TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0044c

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.01897	0.00000	0.98104
2 T	0.01897	0.00000	0.98104
3 S	0.01897	0.00000	0.98104
4 L	0.01897	0.00000	0.98104
5 V	0.01897	0.00000	0.98104
6 R	0.01897	0.00000	0.98104
7 P	0.01897	0.00000	0.98104
8 D	0.01897	0.00000	0.98104
9 L	0.01897	0.00000	0.98104
10 P	0.01897	0.00000	0.98104
11 V	0.01897	0.00000	0.98104
12 R	0.01897	0.00000	0.98104
13 I	0.01897	0.00000	0.98104
14 G	0.01897	0.00000	0.98104
15 V	0.01897	0.00000	0.98104
16 Q	0.01897	0.00000	0.98104
17 L	0.01897	0.00000	0.98104
18 Q	0.01897	0.00000	0.98104
19 P	0.01897	0.00000	0.98104
20 Q	0.01897	0.00000	0.98104
21 H	0.01897	0.00000	0.98104
22 A	0.01897	0.00000	0.98104
23 P	0.01897	0.00000	0.98104
24 H	0.01897	0.00000	0.98104
25 Y	0.01897	0.00000	0.98104
26 R	0.01897	0.00000	0.98104
27 A	0.01897	0.00000	0.98104
28 V	0.01897	0.00000	0.98104
29 R	0.01897	0.00000	0.98104
30 D	0.01897	0.00000	0.98104
31 A	0.01897	0.00000	0.98104
32 V	0.01897	0.00000	0.98104
33 R	0.01897	0.00000	0.98104
34 R	0.01897	0.00000	0.98104
35 C	0.01897	0.00000	0.98104
36 E	0.01897	0.00000	0.98104
37 D	0.01897	0.00000	0.98104
38 I	0.01897	0.00000	0.98104
39 G	0.01897	0.00000	0.98104
40 V	0.01897	0.00000	0.98104
41 D	0.01897	0.00000	0.98104
42 I	0.01897	0.00000	0.98104
43 A	0.01897	0.00000	0.98104
44 F	0.01897	0.00000	0.98104
45 T	0.01897	0.00000	0.98104
46 W	0.01897	0.00000	0.98104
47 D	0.01897	0.00000	0.98104
48 H	0.01897	0.00000	0.98104
49 F	0.01897	0.00000	0.98104
50 F	0.01897	0.00000	0.98104
51 P	0.01897	0.00000	0.98104
52 L	0.01897	0.00000	0.98104
53 Y	0.01897	0.00000	0.98104
54 G	0.01897	0.00000	0.98104
55 D	0.01897	0.00000	0.98104
56 P	0.01897	0.00000	0.98104
57 D	0.01897	0.00000	0.98104
58 G	0.01897	0.00000	0.98104
59 P	0.01897	0.00000	0.98104
60 H	0.01897	0.00000	0.98104
61 F	0.01897	0.00000	0.98103
62 E	0.01897	0.00000	0.98103
63 C	0.01897	0.00000	0.98103
64 W	0.01897	0.00000	0.98103
65 T	0.01897	0.00001	0.98103
66 V	0.01897	0.00001	0.98103
67 L	0.01897	0.00001	0.98103
68 G	0.01897	0.00001	0.98103
69 A	0.01897	0.00001	0.98103
70 W	0.01897	0.00001	0.98103
71 A	0.01897	0.00001	0.98103
72 E	0.01897	0.00001	0.98103
73 Q	0.01897	0.00001	0.98103
74 T	0.01897	0.00001	0.98103
75 S	0.01897	0.00001	0.98103
76 H	0.01897	0.00001	0.98103
77 I	0.01897	0.00001	0.98103
78 E	0.01897	0.00001	0.98103
79 I	0.01897	0.00001	0.98103
80 G	0.01897	0.00001	0.98103
81 A	0.01897	0.00001	0.98103
82 L	0.01897	0.00001	0.98103
83 V	0.01897	0.00001	0.98103
84 T	0.01897	0.00001	0.98103
85 C	0.01897	0.00001	0.98103
86 N	0.01897	0.00000	0.98103
87 S	0.01897	0.00000	0.98103
88 Y	0.01897	0.00000	0.98103
89 R	0.01897	0.00000	0.98103
90 N	0.01897	0.00000	0.98103
