TransMembrane prediction using Hidden Markov Models for Rv2192c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.006530.000000.99346
2 A0.006530.000000.99346
3 L0.006530.000000.99346
4 S0.006530.000000.99346
5 A0.006530.000000.99346
6 E0.006530.000000.99346
7 G0.006530.000000.99346
8 S0.006530.000000.99346
9 S0.006530.000000.99346
10 G0.006530.000000.99346
11 G0.006530.000000.99346
12 S0.006530.000000.99346
13 R0.006530.000000.99346
14 G0.006530.000000.99346
15 G0.006530.000000.99346
16 S0.006530.000000.99346
17 P0.006530.000000.99346
18 K0.006530.000000.99346
19 A0.006530.000000.99346
20 E0.006530.000000.99346
21 A0.006530.000000.99346
22 A0.006530.000000.99346
23 S0.006530.000000.99346
24 V0.006530.000000.99346
25 P0.006530.000000.99346
26 S0.006530.000000.99346
27 W0.006530.000000.99346
28 P0.006530.000000.99346
29 Q0.006530.000000.99346
30 I0.006530.000000.99346
31 L0.006530.000000.99346
32 G0.006530.000000.99346
33 R0.006530.000000.99346
34 L0.006530.000000.99346
35 T0.006530.000000.99346
36 D0.006530.000000.99346
37 N0.006530.000000.99346
38 R0.006530.000000.99346
39 D0.006530.000000.99346
40 L0.006530.000000.99346
41 A0.006530.000000.99346
42 R0.006530.000000.99346
43 G0.006530.000000.99346
44 Q0.006530.000000.99346
45 A0.006530.000010.99345
46 A0.006530.000020.99345
47 W0.006530.000030.99344
48 A0.006530.000040.99344
49 M0.006530.000040.99344
50 D0.006530.000040.99344
51 Q0.006520.000040.99343
52 I0.006510.000060.99343
53 M0.006510.000060.99343
54 T0.006480.000090.99343
55 G0.006470.000100.99343
56 N0.006470.000100.99343
57 A0.006460.000110.99343
58 R0.006460.000110.99343
59 P0.006450.000130.99342
60 A0.006440.000130.99342
61 Q0.006440.000140.99342
62 I0.006430.000150.99342
63 A0.006420.000150.99342
64 A0.006420.000150.99342
65 F0.006420.000150.99342
66 A0.006420.000150.99342
67 V0.006420.000150.99342
68 A0.006430.000140.99342
69 M0.006440.000130.99343
70 T0.006450.000110.99344
71 M0.006450.000110.99344
72 K0.006460.000080.99346
73 A0.006460.000080.99346
74 P0.006460.000080.99346
75 T0.006460.000070.99347
76 A0.006460.000070.99348
77 D0.006460.000030.9935
78 E0.006460.000030.99352
79 V0.006460.000030.99352
80 G0.006460.000020.99352
81 E0.006460.000020.99352
82 L0.006460.000020.99352
83 A0.006460.000020.99352
84 G0.006460.000020.99352
85 V0.006460.000010.99353
86 M0.006460.000010.99354
87 L0.006460.000000.99354
88 S0.006460.000000.99354
89 H0.006460.000000.99354
90 A0.006460.000000.99354
91 H0.006460.000000.99354
92 P0.006460.000000.99354
93 L0.006460.000000.99354
94 P0.006460.000000.99354
95 A0.006460.000000.99354
96 D0.006460.000000.99354
97 T0.006460.000000.99354
98 V0.006460.000000.99354
99 P0.006460.000000.99354
100 D0.006460.000000.99354
101 D0.006460.000000.99354
102 A0.006460.000000.99354
103 V0.006460.000000.99354
104 D0.006460.000000.99354
105 V0.006450.000020.99353
106 V0.006450.000040.99351
107 G0.006450.000060.99348
108 T0.006450.000100.99346
109 G0.006440.000190.99336
110 G0.006430.000250.99331
111 D0.006420.000400.99318
112 G0.005260.004930.98982
113 V0.004910.005960.98913
114 N0.004760.006340.9889
115 T0.004150.008380.98747
116 V0.003750.009490.98676
117 N0.003660.009920.98642
118 L0.003630.010170.9862
119 S0.003620.010230.98614
120 T0.003620.010290.9861
121 M0.003620.010300.98608
122 A0.003620.010310.98608
123 A0.003610.010310.98608
124 I0.003610.010310.98608
125 V0.003610.010310.98608
126 V0.003620.010310.98608
