TransMembrane prediction using Hidden Markov Models for Rv3220c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.001110.000000.99889
2 S0.001110.000000.99889
3 T0.001110.000000.99889
4 L0.001110.000000.99889
5 G0.001110.000000.99889
6 D0.001110.000000.99889
7 L0.001050.000060.99889
8 L0.001050.000060.99889
9 A0.001050.000060.99889
10 E0.001050.000060.99889
11 H0.001050.000060.99889
12 T0.001040.000070.99889
13 V0.000990.000110.99889
14 L0.000990.000110.99889
15 P0.000990.000120.99889
16 G0.000990.000120.99889
17 S0.000990.000120.99889
18 A0.000990.000120.99889
19 V0.000990.000120.99889
20 D0.000990.000120.99889
21 H0.000980.000130.99889
22 L0.000980.000140.99888
23 H0.000980.000140.99888
24 A0.000980.000140.99888
25 V0.000980.000140.99887
26 V0.000980.000140.99888
27 G0.000980.000130.9989
28 E0.000980.000110.99891
29 W0.000980.000110.99891
30 Q0.000980.000090.99893
31 L0.000980.000090.99893
32 L0.000980.000090.99893
33 A0.000980.000060.99897
34 D0.000980.000040.99898
35 L0.000980.000040.99898
36 S0.000980.000040.99898
37 F0.000980.000040.99898
38 A0.000980.000040.99898
39 D0.000980.000040.99898
40 Y0.000980.000040.99898
41 L0.000980.000040.99898
42 M0.000980.000040.99898
43 W0.000980.000040.99898
44 V0.000980.000020.99899
45 R0.001010.000000.99899
46 R0.001010.000000.99899
47 D0.001010.000000.99899
48 D0.001010.000000.99899
49 G0.001010.000000.99899
50 V0.001010.000000.99899
51 L0.001010.000000.99899
52 V0.001010.000000.99899
53 C0.001010.000000.99899
54 V0.001010.000000.99899
55 A0.001010.000000.99899
56 Q0.001010.000000.99899
57 C0.001010.000000.99899
58 R0.001010.000000.99899
59 P0.001010.000000.99899
60 N0.001010.000000.99899
61 T0.001000.000000.99899
62 G0.001000.000010.99899
63 P0.000990.000020.99899
64 T0.000970.000040.99899
65 V0.000910.000100.99899
66 V0.000900.000110.99898
67 H0.000900.000120.99898
68 T0.000890.000120.99898
69 D0.000880.000140.99897
70 A0.000760.000310.99893
71 V0.000690.000410.99891
72 G0.000680.000420.9989
73 T0.000680.000430.99889
74 V0.000640.000470.99888
75 V0.000640.000480.99888
76 A0.000630.000480.99888
77 A0.000630.000480.99888
78 N0.000630.000480.99888
79 S0.000630.000480.99888
80 M0.000630.000480.99888
81 P0.000630.000480.99889
82 L0.000630.000480.99889
83 V0.000630.000470.99889
84 A0.000630.000470.99889
85 A0.000630.000460.9989
86 T0.000640.000440.99892
87 F0.000640.000420.99894
88 S0.000640.000350.999
89 G0.000640.000330.99902
90 G0.000640.000310.99905
91 V0.000650.000280.99906
92 P0.000670.000210.99911
93 G0.000720.000090.99919
94 R0.000740.000010.99925
95 E0.000740.000000.99925
96 G0.000740.000000.99925
97 A0.000740.000000.99926
98 V0.000740.000000.99926
99 G0.000740.000000.99926
100 Q0.000740.000000.99926
101 Q0.000740.000000.99926
102 N0.000740.000000.99926
103 S0.000740.000000.99926
104 C0.000740.000000.99926
105 Q0.000740.000000.99926
106 H0.000740.000000.99926
107 D0.000740.000000.99926
108 G0.000740.000000.99926
109 H0.000740.000000.99926
110 S0.000740.000000.99926
111 V0.000740.000000.99926
112 E0.000740.000000.99926
113 V0.000740.000000.99926
114 S0.000740.000000.99926
115 P0.000740.000000.99926
116 V0.000740.000000.99926
117 R0.000740.000000.99926
118 F0.000740.000000.99926
119 G0.000740.000000.99926
120 D0.000740.000000.99926
121 Q0.000740.000000.99926
122 V0.000740.000000.99926
123 V0.000740.000000.99926
124 A0.000740.000000.99926
125 V0.000740.000000.99926
126 L0.000740.000000.99926
127 T0.000740.000000.99926
128 R0.000740.000000.99926
