TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv3266c

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.02920	0.00000	0.9708
2 A	0.02920	0.00000	0.9708
3 G	0.02920	0.00000	0.9708
4 R	0.02920	0.00000	0.9708
5 S	0.02915	0.00006	0.9708
6 E	0.02915	0.00006	0.9708
7 R	0.02845	0.00076	0.9708
8 L	0.02845	0.00076	0.9708
9 V	0.02838	0.00082	0.9708
10 I	0.02838	0.00082	0.9708
11 T	0.02838	0.00082	0.9708
12 G	0.02838	0.00082	0.9708
13 A	0.02838	0.00082	0.9708
14 G	0.02838	0.00082	0.9708
15 G	0.02838	0.00082	0.9708
16 Q	0.02838	0.00082	0.9708
17 L	0.02838	0.00082	0.9708
18 G	0.02838	0.00082	0.9708
19 S	0.02838	0.00082	0.9708
20 H	0.02838	0.00082	0.9708
21 L	0.02838	0.00082	0.9708
22 T	0.02838	0.00082	0.9708
23 A	0.02838	0.00081	0.97081
24 Q	0.02838	0.00077	0.97085
25 A	0.02838	0.00061	0.97101
26 A	0.02838	0.00053	0.97109
27 R	0.02838	0.00004	0.97158
28 E	0.02838	0.00001	0.97161
29 G	0.02838	0.00001	0.97161
30 R	0.02839	0.00000	0.97162
31 D	0.02839	0.00000	0.97162
32 M	0.02839	0.00000	0.97162
33 L	0.02839	0.00000	0.97162
34 A	0.02839	0.00000	0.97162
35 L	0.02839	0.00000	0.97162
36 T	0.02839	0.00000	0.97162
37 S	0.02839	0.00000	0.97162
38 S	0.02839	0.00000	0.97162
39 Q	0.02839	0.00000	0.97162
40 W	0.02839	0.00000	0.97162
41 D	0.02839	0.00000	0.97162
42 I	0.02839	0.00000	0.97162
43 T	0.02839	0.00000	0.97162
44 D	0.02839	0.00000	0.97162
45 P	0.02839	0.00000	0.97162
46 A	0.02839	0.00000	0.97162
47 A	0.02839	0.00000	0.97162
48 A	0.02839	0.00000	0.97162
49 E	0.02839	0.00000	0.97162
50 R	0.02838	0.00000	0.97162
51 I	0.02838	0.00000	0.97162
52 I	0.02838	0.00000	0.97162
53 R	0.02838	0.00000	0.97162
54 H	0.02838	0.00000	0.97162
55 G	0.02838	0.00000	0.97162
56 D	0.02838	0.00000	0.97162
57 V	0.02838	0.00000	0.97162
58 V	0.02838	0.00000	0.97162
59 I	0.02838	0.00000	0.97162
60 N	0.02838	0.00000	0.97162
61 C	0.02838	0.00000	0.97162
62 A	0.02838	0.00000	0.97162
63 A	0.02838	0.00000	0.97162
64 Y	0.02838	0.00000	0.97162
65 T	0.02838	0.00000	0.97162
66 D	0.02838	0.00000	0.97162
67 V	0.02838	0.00000	0.97162
68 D	0.02838	0.00000	0.97162
69 G	0.02838	0.00000	0.97162
70 A	0.02838	0.00000	0.97162
71 E	0.02838	0.00000	0.97162
72 S	0.02838	0.00000	0.97162
73 N	0.02838	0.00000	0.97162
74 E	0.02838	0.00000	0.97162
75 A	0.02838	0.00000	0.97162
76 V	0.02838	0.00000	0.97162
77 A	0.02838	0.00000	0.97162
78 Y	0.02838	0.00000	0.97162
79 A	0.02838	0.00000	0.97162
80 V	0.02838	0.00000	0.97162
81 N	0.02838	0.00000	0.97162
82 A	0.02838	0.00000	0.97162
83 T	0.02838	0.00000	0.97162
84 G	0.02838	0.00000	0.97162
85 P	0.02838	0.00000	0.97162
86 Q	0.02838	0.00000	0.97162
87 H	0.02838	0.00000	0.97162
88 L	0.02838	0.00000	0.97162
89 A	0.02838	0.00000	0.97162
90 R	0.02838	0.00000	0.97162
91 A	0.02838	0.00000	0.97162
92 C	0.02838	0.00000	0.97162
93 A	0.02838	0.00000	0.97162
94 R	0.02838	0.00000	0.97162
95 V	0.02838	0.00000	0.97162
96 G	0.02838	0.00000	0.97162
97 A	0.02838	0.00000	0.97162
98 R	0.02838	0.00000	0.97162
99 L	0.02838	0.00000	0.97162
100 I	0.02838	0.00000	0.97162
101 H	0.02838	0.00000	0.97162
102 V	0.02838	0.00000	0.97162
103 S	0.02838	0.00000	0.97162
