TransMembrane prediction using Hidden Markov Models for Rv1027c




Residue number
and Amino Acid
Probabilities
InsideMembraneOutside
1 M0.031180.000000.96882
2 T0.031180.000000.96882
3 L0.031180.000000.96882
4 V0.031180.000000.96882
5 L0.031180.000000.96882
6 V0.031180.000000.96882
7 I0.031180.000000.96882
8 D0.031180.000000.96882
9 D0.031180.000000.96882
10 E0.031180.000000.96882
11 P0.031180.000000.96882
12 Q0.031170.000000.96882
13 I0.031130.000050.96882
14 L0.031130.000050.96882
15 R0.031130.000060.96882
16 A0.031080.000110.96882
17 L0.031060.000130.96882
18 R0.031060.000130.96882
19 I0.030980.000200.96881
20 N0.029920.001290.96879
21 L0.027650.003570.96879
22 T0.027600.003620.96878
23 V0.027490.003740.96876
24 R0.027470.003760.96876
25 G0.027370.003880.96876
26 Y0.027360.003890.96876
27 Q0.027360.003890.96876
28 V0.027350.003890.96876
29 I0.027350.003890.96876
30 T0.027350.003890.96876
31 A0.027350.003880.96877
32 S0.027350.003870.96878
33 T0.027350.003870.96878
34 G0.027350.003870.96878
35 A0.027350.003860.96879
36 G0.027350.003830.96882
37 A0.027350.003820.96883
38 L0.027360.003740.9689
39 R0.027360.003150.96949
40 A0.027370.003070.96956
41 A0.027370.002850.96978
42 A0.027380.002590.97004
43 E0.027410.001450.97114
44 H0.027410.000020.97257
45 P0.027410.000010.97258
46 P0.027410.000010.97258
47 D0.027410.000000.97258
48 V0.027410.000030.97256
49 V0.027410.000070.97252
50 I0.027410.000080.97252
51 L0.027410.000080.97252
52 D0.027410.000080.97252
53 L0.027410.000100.9725
54 G0.027410.000110.97249
55 L0.027410.000140.97245
56 P0.027410.000170.97242
57 D0.027400.000310.97228
58 M0.027400.003150.96945
59 S0.027400.003530.96907
60 G0.027400.004160.96845
61 I0.027400.004870.96773
62 D0.027400.004960.96764
63 V0.027390.005420.96719
64 L0.027380.005620.967
65 G0.027380.005660.96696
66 G0.027380.005690.96693
67 L0.027380.005690.96693
68 R0.027390.005680.96693
69 G0.027390.005680.96693
70 W0.027390.005680.96693
71 L0.027400.005660.96693
72 T0.027450.005620.96693
73 A0.027470.005590.96694
74 P0.027470.005590.96694
75 V0.027470.005590.96694
76 I0.027470.005590.96694
77 V0.027480.005580.96694
78 L0.027640.005420.96694
79 S0.028150.004910.96694
80 A0.028950.004110.96694
81 R0.032540.000510.96695
82 T0.032850.000200.96695
83 D0.033020.000020.96696
84 S0.033030.000010.96696
85 S0.033030.000010.96696
86 D0.033040.000000.96696
87 K0.033040.000000.96696
88 V0.033040.000000.96696
89 Q0.033040.000000.96696
90 A0.033040.000000.96696
91 L0.033040.000000.96696
92 D0.033040.000000.96696
93 A0.033040.000000.96696
94 G0.033040.000000.96696
95 A0.033040.000000.96696
96 D0.033040.000000.96696
97 D0.033040.000000.96696
98 Y0.033040.000000.96696
99 V0.033040.000000.96696
100 T0.033040.000000.96696
101 K0.033040.000000.96696
102 P0.033040.000000.96696
103 F0.033040.000000.96696
104 G0.033040.000000.96696
105 M0.033040.000000.96696
106 D0.033040.000000.96696
107 E0.033040.000000.96696
108 F0.033040.000000.96696
109 L0.033040.000000.96696
110 A0.033040.000000.96696
111 R0.033040.000000.96696
112 L0.033040.000000.96696
113 R0.033040.000000.96696
114 A0.033040.000000.96696
115 A0.033040.000000.96696
116 V0.033040.000000.96696
