TransMembrane prediction using Hidden Markov Models for Rv2398c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.991600.000000.0084
2 T0.991600.000000.0084
3 S0.991600.000000.0084
4 L0.991600.000000.0084
5 P0.991570.000030.0084
6 A0.991570.000030.00839
7 A0.990570.001030.00839
8 R0.990570.001040.00839
9 Y0.900240.091520.00824
10 L0.899840.098520.00164
11 V0.895820.102600.00158
12 R0.874700.123730.00157
13 S0.007330.991540.00113
14 V0.007160.991710.00113
28 A0.000010.999840.00015
29 L0.000010.999320.00067
30 I0.000040.997990.00197
31 L0.000080.982920.01699
32 W0.000650.893420.10593
33 R0.007740.763020.22925
34 T0.007820.750560.24162
35 F0.007830.725880.26629
36 E0.008160.002810.98903
37 P0.006770.002510.99072
38 G0.006340.002960.99071
39 F0.003940.006270.9898
40 G0.003920.006680.98939
41 Q0.003870.008210.98792
42 F0.003790.012330.98388
43 Y0.003760.012820.98342
44 A0.003600.013870.98253
45 W0.003480.022460.97407
46 I0.003470.028060.96847
47 S0.003470.031210.96531
48 T0.003470.034620.96191
49 P0.003450.037410.95914
50 A0.003440.293600.70296
51 A0.003370.322650.67399
52 I0.002450.352430.64512
53 S0.001910.353970.64411
54 A0.001850.357870.64027
55 L0.001740.375670.6226
56 N0.001680.375210.62311
57 L0.001240.422040.57673
58 S0.001680.510940.48739
59 L0.000360.936520.06312
60 L0.000400.975610.02398
61 V0.000440.988710.01084
62 V0.000380.995080.00454
63 A0.000350.998330.00132
64 I0.000320.999510.00017
67 P0.001000.998790.00021
68 L0.001630.998130.00023
69 N0.002980.996780.00024
70 V0.003790.995980.00023
71 I0.004770.995000.00023
72 F0.006540.993190.00027
73 G0.157970.841720.00032
74 V0.189750.809840.00041
75 T0.221910.776950.00114
76 T0.223960.774490.00155
77 A0.228990.769390.00161
78 L0.238450.759770.00178
79 V0.247190.750760.00205
80 L0.298970.698180.00285
81 A0.435420.560800.00378
82 R0.956550.037750.0057
83 N0.987250.006800.00595
84 R0.991690.002240.00607
85 F0.991990.001880.00613
86 R0.992980.000640.00638
87 G0.992650.000930.00643
88 K0.991490.002070.00643
89 G0.974190.019450.00636
90 V0.946600.047120.00627
91 L0.937710.056080.00621
92 Q0.898610.095380.00601
93 A0.654080.340330.00558
94 I0.332410.662850.00474
95 I0.303340.692080.00458
96 D0.301760.693780.00447
97 L0.242010.753730.00426
98 P0.225430.770560.00401
99 F0.172420.824140.00345
100 A0.103000.894920.00208
101 V0.016950.982580.00046
102 S0.005480.994140.00038
103 P0.003630.996080.00029
104 V0.000920.998980.0001
108 V0.000280.999440.00028
109 S0.000280.999240.00047
110 L0.000280.998910.0008
111 I0.000280.998550.00117
112 L0.000310.983070.01663
113 L0.000350.940730.05892
114 W0.000400.919400.0802
115 G0.000700.788180.21112
116 S0.001180.649680.34914
117 A0.001930.347460.65061
118 G0.002070.290990.70693
119 A0.002290.275140.72258
120 L0.002430.231820.76575
121 G0.002800.221860.77533
122 F0.003140.170220.82664
123 V0.004750.094570.90068
124 E0.006540.010890.98258
125 Q0.006700.014180.97912
126 D0.006680.020530.97279
127 L0.005490.110460.88406
128 G0.004590.186660.80875
129 F0.002910.398990.5981
130 K0.001980.479700.51833
131 I0.001290.822260.17646
132 I0.000780.962840.03637
133 F0.000700.985380.01392
134 G0.000680.988980.01034
135 L0.000650.991210.00813
136 P0.000650.991390.00796
137 G0.000650.991630.00771
138 I0.000660.991720.00762
139 V0.000660.991720.00762
140 L0.000720.991670.00762
141 G0.000870.991520.00762
142 S0.001360.991020.00762
143 M0.003140.989240.00762
144 F0.004090.988290.00762
145 V0.015660.976650.00768
146 T0.038800.953370.00783
147 C0.052320.939490.00819
148 P0.065560.926140.0083
149 F0.078810.912830.00836
150 V0.164010.826890.00911
151 V0.347660.642330.01001
152 R0.828110.159940.01195
