TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0038

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 V	0.03529	0.00000	0.96471
2 V	0.03529	0.00000	0.96471
3 A	0.03529	0.00000	0.96471
4 P	0.03529	0.00000	0.96471
5 H	0.03529	0.00000	0.96471
6 E	0.03529	0.00000	0.96471
7 D	0.03529	0.00000	0.96471
8 P	0.03529	0.00000	0.96471
9 E	0.03529	0.00000	0.96471
10 D	0.03529	0.00000	0.96471
11 H	0.03529	0.00000	0.96471
12 V	0.03529	0.00000	0.96471
13 A	0.03529	0.00000	0.9647
14 P	0.03529	0.00000	0.9647
15 A	0.03529	0.00005	0.96466
16 A	0.03529	0.00005	0.96466
17 Q	0.03529	0.00005	0.96466
18 R	0.03529	0.00005	0.96465
19 V	0.03529	0.00006	0.96465
20 R	0.03529	0.00006	0.96465
21 A	0.03528	0.00006	0.96465
22 G	0.03528	0.00006	0.96465
23 T	0.03528	0.00006	0.96465
24 L	0.03528	0.00006	0.96465
25 L	0.03528	0.00006	0.96465
26 L	0.03528	0.00006	0.96465
27 A	0.03528	0.00006	0.96465
28 N	0.03528	0.00006	0.96465
29 T	0.03528	0.00006	0.96465
30 D	0.03529	0.00006	0.96465
31 L	0.03529	0.00006	0.96465
32 L	0.03529	0.00006	0.96465
33 E	0.03533	0.00002	0.96465
34 P	0.03533	0.00003	0.96464
35 T	0.03533	0.00004	0.96463
36 F	0.03533	0.00004	0.96463
37 R	0.03534	0.00003	0.96463
38 R	0.03534	0.00004	0.96463
39 S	0.03534	0.00006	0.96461
40 V	0.03534	0.00007	0.96459
41 I	0.03534	0.00007	0.96459
42 Y	0.03534	0.00007	0.9646
43 I	0.03534	0.00007	0.9646
44 V	0.03534	0.00006	0.9646
45 E	0.03534	0.00006	0.9646
46 H	0.03534	0.00006	0.9646
47 N	0.03534	0.00006	0.9646
48 D	0.03534	0.00007	0.9646
49 G	0.03534	0.00007	0.96459
50 G	0.03534	0.00007	0.96459
51 T	0.03534	0.00007	0.96459
52 L	0.03534	0.00008	0.96459
53 G	0.03534	0.00008	0.96459
54 V	0.03534	0.00008	0.96459
55 V	0.03534	0.00008	0.96459
56 L	0.03534	0.00008	0.96459
57 N	0.03538	0.00004	0.96459
58 R	0.03540	0.00002	0.96459
59 P	0.03540	0.00002	0.96459
60 S	0.03540	0.00002	0.96459
61 E	0.03540	0.00001	0.96459
62 T	0.03540	0.00001	0.96458
63 A	0.03540	0.00002	0.96458
64 V	0.03540	0.00002	0.96458
65 Y	0.03540	0.00002	0.96458
66 N	0.03540	0.00002	0.96458
67 V	0.03540	0.00002	0.96458
68 L	0.03540	0.00002	0.96458
69 P	0.03541	0.00001	0.96458
70 Q	0.03541	0.00001	0.96458
71 W	0.03541	0.00001	0.96458
72 A	0.03541	0.00001	0.96458
73 K	0.03541	0.00000	0.96458
74 L	0.03541	0.00000	0.96458
75 A	0.03542	0.00000	0.96458
76 A	0.03542	0.00000	0.96458
77 K	0.03542	0.00000	0.96458
78 P	0.03542	0.00000	0.96458
79 K	0.03542	0.00000	0.96458
80 T	0.03541	0.00001	0.96458
81 M	0.03541	0.00001	0.96458
82 F	0.03541	0.00002	0.96457
83 I	0.03541	0.00002	0.96457
84 G	0.03541	0.00002	0.96457
85 G	0.03541	0.00002	0.96457
86 P	0.03541	0.00002	0.96457
87 V	0.03541	0.00002	0.96457
88 K	0.03541	0.00002	0.96457
89 R	0.03541	0.00002	0.96457
90 D	0.03541	0.00002	0.96457
91 A	0.03541	0.00002	0.96457
92 A	0.03541	0.00002	0.96457
93 L	0.03541	0.00002	0.96457
94 C	0.03541	0.00002	0.96457
95 L	0.03541	0.00002	0.96457
96 A	0.03541	0.00002	0.96457
97 V	0.03541	0.00002	0.96457
98 L	0.03541	0.00002	0.96457
99 R	0.03541	0.00002	0.96457
100 V	0.03541	0.00002	0.96457
101 G	0.03541	0.00002	0.96457
102 A	0.03541	0.00002	0.96457
103 D	0.03542	0.00001	0.96457
104 P	0.03542	0.00000	0.96457
105 E	0.03542	0.00000	0.96457