104 T	0.02838	0.00000	0.97162
105 D	0.02838	0.00000	0.97162
106 Y	0.02838	0.00000	0.97162
107 V	0.02838	0.00000	0.97162
108 F	0.02838	0.00000	0.97162
109 D	0.02838	0.00000	0.97162
110 G	0.02838	0.00000	0.97162
111 D	0.02838	0.00000	0.97162
112 F	0.02838	0.00000	0.97162
113 G	0.02838	0.00000	0.97162
114 G	0.02838	0.00000	0.97162
115 A	0.02838	0.00000	0.97162
116 E	0.02838	0.00000	0.97162
117 P	0.02838	0.00000	0.97162
118 R	0.02838	0.00000	0.97162
119 P	0.02838	0.00000	0.97162
120 Y	0.02838	0.00000	0.97162
121 E	0.02838	0.00000	0.97162
122 P	0.02838	0.00000	0.97162
123 T	0.02838	0.00000	0.97162
124 D	0.02838	0.00000	0.97162
125 E	0.02838	0.00000	0.97162
126 T	0.02838	0.00000	0.97162
127 A	0.02838	0.00000	0.97162
128 P	0.02838	0.00000	0.97162
129 Q	0.02838	0.00000	0.97162
130 G	0.02838	0.00000	0.97162
131 V	0.02838	0.00000	0.97162
132 Y	0.02838	0.00000	0.97162
133 A	0.02838	0.00000	0.97162
134 R	0.02838	0.00000	0.97162
135 S	0.02838	0.00000	0.97162
136 K	0.02838	0.00000	0.97162
137 L	0.02836	0.00003	0.97161
138 A	0.02836	0.00004	0.97161
139 G	0.02835	0.00005	0.9716
140 E	0.02834	0.00006	0.9716
141 Q	0.02828	0.00017	0.97155
142 A	0.02779	0.00076	0.97145
143 V	0.02769	0.00088	0.97143
144 L	0.02767	0.00091	0.97142
145 A	0.02766	0.00092	0.97141
146 A	0.02766	0.00093	0.97141
147 F	0.02766	0.00093	0.97141
148 P	0.02766	0.00093	0.97141
149 E	0.02766	0.00093	0.97141
150 A	0.02766	0.00095	0.9714
151 A	0.02765	0.00096	0.97139
152 V	0.02765	0.00097	0.97138
153 V	0.02765	0.00098	0.97137
154 R	0.02765	0.00098	0.97137
155 T	0.02765	0.00098	0.97137
156 A	0.02765	0.00098	0.97137
157 W	0.02765	0.00098	0.97137
158 V	0.02765	0.00097	0.97137
159 Y	0.02766	0.00094	0.9714
160 T	0.02767	0.00089	0.97145
161 G	0.02768	0.00085	0.97148
162 G	0.02770	0.00068	0.97161
163 T	0.02773	0.00060	0.97167
164 G	0.02779	0.00046	0.97176
165 K	0.02785	0.00007	0.97208
166 D	0.02785	0.00006	0.97209
167 F	0.02785	0.00006	0.97209
168 V	0.02785	0.00006	0.97209
169 A	0.02786	0.00005	0.97209
170 V	0.02786	0.00005	0.97209
171 M	0.02787	0.00003	0.9721
172 R	0.02788	0.00001	0.9721
173 R	0.02789	0.00001	0.9721
174 L	0.02789	0.00001	0.9721
175 A	0.02789	0.00001	0.9721
176 A	0.02789	0.00000	0.9721
177 G	0.02789	0.00000	0.9721
178 H	0.02789	0.00000	0.9721
179 G	0.02789	0.00000	0.9721
180 R	0.02789	0.00000	0.9721
181 V	0.02789	0.00000	0.9721
182 D	0.02789	0.00000	0.9721
183 V	0.02789	0.00000	0.9721
184 V	0.02789	0.00000	0.9721
185 D	0.02789	0.00000	0.9721
186 D	0.02789	0.00000	0.9721
187 Q	0.02789	0.00000	0.9721
188 T	0.02789	0.00000	0.9721
189 G	0.02789	0.00000	0.9721
190 S	0.02789	0.00000	0.9721
191 P	0.02789	0.00000	0.9721
192 T	0.02789	0.00001	0.9721
193 Y	0.02789	0.00001	0.9721
194 V	0.02789	0.00001	0.9721
195 A	0.02789	0.00001	0.9721
196 D	0.02789	0.00001	0.9721
197 L	0.02789	0.00001	0.9721
198 A	0.02789	0.00001	0.9721
199 E	0.02789	0.00001	0.9721
200 A	0.02789	0.00001	0.9721
201 L	0.02789	0.00001	0.9721
202 L	0.02789	0.00001	0.9721
203 A	0.02789	0.00001	0.9721
204 L	0.02789	0.00001	0.9721
205 A	0.02789	0.00001	0.9721
206 D	0.02789	0.00001	0.9721
207 A	0.02789	0.00001	0.9721
208 G	0.02789	0.00001	0.9721
