TransMembrane prediction using Hidden Markov Models for Rv1079




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.013990.000000.986
2 S0.013990.000000.986
3 E0.013990.000000.986
4 D0.013990.000000.986
5 R0.013990.000000.986
6 T0.013990.000000.986
7 G0.013990.000000.986
8 H0.013990.000000.986
9 Q0.013990.000000.986
10 G0.013990.000000.986
11 I0.013990.000000.986
12 S0.013990.000000.986
13 G0.013990.000000.986
14 P0.013990.000000.986
15 A0.013990.000000.986
16 T0.013990.000000.986
17 R0.013990.000000.986
18 A0.013990.000000.986
19 I0.013990.000000.986
20 H0.013970.000020.986
21 A0.013890.000100.986
22 G0.013890.000100.986
23 Y0.013890.000100.986
24 R0.013890.000100.986
25 P0.013890.000110.986
26 D0.013880.000110.986
27 P0.013840.000150.986
28 A0.013820.000190.98599
29 T0.013780.000220.98599
30 G0.013730.000270.98599
31 A0.013710.000300.98599
32 V0.013700.000320.98598
33 N0.013690.000330.98598
34 V0.013690.000330.98598
35 P0.013690.000330.98597
36 I0.013690.000330.98597
37 Y0.013690.000330.98597
38 A0.013690.000330.98597
39 S0.013690.000330.98598
40 S0.013690.000320.98599
41 T0.013690.000320.98599
42 F0.013690.000310.98599
43 A0.013690.000290.98601
44 Q0.013690.000230.98608
45 D0.013690.000200.9861
46 G0.013690.000200.9861
47 V0.013690.000190.98611
48 G0.013690.000160.98614
49 G0.013690.000110.9862
50 L0.013690.000080.98623
51 R0.013700.000040.98625
52 G0.013700.000040.98625
53 G0.013700.000030.98626
54 F0.013710.000020.98627
55 E0.013720.000000.98628
56 Y0.013720.000000.98628
57 A0.013720.000000.98628
58 R0.013720.000000.98628
59 T0.013720.000000.98628
60 G0.013720.000000.98628
61 N0.013720.000000.98628
62 P0.013720.000000.98628
63 T0.013720.000000.98628
64 R0.013720.000000.98628
65 A0.013710.000010.98628
66 A0.013700.000020.98628
67 L0.013690.000030.98628
68 E0.013680.000040.98628
69 A0.013680.000040.98628
70 S0.013680.000040.98628
71 L0.013680.000040.98628
72 A0.013680.000050.98628
73 A0.013680.000050.98628
74 V0.013680.000050.98628
75 E0.013680.000050.98628
76 E0.013680.000050.98628
77 G0.013670.000050.98628
78 A0.013670.000050.98628
79 F0.013670.000060.98628
80 A0.013670.000060.98628
81 R0.013660.000060.98628
82 A0.013660.000060.98628
83 F0.013660.000050.98628
84 S0.013660.000050.98628
85 S0.013660.000050.98629
86 G0.013660.000050.98629
87 M0.013660.000040.98629
88 A0.013660.000040.98629
89 A0.013660.000030.9863
90 T0.013670.000020.98631
91 D0.013670.000010.98632
92 C0.013670.000010.98632
93 A0.013670.000010.98632
94 L0.013670.000010.98632
95 R0.013670.000010.98632
96 A0.013670.000010.98632
97 M0.013670.000010.98632
98 L0.013670.000010.98633
99 R0.013670.000000.98633
100 P0.013670.000000.98633
101 G0.013670.000000.98633
102 D0.013670.000000.98633
103 H0.013670.000000.98633
104 V0.013670.000000.98633
105 V0.013670.000000.98633
106 I0.013670.000000.98633
107 P0.013670.000000.98633
108 D0.013670.000000.98633
109 D0.013670.000000.98633
110 A0.013670.000000.98633
111 Y0.013670.000000.98633
112 G0.013670.000000.98633
113 G0.013670.000000.98633
114 T0.013670.000000.98633
115 F0.013670.000000.98633
116 R0.013670.000000.98633
117 L0.013670.000000.98633
118 I0.013670.000000.98633
119 D0.013670.000000.98633
120 K0.013670.000000.98633
121 V0.013670.000000.98633
122 F0.013670.000000.98633
123 T0.013670.000000.98633
124 R0.013670.000000.98633
125 W0.013670.000000.98633
126 D0.013670.000000.98633
127 V0.013670.000000.98633
128 Q0.013670.000000.98633
129 Y0.013660.000000.98633
130 T0.013660.000000.98633
131 P0.013660.000000.98633
132 V0.013660.000000.98633
133 R0.013660.000000.98633
