TransMembrane prediction using Hidden Markov Models for Rv3765c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.152190.000000.84781
2 R0.152190.000000.84781
3 R0.152190.000000.84781
4 A0.152190.000000.84781
5 D0.152190.000000.84781
6 G0.152190.000000.84781
7 Q0.152190.000000.84781
8 P0.152190.000000.84781
9 V0.152180.000010.84781
10 T0.152180.000010.84781
11 V0.152180.000010.84781
12 L0.152180.000010.84781
13 V0.152180.000010.84781
14 V0.152180.000010.84781
15 D0.152180.000010.84781
16 D0.152180.000010.84781
17 E0.152180.000010.84781
18 P0.152180.000010.84781
19 V0.152180.000010.84781
20 L0.152180.000010.84781
21 A0.152180.000010.84781
22 E0.152180.000010.84781
23 M0.152180.000010.84781
24 V0.152180.000010.84781
25 S0.152180.000020.8478
26 M0.152180.000020.8478
27 A0.152180.000020.8478
28 L0.152170.000030.8478
29 R0.152170.000020.84781
30 Y0.152150.000050.8478
31 E0.152140.000060.8478
32 G0.152130.000080.8478
33 W0.152120.000080.8478
34 N0.152120.000080.8478
35 I0.152120.000080.8478
36 T0.152120.000080.8478
37 T0.152120.000080.8478
38 A0.152120.000080.8478
39 G0.152120.000080.8478
40 D0.152120.000080.8478
41 G0.152120.000080.8478
42 S0.152120.000080.8478
43 S0.152120.000080.8478
44 A0.152130.000080.8478
45 I0.152130.000080.8478
46 A0.152130.000070.8478
47 A0.152130.000070.8478
48 A0.152130.000060.84781
49 R0.152140.000020.84784
50 R0.152140.000000.84785
51 Q0.152140.000000.84785
52 R0.152140.000000.84785
53 P0.152140.000000.84786
54 D0.152140.000010.84786
55 V0.152110.000040.84786
56 V0.152100.000040.84786
57 V0.152100.000040.84786
58 L0.152100.000040.84786
59 D0.152100.000040.84786
60 V0.152100.000040.84786
61 M0.152100.000040.84786
62 L0.152100.000040.84786
63 P0.152100.000040.84786
64 D0.152100.000040.84786
65 M0.152100.000040.84786
66 S0.152100.000040.84786
67 G0.152100.000040.84786
68 L0.152100.000040.84786
69 D0.152100.000040.84786
70 V0.152100.000040.84786
71 L0.152100.000040.84786
72 H0.152100.000030.84786
73 K0.152100.000000.84789
74 L0.152100.000000.84789
75 R0.152100.000000.84789
76 S0.152100.000000.84789
77 E0.152100.000000.84789
78 N0.152100.000000.84789
79 P0.152100.000000.84789
80 G0.152100.000000.84789
81 L0.152100.000000.84789
82 P0.152100.000000.84789
83 V0.152100.000000.84789
84 L0.152100.000000.84789
85 L0.152100.000000.84789
86 L0.152100.000000.84789
87 T0.152100.000000.84789
88 A0.152100.000000.84789
89 K0.152100.000000.84789
90 D0.152100.000000.84789
91 A0.152100.000000.84789
92 V0.152100.000000.84789
93 E0.152100.000000.84789
94 D0.152100.000000.8479
95 R0.152100.000000.8479
96 I0.152100.000000.84789
97 A0.152100.000000.84789
98 G0.152100.000000.84789
99 L0.152100.000000.84789
100 T0.152100.000000.84789
101 A0.152100.000000.84789
102 G0.152100.000000.84789
103 G0.152100.000000.84789
104 D0.152100.000000.8479
105 D0.152100.000000.8479
106 Y0.152100.000000.84789
107 V0.152100.000000.84789
108 T0.152100.000000.84789
109 K0.152100.000000.84789
110 P0.152100.000000.84789
111 F0.152100.000000.84789
112 S0.152100.000000.84789
113 I0.152100.000000.84789
114 E0.152100.000000.8479
115 E0.152100.000000.8479
116 V0.152100.000000.8479
117 V0.152100.000000.8479
118 L0.152100.000000.8479
119 R0.152100.000000.8479
120 L0.152100.000000.8479
121 R0.152100.000000.8479
122 A0.152090.000010.8479
