TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0013

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.10536	0.00000	0.89464
2 R	0.10535	0.00001	0.89464
3 I	0.10533	0.00003	0.89464
4 L	0.10533	0.00003	0.89464
5 V	0.10529	0.00008	0.89463
6 V	0.10529	0.00008	0.89463
7 D	0.10529	0.00009	0.89463
8 N	0.10529	0.00009	0.89463
9 Y	0.10527	0.00010	0.89463
10 D	0.10527	0.00012	0.89462
11 S	0.10519	0.00021	0.89461
12 F	0.10438	0.00102	0.8946
13 V	0.10410	0.00131	0.8946
14 F	0.10410	0.00131	0.8946
15 N	0.10410	0.00131	0.89459
16 L	0.10410	0.00131	0.89459
17 V	0.10410	0.00131	0.89459
18 Q	0.10410	0.00131	0.89459
19 Y	0.10410	0.00131	0.89459
20 L	0.10410	0.00131	0.89459
21 G	0.10410	0.00131	0.89459
22 Q	0.10410	0.00129	0.8946
23 L	0.10410	0.00128	0.89462
24 G	0.10410	0.00127	0.89462
25 I	0.10410	0.00126	0.89463
26 E	0.10411	0.00124	0.89466
27 A	0.10411	0.00120	0.89468
28 E	0.10412	0.00115	0.89473
29 V	0.10412	0.00114	0.89474
30 W	0.10413	0.00091	0.89496
31 R	0.10414	0.00015	0.89571
32 N	0.10414	0.00002	0.89583
33 D	0.10415	0.00000	0.89585
34 D	0.10415	0.00000	0.89585
35 H	0.10415	0.00000	0.89585
36 R	0.10415	0.00000	0.89585
37 L	0.10415	0.00000	0.89585
38 S	0.10415	0.00000	0.89585
39 D	0.10415	0.00000	0.89585
40 E	0.10415	0.00000	0.89585
41 A	0.10415	0.00000	0.89585
42 A	0.10415	0.00000	0.89585
43 V	0.10415	0.00000	0.89585
44 A	0.10415	0.00000	0.89585
45 G	0.10415	0.00000	0.89585
46 Q	0.10415	0.00000	0.89585
47 F	0.10415	0.00000	0.89585
48 D	0.10415	0.00000	0.89585
49 G	0.10415	0.00000	0.89585
50 V	0.10415	0.00000	0.89585
51 L	0.10415	0.00000	0.89585
52 L	0.10415	0.00000	0.89585
53 S	0.10415	0.00000	0.89585
54 P	0.10415	0.00000	0.89585
55 G	0.10415	0.00000	0.89585
56 P	0.10415	0.00000	0.89585
57 G	0.10415	0.00000	0.89585
58 T	0.10415	0.00001	0.89584
59 P	0.10415	0.00000	0.89584
60 E	0.10415	0.00001	0.89584
61 R	0.10414	0.00007	0.89579
62 A	0.10407	0.00059	0.89533
63 G	0.10399	0.00093	0.89509
64 A	0.10394	0.00112	0.89494
65 S	0.10390	0.00119	0.8949
66 V	0.10343	0.00187	0.89471
67 S	0.10270	0.00274	0.89456
68 I	0.10171	0.00379	0.8945
69 V	0.10152	0.00400	0.89448
70 H	0.10146	0.00406	0.89447
71 A	0.10115	0.00441	0.89444
72 C	0.10082	0.00483	0.89436
73 A	0.10051	0.00545	0.89404
74 A	0.10022	0.00587	0.89392
75 A	0.09954	0.00688	0.89357
76 H	0.09938	0.00708	0.89354
77 T	0.09911	0.00739	0.8935
78 P	0.09795	0.00862	0.89343
79 L	0.09710	0.00947	0.89342
80 L	0.09685	0.00973	0.89342
81 G	0.09684	0.00972	0.89344
82 V	0.09684	0.00971	0.89345
83 C	0.09687	0.00966	0.89347
84 L	0.09696	0.00955	0.89349
85 G	0.09745	0.00897	0.89358
86 H	0.09780	0.00850	0.8937
87 Q	0.09795	0.00829	0.89375
88 A	0.09796	0.00826	0.89377
89 I	0.09800	0.00787	0.89414
90 G	0.09810	0.00695	0.89495
91 V	0.09817	0.00590	0.89593
92 A	0.09819	0.00564	0.89617
93 F	0.09821	0.00557	0.89621
94 G	0.09829	0.00524	0.89648
95 A	0.09840	0.00480	0.8968
96 T	0.09873	0.00400	0.89727
97 V	0.09882	0.00324	0.89794
98 D	0.09924	0.00050	0.90026
99 R	0.09925	0.00022	0.90053
100 A	0.09925	0.00018	0.90057
101 P	0.09925	0.00008	0.90067
102 E	0.09925	0.00001	0.90073
103 L	0.09925	0.00001	0.90074
104 L	0.09925	0.00001	0.90074
105 H	0.09925	0.00001	0.90074
106 G	0.09925	0.00001	0.90074
107 K	0.09925	0.00001	0.90074
108 T	0.09925	0.00001	0.90074
109 S	0.09925	0.00001	0.90074
110 S	0.09925	0.00001	0.90074
111 V	0.09924	0.00002	0.90074
112 F	0.09924	0.00002	0.90074
113 H	0.09924	0.00002	0.90074
114 T	0.09924	0.00002	0.90074
115 N	0.09924	0.00002	0.90074
116 V	0.09924	0.00002	0.90074
117 G	0.09924	0.00002	0.90074
118 V	0.09924	0.00002	0.90074
119 L	0.09924	0.00002	0.90074
120 Q	0.09924	0.00002	0.90074