129 H0.000740.000000.99926
130 Q0.000740.000000.99926
131 P0.000740.000000.99926
132 E0.000740.000000.99926
133 L0.000740.000000.99926
134 A0.000740.000000.99926
135 A0.000740.000000.99926
136 R0.000740.000000.99926
137 R0.000740.000000.99926
138 R0.000740.000000.99926
139 S0.000740.000000.99926
140 G0.000740.000000.99926
141 H0.000740.000000.99926
142 L0.000740.000000.99926
143 E0.000740.000000.99926
144 T0.000740.000000.99926
145 A0.000740.000000.99926
146 Y0.000740.000000.99926
147 R0.000740.000000.99926
148 L0.000740.000000.99926
149 C0.000740.000000.99926
150 A0.000740.000000.99926
151 T0.000740.000000.99926
152 D0.000740.000000.99926
153 L0.000740.000000.99926
154 L0.000740.000000.99926
155 R0.000740.000000.99926
156 M0.000740.000000.99926
157 L0.000740.000000.99926
158 A0.000740.000000.99926
159 E0.000740.000000.99926
160 G0.000740.000000.99926
161 T0.000740.000000.99926
162 F0.000740.000000.99926
163 P0.000740.000000.99926
164 D0.000740.000000.99926
165 A0.000740.000000.99926
166 G0.000740.000000.99926
167 D0.000740.000000.99926
168 V0.000740.000000.99926
169 A0.000740.000000.99926
170 M0.000740.000000.99926
171 S0.000740.000000.99926
172 R0.000740.000000.99926
173 S0.000740.000000.99926
174 S0.000740.000000.99926
175 P0.000740.000000.99926
176 R0.000740.000000.99926
177 A0.000740.000000.99926
178 G0.000740.000000.99926
179 D0.000740.000000.99926
180 G0.000740.000000.99926
181 F0.000740.000000.99926
182 I0.000740.000000.99926
183 R0.000740.000000.99926
184 L0.000740.000000.99926
185 D0.000740.000000.99926
186 V0.000740.000000.99926
187 D0.000740.000000.99926
188 G0.000740.000000.99926
189 V0.000740.000000.99926
190 V0.000740.000000.99926
191 S0.000740.000000.99926
192 Y0.000740.000000.99926
193 A0.000740.000000.99926
194 S0.000740.000000.99926
195 P0.000740.000000.99926
196 N0.000740.000000.99926
197 A0.000740.000000.99926
198 L0.000740.000000.99926
199 S0.000740.000000.99926
200 A0.000740.000000.99926
201 Y0.000740.000000.99926
202 H0.000740.000000.99926
203 R0.000740.000000.99926
204 M0.000740.000000.99926
205 G0.000740.000000.99926
206 L0.000740.000000.99926
207 T0.000740.000000.99926
208 T0.000740.000000.99926
209 E0.000740.000000.99926
210 L0.000740.000000.99926
211 E0.000740.000000.99926
212 G0.000740.000000.99926
213 V0.000740.000000.99926
214 N0.000740.000000.99926
215 L0.000740.000000.99926
216 I0.000740.000000.99926
217 D0.000740.000000.99926
218 A0.000740.000000.99926
219 T0.000740.000000.99926
220 R0.000740.000000.99926
221 P0.000740.000000.99926
222 L0.000740.000000.99926
223 I0.000740.000000.99926
224 S0.000740.000000.99926
225 D0.000740.000000.99926
226 P0.000740.000000.99926
227 F0.000740.000000.99926
228 E0.000740.000000.99926
229 A0.000740.000000.99926
230 H0.000740.000000.99926
231 E0.000740.000000.99926
232 V0.000740.000000.99926
233 D0.000740.000000.99926
234 E0.000740.000000.99926
235 H0.000740.000000.99926
236 V0.000740.000000.99926
237 Q0.000740.000000.99926
238 D0.000740.000000.99926
239 L0.000740.000000.99926
240 L0.000740.000000.99926
241 A0.000740.000000.99926
242 G0.000740.000000.99926
243 D0.000740.000000.99926
244 G0.000740.000000.99926
245 K0.000740.000000.99926
246 G0.000740.000000.99926
247 M0.000740.000000.99925
248 R0.000740.000000.99925
249 M0.000740.000010.99925
250 E0.000740.000020.99924
251 V0.000740.000060.9992
252 D0.000740.000080.99918
253 A0.000730.000140.99912
254 G0.000730.000210.99905
255 G0.000720.000560.99872