123 L0.152080.000020.84789
124 L0.152080.000020.84789
125 R0.152080.000020.84789
126 R0.152080.000020.84789
127 T0.152080.000030.84789
128 G0.152070.000040.84789
129 V0.152070.000040.84789
130 T0.152070.000040.84789
131 T0.152070.000040.84789
132 V0.152070.000040.84789
133 D0.152070.000040.84789
134 S0.152070.000040.84789
135 G0.152070.000040.84789
136 A0.152070.000040.84789
137 Q0.152070.000040.84789
138 L0.152070.000040.84789
139 V0.152070.000040.84789
140 V0.152070.000040.84789
141 G0.152070.000040.84789
142 D0.152070.000030.84789
143 L0.152070.000030.84789
144 V0.152070.000030.84789
145 L0.152070.000020.84791
146 D0.152080.000000.84792
147 E0.152080.000000.84792
148 D0.152080.000000.84792
149 S0.152080.000000.84792
150 H0.152080.000000.84792
151 E0.152080.000000.84792
152 V0.152080.000000.84792
153 M0.152080.000000.84792
154 R0.152080.000000.84792
155 A0.152080.000000.84792
156 G0.152080.000000.84792
157 E0.152080.000000.84792
158 P0.152080.000000.84792
159 V0.152080.000000.84792
160 S0.152080.000000.84792
161 L0.152080.000000.84792
162 T0.152080.000000.84792
163 S0.152080.000000.84792
164 T0.152080.000000.84792
165 E0.152080.000000.84792
166 F0.152080.000000.84792
167 E0.152080.000000.84792
168 L0.152080.000000.84792
169 L0.152080.000000.84792
170 R0.152080.000000.84792
171 F0.152080.000000.84792
172 M0.152080.000000.84792
173 M0.152080.000000.84792
174 H0.152080.000000.84792
175 N0.152080.000000.84792
176 S0.152080.000000.84792
177 K0.152080.000000.84792
178 R0.152080.000000.84792
179 V0.152080.000000.84792
180 L0.152080.000000.84792
181 S0.152080.000000.84792
182 K0.152080.000000.84792
183 A0.152080.000000.84792
184 Q0.152080.000000.84792
185 I0.152080.000000.84792
186 L0.152080.000010.84792
187 D0.152080.000010.84791
188 R0.152070.000010.84791
189 V0.152070.000060.84787
190 W0.152070.000070.84786
191 S0.152070.000080.84786
192 Y0.152070.000080.84786
193 D0.152070.000080.84786
194 F0.152060.000080.84786
195 G0.152060.000080.84786
196 G0.152060.000080.84786
197 R0.152060.000080.84786
198 S0.152060.000080.84786
199 N0.152060.000080.84786
200 I0.152060.000080.84786
201 V0.152060.000080.84786
202 E0.152060.000080.84786
203 L0.152060.000080.84786
204 Y0.152060.000080.84786
205 I0.152070.000080.84786
206 S0.152070.000080.84786
207 Y0.152070.000070.84786
208 L0.152080.000050.84787
209 R0.152120.000010.84787
210 K0.152130.000000.84787
211 K0.152130.000000.84787
212 I0.152130.000000.84787
213 D0.152130.000000.84787
214 N0.152130.000000.84787
215 G0.152130.000000.84787
216 R0.152130.000000.84787
217 E0.152130.000000.84787
218 P0.152130.000000.84787
219 M0.152130.000000.84787
220 I0.152130.000000.84787
221 H0.152130.000000.84787
222 T0.152130.000000.84787
223 L0.152130.000000.84787
224 R0.152130.000000.84787
225 G0.152130.000000.84787
226 A0.152130.000000.84787
227 G0.152130.000000.84787
228 Y0.152130.000000.84787
229 V0.152130.000000.84787
230 L0.152130.000000.84787
231 K0.152130.000000.84787
232 P0.152130.000000.84787
233 A0.152130.000000.84787
234 R0.152130.000000.84787

General Statistics
Length: 234
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.00480000000000001
Exp number, first 60 AAs: 0.00197
Total prob of N-in: 0.15219
outside: from residue 1 to 234
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