121 G	0.09924	0.00002	0.90074
122 L	0.09924	0.00002	0.90074
123 P	0.09924	0.00002	0.90075
124 D	0.09924	0.00002	0.90075
125 P	0.09924	0.00002	0.90074
126 F	0.09924	0.00003	0.90073
127 T	0.09924	0.00004	0.90072
128 A	0.09924	0.00005	0.9007
129 T	0.09924	0.00005	0.9007
130 R	0.09924	0.00006	0.9007
131 Y	0.09924	0.00007	0.90069
132 H	0.09924	0.00007	0.90069
133 S	0.09924	0.00007	0.90069
134 L	0.09924	0.00007	0.90069
135 T	0.09924	0.00007	0.90069
136 I	0.09924	0.00007	0.90069
137 L	0.09924	0.00008	0.90069
138 P	0.09924	0.00008	0.90069
139 K	0.09924	0.00008	0.90069
140 S	0.09923	0.00008	0.90069
141 L	0.09923	0.00009	0.90069
142 P	0.09922	0.00010	0.90069
143 A	0.09921	0.00011	0.90069
144 V	0.09920	0.00011	0.90069
145 L	0.09920	0.00011	0.90069
146 R	0.09921	0.00011	0.90069
147 V	0.09920	0.00013	0.90067
148 T	0.09921	0.00011	0.90067
149 A	0.09921	0.00011	0.90067
150 R	0.09923	0.00009	0.90067
151 T	0.09922	0.00010	0.90067
152 S	0.09919	0.00013	0.90067
153 S	0.09918	0.00014	0.90067
154 G	0.09916	0.00016	0.90067
155 V	0.09916	0.00016	0.90067
156 I	0.09916	0.00017	0.90067
157 M	0.09916	0.00016	0.90067
158 A	0.09916	0.00016	0.90067
159 V	0.09916	0.00016	0.90069
160 Q	0.09916	0.00015	0.90069
161 H	0.09916	0.00015	0.90069
162 T	0.09916	0.00015	0.90069
163 G	0.09916	0.00014	0.9007
164 L	0.09916	0.00014	0.9007
165 P	0.09916	0.00012	0.90072
166 I	0.09916	0.00012	0.90072
167 H	0.09916	0.00011	0.90072
168 G	0.09916	0.00011	0.90072
169 V	0.09916	0.00011	0.90073
170 Q	0.09917	0.00008	0.90075
171 F	0.09917	0.00007	0.90076
172 H	0.09917	0.00002	0.9008
173 P	0.09917	0.00001	0.90081
174 E	0.09917	0.00001	0.90082
175 S	0.09917	0.00000	0.90082
176 I	0.09917	0.00000	0.90082
177 L	0.09917	0.00000	0.90082
178 T	0.09917	0.00000	0.90082
179 E	0.09917	0.00000	0.90082
180 G	0.09917	0.00000	0.90082
181 G	0.09917	0.00000	0.90082
182 H	0.09917	0.00000	0.90082
183 R	0.09917	0.00000	0.90082
184 I	0.09917	0.00000	0.90082
185 L	0.09917	0.00000	0.90082
186 A	0.09917	0.00000	0.90082
187 N	0.09917	0.00000	0.90082
188 W	0.09917	0.00000	0.90082
189 L	0.09917	0.00000	0.90082
190 T	0.09917	0.00000	0.90082
191 C	0.09917	0.00000	0.90082
192 C	0.09917	0.00000	0.90082
193 G	0.09917	0.00000	0.90082
194 W	0.09917	0.00000	0.90082
195 T	0.09917	0.00000	0.90082
196 Q	0.09917	0.00000	0.90082
197 D	0.09917	0.00000	0.90082
198 D	0.09917	0.00000	0.90082
199 T	0.09917	0.00000	0.90082
200 L	0.09917	0.00000	0.90082
201 V	0.09917	0.00000	0.90082
202 R	0.09917	0.00000	0.90082
203 R	0.09917	0.00000	0.90082
204 L	0.09917	0.00000	0.90082
205 E	0.09917	0.00000	0.90082
206 N	0.09917	0.00000	0.90082
207 E	0.09917	0.00000	0.90082
208 V	0.09917	0.00001	0.90082
209 L	0.09917	0.00001	0.90082
210 T	0.09917	0.00001	0.90082
211 A	0.09917	0.00001	0.90082
212 I	0.09917	0.00001	0.90082
213 S	0.09917	0.00001	0.90082
214 P	0.09917	0.00001	0.90082
215 H	0.09917	0.00001	0.90082
216 F	0.09917	0.00001	0.90082
217 P	0.09917	0.00001	0.90082
218 T	0.09917	0.00001	0.90082
219 S	0.09917	0.00001	0.90082
220 T	0.09917	0.00001	0.90082
221 A	0.09917	0.00001	0.90082
222 S	0.09917	0.00001	0.90082
223 A	0.09917	0.00001	0.90082
224 G	0.09917	0.00001	0.90082
225 E	0.09917	0.00001	0.90082
226 A	0.09917	0.00001	0.90082
227 T	0.09917	0.00001	0.90083
228 G	0.09917	0.00000	0.90083
229 R	0.09917	0.00000	0.90083
230 T	0.09917	0.00000	0.90083
231 S	0.09917	0.00000	0.90083
232 A	0.09917	0.00000	0.90083

General Statistics

Length: 232

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.24298

Exp number, first 60 AAs: 0.02458

Total prob of N-in: 0.10536

outside: from residue 1 to 232

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