256 A0.000700.001210.99809
257 T0.000660.002490.99684
258 V0.000650.002700.99665
259 L0.000640.002790.99657
260 L0.000640.002810.99655
261 R0.000640.002820.99654
262 T0.000640.002850.99651
263 L0.000640.002860.9965
264 P0.000640.002860.9965
265 L0.000640.002860.99649
266 V0.000640.002860.99649
267 V0.000640.002860.99649
268 A0.000650.002860.99649
269 G0.000650.002860.99649
270 R0.000680.002830.99649
271 N0.000690.002820.99649
272 V0.000690.002810.99649
273 G0.000710.002790.9965
274 A0.000750.002750.9965
275 A0.000790.002710.9965
276 I0.000810.002680.9965
277 L0.000880.002610.99651
278 I0.001340.002130.99653
279 R0.002310.001130.99656
280 D0.003350.000070.99658
281 V0.003370.000040.99659
282 T0.003400.000010.99659
283 E0.003410.000000.99659
284 V0.003410.000000.99659
285 K0.003410.000000.99659
286 R0.003410.000000.99659
287 R0.003410.000000.99659
288 D0.003410.000000.99659
289 R0.003410.000000.99659
290 A0.003410.000000.99659
291 L0.003410.000000.99659
292 I0.003410.000000.99659
293 S0.003410.000000.99659
294 K0.003410.000000.99659
295 D0.003410.000000.99659
296 A0.003410.000000.99659
297 T0.003410.000000.99659
298 I0.003410.000000.99659
299 R0.003410.000000.99659
300 E0.003410.000000.99659
301 I0.003410.000000.99659
302 H0.003410.000000.99659
303 H0.003410.000000.99659
304 R0.003410.000000.99659
305 V0.003410.000000.99659
306 K0.003410.000000.99659
307 N0.003410.000000.99659
308 N0.003410.000000.99659
309 L0.003410.000000.99659
310 Q0.003410.000000.99659
311 T0.003410.000000.99659
312 V0.003410.000000.99659
313 A0.003410.000000.99659
314 A0.003410.000000.99659
315 L0.003410.000000.99659
316 L0.003410.000000.99659
317 R0.003410.000000.99659
318 L0.003410.000000.99659
319 Q0.003410.000000.99659
320 A0.003410.000000.99659
321 R0.003410.000000.99659
322 R0.003410.000000.99659
323 T0.003410.000000.99659
324 S0.003410.000000.99659
325 N0.003410.000000.99659
326 A0.003410.000000.99659
327 E0.003410.000000.99659
328 G0.003410.000000.99659
329 R0.003410.000000.99659
330 E0.003410.000000.99659
331 A0.003410.000000.99659
332 L0.003410.000000.99659
333 I0.003410.000000.99659
334 E0.003410.000000.99659
335 S0.003410.000000.99659
336 V0.003410.000000.99659
337 R0.003410.000000.99659
338 R0.003410.000000.99659
339 V0.003410.000000.99659
340 S0.003410.000000.99659
341 S0.003410.000000.99659
342 I0.003410.000000.99659
343 A0.003410.000000.99659
344 L0.003410.000000.99659
345 V0.003410.000000.99659
346 H0.003410.000000.99659
347 D0.003410.000000.99659
348 A0.003410.000000.99659
349 L0.003410.000000.99659
350 S0.003410.000000.99659
351 M0.003410.000000.99659
352 S0.003410.000000.99659
353 V0.003410.000000.99659
354 D0.003410.000000.99659
355 E0.003410.000000.99659
356 Q0.003410.000000.99659
357 V0.003410.000000.99659
358 N0.003410.000000.99659
359 L0.003410.000000.99659
360 D0.003410.000000.99659
361 E0.003410.000000.99659
362 V0.003410.000000.99659
363 I0.003410.000000.99659
364 D0.003410.000000.99659
365 R0.003410.000000.99659
366 I0.003410.000000.99659
367 L0.003410.000000.99659
368 P0.003410.000000.99659
369 I0.003410.000000.99659
370 M0.003410.000000.99659
371 N0.003410.000000.99659
372 D0.003410.000000.99659
373 V0.003410.000000.99659
374 A0.003410.000000.99659
375 S0.003410.000000.99659
376 V0.003410.000000.99659
377 D0.003410.000000.99659
378 R0.003410.000000.99659
379 P0.003410.000000.99659
380 I0.003410.000000.99659
381 R0.003410.000000.99659
382 I0.003410.000000.99659
383 N0.003410.000000.99659