91 P	0.01898	0.00000	0.98103
92 E	0.01898	0.00000	0.98103
93 L	0.01898	0.00000	0.98103
94 L	0.01898	0.00000	0.98103
95 A	0.01898	0.00000	0.98103
96 D	0.01898	0.00000	0.98103
97 M	0.01898	0.00000	0.98103
98 A	0.01898	0.00001	0.98102
99 R	0.01898	0.00001	0.98101
100 T	0.01898	0.00001	0.98101
101 V	0.01898	0.00002	0.98101
102 D	0.01898	0.00002	0.98101
103 H	0.01898	0.00002	0.98101
104 I	0.01897	0.00002	0.98101
105 S	0.01897	0.00002	0.98101
106 G	0.01897	0.00002	0.98101
107 G	0.01897	0.00002	0.98101
108 R	0.01897	0.00002	0.98101
109 L	0.01897	0.00002	0.98101
110 I	0.01897	0.00002	0.98101
111 L	0.01897	0.00002	0.98101
112 G	0.01897	0.00002	0.98101
113 I	0.01898	0.00002	0.98101
114 G	0.01898	0.00002	0.98101
115 S	0.01898	0.00002	0.98101
116 G	0.01898	0.00002	0.98101
117 W	0.01898	0.00002	0.98101
118 K	0.01899	0.00001	0.98101
119 Q	0.01899	0.00000	0.98101
120 K	0.01899	0.00000	0.98101
121 D	0.01899	0.00000	0.98101
122 Y	0.01899	0.00000	0.98101
123 D	0.01899	0.00000	0.98101
124 E	0.01899	0.00000	0.98101
125 Y	0.01899	0.00000	0.98101
126 G	0.01899	0.00000	0.98101
127 Y	0.01899	0.00000	0.98101
128 R	0.01899	0.00000	0.98101
129 F	0.01899	0.00000	0.98101
130 G	0.01899	0.00000	0.98101
131 T	0.01899	0.00000	0.98101
132 A	0.01899	0.00000	0.98101
133 G	0.01899	0.00000	0.98101
134 S	0.01899	0.00000	0.98101
135 R	0.01899	0.00000	0.98101
136 L	0.01899	0.00000	0.98101
137 D	0.01899	0.00000	0.98101
138 D	0.01899	0.00000	0.98101
139 L	0.01899	0.00000	0.98101
140 A	0.01899	0.00000	0.98101
141 A	0.01899	0.00000	0.98101
142 A	0.01899	0.00000	0.98101
143 L	0.01899	0.00000	0.98101
144 P	0.01899	0.00000	0.98101
145 R	0.01899	0.00000	0.98101
146 I	0.01899	0.00000	0.98101
147 K	0.01899	0.00000	0.98101
148 A	0.01899	0.00000	0.98101
149 R	0.01899	0.00000	0.98101
150 L	0.01899	0.00000	0.98101
151 G	0.01899	0.00000	0.98101
152 K	0.01899	0.00000	0.98101
153 L	0.01899	0.00000	0.98101
154 N	0.01899	0.00000	0.98101
155 P	0.01899	0.00000	0.98101
156 P	0.01899	0.00000	0.98101
157 P	0.01899	0.00000	0.98101
158 T	0.01899	0.00000	0.98101
159 R	0.01899	0.00000	0.98101
160 D	0.01899	0.00000	0.98101
161 I	0.01899	0.00000	0.98101
162 P	0.01899	0.00000	0.98101
163 V	0.01899	0.00000	0.98101
164 L	0.01899	0.00000	0.98101
165 I	0.01899	0.00000	0.98101
166 G	0.01899	0.00000	0.98101
167 G	0.01899	0.00000	0.98101
168 G	0.01899	0.00000	0.98101
169 G	0.01899	0.00000	0.98101
170 E	0.01899	0.00000	0.98101
171 R	0.01899	0.00000	0.98101
172 K	0.01899	0.00000	0.98101
173 T	0.01899	0.00000	0.98101
174 L	0.01899	0.00000	0.98101
175 R	0.01899	0.00000	0.98101
176 L	0.01899	0.00000	0.98101
177 V	0.01899	0.00000	0.98101
178 A	0.01899	0.00000	0.981
179 E	0.01899	0.00000	0.981
180 Y	0.01899	0.00001	0.981
181 A	0.01899	0.00001	0.981
