TransMembrane prediction using Hidden Markov Models for MMAR_5055




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.011930.000000.98807
2 A0.011930.000000.98807
3 L0.011930.000000.98807
4 D0.011930.000000.98807
5 L0.011930.000000.98807
6 T0.011930.000000.98807
7 G0.011930.000000.98807
8 Y0.011930.000000.98807
9 L0.011930.000000.98807
10 D0.011930.000000.98807
11 R0.011930.000000.98807
12 I0.011930.000000.98807
13 N0.011930.000000.98807
14 Y0.011930.000000.98807
15 R0.011930.000000.98807
16 G0.011930.000000.98807
17 A0.011930.000000.98807
18 T0.011930.000000.98807
19 D0.011930.000000.98807
20 P0.011930.000000.98807
21 T0.011930.000000.98807
22 L0.011930.000000.98807
23 D0.011930.000000.98807
24 V0.011930.000010.98806
25 L0.011930.000010.98806
26 R0.011930.000010.98806
27 D0.011930.000010.98806
28 L0.011920.000010.98806
29 V0.011920.000010.98806
30 S0.011920.000010.98806
31 A0.011920.000010.98806
32 H0.011920.000010.98806
33 T0.011920.000010.98806
34 G0.011920.000010.98806
35 A0.011920.000010.98806
36 I0.011920.000010.98806
37 A0.011920.000010.98806
38 F0.011920.000010.98807
39 E0.011920.000010.98807
40 N0.011920.000000.98807
41 L0.011920.000000.98807
42 D0.011930.000000.98807
43 P0.011930.000000.98807
44 L0.011930.000000.98807
45 M0.011930.000000.98807
46 G0.011930.000000.98807
47 V0.011930.000000.98807
48 P0.011930.000000.98807
49 V0.011930.000000.98807
50 D0.011930.000000.98807
51 D0.011930.000000.98807
52 L0.011930.000000.98807
53 S0.011930.000000.98807
54 A0.011930.000000.98807
55 E0.011930.000000.98807
56 A0.011930.000000.98807
57 L0.011930.000000.98807
58 A0.011930.000000.98807
59 D0.011930.000000.98807
60 K0.011930.000000.98807
61 L0.011930.000000.98807
62 V0.011930.000000.98807
63 D0.011930.000000.98807
64 R0.011930.000000.98807
65 R0.011930.000000.98807
66 R0.011920.000020.98807
67 G0.011800.000160.98804
68 G0.011730.000250.98802
69 Y0.011610.000430.98797
70 C0.011560.000480.98796
71 Y0.011540.000510.98794
72 E0.011540.000510.98794
73 H0.011540.000520.98794
74 N0.011530.000530.98794
75 G0.011520.000540.98794
76 L0.011520.000540.98794
77 I0.011520.000540.98794
78 G0.011520.000540.98794
79 Y0.011520.000540.98794
80 V0.011520.000540.98794
81 L0.011520.000540.98794
82 A0.011520.000540.98794
83 E0.011520.000530.98794
84 L0.011520.000530.98795
85 G0.011530.000500.98796
86 Y0.011540.000460.988
87 R0.011600.000230.98818
88 V0.011610.000180.98821
89 R0.011650.000060.98829
90 R0.011650.000030.98832
91 L0.011650.000020.98833
92 A0.011650.000010.98833
93 G0.011650.000010.98834
94 R0.011650.000000.98834
95 V0.011650.000010.98834
96 V0.011650.000010.98834
97 W0.011650.000010.98834
98 L0.011650.000010.98834
99 A0.011650.000010.98834
100 P0.011650.000010.98834
101 P0.011650.000010.98834
102 D0.011650.000010.98834
103 A0.011650.000010.98834
104 P0.011650.000010.98834
105 T0.011650.000010.98834
106 P0.011650.000010.98834
107 A0.011650.000020.98833
108 Q0.011650.000030.98833
109 T0.011640.000050.98831
110 H0.011640.000060.9883
111 T0.011620.000100.98828
112 V0.011580.000150.98827
113 L0.011570.000160.98826
114 A0.011570.000170.98826
115 V0.011570.000170.98826
116 T0.011570.000170.98826
117 F0.011570.000170.98826
118 P0.011570.000170.98826
119 G0.011570.000170.98826
120 C0.011570.000170.98826
121 Q0.011570.000170.98826
122 G0.011570.000170.98826
123 P0.011570.000170.98826
124 Y0.011570.000180.98826
125 L0.011570.000180.98826
126 V0.011570.000170.98826
127 D0.011580.000160.98826
128 V0.011580.000160.98826
129 G0.011580.000160.98826
130 F0.011580.000160.98826
131 G0.011590.000140.98827
132 G0.011610.000110.98828
133 M0.011630.000080.98829
134 T0.011650.000050.9883
135 P0.011650.000020.98832
136 T0.011650.000020.98833
137 A0.011650.000010.98833
138 P0.011650.000010.98833
139 L0.011650.000010.98833
140 R0.011660.000010.98833
141 L0.011660.000010.98833
