TransMembrane prediction using Hidden Markov Models for Rv2395




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.998240.000000.00175
2 S0.998240.000000.00175
3 G0.998240.000000.00175
4 A0.998240.000000.00175
5 T0.996610.001630.00175
6 V0.996610.001640.00175
7 G0.994630.003620.00175
8 A0.994630.003620.00175
9 R0.994530.003720.00175
10 E0.994460.004070.00147
11 I0.870770.128080.00115
12 T0.674950.323940.00111
13 I0.023210.975950.00085
14 R0.023150.976000.00085
15 G0.023150.976510.00034
16 V0.003650.996010.00034
17 V0.000170.999490.00034
18 L0.000140.999520.00033
19 G0.000110.999550.00033
20 A0.000040.999630.00032
21 L0.000000.999670.00032
22 I0.000000.999670.00032
23 T0.000000.999660.00034
24 L0.000000.999650.00034
25 V0.000000.999630.00036
26 F0.000000.999600.00039
27 T0.000010.999350.00064
28 A0.000010.995530.00445
29 A0.000020.992130.00784
30 N0.000030.983180.01678
31 V0.000050.976150.0238
32 Y0.000050.953310.04663
33 L0.000320.747370.25231
34 G0.000660.485650.51369
35 L0.000900.331860.66724
36 R0.001210.018740.98005
37 V0.000990.416430.58258
38 G0.001060.595320.40362
39 L0.001020.777050.22193
40 T0.001010.932290.06671
41 F0.000990.962480.03653
42 A0.000990.979200.01981
43 T0.000990.982860.01614
44 S0.000990.984610.0144
45 I0.000990.998310.0007
46 P0.000990.998460.00055
47 A0.000990.998820.00019
48 A0.000990.998890.00011
49 V0.000990.998910.0001
56 R0.008390.991490.00012
57 L0.009810.990060.00013
58 F0.014180.985660.00016
59 A0.092290.907440.00026
60 N0.728550.270970.00047
61 H0.966490.032990.00051
62 S0.978560.020930.00051
63 V0.979890.019600.00051
64 V0.982210.017270.00052
65 E0.997210.002270.00052
66 N0.992010.007470.00052
67 N0.986480.013000.00052
68 I0.977560.022060.00037
69 V0.975940.023740.00032
70 Q0.969620.030080.0003
71 T0.809510.190210.00027
72 I0.161710.838060.00023
73 A0.033630.966160.00021
74 S0.029840.969990.00016
75 A0.023170.976680.00014
76 A0.012810.987060.00013
77 G0.009120.990750.00013
78 T0.005660.994210.00013
79 L0.000810.999070.00012
80 S0.000190.999690.00012
81 S0.000010.999870.00011
82 I0.000000.999880.00011
83 I0.000000.999880.00012
84 F0.000000.999840.00016
85 V0.000000.999640.00036
86 L0.000000.998700.00129
87 P0.000000.997760.00223
88 A0.000000.996730.00327
89 L0.000010.991560.00843
90 L0.000010.982890.0171
91 M0.000170.966860.03297
92 I0.000210.955530.04426
93 G0.000230.924690.07507
94 W0.000250.777210.22254
95 W0.000290.187950.81177
96 S0.000310.030260.96943
97 G0.000160.124140.8757
98 F0.000130.407460.59241
99 P0.000120.827610.17227
100 Y0.000110.952410.04748
101 W0.000090.973530.02638
102 T0.000090.986050.01386
103 T0.000080.988350.01156
104 A0.000060.999440.0005
105 A0.000060.999740.0002
106 V0.000060.999780.00016
107 C0.000050.999810.00013
108 A0.000050.999840.0001
118 S0.139110.860790.0001
119 I0.175420.824480.0001
120 P0.368860.630860.00029
121 L0.538340.461320.00034
122 R0.979900.019730.00037
123 R0.994960.004650.00038
124 A0.995770.003840.00038
125 L0.996080.003530.00039
126 V0.996610.003000.00039
127 T0.999550.000040.00041
128 G0.999580.000010.00041
129 S0.999580.000010.00041
130 D0.999580.000010.00041
131 L0.999580.000010.00041
132 P0.999580.000010.00041
133 Y0.999580.000010.00041
134 P0.999580.000010.00041
135 E0.999580.000010.00041
136 G0.999580.000010.00041
137 V0.999580.000010.00041
138 A0.999580.000010.00041
139 G0.999580.000010.00041
140 A0.999580.000010.00041
141 E0.999580.000010.00041
142 V0.999580.000010.00041
