TubercuList - TMHMM

TransMembrane prediction using Hidden Markov Models for Rv0017c

Residue number and Amino Acid	Probabilities
Residue number and Amino Acid	Inside	Membrane	Outside
1 M	0.99866	0.00000	0.00134
2 T	0.99866	0.00000	0.00134
3 T	0.99866	0.00000	0.00134
4 R	0.99866	0.00000	0.00134
5 L	0.99866	0.00000	0.00134
6 Q	0.99866	0.00000	0.00134
7 A	0.99866	0.00000	0.00134
8 P	0.99866	0.00000	0.00134
9 V	0.99866	0.00000	0.00134
10 A	0.99866	0.00000	0.00134
11 V	0.99866	0.00000	0.00134
12 T	0.99866	0.00000	0.00134
13 P	0.99866	0.00000	0.00134
14 P	0.99866	0.00000	0.00134
15 L	0.99866	0.00001	0.00133
16 P	0.99864	0.00003	0.00133
17 T	0.99856	0.00010	0.00133
18 R	0.99854	0.00014	0.00131
19 R	0.99592	0.00278	0.0013
20 N	0.61848	0.38102	0.00049
21 A	0.15824	0.84130	0.00047
22 E	0.14309	0.85660	0.0003
37 L	0.00003	0.99978	0.00018
38 L	0.00004	0.99321	0.00675
39 V	0.00006	0.96097	0.03896
40 V	0.00035	0.92496	0.07468
41 Q	0.00092	0.76968	0.22941
42 A	0.00101	0.73899	0.26001
43 N	0.00132	0.21249	0.78619
44 Q	0.00134	0.00814	0.99052
45 D	0.00134	0.00180	0.99685
46 Q	0.00134	0.02968	0.96897
47 G	0.00128	0.14882	0.8499
48 V	0.00122	0.27077	0.72801
49 P	0.00120	0.28874	0.71006
50 W	0.00120	0.35005	0.64875
51 D	0.00119	0.36843	0.63038
52 L	0.00082	0.77846	0.22072
53 T	0.00073	0.88931	0.10996
54 S	0.00069	0.90839	0.09093
55 Y	0.00063	0.97664	0.02273
56 G	0.00063	0.98474	0.01463
57 L	0.00063	0.99696	0.00241
58 A	0.00063	0.99848	0.00089
59 F	0.00063	0.99851	0.00086
60 L	0.00063	0.99852	0.00085
61 T	0.00063	0.99852	0.00085
62 L	0.00064	0.99851	0.00085
63 F	0.00065	0.99850	0.00085
64 G	0.00102	0.99813	0.00085
65 S	0.00251	0.99664	0.00086
66 A	0.00336	0.99578	0.00086
67 H	0.04684	0.95230	0.00086
68 L	0.08672	0.91242	0.00086
69 A	0.17062	0.82852	0.00087
70 I	0.32861	0.67044	0.00095
71 R	0.61972	0.37908	0.00119
72 R	0.70761	0.29109	0.00129
73 F	0.72246	0.27625	0.00129
74 A	0.77232	0.22638	0.0013
75 P	0.92609	0.07245	0.00146
76 Y	0.91888	0.07963	0.00148
77 T	0.87886	0.11965	0.00149
78 D	0.86352	0.13499	0.00149
79 P	0.46895	0.52962	0.00142
80 L	0.16413	0.83457	0.00129
81 L	0.04180	0.95691	0.00129
82 L	0.00833	0.99038	0.00128
83 P	0.00265	0.99606	0.00128
84 V	0.00059	0.99812	0.00128
85 V	0.00033	0.99838	0.00128
86 A	0.00030	0.99841	0.00128
87 L	0.00029	0.99843	0.00128
88 L	0.00028	0.99843	0.00128
89 N	0.00029	0.99842	0.00129
90 G	0.00029	0.99842	0.00129
91 L	0.00029	0.99839	0.00132
92 G	0.00029	0.99829	0.00143
93 L	0.00029	0.99809	0.00163
94 V	0.00029	0.99701	0.0027
95 M	0.00030	0.99302	0.00668
96 I	0.00031	0.98355	0.01615
97 H	0.00035	0.79358	0.20607
98 R	0.00048	0.66742	0.3321
99 L	0.00050	0.45021	0.54929
100 D	0.00053	0.34445	0.65502
101 L	0.00053	0.33852	0.66095
