TransMembrane prediction using Hidden Markov Models for Rv1599




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.009270.000000.99072
2 L0.009270.000000.99072
3 T0.009270.000000.99072
4 R0.009270.000000.99072
5 I0.009270.000000.99072
6 D0.009270.000000.99072
7 L0.009270.000000.99072
8 R0.009270.000000.99072
9 G0.009270.000000.99072
10 A0.009270.000000.99072
11 E0.009270.000000.99072
12 L0.009270.000000.99072
13 T0.009270.000000.99072
14 A0.009270.000000.99072
15 A0.009270.000000.99072
16 E0.009270.000000.99072
17 L0.009270.000000.99072
18 R0.009270.000000.99072
19 A0.009270.000000.99072
20 A0.009270.000000.99072
21 L0.009260.000010.99072
22 P0.009260.000010.99072
23 R0.009260.000010.99072
24 G0.009260.000010.99072
25 G0.009260.000010.99072
26 A0.009260.000010.99072
27 D0.009260.000010.99073
28 V0.009260.000010.99073
29 E0.009260.000010.99073
30 A0.009260.000010.99073
31 V0.009260.000010.99073
32 L0.009260.000010.99073
33 P0.009260.000010.99073
34 T0.009260.000010.99073
35 V0.009260.000010.99073
36 R0.009260.000010.99073
37 P0.009260.000010.99073
38 I0.009260.000010.99073
39 V0.009260.000010.99073
40 A0.009260.000010.99073
41 A0.009260.000010.99073
42 V0.009260.000010.99073
43 A0.009260.000010.99073
44 E0.009260.000000.99073
45 R0.009260.000000.99073
46 G0.009260.000000.99073
47 A0.009260.000000.99073
48 E0.009260.000000.99074
49 A0.009260.000000.99074
50 A0.009260.000000.99074
51 L0.009260.000000.99074
52 D0.009260.000000.99074
53 F0.009260.000000.99074
54 G0.009260.000000.99074
55 A0.009260.000000.99074
56 S0.009260.000000.99074
57 F0.009260.000000.99074
58 D0.009260.000000.99074
59 G0.009260.000000.99074
60 V0.009260.000000.99074
61 R0.009260.000000.99074
62 P0.009260.000000.99074
63 H0.009260.000000.99074
64 A0.009260.000000.99074
65 I0.009260.000000.99074
66 R0.009260.000000.99074
67 V0.009260.000000.99074
68 P0.009260.000000.99074
69 D0.009260.000000.99074
70 A0.009260.000000.99074
71 A0.009260.000000.99074
72 L0.009260.000000.99074
73 D0.009260.000000.99074
74 A0.009260.000000.99074
75 A0.009260.000000.99074
76 L0.009260.000000.99074
77 A0.009260.000000.99074
78 G0.009260.000000.99074
79 L0.009260.000000.99074
80 D0.009260.000000.99074
81 C0.009260.000000.99074
82 D0.009260.000000.99074
83 V0.009260.000000.99074
84 C0.009260.000000.99074
85 E0.009260.000000.99074
86 A0.009260.000000.99074
87 L0.009260.000000.99074
88 Q0.009260.000000.99074
89 V0.009260.000000.99074
90 M0.009260.000000.99074
91 V0.009260.000000.99074
92 E0.009260.000000.99074
93 R0.009260.000000.99074
94 T0.009260.000000.99074
95 R0.009260.000000.99074
96 A0.009260.000000.99074
97 V0.009260.000000.99074
98 H0.009260.000000.99074
99 S0.009260.000000.99074
100 G0.009260.000000.99074
101 Q0.009260.000000.99074
102 R0.009260.000000.99074
103 R0.009260.000000.99074
104 T0.009260.000000.99074
105 D0.009260.000000.99074
106 V0.009260.000000.99074
107 T0.009260.000000.99074
108 T0.009260.000000.99074
109 T0.009260.000000.99074
