TransMembrane prediction using Hidden Markov Models for Rv2396




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.036400.000000.9636
2 S0.035390.001010.9636
3 F0.034240.002160.9636
4 L0.034240.004290.96147
5 I0.032650.009510.95784
6 A0.032650.009650.9577
7 S0.031760.010570.95768
8 P0.031760.010570.95768
9 E0.030500.011970.95753
10 A0.030480.126240.84328
11 L0.027630.134860.83751
12 A0.018660.144880.83646
13 A0.007010.159990.833
14 T0.007010.159990.833
15 A0.007010.168510.82449
16 T0.006850.168660.82449
17 Y0.006400.169140.82447
18 L0.006390.169170.82444
19 T0.006330.169240.82442
20 G0.005710.170410.82388
21 I0.005350.170720.82393
22 G0.005420.170400.82418
23 S0.005490.170200.82431
24 A0.005580.170070.82435
25 I0.005780.169170.82505
26 S0.006020.167810.82616
27 A0.007960.165660.82639
28 A0.014570.157670.82776
29 N0.016570.155400.82803
30 A0.019900.151600.8285
31 V0.021420.149680.8289
32 A0.026190.143050.83075
33 A0.127320.039880.8328
34 A0.135840.027640.83652
35 P0.140870.013250.84587
36 T0.143000.003750.85325
37 T0.142990.003520.85349
38 E0.144070.002290.85364
39 I0.137510.008870.85362
40 L0.136990.009230.85378
41 A0.137000.009170.85384
42 A0.137060.009020.85392
43 G0.137620.007910.85446
44 T0.137630.007640.85473
45 D0.137570.007680.85476
46 E0.137480.007760.85475
47 V0.137040.008300.85466
48 S0.136830.008540.85463
49 T0.136470.009070.85447
50 A0.135720.010280.854
51 I0.135330.010690.85398
52 S0.135100.010920.85398
53 A0.134610.011420.85398
54 L0.134480.011560.85396
55 F0.134460.011570.85397
56 G0.134460.011540.854
57 A0.134490.011040.85447
58 H0.134510.010500.85499
59 A0.134530.009690.85579
60 Q0.134540.009140.85631
61 A0.134540.008960.8565
62 Y0.134550.004820.86063
63 Q0.134550.004050.8614
64 A0.134530.004020.86145
65 L0.134500.003910.86159
66 S0.134500.003830.86167
67 A0.134500.003680.86183
68 H0.134480.003570.86195
69 V0.134420.003600.86198
70 A0.134520.003310.86216
71 A0.134540.003000.86246
72 F0.134670.002320.86301
73 H0.135130.000640.86423
74 D0.135130.000380.86449
75 Q0.135020.000480.8645
76 F0.132800.003220.86399
77 V0.132550.003470.86398
78 H0.132490.003530.86398
79 T0.132300.003740.86395
80 L0.132160.003890.86395
81 T0.132110.003950.86394
82 A0.132050.004010.86394
83 G0.132000.004060.86394
84 A0.131960.004090.86395
85 G0.131950.004090.86395
86 S0.131950.004090.86396
87 Y0.131950.004090.86396
88 M0.131950.004070.86399
89 A0.131950.004040.864
90 A0.131960.004010.86404
91 E0.131980.003930.86409
92 A0.131970.003910.86413
93 A0.131960.003900.86414
94 A0.131980.003740.86428
95 A0.131990.003580.86443
96 S0.132040.002740.86523
97 P0.132050.002540.86541
98 L0.132040.002420.86554
99 Q0.132470.000810.86671
100 A0.132410.000780.86682
101 L0.132340.000780.86688
102 Q0.132360.000550.86709
103 L0.132180.000650.86718
104 E0.132140.000630.86723
105 L0.131910.000880.86722
106 L0.131830.000950.86722
107 N0.131830.000930.86724
108 A0.131830.000930.86724
109 I0.131830.000930.86725
110 N0.131840.000910.86725
111 A0.131840.000910.86725
112 P0.131840.000900.86726
113 T0.131840.000900.86726
114 L0.131840.000900.86726
115 A0.131840.000890.86727
116 L0.131840.000880.86728
117 L0.131840.000860.8673
118 G0.131850.000820.86734
119 R0.131870.000770.86737
120 P0.131860.000760.86737
121 L0.131850.000780.86737
122 I0.131850.000780.86737
123 G0.131880.000440.86768