102 V	0.00054	0.15833	0.84113
103 D	0.00056	0.00536	0.99408
104 N	0.00056	0.00008	0.99936
105 E	0.00056	0.00002	0.99942
106 I	0.00056	0.00001	0.99942
107 G	0.00056	0.00000	0.99943
108 E	0.00056	0.00000	0.99944
109 H	0.00056	0.00004	0.9994
110 R	0.00056	0.00012	0.99932
111 H	0.00056	0.00041	0.99903
112 P	0.00056	0.00461	0.99484
113 S	0.00055	0.06305	0.9364
114 A	0.00055	0.11235	0.88711
115 N	0.00055	0.11662	0.88283
116 Q	0.00054	0.44407	0.55539
117 Q	0.00051	0.72370	0.27579
118 M	0.00021	0.97158	0.02821
119 L	0.00016	0.99723	0.00261
120 W	0.00015	0.99918	0.00067
136 K	0.95773	0.04185	0.00042
137 D	0.98535	0.01422	0.00043
138 H	0.99666	0.00290	0.00043
139 R	0.99861	0.00096	0.00043
140 Q	0.99448	0.00510	0.00042
141 L	0.96528	0.03430	0.00041
142 A	0.87489	0.12470	0.00041
143 R	0.85652	0.14308	0.0004
144 Y	0.17199	0.82766	0.00035
158 V	0.00021	0.99968	0.00011
159 P	0.00021	0.99881	0.00098
160 A	0.00021	0.99756	0.00224
161 L	0.00021	0.99454	0.00525
162 L	0.00021	0.96808	0.03171
163 P	0.00022	0.95304	0.04673
164 A	0.00023	0.91909	0.08069
165 A	0.00024	0.86604	0.13372
166 L	0.00026	0.82405	0.17569
167 S	0.00033	0.03221	0.96746
168 E	0.00063	0.01009	0.98928
169 Q	0.00064	0.00305	0.99631
170 N	0.00064	0.00059	0.99877
171 G	0.00064	0.00028	0.99908
172 A	0.00064	0.00005	0.99931
173 K	0.00064	0.00005	0.9993
174 I	0.00064	0.00264	0.99672
175 W	0.00063	0.00362	0.99575
176 I	0.00063	0.00515	0.99421
177 R	0.00063	0.00537	0.994
178 L	0.00062	0.00757	0.99181
179 P	0.00061	0.01283	0.98656
180 G	0.00055	0.04173	0.95772
181 F	0.00054	0.65689	0.34257
182 S	0.00054	0.66746	0.332
183 I	0.00054	0.68509	0.31437
184 Q	0.00054	0.69559	0.30387
185 P	0.00053	0.70376	0.29571
186 A	0.00049	0.83493	0.16458
187 E	0.00043	0.83960	0.15997
188 F	0.00033	0.85264	0.14703
189 S	0.00032	0.85950	0.14018
190 K	0.00030	0.86671	0.133
191 I	0.00013	0.97676	0.02312
192 L	0.00007	0.98198	0.01795
193 L	0.00006	0.98322	0.01672
194 L	0.00006	0.98439	0.01555
195 I	0.00007	0.98539	0.01453
196 F	0.00016	0.98536	0.01448
197 F	0.00199	0.98355	0.01447
198 S	0.00324	0.98230	0.01446
199 A	0.00509	0.98046	0.01445
200 V	0.00645	0.97910	0.01445
201 L	0.01685	0.96869	0.01446
202 V	0.03146	0.95407	0.01447
203 A	0.08898	0.89649	0.01453
204 K	0.72363	0.26180	0.01457
205 R	0.73443	0.25099	0.01457
206 G	0.74039	0.24503	0.01458
207 L	0.74297	0.24244	0.01458
208 F	0.75063	0.23477	0.0146
209 T	0.94238	0.04292	0.01469
210 S	0.96683	0.01828	0.01489
211 A	0.97024	0.01481	0.01495
212 G	0.97165	0.01335	0.015
213 K	0.97722	0.00776	0.01502
214 H	0.98189	0.00308	0.01503
215 L	0.98145	0.00352	0.01502
216 L	0.98156	0.00342	0.01502
217 G	0.98261	0.00238	0.01501
218 M	0.98359	0.00143	0.01499
219 T	0.98339	0.00167	0.01494