110 L0.009260.000000.99074
111 G0.009260.000000.99074
112 P0.009260.000000.99074
113 G0.009260.000000.99074
114 A0.009260.000000.99074
115 T0.009260.000000.99074
116 V0.009260.000000.99074
117 T0.009260.000000.99074
118 E0.009260.000000.99074
119 R0.009260.000000.99074
120 W0.009260.000000.99074
121 V0.009260.000000.99074
122 P0.009250.000000.99074
123 V0.009250.000010.99074
124 E0.009250.000010.99074
125 R0.009220.000030.99074
126 V0.009010.000250.99073
127 G0.008970.000290.99073
128 L0.008950.000320.99073
129 Y0.008940.000330.99073
130 V0.008930.000340.99073
131 P0.008930.000340.99073
132 G0.008930.000340.99073
133 G0.008920.000340.99073
134 N0.008920.000350.99073
135 A0.008910.000360.99073
136 V0.008910.000360.99073
137 Y0.008910.000360.99073
138 P0.008900.000360.99073
139 S0.008900.000370.99073
140 S0.008900.000370.99073
141 V0.008900.000370.99073
142 V0.008900.000370.99073
143 M0.008900.000370.99073
144 N0.008900.000350.99074
145 V0.008900.000350.99075
146 V0.008900.000340.99077
147 P0.008900.000300.99081
148 A0.008900.000260.99084
149 Q0.008900.000090.99101
150 A0.008900.000070.99102
151 A0.008900.000060.99104
152 G0.008900.000040.99105
153 V0.008900.000030.99106
154 D0.008900.000020.99107
155 S0.008900.000020.99107
156 L0.008900.000020.99107
157 V0.008900.000020.99107
158 V0.008900.000020.99108
159 A0.008910.000010.99109
160 S0.008910.000010.99109
161 P0.008910.000000.99109
162 P0.008910.000000.99109
163 Q0.008910.000000.99109
164 A0.008910.000000.99109
165 Q0.008910.000000.99109
166 W0.008910.000000.99109
167 D0.008910.000000.99109
168 G0.008910.000000.99109
169 M0.008910.000000.99109
170 P0.008910.000000.99109
171 H0.008910.000000.99109
172 P0.008910.000000.99109
173 T0.008900.000010.99109
174 I0.008900.000010.99109
175 L0.008860.000060.99109
176 A0.008850.000070.99107
177 A0.008850.000080.99107
178 A0.008830.000100.99106
179 R0.008820.000120.99106
180 L0.008780.000190.99103
181 L0.008760.000230.99101
182 G0.008760.000240.991
183 V0.008750.000270.99098
184 D0.008750.000280.99098
185 E0.008730.000310.99096
186 V0.008590.000470.99094
187 W0.008580.000490.99093
188 A0.008580.000490.99093
189 V0.008580.000490.99093
190 G0.008580.000490.99093
191 G0.008580.000490.99093
192 A0.008580.000490.99093
193 Q0.008580.000490.99093
194 A0.008580.000490.99093
195 V0.008580.000490.99093
196 A0.008580.000490.99094
197 L0.008580.000480.99094
198 L0.008580.000440.99098
199 A0.008590.000420.99099
200 Y0.008600.000410.99099
201 G0.008620.000370.99102
202 G0.008640.000330.99103
203 T0.008700.000230.99107
204 D0.008730.000080.99118
205 T0.008730.000100.99116
206 D0.008740.000090.99117
207 G0.008730.000210.99106
208 A0.008730.000290.99098
209 A0.008730.000280.991
210 L0.008720.000290.99099
211 T0.008730.000290.99099
212 P0.008730.000280.99099
213 V0.008730.000280.99099
214 D0.008730.000280.99099
215 M0.008730.000280.99099
216 I0.008730.000280.99099
217 T0.008730.000280.99099
218 G0.008730.000280.99099
219 P0.008730.000280.99099
