TransMembrane prediction using Hidden Markov Models for Rv2397c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.031930.000000.96807
2 T0.031930.000000.96807
3 Y0.031930.000000.96807
4 A0.031930.000000.96807
5 I0.031930.000000.96807
6 V0.031930.000000.96807
7 V0.031930.000000.96807
8 A0.031930.000000.96807
9 D0.031930.000000.96807
10 A0.031930.000000.96807
11 T0.031930.000000.96807
12 K0.031930.000010.96807
13 R0.031610.000320.96807
14 Y0.031610.000320.96807
15 G0.031610.000350.96805
16 D0.031510.000440.96805
17 F0.029560.002410.96804
18 V0.029490.002520.96799
19 A0.029090.002930.96798
20 L0.028230.004000.96778
21 D0.028050.004170.96778
22 H0.027910.004370.96772
23 V0.027760.004580.96766
24 D0.027750.004600.96765
25 F0.027700.004840.96746
26 V0.027700.004850.96745
27 V0.027700.004860.96745
28 P0.027700.004860.96745
29 T0.027700.004860.96744
30 G0.027690.004860.96744
31 S0.027690.004860.96745
32 L0.027690.004850.96745
33 T0.027690.004830.96748
34 A0.027690.004820.96749
35 L0.027690.004760.96755
36 L0.027690.004460.96785
37 G0.027700.004000.9683
38 P0.027730.003580.9687
39 S0.027740.003120.96914
40 G0.027800.001770.97042
41 S0.027880.001420.9707
42 G0.027930.001050.97102
43 K0.028180.000190.97164
44 S0.028180.000170.97165
45 T0.028190.000150.97165
46 L0.028200.000140.97166
47 L0.028200.000130.97166
48 R0.028310.000020.97167
49 T0.028310.000010.97167
50 I0.028310.000010.97167
51 A0.028320.000010.97168
52 G0.028320.000010.97168
53 L0.028320.000000.97168
54 D0.028320.000000.97168
55 Q0.028320.000000.97168
56 P0.028320.000000.97168
57 D0.028320.000000.97168
58 T0.028320.000000.97168
59 G0.028320.000000.97168
60 T0.028320.000000.97168
61 I0.028320.000000.97168
62 T0.028320.000000.97168
63 I0.028320.000000.97168
64 N0.028320.000000.97168
65 G0.028320.000000.97168
66 R0.028320.000000.97168
67 D0.028320.000000.97168
68 V0.028320.000000.97168
69 T0.028320.000000.97168
70 R0.028320.000000.97168
71 V0.028320.000000.97168
72 P0.028320.000000.97168
73 P0.028320.000000.97168
74 Q0.028320.000000.97168
75 R0.028310.000010.97168
76 R0.028270.000050.97168
77 G0.028230.000100.97168
78 I0.028210.000110.97168
79 G0.028200.000120.97168
80 F0.028200.000130.97168
81 V0.028200.000130.97168
82 F0.028200.000130.97168
83 Q0.028200.000130.97168
84 H0.028200.000130.97168
85 Y0.028200.000130.97168
86 A0.028200.000130.97168
87 A0.028200.000130.97168
88 F0.028200.000130.97168
89 K0.028200.000130.97168
90 H0.028200.000130.97168
91 L0.028200.000130.97168
92 T0.028200.000130.97168
93 V0.028200.000130.97168
94 R0.028200.000090.97172
95 D0.028200.000050.97175
96 N0.028200.000050.97175
97 V0.028200.000050.97175
98 A0.028200.000040.97176
99 F0.028200.000020.97178
100 G0.028200.000010.97179
101 L0.028200.000010.97179
102 K0.028210.000000.97179
103 I0.028210.000000.97179
104 R0.028210.000000.97179
105 K0.028210.000000.97179
106 R0.028210.000000.97179
107 P0.028210.000000.97179
108 K0.028210.000000.97179
109 A0.028210.000000.97179
110 E0.028210.000000.97179
111 I0.028200.000000.97179
112 K0.028200.000000.97179
113 A0.028200.000010.97179
114 K0.028200.000010.97179
115 V0.028190.000010.97179
116 D0.028190.000010.97179
117 N0.028190.000010.97179
118 L0.028190.000020.97179
119 L0.028190.000020.97179
120 Q0.028190.000020.97179