220 L	0.94166	0.04374	0.0146
221 P	0.94033	0.04515	0.01452
222 R	0.93790	0.04782	0.01428
223 P	0.87310	0.11327	0.01362
224 R	0.80552	0.18203	0.01245
225 D	0.74317	0.24653	0.0103
226 L	0.57816	0.41439	0.00745
227 A	0.55659	0.43644	0.00696
228 P	0.53964	0.45358	0.00678
229 L	0.42632	0.56762	0.00606
230 L	0.40847	0.58578	0.00575
231 A	0.40536	0.58925	0.0054
232 A	0.39605	0.59873	0.00522
233 W	0.39449	0.60036	0.00515
234 V	0.39228	0.60259	0.00513
235 I	0.39183	0.60305	0.00513
236 S	0.39176	0.60296	0.00528
237 V	0.39122	0.60323	0.00555
238 G	0.39104	0.60258	0.00638
239 V	0.39024	0.60346	0.0063
240 M	0.38892	0.60471	0.00638
241 V	0.38603	0.60277	0.0112
242 F	0.38693	0.54789	0.06518
243 E	0.39059	0.25782	0.35159
244 K	0.39136	0.17429	0.43435
245 D	0.37530	0.20178	0.42292
246 L	0.09909	0.72147	0.17945
247 G	0.04360	0.85249	0.10391
248 A	0.02362	0.87925	0.09712
249 S	0.01589	0.88281	0.10129
250 L	0.01246	0.88366	0.10388
251 L	0.01236	0.88180	0.10583
252 L	0.01238	0.79956	0.18806
253 Y	0.01240	0.78248	0.20512
254 T	0.01260	0.77891	0.20849
255 S	0.01271	0.76966	0.21763
256 F	0.01272	0.76927	0.218
257 L	0.01273	0.76757	0.2197
258 V	0.01275	0.76600	0.22124
259 V	0.01277	0.76532	0.22191
260 V	0.01290	0.76204	0.22505
261 Y	0.01712	0.75477	0.22811
262 L	0.02093	0.74600	0.23306
263 A	0.07933	0.66968	0.25099
264 T	0.23522	0.38940	0.37538
265 Q	0.35148	0.14960	0.49891
266 R	0.33322	0.18593	0.48085
267 F	0.28200	0.36938	0.34863
268 S	0.22524	0.47904	0.29572
269 W	0.11002	0.85496	0.03502
270 V	0.01379	0.97653	0.00968
271 V	0.00100	0.99680	0.00221
272 I	0.00030	0.99880	0.0009
273 G	0.00022	0.99929	0.00049
274 L	0.00014	0.99972	0.00013
284 A	0.00012	0.99975	0.00013
285 Y	0.00058	0.99891	0.0005
286 F	0.00139	0.99670	0.00191
287 I	0.02394	0.96868	0.00738
288 F	0.08962	0.86133	0.04905
289 E	0.45483	0.33427	0.2109
290 H	0.53968	0.19521	0.26511
291 V	0.54888	0.16571	0.28541
292 R	0.63170	0.03725	0.33105
293 L	0.63422	0.00872	0.35706
294 R	0.63556	0.00087	0.36357
295 V	0.63579	0.00040	0.36381
296 Q	0.63602	0.00007	0.36391
297 T	0.63603	0.00003	0.36393
298 W	0.63603	0.00003	0.36394
299 L	0.63603	0.00001	0.36396
300 D	0.63603	0.00001	0.36396
301 P	0.63600	0.00004	0.36396
302 F	0.63596	0.00008	0.36396
303 A	0.63595	0.00009	0.36396
304 D	0.63594	0.00010	0.36396
305 P	0.63587	0.00018	0.36396
306 D	0.63550	0.00055	0.36395
307 G	0.55788	0.07888	0.36323
308 T	0.45382	0.18416	0.36202
309 G	0.32979	0.30855	0.36165
310 Y	0.27798	0.36605	0.35596
311 Q	0.26060	0.38429	0.35511
312 I	0.10638	0.53926	0.35436
313 V	0.08684	0.55900	0.35416
314 Q	0.08312	0.56275	0.35413
315 S	0.04485	0.60109	0.35405
316 L	0.00540	0.64057	0.35403
317 F	0.00278	0.64319	0.35403
318 S	0.00235	0.64362	0.35403