127 A0.003620.010310.98608
128 A0.003630.010290.98608
129 A0.003640.010280.98609
130 G0.003690.010210.9861
131 V0.003770.010100.98613
132 P0.004100.009630.98626
133 V0.004300.009340.98637
134 V0.004940.008430.98662
135 K0.010310.000990.98869
136 H0.010680.000520.9888
137 G0.010750.000410.98884
138 N0.010960.000150.98889
139 R0.011050.000030.98891
140 A0.011060.000030.98891
141 A0.011070.000010.98892
142 S0.011070.000010.98892
143 S0.011070.000010.98892
144 L0.011070.000000.98892
145 S0.011070.000000.98892
146 G0.011070.000000.98892
147 G0.011070.000000.98892
148 A0.011070.000000.98892
149 D0.011070.000000.98892
150 T0.011070.000000.98892
151 L0.011070.000000.98892
152 E0.011070.000000.98892
153 A0.011070.000000.98892
154 L0.011070.000000.98892
155 G0.011070.000000.98892
156 V0.011070.000000.98892
157 R0.011070.000000.98892
158 I0.011070.000000.98892
159 D0.011070.000000.98892
160 L0.011070.000010.98892
161 G0.011070.000010.98892
162 P0.011070.000010.98892
163 D0.011070.000030.9889
164 L0.011060.000110.98884
165 V0.011050.000130.98882
166 A0.011050.000140.98881
167 R0.011050.000140.98881
168 S0.011050.000150.9888
169 L0.011050.000150.9888
170 A0.011050.000150.98879
171 E0.011050.000150.98879
172 V0.011050.000150.98879
173 G0.011050.000150.98879
174 I0.011050.000150.98879
175 G0.011050.000150.98879
176 F0.011050.000150.98879
177 C0.011050.000150.9888
178 F0.011050.000150.9888
179 A0.011050.000150.9888
180 P0.011060.000150.9888
181 R0.011060.000140.9888
182 F0.011060.000140.9888
183 H0.011080.000110.98881
184 P0.011110.000080.98882
185 S0.011130.000050.98882
186 Y0.011160.000020.98882
187 R0.011170.000000.98883
188 H0.011180.000000.98883
189 A0.011170.000000.98882
190 A0.011170.000020.98882
191 A0.011160.000030.98882
192 V0.011160.000030.98882
193 R0.011160.000030.98882
194 R0.011160.000030.98882
195 E0.011150.000030.98882
196 I0.011150.000040.98882
197 G0.011140.000040.98882
198 V0.011140.000040.98882
199 P0.011140.000040.98882
200 T0.011140.000040.98882
201 V0.011140.000040.98882
202 F0.011140.000040.98882
203 N0.011140.000040.98882
204 L0.011140.000040.98882
205 L0.011140.000040.98882
206 G0.011140.000040.98882
207 P0.011150.000040.98882
208 L0.011150.000040.98882
209 T0.011150.000030.98882
210 N0.011150.000030.98883
211 P0.011150.000040.98881
212 A0.011150.000150.98871
213 R0.011150.000200.98865
214 P0.011110.000740.98815
215 R0.011080.000950.98797
216 A0.010910.001890.9872
217 G0.010760.002130.98711
218 L0.010680.002270.98705
219 I0.010650.002320.98703
220 G0.010650.002320.98703
221 C0.010650.002320.98703
222 A0.010650.002320.98702
223 F0.010650.002320.98702
224 A0.010650.002320.98702
225 D0.010650.002320.98702
226 L0.010650.002320.98702
227 A0.010650.002320.98702
228 E0.010650.002320.98702
229 V0.010650.002320.98702
230 M0.010650.002320.98702
231 A0.010660.002320.98702
232 G0.010660.002310.98702
233 V0.010670.002300.98703
234 F0.010730.002220.98705
235 A0.010970.001920.98711
236 A0.011590.001170.98724
237 R0.012330.000190.98747
238 R0.012430.000070.9875
239 S0.012460.000020.98751
240 S0.012460.000010.98753
241 V0.012460.000010.98753
242 L0.012470.000000.98753
243 V0.012470.000000.98753
244 V0.012470.000000.98753
245 H0.012470.000000.98753
246 G0.012470.000000.98753
247 D0.012470.000000.98753
248 D0.012470.000000.98753
249 G0.012470.000000.98753
250 L0.012470.000000.98753
251 D0.012470.000000.98753
252 E0.012470.000000.98753
253 L0.012470.000000.98753
