TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0024

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 V	0.01364	0.00000	0.98636
2 N	0.01364	0.00000	0.98636
3 Y	0.01364	0.00000	0.98636
4 S	0.01364	0.00000	0.98636
5 E	0.01364	0.00000	0.98636
6 V	0.01364	0.00000	0.98636
7 E	0.01364	0.00000	0.98636
8 L	0.01364	0.00000	0.98636
9 L	0.01364	0.00000	0.98636
10 S	0.01364	0.00000	0.98636
11 R	0.01364	0.00000	0.98636
12 A	0.01364	0.00000	0.98636
13 H	0.01364	0.00000	0.98636
14 Q	0.01364	0.00000	0.98636
15 L	0.01364	0.00000	0.98636
16 F	0.01364	0.00000	0.98636
17 A	0.01364	0.00000	0.98636
18 G	0.01364	0.00000	0.98636
19 D	0.01364	0.00000	0.98636
20 S	0.01364	0.00000	0.98636
21 R	0.01364	0.00000	0.98636
22 R	0.01364	0.00000	0.98636
23 P	0.01364	0.00000	0.98636
24 G	0.01364	0.00000	0.98636
25 L	0.01364	0.00000	0.98636
26 D	0.01364	0.00000	0.98636
27 A	0.01364	0.00000	0.98636
28 G	0.01364	0.00000	0.98636
29 T	0.01364	0.00000	0.98636
30 T	0.01364	0.00000	0.98636
31 P	0.01364	0.00000	0.98636
32 Y	0.01364	0.00000	0.98636
33 G	0.01364	0.00000	0.98636
34 D	0.01364	0.00000	0.98636
35 L	0.01364	0.00000	0.98636
36 L	0.01364	0.00000	0.98636
37 S	0.01364	0.00000	0.98636
38 R	0.01364	0.00000	0.98636
39 A	0.01364	0.00000	0.98636
40 A	0.01364	0.00000	0.98636
41 D	0.01364	0.00000	0.98636
42 L	0.01364	0.00000	0.98636
43 N	0.01364	0.00000	0.98636
44 V	0.01364	0.00000	0.98636
45 G	0.01364	0.00000	0.98636
46 A	0.01364	0.00000	0.98636
47 G	0.01364	0.00000	0.98636
48 Q	0.01364	0.00000	0.98636
49 R	0.01364	0.00000	0.98636
50 R	0.01364	0.00000	0.98636
51 Y	0.01364	0.00000	0.98636
52 Q	0.01364	0.00000	0.98636
53 L	0.01364	0.00000	0.98636
54 A	0.01364	0.00000	0.98636
55 V	0.01364	0.00000	0.98636
56 D	0.01364	0.00000	0.98636
57 H	0.01363	0.00003	0.98634
58 S	0.01362	0.00005	0.98633
59 R	0.01361	0.00008	0.98631
60 A	0.01358	0.00020	0.98622
61 A	0.01357	0.00024	0.98619
62 L	0.01357	0.00025	0.98618
63 L	0.01357	0.00026	0.98618
64 S	0.01357	0.00026	0.98617
65 A	0.01357	0.00026	0.98617
66 A	0.01357	0.00026	0.98617
67 R	0.01357	0.00026	0.98617
68 T	0.01357	0.00026	0.98617
69 D	0.01357	0.00026	0.98617
70 A	0.01357	0.00026	0.98617
71 A	0.01357	0.00026	0.98617
72 A	0.01357	0.00026	0.98617
73 G	0.01357	0.00026	0.98617
74 A	0.01357	0.00026	0.98617
75 V	0.01357	0.00026	0.98617
76 I	0.01357	0.00026	0.98617
77 T	0.01357	0.00025	0.98617
78 G	0.01358	0.00024	0.98618
79 A	0.01363	0.00018	0.98619
80 Q	0.01374	0.00004	0.98622
81 R	0.01376	0.00001	0.98623
82 D	0.01376	0.00000	0.98623
83 R	0.01376	0.00000	0.98623
84 A	0.01376	0.00000	0.98623
85 W	0.01376	0.00000	0.98623
86 A	0.01376	0.00000	0.98623
87 R	0.01376	0.00000	0.98623
88 R	0.01376	0.00000	0.98623
89 S	0.01376	0.00000	0.98623
90 T	0.01376	0.00000	0.98623
91 G	0.01376	0.00000	0.98623
92 T	0.01376	0.00000	0.98623
93 V	0.01376	0.00000	0.98623
94 L	0.01376	0.00000	0.98623
95 D	0.01376	0.00000	0.98623
96 E	0.01376	0.00000	0.98623