121 V0.028190.000020.97179
122 V0.028190.000020.97179
123 G0.028190.000020.97179
124 L0.028190.000020.97179
125 S0.028190.000020.97179
126 G0.028190.000020.97179
127 F0.028190.000020.97179
128 Q0.028190.000020.97179
129 S0.028190.000020.97179
130 R0.028190.000010.97179
131 Y0.028190.000010.97179
132 P0.028190.000010.9718
133 N0.028190.000000.9718
134 Q0.028190.000000.9718
135 L0.028190.000000.9718
136 S0.028190.000000.9718
137 G0.028190.000000.9718
138 G0.028190.000000.97181
139 Q0.028190.000000.97181
140 R0.028190.000000.97181
141 Q0.028190.000000.97181
142 R0.028190.000000.97181
143 M0.028190.000000.97181
144 A0.028180.000010.97181
145 L0.028180.000010.97181
146 A0.028180.000010.97181
147 R0.028180.000010.97181
148 A0.028180.000010.97181
149 L0.028180.000010.97181
150 A0.028180.000010.97181
151 V0.028180.000010.97181
152 D0.028180.000010.97181
153 P0.028180.000010.97181
154 E0.028180.000010.97181
155 V0.028180.000010.97181
156 L0.028180.000010.97181
157 L0.028180.000010.97181
158 L0.028180.000010.97181
159 D0.028180.000010.97181
160 E0.028180.000010.97181
161 P0.028180.000010.97181
162 F0.028180.000010.97181
163 G0.028180.000010.97182
164 A0.028180.000010.97182
165 L0.028180.000000.97182
166 D0.028180.000000.97182
167 A0.028180.000000.97182
168 K0.028180.000000.97182
169 V0.028180.000000.97182
170 R0.028180.000000.97182
171 E0.028180.000000.97182
172 E0.028180.000000.97182
173 L0.028180.000000.97182
174 R0.028180.000000.97182
175 A0.028180.000000.97182
176 W0.028180.000000.97182
177 L0.028180.000000.97182
178 R0.028180.000000.97182
179 R0.028180.000000.97182
180 L0.028180.000000.97182
181 H0.028180.000000.97182
182 D0.028180.000000.97182
183 E0.028180.000000.97182
184 V0.028180.000000.97182
185 H0.028180.000000.97182
186 V0.028180.000000.97182
187 T0.028180.000000.97182
188 T0.028180.000000.97182
189 V0.028180.000000.97182
190 L0.028180.000000.97182
191 V0.028180.000000.97182
192 T0.028180.000000.97182
193 H0.028180.000000.97182
194 D0.028180.000000.97182
195 Q0.028180.000000.97182
196 A0.028180.000000.97182
197 E0.028180.000000.97182
198 A0.028180.000000.97182
199 L0.028180.000000.97182
200 D0.028180.000000.97182
201 V0.028180.000000.97182
202 A0.028180.000000.97182
203 D0.028180.000000.97182
204 R0.028180.000000.97182
205 I0.028180.000000.97182
206 A0.028180.000000.97182
207 V0.028180.000000.97182
208 L0.028180.000000.97182
209 H0.028180.000000.97182
210 K0.028180.000000.97182
211 G0.028180.000000.97182
212 R0.028180.000000.97182
213 I0.028180.000000.97182
214 E0.028180.000000.97182
215 Q0.028180.000000.97182
216 V0.028180.000010.97182
217 G0.028180.000010.97182
218 S0.028180.000010.97182
219 P0.028180.000010.97181
220 T0.028170.000040.97179
221 D0.028170.000060.97177
222 V0.028130.000290.97158
223 Y0.028130.000680.97119
224 D0.028120.001280.9706
225 A0.028020.002210.96977
226 P0.027960.002900.96914
227 A0.027710.005310.96698
228 N0.027640.006000.96635
229 A0.027420.008810.96377
230 F0.027330.009100.96357
231 V0.027320.009150.96352
232 M0.027320.009170.96351
233 S0.027320.009170.96351
234 F0.027320.009170.96351
235 L0.027320.009170.96351
236 G0.027320.009170.96351
237 A0.027320.009170.96351
238 V0.027320.009170.96351
239 S0.027320.009160.96351
240 T0.027330.009150.96352