220 G0.008730.000280.99099
221 N0.008730.000280.99099
222 I0.008730.000280.99099
223 Y0.008730.000280.99099
224 V0.008730.000280.99099
225 T0.008820.000190.99099
226 A0.008870.000130.99099
227 A0.008910.000090.991
228 K0.008990.000010.991
229 R0.008990.000000.991
230 L0.008990.000000.991
231 C0.008990.000000.991
232 R0.008990.000000.991
233 S0.009000.000000.991
234 R0.009000.000000.991
235 V0.009000.000000.991
236 G0.009000.000000.991
237 I0.009000.000000.991
238 D0.009000.000000.991
239 A0.009000.000000.991
240 E0.009000.000000.991
241 A0.009000.000000.991
242 G0.009000.000000.991
243 P0.009000.000000.991
244 T0.009000.000000.991
245 E0.009000.000000.991
246 I0.009000.000000.991
247 A0.009000.000000.991
248 I0.009000.000000.991
249 L0.009000.000000.991
250 A0.009000.000000.991
251 D0.009000.000000.991
252 H0.009000.000000.991
253 T0.009000.000000.991
254 A0.009000.000000.991
255 D0.009000.000000.991
256 P0.009000.000000.991
257 V0.009000.000000.991
258 H0.009000.000000.991
259 V0.009000.000000.991
260 A0.009000.000000.991
261 A0.009000.000000.991
262 D0.009000.000000.991
263 L0.009000.000000.991
264 I0.009000.000000.991
265 S0.009000.000000.991
266 Q0.009000.000000.991
267 A0.009000.000000.991
268 E0.009000.000000.991
269 H0.009000.000000.991
270 D0.009000.000000.991
271 E0.009000.000000.991
272 L0.009000.000000.991
273 A0.009000.000000.991
274 A0.009000.000000.991
275 S0.009000.000000.991
276 V0.009000.000000.991
277 L0.009000.000000.991
278 V0.009000.000000.991
279 T0.009000.000000.991
280 P0.009000.000000.991
281 S0.009000.000000.991
282 E0.009000.000000.991
283 D0.009000.000000.991
284 L0.009000.000000.991
285 A0.009000.000000.991
286 D0.009000.000000.991
287 A0.009000.000000.991
288 T0.009000.000000.991
289 D0.009000.000000.991
290 A0.009000.000000.991
291 E0.009000.000000.991
292 L0.009000.000000.991
293 A0.009000.000000.991
294 G0.009000.000000.991
295 Q0.009000.000000.991
296 L0.009000.000000.991
297 Q0.009000.000000.991
298 T0.009000.000000.991
299 T0.009000.000000.991
300 V0.009000.000000.991
301 H0.009000.000000.991
302 R0.009000.000000.991
303 E0.009000.000000.991
304 R0.009000.000000.991
305 V0.009000.000000.991
306 T0.009000.000000.991
307 A0.009000.000000.991
308 A0.009000.000000.991
309 L0.008990.000000.991
310 T0.008990.000000.991
311 G0.008990.000010.991
312 R0.008990.000010.991
313 Q0.008990.000010.99099
314 S0.008990.000020.99099
315 A0.008990.000030.99098
316 I0.008990.000040.99097
317 V0.008990.000040.99097
318 L0.008990.000040.99097
319 V0.008990.000040.99097
320 D0.008990.000040.99097
321 D0.008990.000040.99097
322 V0.008990.000040.99097
323 D0.008990.000040.99097
324 A0.008990.000040.99097
325 A0.008990.000040.99097
326 V0.008990.000040.99097
327 L0.008990.000040.99097
328 V0.008990.000040.99097
329 V0.008990.000040.99097
330 N0.008990.000040.99097
331 A0.008990.000040.99097
332 Y0.008990.000040.99097
333 A0.009000.000030.99097
334 A0.009010.000020.99097
335 E0.009020.000000.99097
