TransMembrane prediction using Hidden Markov Models for Rv0500




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.025010.000000.97499
2 L0.023220.001790.97499
3 F0.020400.004610.97499
4 G0.020400.010720.96888
5 M0.017590.022950.95946
6 A0.017590.024470.95794
7 R0.013590.028610.9578
8 I0.013590.028630.95779
9 A0.013060.029170.95777
10 I0.013060.029570.95737
11 I0.013050.029590.95737
12 G0.013030.029600.95737
13 G0.013030.029610.95737
14 G0.013030.029610.95737
15 S0.013030.029610.95737
16 I0.013030.029610.95737
17 G0.013030.029610.95737
18 E0.013030.029600.95738
19 A0.013030.029600.95738
20 L0.013030.029540.95744
21 L0.013030.029390.95758
22 S0.013220.028750.95803
23 G0.013830.027480.9587
24 L0.014620.026500.95888
25 L0.017890.020140.96197
26 R0.022850.011370.96578
27 A0.025720.007830.96644
28 G0.029850.002090.96807
29 R0.030490.000990.96852
30 Q0.030640.000130.96923
31 V0.030640.000080.96928
32 K0.030650.000000.96935
33 D0.030650.000000.96935
34 L0.030650.000000.96935
35 V0.030650.000000.96935
36 V0.030650.000000.96935
37 A0.030650.000000.96935
38 E0.030650.000000.96935
39 R0.030650.000000.96935
40 M0.030650.000000.96935
41 P0.030650.000000.96935
42 D0.030650.000000.96935
43 R0.030630.000010.96935
44 A0.030550.000100.96935
45 N0.030420.000230.96935
46 Y0.030300.000350.96934
47 L0.030130.000530.96934
48 A0.030030.000640.96934
49 Q0.029950.000720.96933
50 T0.029340.001370.96929
51 Y0.029250.001470.96928
52 S0.029200.001520.96928
53 V0.029060.001660.96928
54 L0.029050.001670.96928
55 V0.029050.001670.96928
56 T0.029050.001670.96928
57 S0.029050.001670.96928
58 A0.029050.001670.96928
59 A0.029050.001670.96928
60 D0.029050.001660.96929
61 A0.029050.001660.96929
62 V0.029050.001640.96931
63 E0.029050.001520.96943
64 N0.029050.001480.96947
65 A0.029050.001470.96948
66 T0.029050.001450.96949
67 F0.029050.001430.96952
68 V0.029050.001380.96957
69 V0.029060.001300.96965
70 V0.029060.001130.96981
71 A0.029070.000980.96995
72 V0.029080.000820.97009
73 K0.029120.000060.97082
74 P0.029120.000040.97083
75 A0.029120.000030.97085
76 D0.029120.000000.97088
77 V0.029120.000000.97088
78 E0.029120.000000.97088
79 P0.029120.000000.97088
80 V0.029120.000000.97088
81 I0.029120.000000.97088
82 A0.029120.000000.97088
83 D0.029120.000000.97088
84 L0.029120.000000.97088
85 A0.029120.000000.97088
86 N0.029120.000000.97088
87 A0.029120.000000.97088
88 T0.029120.000000.97088
89 A0.029120.000000.97088
90 A0.029110.000010.97088
91 A0.029110.000010.97088
92 E0.029110.000020.97088
93 N0.029100.000030.97087
94 D0.029080.000060.97086
95 S0.028470.000730.97079
96 A0.028290.000970.97074
97 E0.028220.001060.97072
98 Q0.028060.001270.97067
99 V0.027440.001970.97058
100 F0.027200.002240.97056
101 V0.027100.002360.97054
102 T0.027090.002370.97054
103 V0.027060.002400.97054
104 V0.027050.002410.97054
105 A0.027050.002410.97054
106 G0.027050.002410.97054
107 I0.027050.002410.97054
108 T0.027050.002410.97054
109 I0.027050.002410.97054
110 A0.027050.002410.97054
111 Y0.027050.002400.97054
112 F0.027050.002370.97057
113 E0.027110.001710.97119
114 S0.027130.001520.97135
115 K0.027180.001260.97156
116 L0.027150.001300.97156
117 P0.027190.001170.97165
118 A0.027140.001310.97154
119 G0.027060.001370.97157
120 T0.026930.001580.97149
121 P0.026640.001980.97139
122 V0.026230.002780.97098
123 V0.026200.002750.97105
124 R0.026170.002740.97109
125 A0.026020.002970.97102
126 M0.025980.003020.971
127 P0.025960.003060.97099
128 N0.025880.003150.97097
129 A0.025710.003370.97092
130 A0.025630.003460.97092
131 A0.025610.003480.97092
132 L0.025600.003490.97092
133 V0.025600.003490.97092
134 G0.025600.003490.97092
135 A0.025600.003480.97092
136 G0.025600.003480.97092
137 V0.025610.003470.97092
138 T0.025650.003400.97095
139 A0.025680.003300.97102
140 L0.025760.003090.97115
141 A0.026230.002350.97141
142 K0.026970.000950.97208
143 G0.027010.000860.97212
144 R0.027080.000750.97217
145 F0.027100.000730.97217
146 V0.027120.000690.97219
147 T0.027230.000520.97226
148 P0.027270.000240.97249
149 Q0.027290.000040.97267
150 Q0.027290.000030.97268
151 L0.027280.000030.97268
152 E0.027280.000010.97271
