TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0012

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.90985	0.00000	0.09015
2 R	0.90985	0.00000	0.09015
3 L	0.90985	0.00000	0.09015
4 T	0.90985	0.00000	0.09015
5 H	0.90985	0.00000	0.09015
6 P	0.90985	0.00000	0.09015
7 T	0.90985	0.00000	0.09015
8 P	0.90985	0.00000	0.09015
9 C	0.90985	0.00000	0.09015
10 P	0.90985	0.00000	0.09015
11 E	0.90985	0.00000	0.09015
12 N	0.90985	0.00000	0.09015
13 G	0.90985	0.00000	0.09015
14 E	0.90985	0.00000	0.09015
15 T	0.90985	0.00000	0.09015
16 M	0.90985	0.00000	0.09015
17 I	0.90985	0.00000	0.09015
18 D	0.90985	0.00000	0.09015
19 R	0.90984	0.00000	0.09015
20 R	0.90929	0.00061	0.0901
21 R	0.82853	0.08137	0.09009
22 S	0.74328	0.16886	0.08785
23 A	0.54881	0.37325	0.07794
24 W	0.41607	0.51020	0.07374
25 R	0.36361	0.56624	0.07015
26 F	0.06328	0.88970	0.04702
27 S	0.02777	0.92758	0.04466
28 V	0.01142	0.94448	0.0441
29 P	0.00570	0.95040	0.0439
30 L	0.00181	0.95451	0.04367
31 V	0.00167	0.95472	0.04361
32 C	0.00166	0.95475	0.04359
33 L	0.00165	0.95476	0.04359
34 L	0.00165	0.95476	0.04359
35 A	0.00165	0.95476	0.04359
36 G	0.00165	0.95476	0.04359
37 L	0.00165	0.95476	0.04359
38 L	0.00165	0.95470	0.04364
39 L	0.00165	0.95363	0.04472
40 A	0.00176	0.95049	0.04775
41 A	0.00199	0.94169	0.05631
42 T	0.00261	0.92046	0.07693
43 H	0.00348	0.88211	0.11442
44 G	0.00438	0.76479	0.23082
45 V	0.00653	0.66260	0.33087
46 S	0.01805	0.36368	0.61827
47 G	0.02268	0.24387	0.73346
48 G	0.02713	0.17753	0.79534
49 T	0.04633	0.03581	0.91786
50 E	0.04805	0.00695	0.945
51 I	0.04813	0.00390	0.94797
52 R	0.04820	0.00064	0.95115
53 R	0.04822	0.00002	0.95177
54 S	0.04822	0.00001	0.95178
55 D	0.04822	0.00000	0.95178
56 A	0.04822	0.00000	0.95178
57 P	0.04822	0.00000	0.95178
58 R	0.04822	0.00000	0.95178
59 L	0.04822	0.00000	0.95178
60 V	0.04822	0.00000	0.95178
61 D	0.04822	0.00000	0.95178
62 L	0.04822	0.00000	0.95178
63 V	0.04822	0.00000	0.95178
64 R	0.04822	0.00000	0.95178
65 R	0.04822	0.00000	0.95178
66 A	0.04822	0.00000	0.95178
67 Q	0.04822	0.00000	0.95178
68 A	0.04822	0.00000	0.95178
69 S	0.04822	0.00000	0.95178
70 V	0.04822	0.00000	0.95178
71 N	0.04822	0.00000	0.95178
72 R	0.04822	0.00000	0.95178
73 L	0.04822	0.00000	0.95178
74 A	0.04822	0.00000	0.95178
75 T	0.04822	0.00000	0.95178
76 E	0.04822	0.00000	0.95178
77 R	0.04822	0.00000	0.95178
78 E	0.04822	0.00000	0.95178
79 A	0.04822	0.00000	0.95178
80 L	0.04822	0.00000	0.95178
81 T	0.04822	0.00000	0.95178
82 T	0.04822	0.00000	0.95178
83 R	0.04822	0.00000	0.95178
84 I	0.04822	0.00000	0.95178
85 D	0.04822	0.00000	0.95178
86 S	0.04822	0.00000	0.95178
87 V	0.04822	0.00000	0.95178
88 H	0.04822	0.00000	0.95178
89 G	0.04822	0.00000	0.95178
90 R	0.04822	0.00000	0.95178
91 S	0.04822	0.00000	0.95178