134 L0.013660.000000.98633
135 A0.013660.000000.98633
136 D0.013660.000000.98633
137 L0.013660.000000.98633
138 D0.013660.000000.98633
139 A0.013660.000000.98633
140 V0.013660.000000.98633
141 G0.013660.000000.98633
142 A0.013660.000000.98633
143 A0.013660.000000.98633
144 I0.013660.000000.98633
145 T0.013660.000000.98633
146 P0.013660.000000.98633
147 R0.013660.000000.98633
148 T0.013660.000010.98633
149 R0.013650.000010.98633
150 L0.013600.000070.98633
151 I0.013590.000080.98633
152 W0.013580.000080.98633
153 V0.013580.000080.98633
154 E0.013580.000080.98633
155 T0.013580.000080.98633
156 P0.013580.000080.98633
157 T0.013580.000080.98633
158 N0.013580.000080.98633
159 P0.013580.000080.98633
160 L0.013580.000080.98633
161 L0.013580.000080.98633
162 S0.013580.000080.98633
163 I0.013580.000080.98633
164 A0.013580.000080.98633
165 D0.013580.000080.98633
166 I0.013580.000080.98633
167 T0.013580.000080.98633
168 A0.013580.000080.98634
169 I0.013580.000080.98634
170 A0.013580.000050.98636
171 E0.013580.000040.98637
172 L0.013580.000040.98638
173 G0.013580.000010.9864
174 T0.013590.000000.98641
175 D0.013590.000000.98641
176 R0.013590.000000.98641
177 S0.013590.000000.98641
178 A0.013590.000000.98641
179 K0.013590.000000.98641
180 V0.013590.000000.98641
181 L0.013590.000000.98641
182 V0.013590.000000.98641
183 D0.013590.000000.98641
184 N0.013590.000000.98641
185 T0.013590.000000.98641
186 F0.013590.000000.98641
187 A0.013590.000000.98641
188 S0.013590.000000.98641
189 P0.013590.000000.98641
190 A0.013590.000000.98641
191 L0.013590.000000.98641
192 Q0.013590.000000.98641
193 Q0.013590.000000.98641
194 P0.013590.000000.98641
195 L0.013590.000000.98641
196 R0.013590.000000.98641
197 L0.013590.000000.98641
198 G0.013590.000000.98641
199 A0.013590.000000.98641
200 D0.013590.000000.98641
201 V0.013590.000000.98641
202 V0.013590.000000.98641
203 L0.013590.000000.98641
204 H0.013590.000000.98641
205 S0.013590.000000.98641
206 T0.013590.000000.98641
207 T0.013590.000000.98641
208 K0.013590.000000.98641
209 Y0.013590.000000.98641
210 I0.013590.000000.98641
211 G0.013590.000000.98641
212 G0.013590.000000.98641
213 H0.013590.000000.98641
214 S0.013590.000000.98641
215 D0.013590.000000.98641
216 V0.013590.000000.98641
217 V0.013590.000000.98641
218 G0.013590.000000.98641
219 G0.013590.000000.98641
220 A0.013590.000000.98641
221 L0.013590.000000.98641
222 V0.013590.000000.98641
223 T0.013590.000000.98641
224 N0.013590.000000.98641
225 D0.013590.000000.98641
226 E0.013590.000000.98641
227 E0.013590.000000.98641
228 L0.013590.000000.98641
229 D0.013590.000000.98641
230 E0.013590.000000.98641
231 E0.013580.000000.98641
232 F0.013570.000020.9864
233 A0.013560.000050.98638
234 F0.013560.000050.98638
235 L0.013560.000060.98638
236 Q0.013560.000060.98638
237 N0.013560.000060.98638
238 G0.013560.000070.98636
239 A0.013560.000080.98636
240 G0.013560.000080.98636
241 A0.013560.000080.98636
242 V0.013560.000080.98636
243 P0.013560.000080.98636
244 G0.013560.000080.98636
245 P0.013560.000080.98635
246 F0.013560.000080.98635
247 D0.013560.000080.98635
248 A0.013560.000080.98635
249 Y0.013560.000080.98636
250 L0.013560.000080.98636
251 T0.013560.000080.98636
252 M0.013570.000070.98636
253 R0.013570.000060.98637
254 G0.013570.000050.98637
255 L0.013580.000040.98637
256 K0.013600.000020.98638
257 T0.013600.000020.98638
258 L0.013600.000020.98638
259 V0.013600.000020.98638
260 L0.013610.000010.98638
261 R0.013620.000000.98638
262 M0.013620.000000.98638
263 Q0.013620.000000.98638
264 R0.013620.000000.98638
265 H0.013620.000000.98638