153 E0.027280.000020.97271
154 V0.027260.000030.97271
155 S0.027260.000040.97271
156 A0.027260.000040.97271
157 L0.027260.000040.97271
158 F0.027260.000040.97271
159 D0.027260.000040.97271
160 A0.027260.000040.97271
161 V0.027260.000040.97271
162 G0.027260.000040.97271
163 G0.027260.000040.97271
164 V0.027260.000040.97271
165 L0.027260.000040.97271
166 T0.027260.000040.97271
167 V0.027260.000040.9727
168 P0.027260.000040.9727
169 E0.027260.000040.97271
170 S0.027260.000040.97271
171 Q0.027250.000060.97268
172 L0.027230.000250.97252
173 D0.027230.000260.9725
174 A0.027180.000410.97241
175 V0.027100.000610.97229
176 T0.027070.000670.97226
177 A0.027010.000770.97221
178 V0.026950.000900.97215
179 S0.026930.000990.97208
180 G0.026870.001650.97148
181 S0.026770.002820.97041
182 G0.026710.003600.96969
183 P0.026640.004250.96911
184 A0.026380.006020.9676
185 Y0.026090.006930.96697
186 F0.025950.007230.96683
187 F0.025940.007290.96678
188 L0.025940.007310.96676
189 L0.025940.007310.96675
190 V0.025960.007290.96675
191 E0.025980.007270.96675
192 A0.025990.007260.96675
193 L0.026000.007250.96676
194 V0.026030.007200.96677
195 D0.026320.006820.96687
196 A0.026330.006800.96688
197 G0.026350.006740.9669
198 V0.026380.006690.96693
199 G0.026420.006620.96696
200 V0.026460.006520.96701
201 G0.026620.006280.96709
202 L0.026930.005900.96717
203 S0.028520.004120.96736
204 R0.030570.001900.96753
205 Q0.031020.001430.96755
206 V0.031100.001330.96757
207 A0.031620.000670.9677
208 T0.031880.000190.96792
209 D0.031930.000030.96804
210 L0.031930.000030.96804
211 A0.031930.000030.96804
212 A0.031930.000030.96804
213 Q0.031930.000030.96804
214 T0.031930.000030.96804
215 M0.031930.000030.96804
216 A0.031930.000030.96804
217 G0.031930.000030.96804
218 S0.031930.000030.96804
219 A0.031930.000020.96804
220 A0.031930.000020.96805
221 M0.031930.000020.96805
222 L0.031930.000020.96805
223 L0.031930.000020.96805
224 E0.031940.000010.96805
225 R0.031950.000000.96805
226 M0.031950.000000.96805
227 E0.031950.000000.96805
228 Q0.031950.000000.96805
229 D0.031950.000000.96805
230 Q0.031950.000000.96805
231 G0.031950.000000.96805
232 G0.031950.000000.96805
233 A0.031950.000000.96805
234 N0.031950.000000.96805
235 G0.031950.000000.96805
236 E0.031950.000000.96805
237 L0.031950.000000.96805
238 M0.031950.000000.96805
239 G0.031950.000000.96805
240 L0.031950.000000.96805
241 R0.031950.000000.96805
242 V0.031950.000000.96805
243 D0.031950.000000.96805
244 L0.031950.000000.96804
245 T0.031950.000010.96804
246 A0.031940.000030.96803
247 S0.031930.000040.96802
248 R0.031930.000050.96802
249 L0.031930.000050.96802
250 R0.031930.000060.96801
251 A0.031930.000060.96801
252 A0.031930.000060.96801
253 V0.031930.000060.96801
254 T0.031930.000060.96801
255 S0.031930.000060.96801
256 P0.031930.000060.96801
257 G0.031930.000060.96801
258 G0.031930.000060.96801
259 T0.031930.000060.96801
260 T0.031930.000060.96801
261 A0.031930.000060.96801
262 A0.031930.000060.96801
263 A0.031930.000060.96801
264 L0.031930.000060.96801
265 R0.031950.000030.96802
266 E0.031960.000010.96803
267 L0.031960.000010.96804
268 E0.031960.000000.96804
269 R0.031970.000000.96804
270 G0.031970.000000.96804
271 G0.031970.000000.96804
272 F0.031970.000000.96804
273 R0.031970.000000.96804
274 M0.031970.000000.96804
275 A0.031970.000000.96804
276 V0.031970.000000.96804
277 D0.031970.000000.96804
278 A0.031970.000000.96804
279 A0.031970.000000.96804
280 V0.031970.000000.96804
281 Q0.031970.000000.96804
282 A0.031970.000000.96804
283 A0.031970.000000.96804
284 K0.031970.000000.96804
285 S0.031970.000000.96804
286 R0.031970.000000.96804
287 S0.031970.000000.96804
288 E0.031970.000000.96804
289 Q0.031970.000000.96804
290 L0.031970.000000.96804
291 R0.031970.000000.96804
292 I0.031970.000000.96804
293 T0.031970.000000.96804
294 P0.031970.000000.96804
295 E0.031970.000000.96804

General Statistics
Length: 295
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.946769999999999
Exp number, first 60 AAs: 0.65153
Total prob of N-in: 0.02501
outside: from residue 1 to 295
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