MarinoList - TMHMM

TransMembrane prediction using Hidden Markov Models for MMAR_1258

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.32263	0.00000	0.67738
2 G	0.32263	0.00000	0.67738
3 Y	0.32263	0.00000	0.67738
4 P	0.32263	0.00000	0.67738
5 D	0.32263	0.00000	0.67738
6 N	0.32263	0.00000	0.67738
7 A	0.32263	0.00000	0.67738
8 M	0.32263	0.00000	0.67738
9 A	0.32263	0.00000	0.67738
10 A	0.32263	0.00000	0.67738
11 G	0.32263	0.00000	0.67738
12 E	0.32263	0.00000	0.67738
13 Q	0.32263	0.00000	0.67738
14 V	0.32263	0.00000	0.67738
15 V	0.32263	0.00000	0.67737
16 L	0.32263	0.00000	0.67737
17 H	0.32263	0.00000	0.67737
18 R	0.32263	0.00000	0.67737
19 H	0.32258	0.00006	0.67736
20 P	0.31945	0.00885	0.67169
21 H	0.30250	0.02586	0.67165
22 W	0.30017	0.03175	0.66808
23 T	0.29546	0.08489	0.61965
24 R	0.21921	0.34695	0.43383
25 L	0.07687	0.73651	0.18662
26 V	0.03390	0.91178	0.05432
27 W	0.01161	0.97002	0.01837
28 P	0.00785	0.97845	0.0137
29 V	0.00076	0.99758	0.00167
30 V	0.00021	0.99943	0.00036
31 V	0.00006	0.99982	0.00012
39 A	0.00005	0.99975	0.0002
40 A	0.00010	0.99946	0.00044
41 L	0.00017	0.99880	0.00103
42 G	0.00125	0.99371	0.00504
43 S	0.00956	0.97743	0.01301
44 G	0.01137	0.95605	0.03258
45 F	0.01946	0.94365	0.03689
46 V	0.12089	0.83446	0.04465
47 N	0.39021	0.40204	0.20776
48 S	0.56705	0.14464	0.28831
49 T	0.65631	0.02931	0.31438
50 Q	0.67289	0.00974	0.31737
51 W	0.67349	0.00864	0.31787
52 Q	0.67732	0.00040	0.32228
53 Q	0.67692	0.00053	0.32255
54 L	0.66801	0.00940	0.3226
55 A	0.66353	0.01388	0.3226
56 K	0.66243	0.01503	0.32254
57 N	0.63478	0.04603	0.31919
58 I	0.33721	0.36291	0.29989
59 I	0.24236	0.46060	0.29704
60 H	0.14735	0.56075	0.2919
61 G	0.07413	0.79762	0.12825
62 V	0.06090	0.88375	0.05535
63 I	0.03636	0.93546	0.02817
64 W	0.02923	0.94680	0.02398
65 G	0.02622	0.95213	0.02166
66 I	0.01615	0.97409	0.00975
67 W	0.00352	0.99501	0.00147
68 L	0.00032	0.99890	0.00078
69 V	0.00008	0.99963	0.00029
72 G	0.00005	0.99975	0.0002
73 W	0.00005	0.99973	0.00023
74 L	0.00005	0.99930	0.00065
75 T	0.00008	0.99838	0.00155
76 L	0.00012	0.99458	0.0053
77 W	0.00033	0.97870	0.02096
78 P	0.00134	0.85938	0.13928
79 F	0.00144	0.84730	0.15126
80 L	0.00263	0.80404	0.19333
81 S	0.01610	0.58144	0.40246
82 W	0.01912	0.51322	0.46766
83 L	0.02552	0.44188	0.5326
84 T	0.20328	0.20324	0.59348
85 T	0.26086	0.13264	0.6065
86 H	0.28185	0.08558	0.63257
87 F	0.28404	0.07602	0.63994
88 V	0.28734	0.06941	0.64325
89 V	0.30023	0.04640	0.65337
90 T	0.31693	0.01276	0.67032
91 N	0.32183	0.00161	0.67656