106 G	0.03542	0.00000	0.96457
107 V	0.03542	0.00000	0.96457
108 P	0.03542	0.00000	0.96457
109 G	0.03542	0.00000	0.96457
110 L	0.03542	0.00000	0.96457
111 R	0.03542	0.00000	0.96457
112 H	0.03542	0.00000	0.96457
113 V	0.03542	0.00000	0.96457
114 A	0.03542	0.00000	0.96457
115 G	0.03542	0.00000	0.96457
116 R	0.03542	0.00000	0.96457
117 L	0.03542	0.00000	0.96457
118 V	0.03542	0.00000	0.96457
119 M	0.03542	0.00000	0.96457
120 V	0.03542	0.00000	0.96457
121 D	0.03542	0.00000	0.96457
122 L	0.03542	0.00000	0.96457
123 D	0.03542	0.00000	0.96457
124 A	0.03542	0.00000	0.96457
125 D	0.03542	0.00000	0.96457
126 P	0.03542	0.00001	0.96457
127 E	0.03542	0.00002	0.96456
128 V	0.03542	0.00005	0.96453
129 L	0.03541	0.00006	0.96452
130 A	0.03541	0.00007	0.96452
131 A	0.03541	0.00007	0.96452
132 A	0.03541	0.00007	0.96452
133 V	0.03541	0.00007	0.96452
134 E	0.03541	0.00007	0.96452
135 G	0.03541	0.00007	0.96452
136 V	0.03541	0.00007	0.96452
137 R	0.03541	0.00007	0.96452
138 I	0.03541	0.00007	0.96452
139 Y	0.03541	0.00007	0.96452
140 A	0.03541	0.00007	0.96452
141 G	0.03542	0.00007	0.96452
142 Y	0.03542	0.00007	0.96452
143 S	0.03542	0.00007	0.96452
144 G	0.03542	0.00007	0.96452
145 W	0.03542	0.00007	0.96452
146 T	0.03542	0.00006	0.96452
147 I	0.03543	0.00005	0.96452
148 G	0.03545	0.00003	0.96452
149 Q	0.03546	0.00002	0.96452
150 L	0.03546	0.00001	0.96452
151 E	0.03547	0.00000	0.96452
152 G	0.03547	0.00000	0.96452
153 E	0.03547	0.00000	0.96452
154 I	0.03547	0.00000	0.96452
155 E	0.03547	0.00000	0.96452
156 R	0.03547	0.00000	0.96452
157 D	0.03547	0.00000	0.96452
158 D	0.03547	0.00000	0.96452
159 W	0.03547	0.00001	0.96452
160 I	0.03547	0.00001	0.96452
161 V	0.03547	0.00001	0.96452
162 L	0.03547	0.00001	0.96452
163 S	0.03547	0.00001	0.96452
164 A	0.03547	0.00001	0.96452
165 L	0.03547	0.00001	0.96452
166 P	0.03547	0.00001	0.96452
167 S	0.03547	0.00001	0.96452
168 D	0.03547	0.00001	0.96452
169 V	0.03547	0.00001	0.96452
170 L	0.03547	0.00001	0.96452
171 V	0.03547	0.00001	0.96452
172 G	0.03547	0.00001	0.96452
173 P	0.03547	0.00001	0.96452
174 R	0.03547	0.00001	0.96452
175 A	0.03547	0.00001	0.96452
176 D	0.03547	0.00001	0.96452
177 L	0.03547	0.00001	0.96452
178 W	0.03547	0.00001	0.96452
179 G	0.03547	0.00000	0.96453
180 Q	0.03547	0.00000	0.96453
181 V	0.03547	0.00000	0.96453
182 L	0.03547	0.00000	0.96453
183 R	0.03547	0.00000	0.96453
184 R	0.03547	0.00000	0.96453
185 Q	0.03547	0.00000	0.96453
186 P	0.03547	0.00000	0.96453
187 L	0.03547	0.00000	0.96453
188 P	0.03547	0.00000	0.96453
189 L	0.03547	0.00000	0.96453
190 S	0.03547	0.00000	0.96453
191 L	0.03547	0.00000	0.96453
192 L	0.03547	0.00000	0.96453
193 A	0.03547	0.00000	0.96453
194 T	0.03547	0.00000	0.96453
195 H	0.03547	0.00000	0.96453
196 P	0.03547	0.00000	0.96453
197 I	0.03547	0.00000	0.96453
198 D	0.03547	0.00000	0.96453
199 L	0.03547	0.00000	0.96453
200 S	0.03547	0.00000	0.96453
201 R	0.03547	0.00000	0.96453
202 N	0.03547	0.00000	0.96453

General Statistics

Length: 202

Number of predicted TMHs: 0

Exp number of AAs in TMHs: 0.00485999999999999

Exp number, first 60 AAs: 0.0026

Total prob of N-in: 0.03529

outside: from residue 1 to 202

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