97 A	0.01376	0.00000	0.98623
98 R	0.01376	0.00000	0.98623
99 S	0.01376	0.00000	0.98623
100 D	0.01376	0.00000	0.98623
101 T	0.01376	0.00000	0.98623
102 T	0.01376	0.00000	0.98623
103 V	0.01376	0.00000	0.98623
104 T	0.01376	0.00000	0.98623
105 A	0.01376	0.00000	0.98623
106 V	0.01376	0.00000	0.98623
107 M	0.01376	0.00000	0.98623
108 P	0.01376	0.00000	0.98623
109 I	0.01376	0.00000	0.98623
110 A	0.01376	0.00000	0.98623
111 Q	0.01376	0.00000	0.98623
112 R	0.01376	0.00000	0.98623
113 E	0.01376	0.00000	0.98623
114 A	0.01376	0.00000	0.98623
115 I	0.01376	0.00000	0.98623
116 R	0.01376	0.00000	0.98623
117 R	0.01376	0.00000	0.98623
118 R	0.01376	0.00000	0.98623
119 V	0.01376	0.00000	0.98623
120 A	0.01376	0.00000	0.98623
121 R	0.01376	0.00000	0.98623
122 L	0.01376	0.00000	0.98623
123 R	0.01376	0.00000	0.98623
124 A	0.01376	0.00000	0.98623
125 Q	0.01376	0.00000	0.98623
126 R	0.01376	0.00000	0.98623
127 A	0.01376	0.00000	0.98623
128 H	0.01376	0.00000	0.98623
129 V	0.01376	0.00000	0.98623
130 L	0.01376	0.00000	0.98623
131 T	0.01376	0.00000	0.98623
132 A	0.01376	0.00000	0.98623
133 R	0.01376	0.00000	0.98623
134 R	0.01376	0.00000	0.98623
135 R	0.01376	0.00000	0.98623
136 A	0.01376	0.00000	0.98623
137 R	0.01376	0.00000	0.98623
138 R	0.01376	0.00000	0.98623
139 H	0.01376	0.00000	0.98623
140 L	0.01375	0.00002	0.98623
141 A	0.01375	0.00002	0.98623
142 A	0.01375	0.00002	0.98623
143 L	0.01374	0.00002	0.98623
144 R	0.01374	0.00002	0.98623
145 A	0.01374	0.00003	0.98623
146 L	0.01374	0.00003	0.98623
147 R	0.01374	0.00003	0.98623
148 Y	0.01374	0.00003	0.98623
149 R	0.01374	0.00003	0.98623
150 V	0.01374	0.00003	0.98623
151 A	0.01374	0.00003	0.98623
152 H	0.01374	0.00003	0.98623
153 G	0.01374	0.00003	0.98623
154 P	0.01374	0.00003	0.98623
155 G	0.01374	0.00003	0.98623
156 V	0.01374	0.00003	0.98623
157 A	0.01374	0.00003	0.98623
158 L	0.01374	0.00003	0.98623
159 A	0.01374	0.00003	0.98623
160 K	0.01374	0.00001	0.98625
161 L	0.01374	0.00001	0.98625
162 R	0.01374	0.00001	0.98625
163 L	0.01374	0.00001	0.98625
164 P	0.01374	0.00001	0.98625
165 S	0.01374	0.00001	0.98625
166 P	0.01374	0.00000	0.98625
167 S	0.01374	0.00001	0.98625
168 G	0.01374	0.00001	0.98625
169 R	0.01374	0.00001	0.98625
170 A	0.01374	0.00001	0.98625
171 G	0.01374	0.00001	0.98625
172 I	0.01374	0.00001	0.98625
173 A	0.01374	0.00001	0.98625
174 V	0.01374	0.00001	0.98625
175 H	0.01374	0.00001	0.98625
176 A	0.01374	0.00001	0.98625
177 A	0.01374	0.00001	0.98625
178 L	0.01374	0.00001	0.98625
179 S	0.01374	0.00001	0.98625
180 R	0.01374	0.00001	0.98625
181 L	0.01374	0.00001	0.98625
182 G	0.01374	0.00001	0.98625
183 R	0.01374	0.00001	0.98625
184 P	0.01374	0.00001	0.98624
185 Y	0.01374	0.00002	0.98624
186 V	0.01374	0.00002	0.98624
187 W	0.01374	0.00002	0.98624
188 G	0.01374	0.00002	0.98624
189 A	0.01374	0.00002	0.98624
190 T	0.01374	0.00001	0.98624
191 G	0.01374	0.00001	0.98624
192 P	0.01374	0.00001	0.98624
193 N	0.01374	0.00001	0.98624
