TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0009

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.21623	0.00000	0.78377
2 A	0.21623	0.00000	0.78377
3 D	0.21623	0.00000	0.78377
4 C	0.21623	0.00000	0.78377
5 D	0.21623	0.00001	0.78377
6 S	0.21623	0.00001	0.78377
7 V	0.21616	0.00008	0.78377
8 T	0.21616	0.00008	0.78377
9 N	0.21615	0.00008	0.78377
10 S	0.21615	0.00009	0.78376
11 P	0.21615	0.00009	0.78376
12 L	0.21615	0.00009	0.78376
13 A	0.21615	0.00009	0.78376
14 T	0.21615	0.00009	0.78376
15 A	0.21615	0.00009	0.78375
16 T	0.21615	0.00009	0.78375
17 A	0.21615	0.00009	0.78375
18 T	0.21615	0.00009	0.78375
19 L	0.21615	0.00009	0.78375
20 H	0.21615	0.00009	0.78375
21 T	0.21615	0.00009	0.78375
22 N	0.21615	0.00007	0.78377
23 R	0.21615	0.00007	0.78378
24 G	0.21615	0.00008	0.78376
25 D	0.21615	0.00005	0.78379
26 I	0.21612	0.00016	0.78372
27 K	0.21611	0.00017	0.78371
28 I	0.21605	0.00045	0.7835
29 A	0.21602	0.00051	0.78346
30 L	0.21597	0.00057	0.78345
31 F	0.21597	0.00058	0.78345
32 G	0.21597	0.00058	0.78345
33 N	0.21598	0.00057	0.78346
34 H	0.21598	0.00057	0.78346
35 A	0.21598	0.00057	0.78346
36 P	0.21598	0.00056	0.78346
37 K	0.21598	0.00056	0.78346
38 T	0.21598	0.00056	0.78346
39 V	0.21598	0.00056	0.78346
40 A	0.21598	0.00056	0.78346
41 N	0.21598	0.00056	0.78346
42 F	0.21598	0.00056	0.78346
43 V	0.21598	0.00056	0.78346
44 G	0.21599	0.00056	0.78346
45 L	0.21599	0.00055	0.78346
46 A	0.21619	0.00032	0.78348
47 Q	0.21630	0.00018	0.78352
48 G	0.21632	0.00012	0.78355
49 T	0.21635	0.00006	0.7836
50 K	0.21635	0.00001	0.78364
51 D	0.21636	0.00000	0.78364
52 Y	0.21635	0.00001	0.78364
53 S	0.21635	0.00001	0.78364
54 T	0.21635	0.00001	0.78364
55 Q	0.21635	0.00001	0.78364
56 N	0.21634	0.00002	0.78364
57 A	0.21633	0.00003	0.78363
58 S	0.21632	0.00005	0.78363
59 G	0.21632	0.00005	0.78363
60 G	0.21632	0.00005	0.78363
61 P	0.21632	0.00005	0.78363
62 S	0.21631	0.00006	0.78363
63 G	0.21631	0.00006	0.78363
64 P	0.21631	0.00006	0.78362
65 F	0.21631	0.00006	0.78362
66 Y	0.21631	0.00006	0.78362
67 D	0.21631	0.00006	0.78362
68 G	0.21631	0.00006	0.78362
69 A	0.21631	0.00007	0.78362
70 V	0.21631	0.00007	0.78362
71 F	0.21631	0.00007	0.78362
72 H	0.21631	0.00006	0.78362
73 R	0.21631	0.00006	0.78362
74 V	0.21631	0.00006	0.78362
75 I	0.21631	0.00006	0.78363
76 Q	0.21632	0.00004	0.78364
77 G	0.21632	0.00004	0.78364
78 F	0.21632	0.00003	0.78364
79 M	0.21632	0.00003	0.78364
80 I	0.21632	0.00003	0.78365
81 Q	0.21632	0.00002	0.78366
82 G	0.21633	0.00001	0.78366
83 G	0.21633	0.00001	0.78366
84 D	0.21633	0.00001	0.78366
85 P	0.21633	0.00001	0.78366
86 T	0.21633	0.00001	0.78366
87 G	0.21633	0.00001	0.78366
88 T	0.21633	0.00001	0.78366
89 G	0.21633	0.00001	0.78367
90 R	0.21633	0.00000	0.78367
91 G	0.21633	0.00000	0.78367
92 G	0.21633	0.00000	0.78367
93 P	0.21633	0.00000	0.78367
94 G	0.21633	0.00000	0.78367
95 Y	0.21633	0.00000	0.78367