92 V	0.04822	0.00000	0.95178
93 D	0.04822	0.00000	0.95178
94 T	0.04822	0.00000	0.95178
95 A	0.04822	0.00000	0.95178
96 L	0.04822	0.00000	0.95178
97 A	0.04822	0.00000	0.95178
98 A	0.04822	0.00000	0.95178
99 M	0.04822	0.00000	0.95178
100 Q	0.04822	0.00001	0.95177
101 R	0.04821	0.00002	0.95177
102 R	0.04816	0.00021	0.95163
103 S	0.04775	0.00076	0.95149
104 A	0.04754	0.00108	0.95139
105 K	0.04733	0.00140	0.95126
106 L	0.04531	0.00480	0.94988
107 A	0.04501	0.00572	0.94927
108 G	0.04492	0.00589	0.9492
109 V	0.04485	0.00597	0.94918
110 A	0.04484	0.00598	0.94917
111 A	0.04484	0.00599	0.94917
112 M	0.04484	0.00599	0.94917
113 N	0.04484	0.00599	0.94917
114 P	0.04484	0.00599	0.94917
115 V	0.04484	0.00599	0.94917
116 H	0.04484	0.00599	0.94917
117 G	0.04484	0.00599	0.94917
118 P	0.04484	0.00598	0.94917
119 G	0.04484	0.00598	0.94917
120 L	0.04484	0.00598	0.94917
121 V	0.04485	0.00596	0.9492
122 V	0.04486	0.00592	0.94921
123 T	0.04494	0.00572	0.94934
124 L	0.04510	0.00523	0.94966
125 Q	0.04696	0.00268	0.95036
126 D	0.04740	0.00092	0.95169
127 A	0.04741	0.00078	0.95181
128 Q	0.04744	0.00052	0.95204
129 R	0.04745	0.00003	0.95252
130 D	0.04745	0.00000	0.95255
131 A	0.04745	0.00000	0.95255
132 N	0.04745	0.00000	0.95255
133 G	0.04745	0.00000	0.95255
134 R	0.04745	0.00000	0.95255
135 F	0.04745	0.00000	0.95255
136 P	0.04745	0.00000	0.95255
137 R	0.04745	0.00000	0.95255
138 D	0.04745	0.00000	0.95255
139 A	0.04745	0.00000	0.95255
140 S	0.04745	0.00000	0.95255
141 P	0.04745	0.00000	0.95255
142 D	0.04745	0.00000	0.95255
143 D	0.04745	0.00000	0.95255
144 L	0.04745	0.00001	0.95254
145 V	0.04745	0.00002	0.95252
146 V	0.04745	0.00002	0.95252
147 H	0.04745	0.00002	0.95252
148 Q	0.04745	0.00002	0.95252
149 Q	0.04745	0.00002	0.95252
150 D	0.04745	0.00002	0.95252
151 I	0.04745	0.00003	0.95252
152 E	0.04745	0.00003	0.95251
153 A	0.04745	0.00003	0.95251
154 V	0.04745	0.00003	0.95251
155 L	0.04745	0.00003	0.95251
156 N	0.04745	0.00003	0.95251
157 A	0.04745	0.00003	0.95251
158 L	0.04745	0.00003	0.95251
159 W	0.04745	0.00003	0.95251
160 N	0.04745	0.00003	0.95251
161 A	0.04745	0.00003	0.95251
162 G	0.04745	0.00003	0.95251
163 A	0.04746	0.00003	0.95251
164 E	0.04746	0.00002	0.95251
165 A	0.04747	0.00002	0.95251
166 I	0.04747	0.00002	0.95251
167 Q	0.04747	0.00001	0.95251
168 M	0.04747	0.00004	0.9525
169 Q	0.04748	0.00004	0.95248
170 D	0.04747	0.00005	0.95248
171 Q	0.04743	0.00018	0.95239
172 R	0.04728	0.00043	0.95229
173 I	0.04650	0.00173	0.95177
174 I	0.04638	0.00188	0.95174
175 A	0.04634	0.00192	0.95173
176 M	0.04611	0.00217	0.95172
177 S	0.04599	0.00229	0.95172
178 I	0.04593	0.00235	0.95172
179 A	0.04593	0.00236	0.95172
180 R	0.04592	0.00237	0.95172
181 C	0.04587	0.00241	0.95171
182 V	0.04586	0.00243	0.95171