143 L0.999580.000010.00041
144 K0.999580.000000.00041
145 I0.999580.000000.00041
146 G0.999580.000000.00041
147 D0.999580.000000.00041
148 S0.999580.000000.00041
149 A0.999580.000000.00041
150 R0.999580.000000.00041
151 E0.999580.000000.00041
152 M0.999580.000000.00041
153 E0.999490.000090.00041
154 H0.995650.003940.00041
155 N0.994450.005140.00041
156 R0.990380.009220.0004
157 R0.965290.034320.00039
158 G0.769040.230640.00032
173 A0.000080.999770.00015
174 L0.000080.999330.00059
175 L0.000080.997780.00214
176 A0.000080.984850.01507
177 S0.000090.882560.11734
178 L0.000100.843460.15644
179 R0.000140.764530.23533
180 V0.000140.754480.24538
181 I0.000200.659500.3403
182 N0.000460.043380.95616
183 N0.000480.004250.99526
184 S0.000490.003570.99593
185 L0.000490.031440.96807
186 S0.000480.163540.83598
187 A0.000470.247800.75172
188 T0.000460.302370.69717
189 F0.000460.313500.68604
190 R0.000460.339840.65971
191 V0.000440.775810.22375
192 G0.000440.801640.19792
193 S0.000440.857540.14201
194 G0.000440.878020.12154
195 A0.000440.914710.08485
196 T0.000440.987430.01214
197 M0.000430.991710.00786
198 I0.000410.993440.00615
199 G0.000390.993540.00607
200 A0.000370.993780.00585
201 S0.000320.994200.00548
202 L0.000170.994480.00535
203 S0.000510.994230.00526
204 L0.000970.994190.00483
205 A0.005230.990460.00432
206 L0.014050.982050.0039
207 I0.040910.956860.00222
208 G0.084720.913310.00197
209 V0.235250.763600.00115
210 G0.321670.677330.001
211 H0.461980.537370.00065
212 L0.382140.617570.00029
226 A0.000270.999630.0001
227 I0.000620.999250.00013
228 A0.001420.998340.00024
229 F0.002010.997290.0007
230 G0.004060.992790.00315
231 V0.004800.989450.00575
232 M0.006190.973240.02057
233 L0.006470.945770.04776
234 P0.007050.874910.11803
235 I0.007280.780640.21208
236 R0.007540.561680.43079
237 T0.007550.501620.49083
238 A0.007550.330460.66198
239 G0.007560.236380.75606
240 Q0.007580.057370.93505
241 L0.007580.020480.97194
242 P0.007580.006280.98613
243 P0.007580.000940.99147
244 D0.007580.000360.99206
245 G0.007580.000060.99235
246 D0.007580.000050.99237
247 Y0.007570.000340.99208
248 A0.007570.000600.99183
249 V0.007550.001810.99064
250 A0.007540.002910.98954
251 V0.007520.003430.98904
252 A0.007520.003860.98862
253 R0.007510.004440.98805
254 I0.007420.032520.96006
255 F0.007420.033440.95914
256 S0.007390.034610.95799
257 T0.007360.044790.94785
258 D0.007320.050510.94216
259 V0.006800.101460.89173
260 R0.006520.115630.87786
261 F0.002090.270680.72722
262 I0.001700.318950.67935
263 G0.001580.333730.66469
264 A0.001510.422290.5762
265 G0.001440.883710.11485
266 A0.001430.955160.04341
267 I0.001430.972910.02567
268 A0.001460.982340.0162
269 V0.001520.992820.00566
270 A0.001900.996370.00173
271 A0.002200.997270.00053
272 A0.003080.996540.00038
273 W0.003920.995780.00031
274 T0.004760.994930.00031
275 F0.005410.994280.00031
276 L0.007190.992450.00037
277 K0.051510.947710.00077
278 I0.052890.946330.00078
279 L0.056150.943000.00086
280 G0.074660.924380.00096
281 P0.098740.900140.00113
282 I0.121140.877560.0013
283 L0.131030.867260.00172
284 R0.255090.739050.00587
285 G0.270070.723800.00612
286 I0.277110.716680.00621
287 A0.368410.625300.00629
288 D0.921640.071980.00639
289 A0.978880.014730.00639
290 A0.982400.011210.0064
291 V0.984680.008930.0064
292 S0.990460.003140.0064
293 A0.992250.001350.0064
294 R0.993460.000140.00641
295 T0.993520.000080.00641
296 R0.993580.000020.00641
297 R0.993600.000000.00641
