TransMembrane prediction using Hidden Markov Models for Rv0491




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.032980.000000.96702
2 T0.032980.000000.96702
3 S0.032980.000000.96702
4 V0.032980.000000.96702
5 L0.032980.000000.96702
6 I0.032980.000000.96702
7 V0.032980.000000.96702
8 E0.032980.000000.96702
9 D0.032980.000000.96702
10 E0.032980.000000.96702
11 E0.032980.000000.96702
12 S0.032980.000000.96702
13 L0.032980.000000.96702
14 A0.032980.000000.96702
15 D0.032980.000000.96702
16 P0.032980.000000.96702
17 L0.032980.000000.96702
18 A0.032980.000000.96702
19 F0.032980.000000.96702
20 L0.032980.000000.96702
21 L0.032980.000000.96702
22 R0.032980.000000.96702
23 K0.032980.000000.96702
24 E0.032980.000000.96702
25 G0.032980.000000.96702
26 F0.032980.000000.96702
27 E0.032980.000000.96702
28 A0.032980.000000.96702
29 T0.032980.000000.96702
30 V0.032980.000000.96702
31 V0.032980.000000.96702
32 T0.032980.000000.96702
33 D0.032980.000000.96702
34 G0.032980.000000.96702
35 P0.032980.000000.96702
36 A0.032980.000000.96702
37 A0.032980.000000.96702
38 L0.032980.000000.96702
39 A0.032980.000000.96702
40 E0.032980.000000.96702
41 F0.032980.000010.96701
42 D0.032980.000010.96701
43 R0.032980.000030.967
44 A0.032980.000060.96696
45 G0.032980.000070.96696
46 A0.032980.000070.96695
47 D0.032980.000070.96695
48 I0.032980.000070.96695
49 V0.032980.000070.96695
50 L0.032980.000070.96695
51 L0.032980.000070.96695
52 D0.032980.000070.96695
53 L0.032980.000070.96695
54 M0.032980.000070.96695
55 L0.032980.000070.96695
56 P0.032980.000070.96695
57 G0.032980.000070.96695
58 M0.032980.000070.96695
59 S0.032980.000070.96695
60 G0.032980.000070.96695
61 T0.033000.000050.96695
62 D0.033020.000020.96695
63 V0.033030.000020.96695
64 C0.033040.000010.96695
65 K0.033040.000010.96695
66 Q0.033040.000000.96695
67 L0.033040.000000.96695
68 R0.033050.000000.96695
69 A0.033050.000000.96695
70 R0.033050.000000.96695
71 S0.033050.000000.96695
72 S0.033050.000000.96695
73 V0.033050.000000.96695
74 P0.033050.000000.96695
75 V0.033050.000000.96695
76 I0.033050.000000.96695
77 M0.033050.000000.96695
78 V0.033050.000000.96695
79 T0.033050.000000.96695
80 A0.033050.000000.96695
81 R0.033050.000000.96695
82 D0.033050.000000.96695
83 S0.033050.000000.96695
84 E0.033050.000000.96695
85 I0.033050.000000.96695
86 D0.033050.000000.96695
87 K0.033050.000000.96695
88 V0.033050.000000.96695
89 V0.033050.000000.96695
90 G0.033050.000000.96695
91 L0.033050.000000.96695
92 E0.033050.000000.96695
93 L0.033050.000000.96695
94 G0.033050.000000.96695
95 A0.033050.000000.96695
96 D0.033050.000000.96695
97 D0.033050.000000.96695
98 Y0.033050.000000.96695
99 V0.033050.000000.96695
100 T0.033050.000000.96695
101 K0.033050.000000.96695
102 P0.033050.000000.96695
103 Y0.033050.000000.96695
104 S0.033050.000000.96695
105 A0.033050.000000.96695
106 R0.033050.000000.96695
107 E0.033050.000000.96695
108 L0.033050.000000.96695
109 I0.033050.000000.96695
110 A0.033050.000000.96695
111 R0.033050.000000.96695
112 I0.033050.000000.96695
113 R0.033050.000000.96695
114 A0.033050.000000.96695
115 V0.033050.000000.96695
116 L0.033050.000000.96695
117 R0.033050.000000.96695
118 R0.033050.000000.96695
