MarinoList - TMHMM

TransMembrane prediction using Hidden Markov Models for MMAR_4154

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.94190	0.00000	0.0581
2 K	0.94188	0.00002	0.0581
3 I	0.94177	0.00013	0.0581
4 N	0.94177	0.00015	0.05808
5 K	0.93741	0.00476	0.05783
6 I	0.93741	0.00635	0.05624
7 A	0.82354	0.12027	0.0562
8 T	0.82354	0.12027	0.0562
9 A	0.80078	0.14305	0.05618
10 L	0.80075	0.14391	0.05535
11 K	0.79894	0.14575	0.05531
12 T	0.59625	0.34884	0.05491
13 A	0.04517	0.90258	0.05225
14 T	0.04505	0.90270	0.05225
15 F	0.04505	0.91843	0.03653
16 A	0.03258	0.93089	0.03653
17 I	0.01578	0.94793	0.03629
18 A	0.01571	0.94803	0.03627
19 A	0.01461	0.94913	0.03626
20 G	0.00958	0.95433	0.0361
21 A	0.00574	0.95816	0.0361
22 V	0.00564	0.95826	0.0361
23 A	0.00563	0.95822	0.03614
24 L	0.00563	0.95810	0.03626
25 G	0.00564	0.95544	0.03892
26 L	0.00565	0.95347	0.04087
27 A	0.00570	0.94410	0.0502
28 S	0.00613	0.92498	0.0689
29 P	0.00769	0.90870	0.08361
30 A	0.00783	0.82341	0.16877
31 G	0.00799	0.78259	0.20941
32 A	0.00812	0.71882	0.27306
33 A	0.00941	0.59644	0.39415
34 S	0.00996	0.52283	0.46721
35 G	0.01165	0.37642	0.61194
36 T	0.01421	0.07386	0.91192
37 M	0.01498	0.06417	0.92085
38 Y	0.02595	0.04584	0.92821
39 G	0.02637	0.02675	0.94688
40 D	0.02741	0.00595	0.96664
41 P	0.02745	0.00506	0.96749
42 A	0.02746	0.00459	0.96795
43 A	0.02756	0.00265	0.9698
44 A	0.02757	0.00075	0.97167
45 A	0.02761	0.00025	0.97213
46 K	0.02764	0.00010	0.97227
47 Y	0.02764	0.00010	0.97226
48 W	0.02765	0.00009	0.97226
49 R	0.02767	0.00007	0.97226
50 Y	0.02768	0.00006	0.97225
51 Q	0.02772	0.00003	0.97225
52 K	0.02773	0.00002	0.97225
53 Y	0.02772	0.00004	0.97223
54 D	0.02772	0.00004	0.97223
55 D	0.02772	0.00005	0.97222
56 C	0.02771	0.00008	0.97221
57 L	0.02771	0.00009	0.9722
58 I	0.02771	0.00009	0.9722
59 M	0.02771	0.00009	0.9722
60 A	0.02771	0.00009	0.9722
61 V	0.02771	0.00009	0.9722
62 A	0.02771	0.00009	0.9722
63 D	0.02771	0.00009	0.9722
64 V	0.02771	0.00009	0.9722
65 V	0.02771	0.00009	0.9722
66 G	0.02771	0.00009	0.9722
67 Q	0.02771	0.00008	0.9722
68 V	0.02771	0.00008	0.9722
69 T	0.02772	0.00008	0.9722
70 G	0.02773	0.00007	0.97221
71 K	0.02776	0.00002	0.97222
72 E	0.02776	0.00002	0.97222
73 P	0.02776	0.00002	0.97222
74 S	0.02777	0.00001	0.97222
75 E	0.02777	0.00001	0.97222
76 Q	0.02778	0.00001	0.97221
77 A	0.02778	0.00001	0.97221
78 I	0.02778	0.00002	0.97221
79 I	0.02778	0.00002	0.97221
80 K	0.02778	0.00001	0.97221
81 V	0.02778	0.00001	0.97221
82 A	0.02778	0.00001	0.97221
83 Q	0.02778	0.00001	0.97221
84 T	0.02778	0.00001	0.97221
85 T	0.02778	0.00001	0.97221
86 P	0.02778	0.00001	0.97221
87 S	0.02778	0.00001	0.97221
88 A	0.02778	0.00001	0.97221
89 V	0.02778	0.00001	0.97221
90 H	0.02778	0.00001	0.97221
91 P	0.02778	0.00001	0.97221
92 G	0.02778	0.00001	0.97221
93 S	0.02778	0.00001	0.97221
94 I	0.02778	0.00001	0.97221
95 Y	0.02778	0.00001	0.97221
96 T	0.02779	0.00000	0.97221
97 K	0.02779	0.00000	0.97221
98 P	0.02779	0.00000	0.97221
99 A	0.02779	0.00000	0.97221
100 D	0.02779	0.00000	0.97221
101 T	0.02779	0.00000	0.97221
102 K	0.02779	0.00000	0.97221
103 N	0.02779	0.00000	0.97221
104 P	0.02779	0.00000	0.9722
105 N	0.02779	0.00000	0.9722
106 S	0.02779	0.00001	0.9722
107 G	0.02779	0.00001	0.97219
108 Q	0.02779	0.00002	0.97219
109 G	0.02779	0.00002	0.97218
110 T	0.02779	0.00003	0.97217
111 S	0.02779	0.00004	0.97217
112 Q	0.02779	0.00005	0.97216
113 A	0.02779	0.00005	0.97216
114 D	0.02779	0.00005	0.97216
115 I	0.02779	0.00005	0.97215
116 A	0.02779	0.00005	0.97215
117 T	0.02779	0.00005	0.97215
118 L	0.02779	0.00006	0.97215
119 L	0.02779	0.00006	0.97215
