TransMembrane prediction using Hidden Markov Models for Rv2399c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.990470.000000.00953
2 T0.990470.000000.00953
3 E0.990470.000000.00953
4 S0.990470.000000.00953
5 L0.990470.000000.00953
6 V0.990470.000000.00953
7 G0.990470.000000.00953
8 E0.990470.000000.00953
9 R0.990470.000000.00953
10 R0.990470.000000.00953
11 A0.990470.000000.00953
12 P0.990470.000000.00953
13 Q0.990470.000000.00953
14 F0.990470.000000.00953
15 R0.990470.000010.00952
16 A0.990470.000020.00952
17 R0.990460.000020.00952
18 L0.990460.000030.00951
19 S0.990440.000050.00951
20 G0.990260.000260.00949
21 P0.990110.000410.00949
22 A0.990060.000450.00949
23 G0.989980.000540.00948
24 P0.988680.001870.00946
25 P0.978900.011690.00941
26 S0.965650.025270.00907
27 V0.915190.077390.00742
28 R0.912010.080730.00726
29 V0.850230.143340.00643
30 G0.805770.188270.00597
31 M0.674880.322090.00303
32 A0.459360.538790.00185
33 V0.315930.683050.00102
34 V0.114530.884940.00053
35 W0.094240.905290.00048
36 L0.082610.916930.00046
37 S0.075050.924500.00045
38 V0.013650.985970.00038
39 I0.001180.998630.0002
40 V0.000530.999270.00019
41 L0.000090.999720.00019
42 L0.000050.999750.00021
43 P0.000060.999620.00031
44 L0.000030.999590.00037
45 A0.000040.999460.00049
46 A0.000040.999200.00076
47 I0.000080.997800.00213
48 V0.000160.987930.0119
49 W0.000890.971860.02725
50 Q0.003000.895150.10184
51 A0.003150.873190.12367
52 A0.003590.769200.2272
53 G0.003750.637800.35846
54 G0.006270.453000.54073
55 G0.007000.325710.66729
56 W0.007550.279740.71271
57 R0.008030.097960.89401
58 A0.008000.095060.89695
59 F0.007990.091900.9001
60 W0.008010.087810.90419
61 L0.008100.025270.96664
62 A0.008400.002400.9892
63 V0.008420.002070.98951
64 S0.008490.001110.99041
65 S0.008500.000960.99054
66 H0.008500.000970.99053
67 A0.008500.001150.99035
68 A0.008500.001280.99022
69 M0.008500.002030.98947
70 E0.008500.002070.98943
71 S0.008460.004810.98673
72 F0.008290.013290.97842
73 R0.007670.026000.96632
74 V0.004130.080610.91526
75 T0.002850.292200.70496
76 L0.000600.927110.0723
77 T0.000370.953410.04623
78 I0.000120.978020.02186
79 S0.000080.988810.01111
80 T0.000060.994200.00574
81 A0.000030.999610.00036
95 W0.008830.991050.00012
96 V0.017540.981050.00141
97 L0.037020.958330.00465
98 V0.279910.713890.00619
99 R0.980290.011450.00826
100 D0.991230.000290.00848
101 D0.991430.000050.00852
102 F0.991340.000140.00852
103 A0.991290.000190.00852
104 G0.991200.000280.00852
105 K0.990890.000590.00852
106 R0.989970.001540.00848
107 I0.945740.045890.00837
108 V0.934430.057470.0081
109 D0.921710.070310.00797
110 A0.166610.828290.0051
111 I0.025540.972820.00163
112 I0.021660.977160.00118
113 D0.021200.977940.00086
114 L0.005590.993710.00069
115 P0.002520.996860.00061
116 F0.001180.998510.0003
117 A0.000740.999000.00026
118 L0.000430.999360.00021
119 P0.000380.999420.00021
120 T0.000360.999440.0002
121 I0.000340.999460.0002
122 V0.000340.999460.0002
123 A0.000340.999450.00021
124 S0.000340.999430.00023
125 L0.000340.999220.00044
126 V0.000340.999120.00054
127 M0.000360.997990.00165
128 L0.000370.993600.00603
129 A0.000430.985250.01433
130 L0.000500.874650.12485
131 Y0.001100.820520.17837
132 G0.001540.731960.2665
133 N0.005640.060650.93371
134 N0.007850.005010.98714
135 S0.008260.002680.98906
136 P0.008410.003210.98837
137 V0.007880.010150.98196
138 G0.007520.017410.97506
139 L0.005120.119620.87526
140 H0.004940.128990.86608
141 F0.004820.190200.80498
142 Q0.004780.442790.55243
143 H0.004550.488980.50647
144 T0.003850.545730.45042
145 A0.002180.617460.38035
146 T0.001390.645960.35264
147 G0.000910.979040.02005
148 V0.000850.986940.01222
149 G0.000830.989070.0101
150 V0.000810.991670.00752
151 A0.000800.992110.00709
152 L0.000800.993350.00585
153 A0.000800.993370.00583
154 F0.000820.993370.00581