119 G0.033050.000000.96695
120 G0.033050.000000.96695
121 D0.033050.000000.96695
122 D0.033050.000000.96695
123 D0.033050.000000.96695
124 S0.033050.000000.96695
125 E0.033050.000000.96695
126 M0.033050.000000.96695
127 S0.033050.000000.96695
128 D0.033050.000000.96695
129 G0.033050.000000.96695
130 V0.033050.000000.96695
131 L0.033050.000000.96695
132 E0.033050.000000.96695
133 S0.033050.000000.96695
134 G0.033050.000000.96695
135 P0.033050.000000.96695
136 V0.033050.000000.96695
137 R0.033050.000000.96695
138 M0.033050.000000.96695
139 D0.033050.000000.96695
140 V0.033050.000000.96695
141 E0.033050.000000.96695
142 R0.033050.000000.96695
143 H0.033050.000000.96695
144 V0.033050.000000.96695
145 V0.033050.000000.96695
146 S0.033050.000000.96695
147 V0.033050.000000.96695
148 N0.033050.000000.96695
149 G0.033050.000000.96695
150 D0.033050.000000.96695
151 T0.033050.000000.96695
152 I0.033050.000000.96695
153 T0.033050.000000.96695
154 L0.033050.000000.96695
155 P0.033050.000000.96695
156 L0.033050.000000.96695
157 K0.033050.000000.96695
158 E0.033050.000000.96695
159 F0.033050.000000.96695
160 D0.033050.000000.96695
161 L0.033050.000000.96695
162 L0.033050.000000.96695
163 E0.033050.000000.96695
164 Y0.033050.000000.96695
165 L0.033050.000000.96695
166 M0.033050.000000.96695
167 R0.033050.000000.96695
168 N0.033050.000000.96695
169 S0.033050.000000.96695
170 G0.033050.000000.96695
171 R0.033050.000000.96695
172 V0.033050.000000.96695
173 L0.033050.000000.96695
174 T0.033050.000000.96695
175 R0.033050.000000.96695
176 G0.033050.000000.96695
177 Q0.033050.000000.96695
178 L0.033050.000000.96695
179 I0.033050.000000.96695
180 D0.033050.000000.96695
181 R0.033050.000000.96695
182 V0.033050.000000.96695
183 W0.033050.000000.96695
184 G0.033050.000000.96695
185 A0.033050.000000.96695
186 D0.033050.000000.96695
187 Y0.033050.000000.96695
188 V0.033050.000000.96695
189 G0.033050.000000.96695
190 D0.033050.000000.96695
191 T0.033050.000000.96695
192 K0.033050.000000.96695
193 T0.033050.000000.96695
194 L0.033050.000000.96695
195 D0.033050.000000.96695
196 V0.033050.000000.96695
197 H0.033050.000000.96695
198 V0.033050.000000.96695
199 K0.033050.000000.96695
200 R0.033050.000000.96695
201 L0.033050.000000.96695
202 R0.033050.000000.96695
203 S0.033050.000000.96695
204 K0.033050.000000.96695
205 I0.033050.000000.96695
206 E0.033050.000000.96695
207 A0.033050.000000.96695
208 D0.033050.000000.96695
209 P0.033050.000000.96695
210 A0.033050.000000.96695
211 N0.033050.000000.96695
212 P0.033050.000000.96695
213 V0.033050.000000.96695
214 H0.033050.000000.96695
215 L0.033050.000000.96695
216 V0.033050.000000.96695
217 T0.033050.000000.96695
218 V0.033050.000000.96695
219 R0.033050.000000.96695
220 G0.033050.000000.96695
221 L0.033050.000000.96695
222 G0.033050.000000.96695
223 Y0.033050.000000.96695
224 K0.033050.000000.96695
225 L0.033050.000000.96695
226 E0.033050.000000.96695
227 G0.033050.000000.96695

General Statistics
Length: 227
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.00134
Exp number, first 60 AAs: 0.00123
Total prob of N-in: 0.03298
outside: from residue 1 to 227
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