183 G	0.04585	0.00243	0.95171
184 N	0.04585	0.00244	0.95171
185 T	0.04583	0.00246	0.95171
186 L	0.04579	0.00250	0.95171
187 L	0.04577	0.00252	0.95171
188 L	0.04577	0.00250	0.95173
189 N	0.04583	0.00235	0.95182
190 G	0.04583	0.00225	0.95192
191 R	0.04634	0.00160	0.95206
192 T	0.04634	0.00187	0.95179
193 Y	0.04602	0.00289	0.95109
194 S	0.04595	0.00296	0.95108
195 P	0.04581	0.00507	0.94913
196 P	0.04499	0.02509	0.92992
197 Y	0.04270	0.04356	0.91374
198 T	0.04052	0.06255	0.89693
199 I	0.03321	0.09516	0.87164
200 A	0.03289	0.09836	0.86875
201 A	0.03260	0.10012	0.86728
202 I	0.03251	0.10120	0.86629
203 G	0.03250	0.10138	0.86613
204 D	0.03250	0.10149	0.86602
205 A	0.03247	0.10242	0.86512
206 A	0.03244	0.10283	0.86473
207 A	0.03242	0.10305	0.86453
208 M	0.03240	0.10312	0.86447
209 Q	0.03239	0.10318	0.86444
210 A	0.03234	0.10327	0.86439
211 A	0.03231	0.10332	0.86436
212 L	0.03230	0.10334	0.86436
213 A	0.03235	0.10321	0.86444
214 A	0.03248	0.10301	0.8645
215 A	0.03305	0.10234	0.86461
216 P	0.03418	0.10082	0.86501
217 L	0.03456	0.10031	0.86513
218 V	0.03781	0.09682	0.86537
219 T	0.06090	0.07237	0.86672
220 L	0.07378	0.05732	0.8689
221 Y	0.09176	0.03671	0.87153
222 K	0.11863	0.00308	0.87829
223 Q	0.12001	0.00161	0.87838
224 Y	0.12009	0.00151	0.8784
225 V	0.12032	0.00127	0.87841
226 V	0.12060	0.00097	0.87843
227 R	0.12093	0.00061	0.87846
228 F	0.12102	0.00050	0.87849
229 G	0.12113	0.00037	0.8785
230 L	0.12117	0.00031	0.87852
231 G	0.12123	0.00022	0.87855
232 Y	0.12132	0.00010	0.87858
233 C	0.12135	0.00005	0.87861
234 E	0.12136	0.00003	0.87861
235 E	0.12136	0.00003	0.87861
236 V	0.12136	0.00003	0.87861
237 H	0.12136	0.00003	0.87861
238 P	0.12136	0.00003	0.87861
239 D	0.12136	0.00003	0.87861
240 L	0.12136	0.00003	0.87861
241 Q	0.12136	0.00003	0.87861
242 I	0.12136	0.00003	0.87861
243 V	0.12136	0.00002	0.87861
244 G	0.12136	0.00002	0.87862
245 Y	0.12136	0.00002	0.87862
246 A	0.12136	0.00001	0.87863
247 D	0.12137	0.00000	0.87863
248 P	0.12137	0.00000	0.87863
249 V	0.12137	0.00000	0.87863
250 R	0.12137	0.00000	0.87863
251 M	0.12137	0.00000	0.87863
252 H	0.12137	0.00000	0.87863
253 F	0.12137	0.00000	0.87863
254 A	0.12137	0.00000	0.87863
255 Q	0.12137	0.00000	0.87863
256 P	0.12137	0.00000	0.87863
257 A	0.12137	0.00000	0.87863
258 G	0.12137	0.00000	0.87863
259 P	0.12137	0.00000	0.87863
260 L	0.12137	0.00000	0.87863
261 D	0.12137	0.00000	0.87863
262 Y	0.12137	0.00000	0.87863

General Statistics

Length: 262

Number of predicted TMHs: 1

Exp number of AAs in TMHs: 23.42719

Exp number, first 60 AAs: 20.91335

Total prob of N-in: 0.90985

POSSIBLE N-term signal sequence

inside: from residue 1 to 22

TMhelix: from residue 23 to 45

outside: from residue 46 to 262

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