153 E0.901010.085830.01315
154 V0.956010.030600.01339
155 E0.984510.001820.01367
156 P0.986060.000270.01368
157 V0.986180.000140.01368
158 L0.986230.000090.01368
159 H0.986270.000050.01368
160 E0.986300.000020.01368
161 L0.986300.000020.01368
162 G0.986310.000020.01368
163 T0.986310.000020.01368
164 D0.986310.000020.01368
165 Q0.986300.000030.01367
166 E0.986290.000070.01364
167 Q0.986260.000150.01358
168 A0.986100.000370.01353
169 A0.986070.000400.01353
170 A0.986000.000480.01352
171 T0.985910.000580.01352
172 L0.985640.000850.01352
173 G0.985580.000910.01351
174 S0.985530.000970.0135
175 G0.985460.001070.01347
176 W0.985400.001250.01335
177 W0.985340.001370.01329
178 Q0.984950.002770.01228
179 T0.979770.009450.01079
180 F0.977120.012720.01016
181 W0.976270.013850.00988
182 R0.976000.014240.00975
183 I0.972840.017840.00932
184 T0.972400.018300.0093
185 L0.963480.027310.00921
186 P0.954840.035910.00924
187 S0.939450.051400.00915
188 I0.905510.085500.00899
189 R0.895300.095730.00896
190 W0.574310.417280.00841
191 G0.350180.641770.00804
192 L0.255780.736430.00779
193 T0.241540.750670.0078
194 Y0.225490.766730.00778
195 G0.221400.771420.00719
196 I0.215020.778120.00686
197 V0.212800.780340.00686
198 L0.202030.790890.00708
199 T0.201960.790220.00782
200 V0.201620.790150.00824
201 A0.203010.787450.00954
202 R0.203960.780640.0154
203 T0.198700.783130.01818
204 L0.190820.788710.02047
205 G0.190010.779100.03089
206 E0.185750.763150.05109
207 Y0.166440.780740.05282
208 G0.164040.781100.05486
209 A0.160830.783190.05598
210 V0.159250.776230.06452
211 I0.158830.751790.08938
212 I0.158730.726190.11508
213 V0.159180.428660.41215
214 S0.159700.185590.65471
215 S0.160020.102220.73775
216 N0.160160.079360.76047
217 L0.160230.074070.7657
218 P0.161110.069690.7692
219 G0.161460.063510.77502
220 T0.161560.060010.77843
221 S0.161590.049990.78841
222 Q0.161600.049380.78902
223 T0.161600.049070.78933
224 L0.161600.047590.79081
225 T0.161600.044830.79357
226 L0.161630.039710.79866
227 L0.161910.032130.80595
228 V0.162430.030500.80707
229 S0.163720.018400.81788
230 D0.165180.000580.83425
231 R0.165260.000210.83453
232 Y0.165300.000630.83406
233 H0.165340.002160.8325
234 R0.165250.009920.82483
235 G0.162440.148220.68934
236 A0.161450.176550.662
237 E0.158830.196820.64434
238 Y0.097320.542420.36026
239 G0.030480.867800.10173
240 A0.012470.952450.03508
241 Y0.003020.980970.01601
242 A0.000810.995730.00346
243 L0.000210.998230.00157
244 S0.000120.999400.00048
245 T0.000110.999670.00022
255 L0.000730.999170.0001
256 I0.008180.991470.00035
257 V0.033210.965210.00157
258 Q0.403310.585150.01154
259 M0.434970.549490.01554
260 V0.449720.527780.0225
261 L0.570690.345500.08381
262 D0.821870.023370.15475
263 A0.829290.008160.16254
264 R0.834110.000720.16518
265 R0.834610.000090.1653
266 A0.834640.000050.16531
267 R0.834660.000020.16532
268 A0.834670.000010.16532
269 V0.834680.000000.16532
270 S0.834680.000000.16532
271 E0.834680.000000.16532
272 G0.834680.000000.16532

General Statistics
Length: 272
Number of predicted TMHs: 6
Exp number of AAs in TMHs: 131.81389
Exp number, first 60 AAs: 28.00407
Total prob of N-in: 0.99160
POSSIBLE N-term signal sequence
inside: from residue 1 to 12
TMhelix: from residue 13 to 35
outside: from residue 36 to 58
TMhelix: from residue 59 to 81
inside: from residue 82 to 93
TMhelix: from residue 94 to 116
outside: from residue 117 to 130
TMhelix: from residue 131 to 151
inside: from residue 152 to 189
TMhelix: from residue 190 to 212
outside: from residue 213 to 238
TMhelix: from residue 239 to 261
inside: from residue 262 to 272
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