194 Q	0.01374	0.00001	0.98624
195 F	0.01374	0.00001	0.98624
196 D	0.01374	0.00001	0.98624
197 C	0.01374	0.00001	0.98624
198 S	0.01374	0.00001	0.98624
199 G	0.01374	0.00001	0.98624
200 L	0.01374	0.00001	0.98624
201 V	0.01374	0.00001	0.98624
202 Q	0.01374	0.00001	0.98624
203 W	0.01374	0.00001	0.98624
204 A	0.01374	0.00001	0.98624
205 Y	0.01374	0.00001	0.98624
206 A	0.01375	0.00001	0.98624
207 Q	0.01375	0.00000	0.98624
208 A	0.01375	0.00000	0.98624
209 G	0.01375	0.00000	0.98624
210 V	0.01375	0.00000	0.98624
211 H	0.01375	0.00000	0.98624
212 L	0.01375	0.00000	0.98624
213 D	0.01375	0.00000	0.98624
214 R	0.01375	0.00000	0.98624
215 T	0.01375	0.00000	0.98624
216 T	0.01375	0.00000	0.98624
217 Y	0.01375	0.00000	0.98624
218 Q	0.01375	0.00000	0.98624
219 Q	0.01375	0.00000	0.98624
220 I	0.01375	0.00000	0.98624
221 N	0.01375	0.00000	0.98624
222 E	0.01375	0.00000	0.98624
223 G	0.01375	0.00000	0.98624
224 I	0.01375	0.00000	0.98624
225 P	0.01375	0.00000	0.98624
226 V	0.01375	0.00000	0.98624
227 P	0.01375	0.00000	0.98624
228 R	0.01375	0.00000	0.98624
229 S	0.01375	0.00000	0.98624
230 Q	0.01375	0.00000	0.98624
231 V	0.01375	0.00000	0.98624
232 R	0.01375	0.00000	0.98624
233 P	0.01375	0.00000	0.98624
234 G	0.01375	0.00000	0.98624
235 D	0.01375	0.00000	0.98624
236 L	0.01375	0.00001	0.98624
237 V	0.01375	0.00001	0.98623
238 F	0.01375	0.00001	0.98623
239 P	0.01375	0.00001	0.98623
240 H	0.01375	0.00001	0.98623
241 P	0.01375	0.00001	0.98623
242 G	0.01375	0.00002	0.98623
243 H	0.01375	0.00002	0.98622
244 V	0.01375	0.00003	0.98621
245 Q	0.01375	0.00003	0.98621
246 L	0.01375	0.00005	0.98619
247 A	0.01375	0.00006	0.98618
248 I	0.01375	0.00006	0.98618
249 G	0.01375	0.00006	0.98618
250 N	0.01375	0.00006	0.98618
251 N	0.01375	0.00006	0.98618
252 L	0.01375	0.00006	0.98618
253 V	0.01375	0.00006	0.98618
254 V	0.01375	0.00006	0.98618
255 E	0.01376	0.00005	0.98618
256 A	0.01376	0.00005	0.98618
257 P	0.01376	0.00005	0.98618
258 H	0.01376	0.00005	0.98618
259 A	0.01376	0.00005	0.98618
260 G	0.01376	0.00005	0.98618
261 A	0.01376	0.00005	0.98618
262 S	0.01377	0.00005	0.98618
263 V	0.01377	0.00005	0.98618
264 R	0.01377	0.00004	0.98618
265 V	0.01377	0.00004	0.98618
266 S	0.01378	0.00004	0.98618
267 S	0.01379	0.00003	0.98618
268 L	0.01379	0.00002	0.98618
269 G	0.01381	0.00000	0.98618
270 N	0.01381	0.00000	0.98618
271 N	0.01381	0.00000	0.98618
272 V	0.01381	0.00000	0.98618
273 Q	0.01381	0.00000	0.98618
274 I	0.01381	0.00000	0.98618
275 R	0.01382	0.00000	0.98618
276 R	0.01382	0.00000	0.98618
277 P	0.01382	0.00000	0.98618
278 L	0.01382	0.00000	0.98618
279 S	0.01382	0.00000	0.98618
280 G	0.01382	0.00000	0.98618
281 R	0.01382	0.00000	0.98618

General Statistics

Length: 281

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.00757999999999997

Exp number, first 60 AAs: 0.00036

Total prob of N-in: 0.01364

outside: from residue 1 to 281

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