142 E0.011660.000000.98833
143 T0.011660.000000.98833
144 G0.011660.000000.98833
145 T0.011660.000000.98833
146 V0.011660.000000.98833
147 Q0.011660.000000.98833
148 Q0.011660.000000.98833
149 T0.011660.000000.98833
150 A0.011660.000000.98833
151 L0.011660.000000.98833
152 E0.011660.000000.98833
153 P0.011660.000000.98833
154 Y0.011660.000000.98833
155 R0.011660.000000.98833
156 L0.011660.000000.98833
157 D0.011660.000000.98833
158 D0.011660.000000.98833
159 R0.011660.000000.98833
160 G0.011660.000000.98833
161 D0.011660.000000.98833
162 G0.011660.000000.98833
163 L0.011660.000000.98833
164 V0.011660.000000.98833
165 L0.011660.000000.98833
166 Q0.011660.000000.98833
167 A0.011660.000000.98833
168 M0.011660.000000.98833
169 V0.011660.000000.98833
170 R0.011660.000000.98833
171 D0.011660.000000.98833
172 E0.011660.000000.98833
173 W0.011660.000000.98833
174 Q0.011660.000000.98833
175 A0.011660.000000.98833
176 L0.011660.000000.98833
177 Y0.011660.000000.98833
178 E0.011660.000000.98833
179 F0.011660.000000.98833
180 S0.011660.000000.98833
181 T0.011660.000000.98833
182 L0.011660.000000.98833
183 T0.011660.000000.98833
184 R0.011660.000000.98833
185 P0.011660.000000.98833
186 Q0.011660.000000.98833
187 V0.011660.000000.98833
188 D0.011660.000010.98833
189 L0.011650.000030.98831
190 R0.011640.000070.98829
191 V0.011190.000870.98793
192 G0.011000.001630.98736
193 S0.010960.001740.9873
194 W0.010930.001850.98722
195 F0.010920.001960.98712
196 V0.010920.001990.98709
197 S0.010920.002010.98708
198 T0.010920.002010.98707
199 H0.010920.002060.98703
200 P0.010910.002100.98699
201 T0.010910.002110.98698
202 S0.010910.002130.98696
203 H0.010910.002150.98693
204 F0.010910.002180.9869
205 V0.010910.002190.98689
206 T0.010910.002190.98689
207 G0.010910.002190.98689
208 L0.010910.002190.98689
209 M0.010930.002180.9869
210 A0.010930.002170.9869
211 A0.010950.002140.98691
212 T0.010990.002090.98693
213 V0.011030.002010.98695
214 A0.011380.001220.9874
215 D0.012140.000240.98762
216 D0.012180.000190.98764
217 A0.012180.000180.98764
218 R0.012180.000180.98764
219 W0.012180.000180.98764
220 N0.012180.000170.98765
221 L0.012190.000170.98765
222 M0.012280.000070.98765
223 G0.012350.000010.98765
224 R0.012350.000000.98765
225 N0.012350.000000.98765
226 L0.012350.000000.98765
227 A0.012350.000000.98765
228 I0.012360.000000.98765
229 H0.012360.000000.98765
230 R0.012360.000000.98765
231 R0.012360.000000.98765
232 G0.012360.000000.98765
233 G0.012360.000000.98765
234 T0.012360.000000.98765
235 E0.012360.000000.98765
236 K0.012360.000000.98765
237 I0.012360.000000.98765
238 L0.012360.000000.98765
239 L0.012360.000000.98765
240 E0.012360.000000.98765
241 D0.012360.000000.98765
242 A0.012360.000000.98765
243 A0.012360.000000.98765
244 A0.012360.000000.98765
245 V0.012360.000000.98765
246 V0.012360.000000.98765
247 D0.012360.000000.98765
248 T0.012360.000000.98765
249 L0.012360.000000.98765
250 G0.012360.000000.98765
251 D0.012360.000000.98765
252 R0.012360.000000.98765
253 F0.012360.000000.98765
254 G0.012360.000000.98765
255 I0.012360.000000.98765
256 N0.012360.000000.98765
257 V0.012360.000000.98765
258 A0.012360.000000.98765
259 D0.012360.000000.98765
260 V0.012360.000000.98765
261 G0.012360.000000.98765
262 E0.012360.000000.98765
263 R0.012360.000000.98765
264 G0.012360.000000.98765
265 R0.012360.000000.98765
266 L0.012360.000000.98765
267 E0.012360.000000.98765
268 A0.012360.000000.98765
269 R0.012360.000000.98765
270 I0.012360.000000.98765
271 D0.012360.000000.98765
272 K0.012360.000000.98765
273 V0.012360.000000.98765
274 C0.012360.000000.98765
275 F0.012360.000000.98765
276 G0.012360.000000.98765
277 A0.012360.000000.98765
278 E0.012360.000000.98765
279 N0.012360.000000.98765
280 R0.012360.000000.98765

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