182 D	0.01899	0.00001	0.98099
183 I	0.01899	0.00002	0.98098
184 W	0.01899	0.00003	0.98098
185 H	0.01899	0.00003	0.98098
186 S	0.01899	0.00003	0.98098
187 F	0.01899	0.00003	0.98098
188 T	0.01899	0.00003	0.98098
189 A	0.01899	0.00003	0.98098
190 G	0.01899	0.00003	0.98098
191 D	0.01899	0.00003	0.98098
192 S	0.01899	0.00003	0.98098
193 Y	0.01899	0.00003	0.98098
194 L	0.01899	0.00003	0.98098
195 A	0.01899	0.00003	0.98098
196 K	0.01899	0.00003	0.98098
197 S	0.01899	0.00003	0.98098
198 A	0.01899	0.00003	0.98098
199 V	0.01899	0.00003	0.98098
200 L	0.01899	0.00003	0.98098
201 S	0.01900	0.00002	0.98098
202 T	0.01901	0.00001	0.98098
203 H	0.01901	0.00001	0.98098
204 C	0.01901	0.00001	0.98098
205 S	0.01901	0.00001	0.98098
206 T	0.01902	0.00000	0.98098
207 V	0.01902	0.00000	0.98098
208 G	0.01902	0.00000	0.98098
209 R	0.01902	0.00000	0.98098
210 N	0.01902	0.00000	0.98098
211 P	0.01902	0.00000	0.98098
212 A	0.01902	0.00000	0.98098
213 T	0.01902	0.00000	0.98098
214 I	0.01902	0.00000	0.98098
215 E	0.01902	0.00000	0.98098
216 R	0.01901	0.00001	0.98098
217 S	0.01893	0.00019	0.98087
218 A	0.01866	0.00096	0.98038
219 A	0.01834	0.00142	0.98024
220 V	0.01810	0.00179	0.98011
221 D	0.01803	0.00197	0.98001
222 G	0.01668	0.00431	0.97901
223 G	0.01615	0.00509	0.97876
224 G	0.01580	0.00581	0.97839
225 L	0.01564	0.00629	0.97807
226 I	0.01559	0.00655	0.97785
227 A	0.01559	0.00659	0.97781
228 S	0.01559	0.00660	0.9778
229 A	0.01559	0.00661	0.9778
230 E	0.01559	0.00661	0.97779
231 A	0.01559	0.00663	0.97778
232 L	0.01559	0.00664	0.97777
233 A	0.01559	0.00665	0.97776
234 G	0.01559	0.00666	0.97775
235 L	0.01559	0.00668	0.97773
236 G	0.01559	0.00668	0.97773
237 V	0.01560	0.00667	0.97773
238 T	0.01562	0.00665	0.97774
239 L	0.01563	0.00663	0.97775
240 L	0.01575	0.00641	0.97785
241 T	0.01628	0.00553	0.97818
242 V	0.01643	0.00489	0.97867
243 G	0.01669	0.00384	0.97947
244 C	0.01719	0.00280	0.98001
245 D	0.01852	0.00047	0.98102
246 G	0.01858	0.00034	0.98108
247 P	0.01872	0.00016	0.98112
248 D	0.01876	0.00009	0.98115
249 Y	0.01877	0.00009	0.98115
250 D	0.01877	0.00008	0.98115
251 L	0.01877	0.00008	0.98115
252 S	0.01877	0.00008	0.98115
253 A	0.01878	0.00008	0.98115
254 A	0.01879	0.00006	0.98115
255 A	0.01880	0.00005	0.98115
256 A	0.01881	0.00004	0.98115
257 L	0.01882	0.00004	0.98115
258 C	0.01884	0.00002	0.98115
259 R	0.01885	0.00000	0.98115
260 W	0.01885	0.00000	0.98115
261 R	0.01885	0.00000	0.98115
262 D	0.01885	0.00000	0.98115
263 G	0.01885	0.00000	0.98115
264 R	0.01885	0.00000	0.98115

General Statistics

Length: 264

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.14705

Exp number, first 60 AAs: 0

Total prob of N-in: 0.01897

outside: from residue 1 to 264

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