92 R	0.32262	0.00041	0.67697
93 R	0.32268	0.00035	0.67697
94 V	0.32268	0.00301	0.6743
95 M	0.32272	0.00344	0.67384
96 Y	0.32277	0.00355	0.67368
97 R	0.32293	0.00347	0.6736
98 Q	0.32294	0.00356	0.6735
99 G	0.32284	0.00549	0.67167
100 V	0.32281	0.00613	0.67106
101 L	0.32280	0.00622	0.67098
102 T	0.32280	0.00622	0.67097
103 R	0.32280	0.00623	0.67097
104 S	0.32280	0.00623	0.67096
105 G	0.32280	0.00623	0.67096
106 I	0.32280	0.00623	0.67096
107 D	0.32280	0.00623	0.67096
108 I	0.32280	0.00623	0.67096
109 P	0.32280	0.00623	0.67096
110 L	0.32280	0.00623	0.67096
111 A	0.32281	0.00623	0.67096
112 R	0.32287	0.00616	0.67097
113 I	0.32289	0.00614	0.67097
114 N	0.32304	0.00598	0.67099
115 S	0.32312	0.00589	0.67099
116 V	0.32324	0.00577	0.67099
117 E	0.32798	0.00092	0.6711
118 F	0.32806	0.00084	0.6711
119 R	0.32879	0.00008	0.67113
120 D	0.32885	0.00001	0.67113
121 R	0.32885	0.00001	0.67113
122 I	0.32885	0.00001	0.67113
123 F	0.32885	0.00001	0.67114
124 E	0.32886	0.00000	0.67114
125 R	0.32886	0.00001	0.67114
126 M	0.32885	0.00001	0.67114
127 L	0.32885	0.00001	0.67114
128 R	0.32885	0.00001	0.67114
129 T	0.32885	0.00001	0.67114
130 G	0.32885	0.00001	0.67114
131 T	0.32885	0.00001	0.67114
132 L	0.32885	0.00001	0.67114
133 I	0.32885	0.00001	0.67114
134 I	0.32885	0.00001	0.67114
135 E	0.32885	0.00001	0.67114
136 S	0.32885	0.00001	0.67114
137 A	0.32885	0.00001	0.67114
138 S	0.32885	0.00001	0.67114
139 Q	0.32885	0.00001	0.67114
140 D	0.32885	0.00001	0.67114
141 P	0.32885	0.00001	0.67114
142 L	0.32885	0.00001	0.67114
143 E	0.32885	0.00001	0.67114
144 F	0.32885	0.00001	0.67114
145 Y	0.32885	0.00001	0.67114
146 N	0.32885	0.00001	0.67114
147 I	0.32885	0.00001	0.67114
148 P	0.32886	0.00000	0.67114
149 R	0.32886	0.00000	0.67114
150 L	0.32886	0.00000	0.67114
151 R	0.32886	0.00000	0.67114
152 E	0.32886	0.00000	0.67114
153 V	0.32886	0.00000	0.67114
154 H	0.32886	0.00000	0.67114
155 A	0.32886	0.00000	0.67114
156 L	0.32886	0.00000	0.67114
157 L	0.32886	0.00000	0.67114
158 Y	0.32886	0.00000	0.67114
159 H	0.32886	0.00000	0.67114
160 E	0.32886	0.00000	0.67114
161 V	0.32886	0.00000	0.67114
162 F	0.32886	0.00000	0.67114
163 D	0.32886	0.00000	0.67114
164 T	0.32886	0.00000	0.67114
165 L	0.32886	0.00000	0.67114
166 G	0.32886	0.00000	0.67114
167 S	0.32886	0.00000	0.67114
168 E	0.32886	0.00000	0.67114
169 E	0.32886	0.00000	0.67114
170 A	0.32886	0.00000	0.67114
171 P	0.32886	0.00000	0.67114
172 S	0.32886	0.00000	0.67114

General Statistics

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