336 H0.009020.000000.99097
337 L0.009020.000000.99097
338 E0.009020.000000.99097
339 I0.009020.000000.99097
340 Q0.009020.000000.99097
341 T0.009020.000000.99097
342 A0.009020.000000.99097
343 D0.009020.000000.99097
344 A0.009020.000000.99097
345 P0.009020.000000.99097
346 Q0.009020.000000.99097
347 V0.009020.000000.99097
348 A0.009020.000000.99097
349 S0.009020.000010.99097
350 R0.009020.000010.99097
351 I0.009020.000010.99096
352 R0.009020.000010.99096
353 S0.009020.000020.99096
354 A0.009020.000030.99095
355 G0.009020.000040.99094
356 A0.009020.000070.99091
357 I0.009020.000080.9909
358 F0.009020.000090.99089
359 V0.009020.000090.99089
360 G0.009020.000090.99089
361 P0.009020.000090.99089
362 W0.009020.000090.99089
363 S0.009020.000090.99089
364 P0.009020.000090.99089
365 V0.009020.000090.99089
366 S0.009020.000090.99089
367 L0.009020.000090.99089
368 G0.009020.000090.99089
369 D0.009020.000090.99089
370 Y0.009020.000090.99089
371 C0.009030.000080.99089
372 A0.009030.000080.99089
373 G0.009030.000080.99089
374 S0.009030.000070.99089
375 N0.009040.000070.99089
376 H0.009040.000060.99089
377 V0.009050.000060.99089
378 L0.009060.000050.99089
379 P0.009090.000010.9909
380 T0.009100.000000.9909
381 A0.009100.000000.9909
382 G0.009100.000000.9909
383 C0.009100.000000.9909
384 A0.009100.000000.9909
385 R0.009100.000000.9909
386 H0.009100.000000.9909
387 S0.009100.000000.9909
388 S0.009100.000000.9909
389 G0.009100.000000.9909
390 L0.009100.000000.9909
391 S0.009100.000000.9909
392 V0.009100.000000.9909
393 Q0.009100.000000.9909
394 T0.009100.000000.9909
395 F0.009100.000000.9909
396 L0.009100.000000.9909
397 R0.009100.000000.9909
398 G0.009100.000000.9909
399 I0.009100.000000.9909
400 H0.009100.000000.9909
401 V0.009100.000000.9909
402 V0.009100.000000.9909
403 E0.009100.000000.9909
404 Y0.009100.000000.9909
405 T0.009110.000000.9909
406 E0.009110.000000.9909
407 A0.009110.000000.9909
408 A0.009110.000000.9909
409 L0.009110.000000.9909
410 K0.009110.000000.9909
411 D0.009110.000000.9909
412 V0.009110.000000.9909
413 S0.009110.000000.9909
414 G0.009110.000000.9909
415 H0.009110.000000.9909
416 V0.009110.000000.9909
417 I0.009110.000000.9909
418 T0.009110.000000.9909
419 L0.009110.000000.9909
420 A0.009110.000000.9909
421 T0.009110.000000.9909
422 A0.009110.000000.9909
423 E0.009110.000000.9909
424 D0.009110.000000.9909
425 L0.009110.000000.9909
426 P0.009110.000000.9909
427 A0.009110.000000.9909
428 H0.009110.000000.9909
429 G0.009110.000000.9909
430 E0.009110.000000.9909
431 A0.009110.000000.9909
432 V0.009110.000000.9909
433 R0.009110.000000.9909
434 R0.009110.000000.9909
435 R0.009110.000000.9909
436 F0.009110.000000.9909
437 E0.009110.000000.9909
438 R0.009110.000000.9909

General Statistics
Length: 438
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.0270099999999999
Exp number, first 60 AAs: 0.00023
Total prob of N-in: 0.00927
outside: from residue 1 to 438
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