384 R0.003410.000000.99659
385 V0.003410.000000.99659
386 G0.003410.000000.99659
387 D0.003410.000000.99659
388 L0.003410.000000.99659
389 G0.003410.000000.99659
390 V0.003410.000000.99659
391 L0.003410.000000.99659
392 D0.003410.000000.99659
393 S0.003410.000000.99659
394 D0.003410.000000.99659
395 R0.003410.000000.99659
396 A0.003410.000000.99658
397 T0.003410.000000.99658
398 A0.003410.000000.99658
399 L0.003410.000000.99658
400 I0.003410.000000.99658
401 M0.003410.000000.99658
402 V0.003410.000000.99658
403 I0.003410.000000.99658
404 T0.003410.000000.99658
405 E0.003410.000000.99658
406 L0.003410.000000.99658
407 V0.003410.000000.99658
408 Q0.003410.000000.99658
409 N0.003410.000000.99658
410 A0.003410.000000.99658
411 I0.003410.000000.99658
412 E0.003410.000000.99658
413 H0.003410.000000.99658
414 A0.003410.000000.99658
415 F0.003410.000000.99658
416 D0.003420.000000.99658
417 P0.003420.000000.99658
418 A0.003420.000000.99658
419 A0.003420.000000.99658
420 A0.003420.000000.99658
421 E0.003420.000000.99658
422 G0.003420.000000.99658
423 S0.003420.000000.99658
424 V0.003420.000000.99658
425 T0.003420.000000.99658
426 I0.003420.000000.99658
427 R0.003420.000000.99658
428 A0.003420.000000.99658
429 E0.003420.000000.99658
430 R0.003420.000000.99658
431 S0.003420.000000.99658
432 A0.003420.000000.99658
433 R0.003420.000000.99658
434 W0.003420.000000.99658
435 L0.003420.000000.99658
436 D0.003420.000000.99658
437 V0.003420.000000.99658
438 V0.003420.000000.99658
439 V0.003420.000000.99658
440 H0.003420.000000.99658
441 D0.003420.000000.99658
442 D0.003420.000000.99658
443 G0.003420.000000.99658
444 L0.003420.000000.99658
445 G0.003420.000000.99658
446 L0.003420.000000.99658
447 P0.003420.000000.99658
448 Q0.003420.000000.99658
449 G0.003420.000000.99658
450 F0.003420.000000.99658
451 S0.003420.000000.99658
452 L0.003420.000000.99658
453 E0.003420.000000.99658
454 K0.003420.000000.99658
455 S0.003420.000000.99658
456 D0.003420.000000.99658
457 S0.003420.000000.99658
458 L0.003420.000000.99658
459 G0.003420.000000.99658
460 L0.003420.000010.99658
461 Q0.003420.000010.99658
462 I0.003420.000010.99658
463 V0.003420.000010.99658
464 R0.003420.000010.99658
465 T0.003420.000010.99658
466 L0.003420.000010.99658
467 V0.003420.000010.99658
468 S0.003420.000010.99658
469 A0.003420.000010.99658
470 E0.003420.000010.99658
471 L0.003420.000010.99658
472 D0.003420.000010.99658
473 G0.003420.000010.99658
474 S0.003420.000010.99658
475 L0.003420.000010.99658
476 G0.003420.000000.99658
477 M0.003420.000000.99658
478 R0.003420.000000.99658
479 D0.003420.000000.99658
480 A0.003420.000000.99658
481 R0.003420.000000.99658
482 E0.003420.000000.99658
483 R0.003420.000000.99658
484 G0.003420.000000.99658
485 T0.003420.000000.99658
486 D0.003420.000000.99658
487 V0.003420.000000.99658
488 V0.003420.000000.99658
489 L0.003420.000000.99658
490 R0.003420.000000.99658
491 V0.003420.000000.99658
492 P0.003420.000000.99658
493 V0.003420.000000.99658
494 G0.003420.000000.99658
495 R0.003420.000000.99658
496 R0.003420.000000.99658
497 G0.003420.000000.99658
498 R0.003420.000000.99658
499 L0.003420.000000.99658
500 M0.003420.000000.99658
501 L0.003420.000000.99658

General Statistics
Length: 501
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.0779299999999999
Exp number, first 60 AAs: 0.00324
Total prob of N-in: 0.00111
outside: from residue 1 to 501
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