TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv1874

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 V	0.03552	0.00000	0.96448
2 L	0.03552	0.00000	0.96448
3 M	0.03552	0.00000	0.96448
4 R	0.03552	0.00000	0.96448
5 P	0.03552	0.00000	0.96448
6 E	0.03552	0.00000	0.96448
7 P	0.03552	0.00000	0.96448
8 D	0.03552	0.00000	0.96448
9 D	0.03552	0.00000	0.96448
10 D	0.03552	0.00000	0.96448
11 W	0.03552	0.00002	0.96447
12 C	0.03546	0.00009	0.96446
13 A	0.03530	0.00097	0.96374
14 R	0.03530	0.00097	0.96374
15 Q	0.03530	0.00580	0.9589
16 R	0.03518	0.00592	0.9589
17 A	0.03470	0.00779	0.95751
18 Q	0.03469	0.00968	0.95564
19 V	0.03392	0.01099	0.95509
20 A	0.03344	0.01226	0.95431
21 D	0.03286	0.01284	0.9543
22 A	0.03251	0.01325	0.95424
23 L	0.03226	0.01352	0.95421
24 L	0.03226	0.01353	0.95421
25 G	0.03226	0.01353	0.95421
26 L	0.03226	0.01353	0.95421
27 G	0.03226	0.01353	0.95421
28 V	0.03226	0.01353	0.95421
29 A	0.03226	0.01353	0.95421
30 G	0.03226	0.01353	0.95421
31 L	0.03226	0.01352	0.95422
32 S	0.03231	0.01346	0.95423
33 I	0.03275	0.01301	0.95424
34 N	0.03346	0.01218	0.95436
35 V	0.03470	0.01074	0.95455
36 R	0.04058	0.00412	0.9553
37 D	0.04202	0.00222	0.95576
38 S	0.04227	0.00202	0.9557
39 T	0.04233	0.00295	0.95472
40 V	0.04228	0.00333	0.95439
41 R	0.04237	0.00228	0.95534
42 D	0.04229	0.00283	0.95489
43 S	0.04089	0.00796	0.95115
44 L	0.03998	0.01556	0.94447
45 M	0.03985	0.01702	0.94313
46 T	0.03976	0.01730	0.94295
47 L	0.03946	0.01774	0.9428
48 T	0.03940	0.01786	0.94274
49 T	0.03938	0.01792	0.94271
50 L	0.03936	0.01797	0.94267
51 Y	0.03935	0.01797	0.94267
52 P	0.03935	0.01798	0.94267
53 P	0.03935	0.01798	0.94266
54 V	0.03935	0.01798	0.94266
55 A	0.03935	0.01799	0.94266
56 A	0.03935	0.01799	0.94265
57 V	0.03935	0.01799	0.94265
58 V	0.03936	0.01798	0.94266
59 S	0.03941	0.01792	0.94266
60 L	0.03947	0.01785	0.94267
61 W	0.04037	0.01687	0.94276
62 T	0.04801	0.00879	0.9432
63 Q	0.05271	0.00316	0.94412
64 Q	0.05334	0.00220	0.94447
65 C	0.05338	0.00192	0.9447
66 Y	0.05359	0.00122	0.94519
67 G	0.05385	0.00053	0.94562
68 E	0.05412	0.00009	0.94579
69 Q	0.05414	0.00006	0.9458
70 V	0.05414	0.00006	0.94581
71 A	0.05415	0.00004	0.94581
72 A	0.05415	0.00004	0.94582
73 A	0.05416	0.00002	0.94582
74 L	0.05416	0.00002	0.94582
75 R	0.05416	0.00002	0.94583
76 L	0.05416	0.00002	0.94583
77 L	0.05416	0.00001	0.94583
78 A	0.05417	0.00001	0.94583
79 Q	0.05417	0.00000	0.94583
80 E	0.05417	0.00000	0.94583
81 C	0.05417	0.00000	0.94583
82 D	0.05417	0.00000	0.94583
83 E	0.05417	0.00001	0.94583
84 L	0.05415	0.00004	0.94581
85 G	0.05415	0.00004	0.94581
86 A	0.05415	0.00004	0.94581
87 Y	0.05415	0.00004	0.94581
88 L	0.05415	0.00004	0.94581
89 V	0.05415	0.00004	0.94581
90 T	0.05415	0.00004	0.94581
91 E	0.05415	0.00004	0.94581
92 S	0.05415	0.00004	0.94581
93 V	0.05415	0.00004	0.94581
94 P	0.05415	0.00004	0.94581
95 L	0.05415	0.00004	0.94581
96 T	0.05415	0.00005	0.94581
97 F	0.05415	0.00005	0.9458
98 P	0.05415	0.00005	0.9458
99 S	0.05415	0.00005	0.9458
100 L	0.05415	0.00005	0.9458
101 V	0.05415	0.00004	0.9458
102 E	0.05415	0.00002	0.94583
103 S	0.05415	0.00002	0.94583
104 G	0.05416	0.00002	0.94583
105 S	0.05416	0.00001	0.94583
106 R	0.05416	0.00001	0.94584
107 T	0.05416	0.00001	0.94584
108 P	0.05416	0.00001	0.94584
109 G	0.05416	0.00001	0.94584
110 L	0.05416	0.00001	0.94584
111 A	0.05416	0.00001	0.94584
112 N	0.05416	0.00001	0.94584
113 I	0.05416	0.00001	0.94584
114 A	0.05416	0.00001	0.94584
115 L	0.05416	0.00001	0.94584
116 L	0.05416	0.00001	0.94584
117 R	0.05417	0.00000	0.94584
118 R	0.05417	0.00000	0.94584