298 R0.993600.000000.00641
299 G0.993600.000000.00641
300 Q0.993600.000000.00641
301 A0.993590.000000.00641
302 V0.993590.000010.00641
303 G0.993490.000110.00641
304 Q0.993420.000180.00641
305 T0.993250.000350.00641
306 E0.992380.001220.0064
307 R0.949590.044080.00633
308 D0.489630.505080.00529
309 I0.302960.694180.00286
310 P0.212420.785360.00221
311 I0.057220.942190.00059
312 H0.037160.962490.00035
325 I0.000140.999740.00012
326 G0.000140.998670.00119
327 W0.000150.997050.0028
328 L0.000170.990490.00934
329 L0.000660.948690.05065
330 A0.002100.716180.28171
331 D0.005260.102550.8922
332 F0.006020.040080.9539
333 T0.006280.027180.96654
334 D0.006510.003880.98962
335 G0.006510.001890.9916
336 T0.006520.000260.99323
337 P0.006520.000060.99343
338 L0.006520.000040.99345
339 D0.006520.000010.99348
340 D0.006520.000120.99337
341 R0.006500.001240.99226
342 R0.006440.009060.98451
343 P0.005740.084050.91021
344 G0.005030.328830.66614
345 A0.004870.862410.13271
346 I0.004510.903460.09203
347 A0.004400.913650.08194
348 A0.004230.927270.06849
349 G0.002650.948440.04891
350 V0.000540.994700.00476
351 L0.000020.998320.00165
352 L0.000000.999530.00046
353 V0.000000.999860.00014
363 V0.007470.992410.00012
364 C0.034340.965190.00047
365 G0.175480.824000.00052
366 Y0.269560.729520.00092
367 M0.573290.425280.00143
368 A0.822240.176220.00154
369 G0.838230.159860.00191
370 L0.818870.179250.00188
371 I0.607750.390290.00196
372 G0.626600.369630.00377
373 S0.644870.349460.00567
374 S0.586270.407720.00601
375 N0.572250.421970.00579
376 S0.514110.482720.00317
377 P0.475470.521950.00258
378 I0.216770.782290.00094
379 S0.074880.924310.00081
380 G0.016920.982460.00063
381 V0.004230.995620.00014
387 V0.000140.999750.0001
388 L0.000140.999610.00024
389 A0.000140.998790.00106
390 G0.000150.996810.00305
391 L0.000150.976080.02377
392 L0.000170.969260.03057
393 I0.000480.916190.08333
394 K0.001790.583660.41455
395 T0.002000.574150.42385
396 A0.002180.536360.46146
397 Y0.002310.525260.47242
398 G0.002540.487790.50966
399 P0.004700.426770.56853
400 A0.004820.390620.60456
401 T0.006390.146830.84677
402 G0.006400.033980.95962
403 S0.006330.121390.87228
404 Q0.006040.188680.80527
405 I0.002730.653210.34406
406 P0.002260.679570.31817
407 A0.000290.754960.24475
408 L0.000080.985460.01445
409 V0.000020.992490.00749
410 A0.000010.998950.00103
411 Y0.000010.999440.00055
412 T0.000010.999560.00043
413 V0.000010.999700.00029
414 F0.000010.999700.00029
415 T0.000010.999700.00029
416 A0.000010.999700.00029
417 A0.000010.999700.00029
418 L0.000010.999700.00029
419 V0.000030.999680.00029
420 F0.000150.999550.00029
421 G0.001030.998670.0003
422 V0.002770.996930.0003
423 A0.016740.982870.00039
424 T0.028680.970760.00056
425 I0.049040.949780.00118
426 S0.186840.810740.00242
427 N0.306780.688290.00493
428 D0.964130.029130.00675
429 N0.972470.020680.00685
430 L0.978000.015130.00687
431 Q0.992870.000250.00688
432 D0.993110.000010.00689
433 L0.993110.000010.00689
434 K0.993110.000000.00689
435 T0.993100.000010.00689
436 G0.993090.000030.00688
437 Q0.993040.000080.00688
438 L0.991960.001180.00686
439 V0.991730.001410.00686
440 G0.991620.001570.00682
441 A0.991590.001600.00681
442 T0.991340.001910.00675
443 P0.989780.003550.00667
444 W0.988750.004650.0066
445 K0.987920.005600.00648
446 Q0.964120.031330.00455
447 Q0.861230.135910.00286
448 V0.075990.922940.00107
449 A0.051980.947370.00065
450 L0.021300.978350.00035
451 I0.010320.989520.00016
