TransMembrane prediction using Hidden Markov Models for Rv3133c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 V0.039340.000000.96066
2 V0.039340.000000.96066
3 K0.039340.000000.96066
4 V0.039340.000000.96066
5 F0.039340.000000.96066
6 L0.039340.000000.96066
7 V0.039340.000000.96066
8 D0.039340.000000.96066
9 D0.039340.000000.96066
10 H0.039340.000000.96066
11 E0.039340.000000.96066
12 V0.039340.000000.96066
13 V0.039340.000000.96066
14 R0.039340.000000.96066
15 R0.039340.000000.96066
16 G0.039340.000000.96066
17 L0.039340.000000.96066
18 V0.039340.000000.96066
19 D0.039340.000000.96066
20 L0.039340.000000.96066
21 L0.039340.000000.96066
22 G0.039340.000000.96066
23 A0.039340.000000.96066
24 D0.039340.000000.96066
25 P0.039340.000000.96066
26 E0.039340.000000.96066
27 L0.039340.000000.96066
28 D0.039340.000000.96066
29 V0.039340.000000.96066
30 V0.039340.000000.96066
31 G0.039340.000000.96066
32 E0.039340.000000.96066
33 A0.039340.000000.96066
34 G0.039340.000000.96066
35 S0.039340.000000.96066
36 V0.039340.000000.96066
37 A0.039340.000000.96066
38 E0.039340.000000.96066
39 A0.039340.000000.96066
40 M0.039340.000000.96066
41 A0.039340.000000.96066
42 R0.039340.000000.96066
43 V0.039340.000000.96066
44 P0.039340.000000.96066
45 A0.039340.000000.96066
46 A0.039340.000000.96066
47 R0.039340.000000.96066
48 P0.039340.000000.96066
49 D0.039340.000000.96066
50 V0.039340.000000.96066
51 A0.039340.000000.96066
52 V0.039340.000000.96066
53 L0.039340.000000.96066
54 D0.039340.000000.96066
55 V0.039340.000000.96066
56 R0.039340.000000.96066
57 L0.039340.000000.96066
58 P0.039340.000000.96066
59 D0.039340.000000.96066
60 G0.039340.000000.96066
61 N0.039340.000000.96066
62 G0.039340.000000.96066
63 I0.039340.000000.96066
64 E0.039340.000000.96066
65 L0.039340.000000.96066
66 C0.039340.000000.96066
67 R0.039340.000000.96066
68 D0.039340.000000.96066
69 L0.039340.000000.96066
70 L0.039340.000000.96066
71 S0.039340.000000.96066
72 R0.039340.000000.96066
73 M0.039340.000000.96066
74 P0.039340.000000.96066
75 D0.039340.000000.96066
76 L0.039330.000010.96066
77 R0.039330.000020.96065
78 C0.039320.000050.96063
79 L0.039290.000150.96056
80 I0.039240.000340.96041
81 L0.039210.000620.96017
82 T0.039210.000640.96015
83 S0.039200.000660.96013
84 Y0.039200.000750.96005
85 T0.039200.000770.96004
86 S0.039200.000790.96001
87 D0.039200.000790.96001
88 E0.039200.000820.95998
89 A0.039200.001030.95977
90 M0.039200.001040.95976
91 L0.039200.001040.95976
92 D0.039200.001040.95976
93 A0.039200.001040.95975
94 I0.039200.001050.95975
95 L0.039200.001040.95975
96 A0.039200.001040.95975
97 G0.039200.001040.95976
98 A0.039200.001040.95976
99 S0.039210.001020.95978
100 G0.039220.001000.95978
101 Y0.039230.000980.95979
102 V0.039280.000910.95981
103 V0.039420.000730.95985
104 K0.040000.000100.9599
105 D0.040030.000070.9599
106 I0.040030.000070.9599
107 K0.040080.000020.9599
108 G0.040080.000020.9599
109 M0.040090.000010.9599
110 E0.040090.000010.9599
111 L0.040090.000010.9599
