0.81908
249 G	0.17183	0.01273	0.81544
250 S	0.17149	0.01539	0.81312
251 S	0.17073	0.02284	0.80643
252 A	0.16806	0.06081	0.77112
253 E	0.16389	0.07614	0.75998
254 L	0.13118	0.15990	0.70892
255 V	0.12238	0.18678	0.69084
256 S	0.12122	0.19575	0.68304
257 S	0.11887	0.21563	0.6655
258 G	0.11667	0.25143	0.6319
259 T	0.11184	0.31042	0.57775
260 I	0.09656	0.40028	0.50316
261 F	0.08477	0.43338	0.48185
262 G	0.07602	0.46026	0.46372
263 G	0.06164	0.53713	0.40124
264 A	0.03371	0.78362	0.18268
265 F	0.02375	0.84017	0.13608
266 L	0.01920	0.89525	0.08555
267 I	0.00861	0.97814	0.01325
268 G	0.00306	0.98960	0.00734
269 L	0.00217	0.99153	0.00629
270 V	0.00380	0.98910	0.00711
271 N	0.00749	0.98533	0.00718
272 I	0.00961	0.98543	0.00496
273 V	0.01389	0.98144	0.00467
274 L	0.02903	0.96395	0.00702
275 M	0.07900	0.90814	0.01286
276 T	0.09226	0.88949	0.01825
277 A	0.09897	0.87220	0.02884
278 L	0.09010	0.88203	0.02787
279 A	0.07941	0.89874	0.02185
280 T	0.08569	0.89193	0.02238
281 I	0.07380	0.90561	0.0206
282 G	0.09991	0.87493	0.02516
283 A	0.13271	0.83040	0.03689
284 F	0.14039	0.81219	0.04742
285 V	0.16119	0.78047	0.05835
286 Y	0.23981	0.67916	0.08103
287 N	0.47181	0.41108	0.11711
288 L	0.51013	0.36641	0.12346
289 I	0.57840	0.29348	0.12812
290 T	0.69813	0.16211	0.13976
291 D	0.71678	0.13484	0.14837
292 L	0.71706	0.13415	0.14879
293 I	0.71735	0.13350	0.14914
294 G	0.71832	0.13133	0.15035
295 G	0.71998	0.12723	0.15279
296 I	0.72169	0.12327	0.15504
297 E	0.72678	0.11275	0.16047
298 V	0.72719	0.11141	0.16141
299 T	0.72910	0.10415	0.16675
300 L	0.73071	0.09517	0.17412
301 A	0.73853	0.05841	0.20307
302 D	0.74895	0.00492	0.24613
303 R	0.74950	0.00174	0.24877
304 D	0.74957	0.00000	0.25043

General Statistics

Length: 304

Number of predicted TMHs: 2

Exp number of AAs in TMHs: 49.96055

Exp number, first 60 AAs: 0

Total prob of N-in: 0.82335

inside: from residue 1 to 203

TMhelix: from residue 204 to 226

outside: from residue 227 to 263

TMhelix: from residue 264 to 286

inside: from residue 287 to 304

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