458 S0.007870.992020.00011
459 V0.007870.992010.00012
460 V0.007880.991930.00018
461 M0.007920.990910.00117
462 A0.007940.990530.00153
463 P0.008000.989790.00222
464 I0.008040.989440.00252
465 L0.008360.973480.01817
466 Q0.010550.844860.14459
467 L0.010910.812820.17627
468 M0.012280.693380.29434
469 Q0.013600.648090.33831
470 A0.013820.596360.38983
471 G0.014010.104700.8813
472 F0.014110.133820.85206
473 G0.014310.131010.85468
474 F0.014500.297630.68787
475 Q0.014660.386360.59898
476 G0.014660.408830.57651
477 A0.014670.454270.53106
478 P0.014670.475130.5102
479 G0.014670.517430.4679
480 A0.014680.763030.2223
481 T0.014680.771320.214
482 A0.014680.784880.20044
483 N0.014680.792430.19289
484 A0.014690.805130.18019
485 L0.014690.921920.06339
486 A0.014790.923500.06171
487 A0.016410.923030.06056
488 P0.029400.910320.06029
489 Q0.036850.902990.06016
490 A0.037970.902850.05918
491 A0.039100.901740.05916
492 L0.042110.898750.05915
493 M0.077490.863360.05915
494 S0.130970.809880.05916
495 A0.171250.769600.05915
496 L0.190620.750230.05915
497 A0.391250.549620.05914
498 K0.558820.382050.05914
499 G0.535210.406130.05867
500 V0.490540.451910.05756
501 F0.379010.565260.05572
502 G0.361780.582610.05561
503 G0.483250.461420.05534
504 S0.321550.623420.05503
505 L0.236010.709220.05477
506 N0.189340.756000.05467
507 W0.087640.857740.05461
508 S0.094860.850530.0546
509 L0.004940.940470.05459
510 V0.001840.943570.05459
511 G0.000440.944970.05459
512 V0.000110.945300.05459
513 G0.000110.945290.0546
514 A0.000040.945350.0546
515 L0.000030.945340.05462
516 T0.000030.945330.05463
517 G0.000030.945250.05472
518 V0.000030.945120.05485
519 I0.000050.944750.0552
520 A0.000110.936490.0634
521 V0.000140.917490.08238
522 A0.000620.868530.13085
523 L0.001820.774200.22398
524 D0.004420.423350.57224
525 E0.004490.216660.77885
526 T0.004510.179180.8163
527 L0.004530.156190.83928
528 A0.004620.123250.87213
529 K0.004650.009450.98591
530 T0.004650.002530.99282
531 T0.004650.001340.99401
532 T0.004650.000420.99493
533 N0.004630.000600.99477
534 L0.004550.001020.99443
535 R0.004440.001180.99438
536 L0.003490.006350.99016
537 P0.003470.011110.98541
538 P0.003370.081430.9152
539 L0.002890.372950.62416
540 A0.002600.506840.49056
541 V0.002530.547770.44971
542 G0.002080.623790.37413
543 M0.001140.972220.02664
544 G0.000850.981440.01771
545 M0.000810.989830.00936
546 Y0.000790.996690.00252
547 L0.000780.998280.00094
548 S0.000780.999040.00017
557 I0.001240.998640.00012
558 G0.001720.998020.00027
559 A0.002720.996260.00101
560 F0.004010.994920.00106
561 L0.052720.946050.00123
562 G0.398690.599570.00175
563 R0.649760.348060.00218
564 I0.673210.324540.00225
565 Y0.720860.276380.00276
566 D0.993990.002240.00377
567 S0.995190.000970.00385
568 W0.995540.000590.00386
569 A0.995600.000540.00386
570 R0.996060.000070.00387
571 W0.996070.000050.00387
572 S0.996110.000020.00387
573 G0.996120.000010.00387
574 D0.996130.000000.00387
575 D0.996130.000000.00387
576 D0.996130.000000.00387
577 E0.996130.000000.00387
578 R0.996130.000000.00387
579 K0.996120.000010.00387
580 K0.995990.000140.00387
581 R0.982620.013660.00372
582 L0.542630.454180.00318
583 G0.412110.585030.00287
584 V0.356330.641810.00186
585 M0.305640.693850.0005
586 L0.027820.971860.00032
587 A0.013050.986680.00027
588 T0.007880.991880.00025
589 G0.002290.997480.00023
590 L0.000220.999580.00021
591 I0.000020.999780.0002
592 V0.000010.999790.0002
593 G0.000010.999790.0002