96 K	0.21633	0.00000	0.78367
97 F	0.21633	0.00000	0.78367
98 A	0.21633	0.00000	0.78367
99 D	0.21633	0.00000	0.78367
100 E	0.21633	0.00000	0.78367
101 F	0.21633	0.00000	0.78367
102 H	0.21633	0.00000	0.78367
103 P	0.21633	0.00000	0.78367
104 E	0.21633	0.00000	0.78367
105 L	0.21633	0.00000	0.78367
106 Q	0.21633	0.00000	0.78367
107 F	0.21633	0.00001	0.78367
108 D	0.21633	0.00001	0.78366
109 K	0.21632	0.00006	0.78363
110 P	0.21615	0.00158	0.78228
111 Y	0.21597	0.00275	0.78127
112 L	0.21591	0.00323	0.78086
113 L	0.21588	0.00349	0.78063
114 A	0.21588	0.00356	0.78056
115 M	0.21587	0.00360	0.78053
116 A	0.21587	0.00361	0.78052
117 N	0.21587	0.00361	0.78052
118 A	0.21587	0.00361	0.78052
119 G	0.21587	0.00361	0.78052
120 P	0.21587	0.00361	0.78052
121 G	0.21587	0.00361	0.78052
122 T	0.21587	0.00361	0.78052
123 N	0.21587	0.00361	0.78052
124 G	0.21587	0.00361	0.78052
125 S	0.21587	0.00361	0.78052
126 Q	0.21587	0.00361	0.78052
127 F	0.21587	0.00361	0.78052
128 F	0.21587	0.00361	0.78052
129 I	0.21589	0.00358	0.78053
130 T	0.21607	0.00333	0.7806
131 V	0.21637	0.00291	0.78072
132 G	0.21693	0.00228	0.78079
133 K	0.21872	0.00033	0.78096
134 T	0.21894	0.00009	0.78096
135 P	0.21899	0.00003	0.78098
136 H	0.21901	0.00001	0.78098
137 L	0.21901	0.00001	0.78098
138 N	0.21902	0.00000	0.78098
139 R	0.21902	0.00000	0.78098
140 R	0.21902	0.00000	0.78098
141 H	0.21902	0.00000	0.78098
142 T	0.21902	0.00000	0.78098
143 I	0.21902	0.00000	0.78098
144 F	0.21902	0.00000	0.78098
145 G	0.21902	0.00000	0.78098
146 E	0.21902	0.00000	0.78098
147 V	0.21902	0.00000	0.78098
148 I	0.21902	0.00000	0.78098
149 D	0.21902	0.00000	0.78098
150 A	0.21902	0.00000	0.78098
151 E	0.21902	0.00000	0.78098
152 S	0.21902	0.00000	0.78098
153 Q	0.21902	0.00000	0.78098
154 R	0.21902	0.00000	0.78098
155 V	0.21902	0.00000	0.78098
156 V	0.21902	0.00000	0.78098
157 E	0.21902	0.00000	0.78098
158 A	0.21902	0.00000	0.78098
159 I	0.21902	0.00000	0.78098
160 S	0.21902	0.00000	0.78098
161 K	0.21902	0.00000	0.78098
162 T	0.21902	0.00000	0.78098
163 A	0.21902	0.00000	0.78098
164 T	0.21902	0.00000	0.78098
165 D	0.21902	0.00000	0.78098
166 G	0.21902	0.00000	0.78098
167 N	0.21902	0.00000	0.78098
168 D	0.21902	0.00000	0.78098
169 R	0.21902	0.00000	0.78098
170 P	0.21902	0.00000	0.78098
171 T	0.21902	0.00000	0.78098
172 D	0.21902	0.00000	0.78098
173 P	0.21902	0.00000	0.78098
174 V	0.21902	0.00000	0.78098
175 V	0.21902	0.00000	0.78098
176 I	0.21902	0.00000	0.78098
177 E	0.21902	0.00000	0.78098
178 S	0.21902	0.00000	0.78098
179 I	0.21902	0.00000	0.78098
180 T	0.21902	0.00000	0.78098
181 I	0.21902	0.00000	0.78098
182 S	0.21902	0.00000	0.78098

General Statistics

Length: 182

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.09184

Exp number, first 60 AAs: 0.01286

Total prob of N-in: 0.21623

outside: from residue 1 to 182

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