120 A	0.02779	0.00006	0.97215
121 H	0.02779	0.00006	0.97215
122 Y	0.02779	0.00006	0.97215
123 G	0.02779	0.00006	0.97215
124 I	0.02779	0.00005	0.97215
125 D	0.02780	0.00005	0.97215
126 A	0.02780	0.00004	0.97215
127 V	0.02780	0.00004	0.97215
128 L	0.02780	0.00004	0.97215
129 T	0.02782	0.00003	0.97215
130 D	0.02783	0.00002	0.97215
131 L	0.02783	0.00002	0.97215
132 D	0.02784	0.00001	0.97215
133 N	0.02784	0.00001	0.97215
134 A	0.02784	0.00001	0.97215
135 P	0.02784	0.00001	0.97215
136 S	0.02784	0.00001	0.97215
137 N	0.02784	0.00001	0.97215
138 G	0.02784	0.00001	0.97215
139 V	0.02784	0.00001	0.97215
140 L	0.02784	0.00001	0.97215
141 T	0.02784	0.00001	0.97215
142 G	0.02784	0.00001	0.97214
143 M	0.02784	0.00001	0.97214
144 E	0.02784	0.00001	0.97214
145 A	0.02784	0.00001	0.97214
146 L	0.02784	0.00002	0.97213
147 E	0.02784	0.00002	0.97213
148 H	0.02784	0.00005	0.97211
149 H	0.02784	0.00006	0.9721
150 L	0.02782	0.00021	0.97197
151 G	0.02780	0.00030	0.9719
152 N	0.02780	0.00032	0.97187
153 G	0.02779	0.00041	0.9718
154 R	0.02779	0.00041	0.97179
155 A	0.02779	0.00042	0.97178
156 V	0.02779	0.00042	0.97178
157 I	0.02779	0.00042	0.97178
158 V	0.02779	0.00042	0.97178
159 S	0.02779	0.00042	0.97178
160 V	0.02779	0.00042	0.97178
161 N	0.02780	0.00042	0.97178
162 A	0.02780	0.00042	0.97178
163 E	0.02780	0.00042	0.97178
164 M	0.02780	0.00042	0.97178
165 I	0.02780	0.00042	0.97178
166 W	0.02780	0.00041	0.97178
167 G	0.02780	0.00041	0.97178
168 V	0.02782	0.00039	0.97179
169 T	0.02789	0.00032	0.9718
170 I	0.02794	0.00025	0.9718
171 D	0.02815	0.00001	0.97184
172 N	0.02815	0.00001	0.97184
173 K	0.02816	0.00000	0.97184
174 D	0.02816	0.00000	0.97184
175 E	0.02816	0.00000	0.97184
176 A	0.02816	0.00000	0.97184
177 G	0.02816	0.00000	0.97184
178 N	0.02816	0.00000	0.97184
179 P	0.02816	0.00000	0.97184
180 V	0.02816	0.00000	0.97184
181 S	0.02816	0.00001	0.97184
182 D	0.02816	0.00001	0.97184
183 H	0.02816	0.00001	0.97184
184 A	0.02816	0.00001	0.97183
185 V	0.02816	0.00001	0.97183
186 V	0.02816	0.00001	0.97183
187 V	0.02816	0.00001	0.97183
188 T	0.02816	0.00001	0.97183
189 G	0.02816	0.00001	0.97183
190 V	0.02816	0.00001	0.97183
191 D	0.02816	0.00001	0.97183
192 T	0.02816	0.00001	0.97183
193 A	0.02816	0.00001	0.97183
194 N	0.02816	0.00001	0.97183
195 G	0.02816	0.00001	0.97183
196 V	0.02816	0.00001	0.97183
197 V	0.02816	0.00001	0.97183
198 H	0.02816	0.00001	0.97183
199 L	0.02816	0.00001	0.97183
200 N	0.02816	0.00000	0.97184
201 D	0.02817	0.00000	0.97184
202 S	0.02817	0.00000	0.97184
203 G	0.02817	0.00000	0.97184
204 S	0.02817	0.00000	0.97184
205 D	0.02817	0.00000	0.97184
206 E	0.02817	0.00000	0.97184
207 G	0.02817	0.00000	0.97184
208 R	0.02817	0.00000	0.97184
209 D	0.02817	0.00000	0.97184
210 E	0.02817	0.00000	0.97183
211 Q	0.02817	0.00001	0.97183
212 V	0.02816	0.00001	0.97182
213 P	0.02816	0.00002	0.97182
214 M	0.02816	0.00002	0.97181
215 A	0.02816	0.00002	0.97181
216 L	0.02816	0.00002	0.97181
217 F	0.02816	0.00002	0.97181
218 M	0.02816	0.00002	0.97181
219 Q	0.02816	0.00002	0.97181
220 A	0.02816	0.00002	0.97181
221 W	0.02816	0.00002	0.97181
222 A	0.02816	0.00002	0.97181
223 T	0.02816	0.00002	0.97181
224 S	0.02816	0.00002	0.97181
225 Q	0.02816	0.00002	0.97181
226 D	0.02816	0.00002	0.97181
227 F	0.02816	0.00002	0.97181
228 M	0.02816	0.00002	0.97181
229 A	0.02816	0.00002	0.97181
230 V	0.02816	0.00002	0.97181
231 T	0.02817	0.00001	0.97182
232 T	0.02818	0.00001	0.97182
233 Q	0.02818	0.00000	0.97182
234 D	0.02818	0.00000	0.97182
235 S	0.02818	0.00000	0.97182
236 N	0.02818	0.00000	0.97182

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