266 S0.013620.000000.98638
267 E0.013620.000000.98638
268 N0.013620.000000.98638
269 A0.013620.000000.98638
270 C0.013620.000000.98638
271 A0.013620.000000.98638
272 V0.013620.000000.98638
273 A0.013620.000000.98638
274 E0.013620.000000.98638
275 F0.013620.000000.98638
276 L0.013620.000000.98638
277 A0.013620.000000.98638
278 D0.013620.000000.98638
279 H0.013620.000000.98638
280 P0.013620.000000.98638
281 S0.013620.000000.98638
282 V0.013620.000000.98638
283 S0.013620.000000.98638
284 S0.013620.000000.98638
285 V0.013620.000000.98638
286 L0.013620.000000.98638
287 Y0.013620.000000.98638
288 P0.013620.000000.98638
289 G0.013620.000000.98638
290 L0.013620.000000.98638
291 P0.013620.000000.98638
292 S0.013620.000000.98638
293 H0.013620.000000.98638
294 P0.013620.000000.98638
295 G0.013620.000000.98638
296 H0.013620.000000.98638
297 E0.013620.000000.98638
298 I0.013620.000000.98638
299 A0.013620.000000.98638
300 A0.013620.000000.98638
301 R0.013620.000000.98638
302 Q0.013620.000000.98638
303 M0.013620.000000.98638
304 R0.013620.000000.98638
305 G0.013620.000000.98638
306 F0.013620.000000.98638
307 G0.013620.000000.98638
308 G0.013620.000000.98638
309 M0.013620.000000.98638
310 V0.013620.000000.98638
311 S0.013620.000000.98638
312 V0.013620.000000.98638
313 R0.013620.000000.98638
314 M0.013620.000000.98638
315 R0.013620.000000.98638
316 A0.013620.000000.98638
317 G0.013620.000000.98638
318 R0.013620.000000.98638
319 R0.013620.000000.98638
320 A0.013620.000000.98638
321 A0.013620.000000.98638
322 Q0.013620.000000.98638
323 D0.013620.000000.98638
324 L0.013620.000000.98638
325 C0.013620.000000.98638
326 A0.013620.000010.98638
327 K0.013620.000010.98638
328 T0.013610.000010.98638
329 R0.013610.000010.98638
330 V0.013610.000010.98638
331 F0.013610.000010.98637
332 I0.013610.000010.98637
333 L0.013610.000010.98637
334 A0.013610.000010.98637
335 E0.013610.000010.98637
336 S0.013610.000010.98637
337 L0.013610.000010.98637
338 G0.013610.000010.98637
339 G0.013610.000010.98637
340 V0.013610.000010.98637
341 E0.013610.000010.98637
342 S0.013610.000010.98638
343 L0.013610.000010.98638
344 I0.013610.000010.98638
345 E0.013610.000010.98638
346 H0.013610.000010.98639
347 P0.013610.000010.98639
348 S0.013610.000010.98639
349 A0.013610.000000.98639
350 M0.013610.000000.98639
351 T0.013610.000000.98639
352 H0.013610.000000.98639
353 A0.013610.000000.98639
354 S0.013610.000000.98639
355 T0.013610.000000.98639
356 A0.013610.000000.98639
357 G0.013610.000000.98639
358 S0.013610.000000.98639
359 Q0.013610.000000.98639
360 L0.013610.000000.98639
361 E0.013610.000000.98639
362 V0.013610.000000.98639
363 P0.013610.000000.98639
364 D0.013610.000000.98639
365 D0.013610.000000.98639
366 L0.013610.000000.98639
367 V0.013610.000000.98639
368 R0.013610.000000.98639
369 L0.013610.000000.98639
370 S0.013610.000000.98639
371 V0.013610.000000.98639
372 G0.013610.000000.98639
373 I0.013610.000000.98639
374 E0.013610.000000.98639
375 D0.013610.000000.98639
376 I0.013610.000000.98639
377 A0.013610.000000.98639
378 D0.013610.000000.98639
379 L0.013610.000000.98639
380 L0.013610.000000.98639
381 G0.013610.000000.98639
382 D0.013610.000000.98639
383 L0.013610.000000.98639
384 E0.013610.000000.98639
385 Q0.013610.000000.98639
386 A0.013610.000000.98639
387 L0.013610.000000.98639
388 G0.013610.000000.98639

General Statistics
Length: 388
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.01186
Exp number, first 60 AAs: 0.00694
Total prob of N-in: 0.01399
outside: from residue 1 to 388
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