319 F	0.00212	0.64385	0.35403
320 A	0.00207	0.64390	0.35403
321 T	0.00205	0.64391	0.35404
322 G	0.00204	0.64392	0.35404
323 G	0.00203	0.64391	0.35405
324 I	0.00202	0.64389	0.35408
325 F	0.00202	0.64304	0.35494
326 G	0.00205	0.63887	0.35908
327 T	0.00214	0.62857	0.36929
328 G	0.00222	0.61553	0.38225
329 L	0.00229	0.58679	0.41092
330 G	0.00323	0.40651	0.59026
331 N	0.00439	0.25234	0.74327
332 G	0.00490	0.17597	0.81913
333 Q	0.01134	0.11879	0.86986
334 P	0.01179	0.06530	0.92292
335 D	0.01190	0.01643	0.97168
336 T	0.01182	0.01487	0.97331
337 V	0.01178	0.01454	0.97368
338 P	0.01178	0.00707	0.98115
339 A	0.01177	0.00364	0.98459
340 A	0.01177	0.00498	0.98325
341 S	0.01177	0.00559	0.98265
342 T	0.01176	0.00751	0.98074
343 D	0.01173	0.01418	0.97408
344 F	0.01117	0.19574	0.79308
345 I	0.01050	0.32319	0.66631
346 I	0.01041	0.36369	0.6259
347 A	0.01030	0.43275	0.55696
348 A	0.01001	0.52260	0.46738
349 F	0.00969	0.54133	0.44899
350 G	0.00953	0.54849	0.44197
351 E	0.00927	0.57714	0.41359
352 E	0.00863	0.62951	0.36186
353 L	0.00180	0.86266	0.13555
354 G	0.00125	0.94849	0.05026
355 L	0.00098	0.97688	0.02214
356 V	0.00091	0.99550	0.00359
357 G	0.00091	0.99757	0.00152
358 L	0.00090	0.99867	0.00042
359 T	0.00091	0.99895	0.00014
367 I	0.14060	0.85904	0.00036
368 V	0.22313	0.77599	0.00088
369 I	0.26367	0.73532	0.00101
370 I	0.39417	0.60451	0.00132
371 R	0.57822	0.41898	0.0028
372 G	0.59825	0.39824	0.00351
373 L	0.61889	0.37633	0.00479
374 R	0.81488	0.17901	0.00611
375 T	0.87272	0.12067	0.0066
376 A	0.97779	0.01176	0.01044
377 I	0.98048	0.00897	0.01054
378 A	0.98620	0.00303	0.01077
379 T	0.98893	0.00019	0.01088
380 R	0.98892	0.00019	0.01088
381 D	0.98702	0.00209	0.01088
382 S	0.74638	0.24278	0.01084
383 F	0.65941	0.32989	0.0107
384 G	0.63073	0.35889	0.01038
385 K	0.60235	0.38779	0.00985
386 L	0.33418	0.65713	0.00869
387 L	0.12976	0.86336	0.00688
388 A	0.06947	0.92497	0.00556
389 A	0.03652	0.95818	0.0053
390 G	0.01133	0.98667	0.002
391 L	0.00622	0.99184	0.00194
392 S	0.00546	0.99264	0.0019
393 S	0.00363	0.99465	0.00173
394 T	0.00233	0.99617	0.00149
395 L	0.00046	0.99865	0.00088
396 A	0.00025	0.99888	0.00087
397 I	0.00019	0.99895	0.00086
398 Q	0.00017	0.99896	0.00086
399 L	0.00008	0.99905	0.00087
400 F	0.00005	0.99872	0.00123
401 I	0.00005	0.99785	0.00209
402 V	0.00005	0.99192	0.00802
403 V	0.00006	0.97963	0.02031
404 G	0.00011	0.95624	0.04365
405 G	0.00018	0.66496	0.33487
406 V	0.00056	0.58267	0.41677
407 T	0.00264	0.48829	0.50907
408 R	0.00353	0.42834	0.56812
409 L	0.00378	0.30813	0.68809
410 I	0.00447	0.13472	0.8608
411 P	0.00551	0.07061	0.92388
412 L	0.00569	0.03956	0.95475
413 T	0.00971	0.01002	0.98027
414 G	0.00969	0.01453	0.97577
415 L	0.00961	0.06836	0.92203