155 V0.000970.993210.00582
156 T0.001870.992290.00583
157 L0.002470.991650.00589
158 P0.004110.989930.00596
159 F0.005930.988030.00604
160 V0.014770.978680.00655
161 V0.033990.958940.00707
162 R0.242900.747370.00972
163 A0.257200.732650.01015
164 V0.343350.645960.01069
165 Q0.640810.347280.01191
166 P0.667710.319840.01245
167 V0.679460.307740.0128
168 L0.682580.304410.01301
169 L0.705300.281480.01322
170 E0.981320.005030.01366
171 I0.983630.002710.01366
172 D0.986150.000180.01367
173 R0.986320.000010.01367
174 E0.986320.000020.01367
175 T0.986300.000040.01367
176 E0.985920.000420.01366
177 E0.982560.003790.01365
178 A0.976980.009410.01361
179 A0.975280.011170.01355
180 A0.970970.015500.01353
181 S0.919970.066550.01348
182 L0.878980.107570.01345
183 G0.876780.109790.01343
184 A0.867450.119150.0134
185 N0.857940.128660.01339
186 G0.847380.139280.01334
187 A0.839790.146940.01328
188 K0.815620.171320.01306
189 I0.430640.559100.01026
190 F0.349930.639980.0101
191 T0.332110.657890.01
192 S0.248090.742030.00988
193 V0.095890.894390.00972
194 V0.075570.914720.00971
195 L0.071960.918160.00988
196 P0.071360.917850.0108
197 S0.070260.918380.01135
198 L0.068620.919570.01181
199 T0.068460.917710.01383
200 P0.067890.913110.01901
201 A0.063850.911150.025
202 L0.061470.908340.03019
203 L0.060610.901510.03788
204 S0.060120.848400.09148
205 G0.057870.821620.1205
206 A0.056460.820670.12287
207 G0.053090.816410.13049
208 L0.039780.819590.14063
209 A0.037430.783940.17863
210 F0.035950.742250.2218
211 S0.036450.638990.32456
212 R0.038280.323450.63827
213 A0.036790.287520.67569
214 I0.036330.273680.68998
215 G0.036240.184510.77925
216 E0.035880.053470.91065
217 F0.034190.047420.91839
218 G0.032720.048310.91897
219 S0.032450.048390.91917
220 V0.032250.048460.91929
221 V0.032210.047740.92004
222 L0.032200.047410.92039
223 I0.032210.046770.92102
224 G0.032240.042380.92539
225 G0.032260.039830.92792
226 A0.032290.038140.92956
227 V0.032340.036090.93157
228 P0.032960.023920.94311
229 G0.033890.019470.94663
230 K0.036160.009770.95407
231 T0.037150.006560.95629
232 E0.037360.005710.95693
233 V0.037380.005660.95696
234 S0.037420.005510.95708
235 S0.037450.005070.95748
236 Q0.037510.003940.95854
237 W0.037550.003600.95885
238 I0.037600.003420.95898
239 R0.037800.002490.95971
240 T0.037820.001370.96081
241 L0.037830.000230.96194
242 I0.037840.000090.96207
243 E0.037880.000010.96212
244 N0.037880.000000.96211
245 D0.037880.000030.96209
246 D0.037850.002570.95957
247 R0.037660.009890.95246
248 T0.034680.057610.90771
249 G0.018310.308780.6729
250 A0.011220.712450.27633
251 A0.004030.954130.04184
252 A0.002710.973970.02331
253 I0.001570.989400.00903
254 S0.000570.994900.00453
255 V0.000150.999020.00084
267 I0.001080.998790.00013
268 L0.007390.991870.00074
269 R0.069730.927670.0026
270 V0.077890.919100.003
271 V0.111570.882890.00554
272 G0.333080.645830.0211
273 A0.726900.244530.02857
274 R0.959570.003500.03693
275 A0.960670.002190.03714
276 A0.961630.000900.03746
277 K0.962080.000070.03786
278 R0.962120.000000.03788
279 E0.962120.000000.03788
280 E0.962120.000000.03788
281 M0.962120.000000.03788
282 A0.962120.000000.03788
283 A0.962120.000000.03788

General Statistics
Length: 283
Number of predicted TMHs: 6
Exp number of AAs in TMHs: 133.59012
Exp number, first 60 AAs: 22.25126
Total prob of N-in: 0.99047
POSSIBLE N-term signal sequence
inside: from residue 1 to 33
TMhelix: from residue 34 to 56
outside: from residue 57 to 75
TMhelix: from residue 76 to 98
inside: from residue 99 to 109
TMhelix: from residue 110 to 132
outside: from residue 133 to 146
TMhelix: from residue 147 to 169
inside: from residue 170 to 188
TMhelix: from residue 189 to 211
outside: from residue 212 to 249
TMhelix: from residue 250 to 272
inside: from residue 273 to 283
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