209 V	0.02789	0.00001	0.9721
210 R	0.02789	0.00001	0.9721
211 G	0.02789	0.00001	0.9721
212 R	0.02789	0.00001	0.9721
213 V	0.02789	0.00001	0.9721
214 L	0.02789	0.00001	0.9721
215 H	0.02790	0.00000	0.9721
216 A	0.02790	0.00000	0.9721
217 A	0.02790	0.00000	0.9721
218 N	0.02790	0.00000	0.9721
219 E	0.02790	0.00000	0.9721
220 G	0.02790	0.00000	0.9721
221 V	0.02790	0.00000	0.9721
222 V	0.02790	0.00000	0.9721
223 S	0.02790	0.00000	0.9721
224 R	0.02790	0.00000	0.9721
225 F	0.02790	0.00000	0.9721
226 G	0.02790	0.00000	0.9721
227 Q	0.02790	0.00000	0.9721
228 A	0.02790	0.00000	0.9721
229 R	0.02790	0.00000	0.9721
230 A	0.02790	0.00000	0.9721
231 V	0.02790	0.00000	0.9721
232 F	0.02790	0.00000	0.9721
233 E	0.02790	0.00000	0.9721
234 E	0.02790	0.00000	0.9721
235 C	0.02790	0.00000	0.9721
236 G	0.02790	0.00000	0.9721
237 A	0.02790	0.00000	0.9721
238 D	0.02790	0.00000	0.9721
239 P	0.02790	0.00000	0.9721
240 Q	0.02790	0.00000	0.9721
241 R	0.02790	0.00000	0.9721
242 V	0.02790	0.00000	0.9721
243 R	0.02790	0.00000	0.9721
244 P	0.02790	0.00000	0.9721
245 V	0.02790	0.00000	0.9721
246 S	0.02790	0.00000	0.9721
247 S	0.02790	0.00000	0.9721
248 A	0.02790	0.00000	0.9721
249 Q	0.02790	0.00000	0.9721
250 F	0.02790	0.00000	0.9721
251 P	0.02790	0.00000	0.9721
252 R	0.02790	0.00000	0.9721
253 P	0.02790	0.00000	0.9721
254 A	0.02790	0.00000	0.9721
255 P	0.02790	0.00000	0.9721
256 R	0.02790	0.00000	0.9721
257 S	0.02790	0.00000	0.9721
258 S	0.02790	0.00000	0.9721
259 Y	0.02790	0.00000	0.9721
260 S	0.02790	0.00000	0.9721
261 A	0.02790	0.00000	0.9721
262 L	0.02790	0.00000	0.9721
263 S	0.02790	0.00000	0.9721
264 S	0.02790	0.00000	0.9721
265 R	0.02790	0.00000	0.9721
266 Q	0.02790	0.00000	0.9721
267 W	0.02790	0.00001	0.97209
268 A	0.02790	0.00001	0.97209
269 L	0.02790	0.00001	0.97209
270 A	0.02790	0.00001	0.97209
271 G	0.02790	0.00001	0.97209
272 L	0.02790	0.00001	0.97209
273 T	0.02790	0.00002	0.97209
274 P	0.02790	0.00002	0.97208
275 L	0.02789	0.00005	0.97205
276 R	0.02789	0.00007	0.97204
277 H	0.02789	0.00013	0.97197
278 W	0.02789	0.00025	0.97186
279 R	0.02789	0.00025	0.97186
280 S	0.02789	0.00026	0.97185
281 A	0.02789	0.00027	0.97185
282 L	0.02789	0.00027	0.97185
283 A	0.02789	0.00027	0.97185
284 T	0.02789	0.00027	0.97185
285 A	0.02789	0.00027	0.97185
286 L	0.02789	0.00027	0.97185
287 A	0.02789	0.00027	0.97185
288 A	0.02789	0.00027	0.97185
289 P	0.02789	0.00026	0.97185
290 A	0.02789	0.00026	0.97185
291 N	0.02789	0.00026	0.97185
292 S	0.02789	0.00026	0.97185
293 T	0.02790	0.00025	0.97185
294 S	0.02791	0.00024	0.97186
295 I	0.02794	0.00021	0.97186
296 D	0.02813	0.00001	0.97186
297 R	0.02813	0.00001	0.97186
298 R	0.02813	0.00001	0.97186
299 L	0.02813	0.00001	0.97186
300 P	0.02814	0.00000	0.97186
301 S	0.02814	0.00000	0.97186
302 T	0.02814	0.00000	0.97186
303 R	0.02814	0.00000	0.97186
304 D	0.02814	0.00000	0.97186

General Statistics

Length: 304

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.0423100000000001

Exp number, first 60 AAs: 0.0159

Total prob of N-in: 0.02920

outside: from residue 1 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