119 P	0.05417	0.00000	0.94584
120 D	0.05417	0.00000	0.94584
121 G	0.05417	0.00000	0.94584
122 L	0.05417	0.00000	0.94584
123 D	0.05417	0.00000	0.94584
124 Q	0.05417	0.00000	0.94584
125 A	0.05417	0.00000	0.94584
126 T	0.05417	0.00000	0.94584
127 W	0.05417	0.00000	0.94584
128 L	0.05417	0.00000	0.94584
129 T	0.05417	0.00000	0.94584
130 R	0.05417	0.00000	0.94584
131 W	0.05417	0.00000	0.94584
132 Q	0.05417	0.00000	0.94584
133 R	0.05417	0.00000	0.94584
134 D	0.05417	0.00000	0.94584
135 H	0.05417	0.00000	0.94584
136 T	0.05416	0.00000	0.94584
137 Q	0.05416	0.00000	0.94584
138 V	0.05416	0.00000	0.94584
139 A	0.05416	0.00001	0.94584
140 I	0.05416	0.00001	0.94584
141 E	0.05416	0.00001	0.94584
142 A	0.05416	0.00001	0.94584
143 Q	0.05416	0.00001	0.94584
144 A	0.05416	0.00001	0.94584
145 T	0.05416	0.00001	0.94584
146 F	0.05416	0.00001	0.94584
147 G	0.05416	0.00001	0.94584
148 Y	0.05416	0.00001	0.94584
149 T	0.05416	0.00001	0.94584
150 Q	0.05416	0.00001	0.94584
151 N	0.05415	0.00002	0.94584
152 W	0.05409	0.00009	0.94582
153 V	0.05407	0.00011	0.94582
154 V	0.05406	0.00012	0.94582
155 R	0.05406	0.00012	0.94582
156 A	0.05405	0.00013	0.94582
157 L	0.05405	0.00013	0.94582
158 T	0.05405	0.00013	0.94582
159 P	0.05405	0.00014	0.94582
160 E	0.05405	0.00014	0.94582
161 A	0.05404	0.00014	0.94581
162 P	0.05404	0.00015	0.94581
163 G	0.05404	0.00017	0.94579
164 I	0.05404	0.00019	0.94577
165 A	0.05404	0.00021	0.94575
166 G	0.05404	0.00022	0.94574
167 I	0.05404	0.00022	0.94574
168 V	0.05404	0.00022	0.94574
169 E	0.05404	0.00021	0.94575
170 E	0.05404	0.00021	0.94575
171 L	0.05404	0.00021	0.94575
172 F	0.05404	0.00021	0.94575
173 P	0.05404	0.00021	0.94575
174 V	0.05404	0.00020	0.94576
175 A	0.05405	0.00014	0.94582
176 A	0.05405	0.00011	0.94583
177 T	0.05405	0.00010	0.94585
178 T	0.05405	0.00010	0.94585
179 D	0.05406	0.00009	0.94585
180 L	0.05406	0.00009	0.94586
181 K	0.05406	0.00009	0.94586
182 A	0.05406	0.00009	0.94586
183 F	0.05406	0.00009	0.94586
184 F	0.05406	0.00008	0.94586
185 G	0.05406	0.00007	0.94586
186 A	0.05410	0.00004	0.94586
187 A	0.05411	0.00002	0.94586
188 D	0.05413	0.00000	0.94586
189 D	0.05413	0.00000	0.94586
190 N	0.05413	0.00000	0.94586
191 D	0.05413	0.00000	0.94586
192 L	0.05413	0.00000	0.94586
193 R	0.05413	0.00000	0.94586
194 N	0.05413	0.00000	0.94586
195 R	0.05413	0.00000	0.94586
196 I	0.05413	0.00001	0.94586
197 S	0.05413	0.00001	0.94586
198 R	0.05412	0.00001	0.94586
199 M	0.05412	0.00002	0.94586
200 V	0.05410	0.00006	0.94584
201 A	0.05410	0.00006	0.94584
202 S	0.05410	0.00006	0.94584
203 T	0.05410	0.00006	0.94584
204 S	0.05410	0.00007	0.94584
205 A	0.05410	0.00007	0.94583
206 F	0.05410	0.00007	0.94583
207 G	0.05410	0.00007	0.94583
208 A	0.05410	0.00007	0.94583
209 N	0.05410	0.00007	0.94583
210 Q	0.05410	0.00007	0.94583
211 N	0.05410	0.00007	0.94583
212 I	0.05410	0.00007	0.94583
213 D	0.05410	0.00007	0.94583
214 T	0.05410	0.00007	0.94583
215 V	0.05410	0.00006	0.94584
216 P	0.05410	0.00006	0.94584
217 T	0.05410	0.00006	0.94584
218 S	0.05410	0.00006	0.94585
219 R	0.05410	0.00005	0.94585
220 Y	0.05410	0.00005	0.94585
221 V	0.05410	0.00005	0.94586
222 F	0.05410	0.00004	0.94586
223 R	0.05412	0.00000	0.94587
224 T	0.05413	0.00000	0.94588
225 P	0.05413	0.00000	0.94588
226 F	0.05413	0.00000	0.94588
227 K	0.05413	0.00000	0.94588
228 D	0.05413	0.00000	0.94588

General Statistics

Length: 228

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.62309

Exp number, first 60 AAs: 0.58043

Total prob of N-in: 0.03552

outside: from residue 1 to 228

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