124 D0.131910.000100.86799
125 G0.131890.000200.86791
126 T0.131880.000310.86781
127 D0.131850.000420.86773
128 A0.130620.002090.86729
129 A0.129320.003660.86701
130 P0.129040.004110.86685
131 G0.128680.004580.86674
132 S0.128340.005080.86658
133 G0.127880.005870.86626
134 G0.127640.006320.86605
135 A0.127470.006620.86592
136 G0.127390.006790.86581
137 G0.127370.006860.86576
138 A0.127350.006920.86574
139 G0.127340.006940.86572
140 G0.127330.006960.8657
141 I0.127310.007000.86569
142 L0.127310.007000.86569
143 I0.127310.007000.86569
144 G0.127340.006950.86572
145 N0.127380.006890.86573
146 G0.127430.006780.86579
147 G0.127510.006640.86586
148 T0.127760.006210.86603
149 G0.127910.005900.86619
150 G0.128080.005550.86637
151 A0.128310.004030.86766
152 S0.128600.002330.86908
153 D0.128900.001530.86957
154 L0.128860.001560.86958
155 A0.128390.002120.86949
156 G0.128240.002130.86963
157 T0.128030.002330.86965
158 G0.126970.003380.86965
159 R0.126660.003740.86959
160 G0.122580.008510.86892
161 G0.119730.012100.86818
162 V0.117100.015590.86731
163 G0.115480.017900.86662
164 G0.109530.025110.86536
165 A0.092250.045100.86265
166 G0.079760.059200.86104
167 G0.066100.074280.85963
168 A0.060890.079920.85918
169 G0.056090.084940.85897
170 G0.054780.086470.85875
171 L0.053530.087850.85862
172 F0.053140.088290.85858
173 G0.053090.088350.85857
174 I0.053000.088440.85857
175 G0.052990.088370.85864
176 G0.053000.088280.85873
177 A0.053020.088080.85891
178 G0.053140.086910.85995
179 G0.053290.085780.86094
180 G0.053520.083800.86268
181 C0.053770.081640.86459
182 G0.053870.081050.86507
183 S0.054340.078820.86684
184 A0.054600.077980.86742
185 V0.055100.076600.8683
186 A0.055850.074890.86926
187 I0.057110.066690.8762
188 G0.060150.041720.89813
189 G0.061770.024280.91395
190 D0.063310.009200.9275
191 G0.062470.008500.92903
192 G0.061360.008870.92977
193 A0.060890.009530.92959
194 G0.060190.009460.93035
195 G0.059690.009700.93061
196 A0.059020.010490.93049
197 G0.058800.010880.93033
198 G0.058580.011260.93017
199 V0.058310.011600.93009
200 F0.058200.011650.93015
201 S0.058220.011480.9303
202 G0.058210.011510.93028
203 G0.058230.011570.93019
204 G0.058300.011710.92999
205 A0.058500.011500.93001
206 G0.058670.011400.92993
207 G0.058880.011370.92974
208 A0.059020.011390.92959
209 G0.059340.011080.92957
210 D0.060290.009980.92974
211 A0.059830.011460.9287
212 I0.059270.012660.92807
213 G0.059060.012660.92827
214 G0.059110.011950.92894
215 S0.059080.011200.92973
216 G0.058750.012230.92902
217 G0.058460.013460.92808
218 A0.058490.014010.9275
219 G0.058480.014050.92747
220 G0.058350.014600.92706
221 T0.058090.015280.92663
222 G0.056670.017890.92543
223 G0.056400.018800.9248
224 L0.056250.019370.92438
225 L0.056270.019500.92424
226 G0.056440.019350.92421
227 G0.056740.019080.92418
228 G0.056890.019030.92407
229 G0.057130.018820.92405
230 G0.057460.018500.92404
231 A0.057850.018080.92408
232 G0.058110.017730.92416
233 G0.058260.017490.92424
234 A0.059050.016260.92469
235 G0.059670.015050.92528
236 G0.059940.014420.92564
237 A0.060470.013610.92591
238 G0.061100.012320.92658
239 G0.062260.010010.92772
240 N0.063670.007840.92849
241 G0.064360.007040.92859
242 G0.064910.006370.92872
243 G0.065550.005470.92898
244 A0.066260.004390.92935
245 S0.067870.001390.93074
246 N0.068360.000740.9309
247 S0.068470.000620.9309