416 T	0.00963	0.09214	0.89823
417 T	0.00956	0.10620	0.88423
418 P	0.00862	0.20907	0.78231
419 W	0.00301	0.70486	0.29212
420 M	0.00276	0.77634	0.2209
421 S	0.00197	0.85960	0.13842
422 Y	0.00123	0.92524	0.07353
423 G	0.00095	0.94851	0.05054
424 G	0.00073	0.96770	0.03158
425 S	0.00064	0.97802	0.02135
426 S	0.00058	0.98864	0.01078
427 L	0.00053	0.99689	0.00258
428 L	0.00053	0.99783	0.00164
429 A	0.00054	0.99793	0.00154
430 N	0.00057	0.99790	0.00152
431 Y	0.00059	0.99790	0.00151
432 I	0.00070	0.99779	0.00151
433 L	0.00088	0.99760	0.00151
434 L	0.00112	0.99735	0.00153
435 A	0.00330	0.99515	0.00156
436 I	0.00571	0.99271	0.00157
437 L	0.02238	0.97586	0.00176
438 A	0.10691	0.89094	0.00215
439 R	0.17500	0.82122	0.00378
440 I	0.19165	0.80431	0.00404
441 S	0.30421	0.69023	0.00556
442 H	0.78986	0.20057	0.00956
443 G	0.84112	0.14890	0.00998
444 A	0.95495	0.03431	0.01074
445 R	0.98213	0.00686	0.01101
446 R	0.98802	0.00093	0.01106
447 P	0.98855	0.00039	0.01106
448 L	0.98860	0.00034	0.01106
449 R	0.98882	0.00011	0.01106
450 T	0.98893	0.00000	0.01106
451 R	0.98894	0.00000	0.01106
452 P	0.98894	0.00000	0.01106
453 R	0.98894	0.00000	0.01106
454 N	0.98894	0.00000	0.01106
455 K	0.98894	0.00000	0.01106
456 S	0.98894	0.00000	0.01106
457 P	0.98894	0.00000	0.01106
458 I	0.98894	0.00000	0.01106
459 T	0.98894	0.00000	0.01106
460 A	0.98894	0.00000	0.01106
461 A	0.98894	0.00000	0.01106
462 G	0.98894	0.00000	0.01106
463 T	0.98894	0.00000	0.01106
464 E	0.98894	0.00000	0.01106
465 V	0.98894	0.00000	0.01106
466 I	0.98894	0.00000	0.01106
467 E	0.98894	0.00000	0.01106
468 R	0.98894	0.00000	0.01106
469 V	0.98894	0.00000	0.01106

General Statistics

Length: 469

Number of predicted TMHs: 12

Exp number of AAs in TMHs: 253.57701

Exp number, first 60 AAs: 31.63192

Total prob of N-in: 0.99866

POSSIBLE N-term signal sequence

inside: from residue 1 to 19

TMhelix: from residue 20 to 42

outside: from residue 43 to 51

TMhelix: from residue 52 to 74

inside: from residue 75 to 78

TMhelix: from residue 79 to 101

outside: from residue 102 to 115

TMhelix: from residue 116 to 135

inside: from residue 136 to 143

TMhelix: from residue 144 to 166

outside: from residue 167 to 180

TMhelix: from residue 181 to 203

inside: from residue 204 to 245

TMhelix: from residue 246 to 263

outside: from residue 264 to 266

TMhelix: from residue 267 to 289

inside: from residue 290 to 309

TMhelix: from residue 310 to 332

outside: from residue 333 to 346

TMhelix: from residue 347 to 369

inside: from residue 370 to 381

TMhelix: from residue 382 to 404

outside: from residue 405 to 418

TMhelix: from residue 419 to 441

inside: from residue 442 to 469

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