594 E0.000010.999790.0002
595 S0.000000.999800.0002
596 L0.000000.999800.0002
597 Y0.000000.999800.00021
598 G0.000000.999790.00021
599 V0.000000.999760.00024
600 L0.000000.999450.00054
601 F0.000020.998640.00135
602 A0.000050.995040.00491
603 V0.000070.993460.00647
604 I0.000250.973190.02657
605 V0.000730.584460.41481
606 A0.001050.443000.55595
607 T0.002000.377000.621
608 T0.003430.305630.69094
609 G0.003610.021950.97444
610 K0.003670.000610.99572
611 E0.003670.000060.99628
612 E0.003670.000010.99632
613 P0.003670.000020.99631
614 L0.003670.000310.99603
615 A0.003670.000780.99555
616 M0.003660.001060.99528
617 V0.003640.001530.99483
618 G0.003400.008060.98854
619 D0.003000.146380.85062
620 G0.001470.261370.73717
621 F0.001240.318420.68034
622 R0.001170.402350.59649
623 F0.000750.750330.24892
624 A0.000590.984310.01509
625 S0.000510.991070.00842
626 Q0.000470.995370.00415
627 P0.000370.998320.00131
628 L0.000340.998980.00068
629 G0.000340.999030.00064
630 A0.000340.999040.00063
631 I0.000340.999040.00063
632 V0.000340.999040.00063
633 F0.000340.999040.00063
634 A0.000340.999030.00063
635 G0.000340.999030.00063
636 L0.000350.999020.00063
637 L0.000590.998780.00063
638 A0.001960.997400.00064
639 W0.003720.995610.00067
640 L0.012290.986940.00077
641 Y0.127260.871520.00122
642 Q0.857100.140820.00208
643 R0.979620.016690.00369
644 T0.993150.003020.00383
645 R0.994980.001140.00388
646 V0.995450.000640.00391
647 T0.995940.000110.00394
648 A0.996010.000040.00396
649 S0.996010.000030.00396
650 Y0.996020.000020.00397
651 R0.996030.000010.00397
652 L0.996030.000010.00397
653 A0.996030.000010.00397
654 A0.996030.000010.00397
655 P0.996030.000010.00397
656 A0.996030.000010.00397
657 G0.996030.000010.00397
658 S0.996030.000010.00397
659 S0.996030.000010.00397
660 K0.996030.000010.00397
661 P0.996030.000010.00397
662 L0.996030.000010.00397
663 P0.996030.000010.00397
664 D0.996030.000010.00397
665 L0.996030.000010.00397
666 P0.996030.000000.00397
667 G0.996030.000000.00397

General Statistics
Length: 667
Number of predicted TMHs: 18
Exp number of AAs in TMHs: 391.6666
Exp number, first 60 AAs: 43.63545
Total prob of N-in: 0.99824
POSSIBLE N-term signal sequence
inside: from residue 1 to 12
TMhelix: from residue 13 to 32
outside: from residue 33 to 36
TMhelix: from residue 37 to 59
inside: from residue 60 to 71
TMhelix: from residue 72 to 94
outside: from residue 95 to 98
TMhelix: from residue 99 to 121
inside: from residue 122 to 158
TMhelix: from residue 159 to 181
outside: from residue 182 to 190
TMhelix: from residue 191 to 213
inside: from residue 214 to 214
TMhelix: from residue 215 to 237
outside: from residue 238 to 264
TMhelix: from residue 265 to 287
inside: from residue 288 to 307
TMhelix: from residue 308 to 330
outside: from residue 331 to 344
TMhelix: from residue 345 to 367
inside: from residue 368 to 378
TMhelix: from residue 379 to 401
outside: from residue 402 to 404
TMhelix: from residue 405 to 427
inside: from residue 428 to 447
TMhelix: from residue 448 to 470
outside: from residue 471 to 473
TMhelix: from residue 474 to 496
inside: from residue 497 to 500
TMhelix: from residue 501 to 523
outside: from residue 524 to 542
TMhelix: from residue 543 to 565
inside: from residue 566 to 585
TMhelix: from residue 586 to 608
outside: from residue 609 to 622
TMhelix: from residue 623 to 641
inside: from residue 642 to 667
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