248 A0.068460.000700.93084
249 S0.068450.000800.93074
250 I0.068440.000910.93066
251 G0.068580.000780.93065
252 G0.068610.000760.93062
253 D0.068650.000740.9306
254 G0.068330.001340.93033
255 G0.067870.002050.93008
256 S0.067160.003410.92942
257 G0.064460.009640.9259
258 G0.063290.016020.92068
259 A0.062330.024920.91275
260 G0.061660.027260.91108
261 G0.061260.029600.90914
262 M0.060920.032560.90652
263 L0.060340.034160.9055
264 Y0.060200.034730.90507
265 G0.060150.034920.90492
266 A0.060140.034970.90489
267 G0.060120.034980.9049
268 G0.060090.035020.90489
269 V0.060060.035040.90489
270 G0.060070.035000.90494
271 G0.060140.034860.905
272 N0.060260.034690.90506
273 G0.060320.034620.90506
274 G0.060360.034550.90508
275 A0.060420.034470.9051
276 A0.060530.034330.90514
277 V0.060830.033750.90542
278 A0.061120.033000.90589
279 I0.062190.031150.90666
280 G0.067300.022850.90984
281 G0.073980.014550.91147
282 D0.083820.003490.91269
283 G0.084160.002950.91289
284 G0.084540.002450.91301
285 A0.085210.001680.91311
286 G0.085680.000870.91345
287 G0.085930.000490.91358
288 R0.086110.000270.91363
289 A0.086130.000240.91363
290 G0.086140.000220.91364
291 A0.086150.000180.91366
292 I0.086170.000120.9137
293 G0.086200.000030.91377
294 N0.086200.000020.91378
295 G0.086200.000010.91378
296 G0.086210.000010.91378
297 D0.086210.000000.91378
298 G0.086210.000000.91378
299 G0.086210.000000.91378
300 N0.086210.000000.91378
301 G0.086210.000000.91378
302 G0.086210.000000.91378
303 T0.086210.000000.91378
304 S0.086210.000000.91378
305 N0.086210.000000.91378
306 T0.086210.000000.91378
307 P0.086210.000000.91378
308 G0.086210.000000.91378
309 G0.086210.000000.91378
310 S0.086210.000000.91378
311 G0.086210.000000.91378
312 G0.086210.000000.91378
313 D0.086210.000000.91378
314 G0.086210.000000.91378
315 G0.086210.000000.91378
316 N0.086210.000010.91378
317 G0.086210.000010.91378
318 G0.086210.000010.91378
319 N0.086210.000010.91378
320 A0.086200.000020.91378
321 G0.086180.000040.91378
322 L0.086160.000070.91378
323 I0.086150.000080.91378
324 G0.086140.000090.91378
325 N0.086140.000090.91378
326 G0.086120.000110.91378
327 G0.086100.000130.91376
328 N0.086070.000170.91376
329 G0.085820.000550.91364
330 G0.085550.001000.91344
331 N0.085320.001510.91316
332 A0.083900.006570.90953
333 E0.083290.008080.90863
334 I0.078300.021160.90054
335 V0.075810.025190.899
336 I0.075480.025940.89857
337 S0.075340.026210.89846
338 G0.075120.026640.89825
339 G0.075080.026740.89818
340 S0.075060.026800.89814
341 V0.075040.026890.89808
342 A0.075040.026900.89807
343 G0.075040.026900.89806
344 T0.075040.026880.89809
345 G0.075040.026850.89811
346 G0.075040.026830.89812
347 N0.075040.026810.89816
348 G0.075040.026800.89816
349 G0.075040.026780.89818
350 L0.075050.026750.8982
351 L0.075080.026660.89826
352 L0.075350.025970.89868
353 G0.075720.024880.89941
354 F0.076540.022900.90056
355 N0.081350.015230.90342
356 G0.082660.013210.90413
357 T0.089370.003260.90737
358 N0.090220.000910.90887
359 G0.090450.000540.90902
360 L0.090550.000370.90908
361 P0.090770.000000.90923

General Statistics
Length: 361
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 8.44252999999999
Exp number, first 60 AAs: 4.04412
Total prob of N-in: 0.03640
outside: from residue 1 to 361
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