241 L0.027340.009140.96352
242 N0.027370.009090.96354
243 G0.027430.009020.96355
244 S0.027500.008940.96357
245 L0.027630.008760.96361
246 V0.028750.007570.96368
247 R0.034820.001110.96407
248 P0.035170.000670.96416
249 H0.035370.000420.96421
250 D0.035580.000110.96431
251 I0.035590.000090.96432
252 R0.035620.000010.96437
253 V0.035620.000010.96437
254 G0.035620.000010.96437
255 R0.035620.000010.96436
256 T0.035610.000050.96434
257 P0.035600.000070.96434
258 N0.035580.000090.96432
259 M0.035530.000170.9643
260 A0.035510.000210.96429
261 V0.035500.000250.96426
262 A0.035500.000250.96425
263 A0.035500.000250.96425
264 A0.035500.000260.96425
265 D0.035500.000260.96425
266 G0.035500.000260.96425
267 T0.035500.000260.96425
268 A0.035490.000260.96425
269 G0.035490.000260.96425
270 S0.035490.000260.96425
271 T0.035490.000260.96425
272 G0.035490.000260.96425
273 V0.035490.000260.96425
274 L0.035500.000260.96425
275 R0.035500.000250.96425
276 A0.035500.000250.96425
277 V0.035510.000240.96426
278 V0.035520.000210.96427
279 D0.035600.000050.96435
280 R0.035610.000030.96436
281 V0.035580.000070.96435
282 V0.035570.000080.96435
283 V0.035560.000090.96435
284 L0.035560.000080.96435
285 G0.035570.000080.96435
286 F0.035570.000080.96435
287 E0.035570.000080.96435
288 V0.035570.000080.96435
289 R0.035570.000080.96435
290 V0.035560.000080.96435
291 E0.035570.000080.96435
292 L0.035570.000080.96435
293 T0.035570.000080.96435
294 S0.035570.000080.96435
295 A0.035570.000080.96435
296 A0.035570.000080.96435
297 T0.035570.000080.96435
298 G0.035570.000080.96435
299 G0.035570.000080.96435
300 A0.035570.000080.96435
301 F0.035570.000070.96435
302 T0.035570.000070.96435
303 A0.035570.000070.96437
304 Q0.035580.000030.96439
305 I0.035580.000030.96439
306 T0.035580.000010.96441
307 R0.035580.000010.96441
308 G0.035580.000000.96441
309 D0.035580.000000.96441
310 A0.035580.000000.96441
311 E0.035580.000000.96441
312 A0.035580.000000.96441
313 L0.035580.000000.96441
314 A0.035580.000000.96441
315 L0.035580.000000.96441
316 R0.035590.000000.96441
317 E0.035590.000000.96441
318 G0.035590.000000.96441
319 D0.035590.000000.96441
320 T0.035580.000000.96441
321 V0.035580.000000.96441
322 Y0.035580.000000.96441
323 V0.035580.000000.96441
324 R0.035580.000000.96441
325 A0.035580.000000.96441
326 T0.035580.000000.96441
327 R0.035580.000000.96441
328 V0.035580.000000.96441
329 P0.035580.000000.96441
330 P0.035580.000000.96441
331 I0.035580.000000.96441
332 A0.035580.000000.96441
333 G0.035580.000000.96441
334 G0.035580.000000.96441
335 V0.035580.000000.96441
336 S0.035580.000000.96441
337 G0.035580.000000.96441
338 V0.035580.000000.96441
339 D0.035590.000000.96441
340 D0.035590.000000.96441
341 A0.035590.000000.96441
342 G0.035590.000000.96441
343 V0.035590.000000.96441
344 E0.035590.000000.96441
345 R0.035590.000000.96441
346 V0.035590.000000.96441
347 K0.035590.000000.96441
348 V0.035590.000000.96441
349 T0.035590.000000.96441
350 S0.035590.000000.96441
351 T0.035590.000000.96441

General Statistics
Length: 351
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.29802
Exp number, first 60 AAs: 0.10451
Total prob of N-in: 0.03193
outside: from residue 1 to 351
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