254 T0.012470.000000.98753
255 T0.012470.000000.98753
256 T0.012470.000000.98753
257 T0.012470.000000.98753
258 T0.012470.000000.98753
259 S0.012470.000000.98753
260 T0.012470.000000.98753
261 I0.012470.000000.98753
262 W0.012470.000000.98753
263 R0.012470.000000.98753
264 V0.012470.000000.98753
265 A0.012470.000000.98753
266 A0.012470.000000.98753
267 G0.012470.000000.98753
268 S0.012470.000000.98753
269 V0.012470.000000.98753
270 D0.012470.000000.98753
271 K0.012470.000000.98753
272 L0.012470.000000.98753
273 T0.012470.000000.98753
274 F0.012470.000000.98753
275 D0.012470.000000.98753
276 P0.012470.000000.98753
277 A0.012470.000000.98753
278 G0.012470.000000.98753
279 F0.012470.000000.98753
280 G0.012470.000000.98753
281 F0.012470.000000.98753
282 A0.012470.000000.98753
283 R0.012470.000000.98753
284 A0.012470.000000.98753
285 Q0.012470.000000.98753
286 L0.012470.000000.98753
287 D0.012470.000000.98753
288 Q0.012470.000000.98753
289 L0.012470.000010.98753
290 A0.012470.000010.98753
291 G0.012470.000010.98753
292 G0.012470.000010.98753
293 D0.012470.000010.98753
294 A0.012470.000010.98753
295 Q0.012470.000010.98753
296 A0.012470.000010.98753
297 N0.012470.000010.98753
298 A0.012470.000010.98753
299 A0.012470.000010.98753
300 A0.012470.000010.98753
301 V0.012470.000010.98753
302 R0.012470.000010.98753
303 A0.012470.000010.98753
304 V0.012470.000010.98753
305 L0.012470.000010.98752
306 G0.012470.000010.98752
307 G0.012470.000010.98752
308 A0.012470.000010.98752
309 R0.012470.000020.98752
310 G0.012470.000050.98749
311 P0.012460.000090.98745
312 V0.012460.000150.9874
313 R0.012460.000160.98739
314 D0.012450.000190.98736
315 A0.012340.000690.98697
316 V0.012320.000730.98694
317 V0.012310.000750.98693
318 L0.012310.000760.98693
319 N0.012310.000760.98693
320 A0.012310.000760.98692
321 A0.012310.000770.98692
322 G0.012310.000770.98692
323 A0.012310.000770.98692
324 I0.012310.000770.98692
325 V0.012310.000770.98692
326 A0.012310.000760.98692
327 H0.012310.000760.98692
328 A0.012310.000760.98692
329 G0.012320.000750.98692
330 L0.012340.000730.98694
331 S0.012400.000640.98695
332 S0.012480.000560.98697
333 R0.012540.000480.98698
334 A0.012540.000470.98699
335 E0.012560.000430.98701
336 W0.012560.000430.98701
337 L0.012580.000400.98702
338 P0.012900.000020.98709
339 A0.012900.000010.98709
340 W0.012900.000000.98709
341 E0.012910.000000.98709
342 E0.012910.000000.98709
343 G0.012910.000000.98709
344 L0.012910.000000.98709
345 R0.012910.000000.98709
346 R0.012910.000000.98709
347 A0.012910.000010.98708
348 S0.012910.000010.98708
349 A0.012910.000010.98708
350 A0.012910.000020.98708
351 I0.012910.000020.98708
352 D0.012910.000020.98708
353 T0.012910.000020.98708
354 G0.012910.000020.98708
355 A0.012910.000020.98708
356 A0.012910.000020.98708
357 E0.012910.000020.98708
358 Q0.012910.000020.98708
359 L0.012910.000020.98708
360 L0.012910.000020.98708
361 A0.012910.000020.98708
362 R0.012910.000010.98708
363 W0.012910.000010.98708
364 V0.012910.000010.98708
365 R0.012910.000010.98708
366 F0.012910.000010.98708
367 G0.012920.000000.98708
368 R0.012920.000000.98708
369 Q0.012920.000000.98708
370 I0.012920.000000.98708

General Statistics
Length: 370
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.291850000000001
Exp number, first 60 AAs: 0.00111
Total prob of N-in: 0.00653
outside: from residue 1 to 370
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