112 A0.040090.000010.9599
113 R0.040090.000000.9599
114 A0.040090.000000.9599
115 V0.040100.000000.9599
116 K0.040100.000000.9599
117 D0.040100.000000.9599
118 V0.040100.000000.9599
119 G0.040100.000000.9599
120 A0.040100.000000.9599
121 G0.040100.000000.9599
122 R0.040100.000000.9599
123 S0.040100.000000.9599
124 L0.040100.000000.9599
125 L0.040100.000000.9599
126 D0.040100.000000.9599
127 N0.040100.000000.9599
128 R0.040100.000000.9599
129 A0.040100.000000.9599
130 A0.040100.000000.9599
131 A0.040100.000000.9599
132 A0.040100.000000.9599
133 L0.040100.000000.9599
134 M0.040100.000000.9599
135 A0.040100.000000.9599
136 K0.040100.000000.9599
137 L0.040100.000000.9599
138 R0.040100.000000.9599
139 G0.040100.000000.9599
140 A0.040100.000000.9599
141 A0.040100.000000.9599
142 E0.040100.000000.9599
143 K0.040100.000000.9599
144 Q0.040100.000000.9599
145 D0.040100.000000.9599
146 P0.040100.000000.9599
147 L0.040100.000000.9599
148 S0.040100.000000.9599
149 G0.040100.000000.9599
150 L0.040100.000000.9599
151 T0.040100.000000.9599
152 D0.040100.000000.9599
153 Q0.040100.000000.9599
154 E0.040100.000000.9599
155 R0.040100.000000.9599
156 T0.040100.000000.9599
157 L0.040100.000000.9599
158 L0.040100.000000.9599
159 G0.040100.000000.9599
160 L0.040100.000000.9599
161 L0.040100.000000.9599
162 S0.040100.000000.9599
163 E0.040100.000000.9599
164 G0.040100.000000.9599
165 L0.040100.000000.9599
166 T0.040100.000000.9599
167 N0.040100.000000.9599
168 K0.040100.000000.9599
169 Q0.040100.000000.9599
170 I0.040100.000000.9599
171 A0.040100.000000.9599
172 D0.040100.000000.9599
173 R0.040100.000000.9599
174 M0.040100.000000.9599
175 F0.040100.000000.9599
176 L0.040100.000000.9599
177 A0.040100.000000.9599
178 E0.040100.000000.9599
179 K0.040100.000000.9599
180 T0.040100.000000.9599
181 V0.040100.000000.9599
182 K0.040100.000000.9599
183 N0.040100.000000.9599
184 Y0.040100.000000.9599
185 V0.040100.000000.9599
186 S0.040100.000000.9599
187 R0.040100.000000.9599
188 L0.040100.000000.9599
189 L0.040100.000000.9599
190 A0.040100.000000.9599
191 K0.040100.000000.9599
192 L0.040100.000000.9599
193 G0.040100.000000.9599
194 M0.040100.000000.9599
195 E0.040100.000000.9599
196 R0.040100.000000.9599
197 R0.040100.000000.9599
198 T0.040100.000000.9599
199 Q0.040100.000000.9599
200 A0.040100.000000.9599
201 A0.040100.000000.9599
202 V0.040100.000000.9599
203 F0.040100.000000.9599
204 A0.040100.000000.9599
205 T0.040100.000000.9599
206 E0.040100.000000.9599
207 L0.040100.000000.9599
208 K0.040100.000000.9599
209 R0.040100.000000.9599
210 S0.040100.000000.9599
211 R0.040100.000000.9599
212 P0.040100.000000.9599
213 P0.040100.000000.9599
214 G0.040100.000000.9599
215 D0.040100.000000.9599
216 G0.040100.000000.9599
217 P0.040100.000000.9599

General Statistics
Length: 217
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.02177
Exp number, first 60 AAs: 0
Total prob of N-in: 0.03934
outside: from residue 1 to 217
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