117 R0.033040.000000.96696
118 R0.033040.000000.96696
119 N0.033040.000000.96696
120 T0.033040.000000.96696
121 A0.033040.000000.96696
122 A0.033040.000000.96696
123 A0.033040.000000.96696
124 E0.033040.000000.96696
125 L0.033040.000000.96696
126 E0.033040.000000.96696
127 Q0.033040.000000.96696
128 P0.033040.000000.96696
129 V0.033040.000000.96696
130 I0.033040.000000.96696
131 E0.033040.000000.96696
132 T0.033040.000000.96696
133 D0.033040.000000.96696
134 S0.033040.000000.96696
135 F0.033040.000000.96696
136 T0.033040.000000.96696
137 V0.033040.000000.96696
138 D0.033040.000000.96696
139 L0.033040.000000.96696
140 A0.033040.000000.96696
141 G0.033040.000000.96696
142 K0.033040.000000.96696
143 K0.033040.000000.96696
144 V0.033040.000000.96696
145 I0.033040.000000.96696
146 K0.033040.000000.96696
147 D0.033040.000000.96696
148 G0.033040.000000.96696
149 A0.033040.000000.96696
150 E0.033040.000000.96696
151 V0.033040.000000.96696
152 H0.033040.000000.96696
153 L0.033040.000000.96696
154 T0.033040.000000.96696
155 P0.033040.000000.96696
156 T0.033040.000000.96696
157 E0.033040.000000.96696
158 W0.033040.000000.96696
159 G0.033040.000000.96696
160 M0.033040.000000.96696
161 L0.033040.000000.96696
162 E0.033040.000000.96696
163 M0.033040.000000.96696
164 L0.033040.000000.96696
165 A0.033040.000000.96696
166 R0.033040.000000.96696
167 N0.033040.000000.96696
168 R0.033040.000000.96696
169 G0.033040.000000.96696
170 K0.033040.000000.96696
171 L0.033040.000000.96696
172 V0.033040.000000.96696
173 G0.033040.000000.96696
174 R0.033040.000000.96696
175 G0.033040.000000.96696
176 E0.033040.000000.96696
177 L0.033030.000000.96696
178 L0.033030.000010.96696
179 K0.033030.000010.96696
180 E0.033030.000010.96695
181 V0.033030.000040.96692
182 W0.033030.000040.96692
183 G0.033030.000040.96692
184 P0.033030.000040.96692
185 A0.033030.000040.96692
186 Y0.033030.000040.96692
187 A0.033030.000040.96692
188 T0.033030.000040.96692
189 E0.033030.000040.96692
190 T0.033030.000040.96692
191 H0.033030.000040.96692
192 Y0.033030.000040.96692
193 L0.033030.000040.96692
194 R0.033040.000040.96692
195 V0.033040.000040.96692
196 Y0.033040.000040.96692
197 L0.033040.000040.96692
198 A0.033050.000030.96692
199 Q0.033070.000000.96692
200 L0.033070.000000.96692
201 R0.033070.000000.96692
202 R0.033070.000000.96692
203 K0.033070.000000.96692
204 L0.033070.000000.96692
205 E0.033070.000000.96692
206 D0.033070.000000.96692
207 D0.033070.000000.96692
208 P0.033070.000000.96692
209 S0.033070.000000.96692
210 H0.033070.000000.96692
211 P0.033070.000000.96692
212 K0.033070.000000.96692
213 H0.033070.000000.96692
214 L0.033070.000000.96692
215 L0.033070.000000.96692
216 T0.033070.000000.96692
217 E0.033070.000000.96692
218 S0.033070.000000.96692
219 G0.033070.000000.96692
220 M0.033070.000000.96692
221 G0.033070.000000.96692
222 Y0.033070.000000.96692
223 R0.033070.000000.96692
224 F0.033070.000000.96692
225 E0.033070.000000.96692
226 A0.033070.000000.96692

General Statistics
Length: 226
Number of predicted TMHs: 0
Exp number of AAs in TMHs: 0.20604
Exp number, first 60 AAs: 0.09594
Total prob of N-in: 0.03118
outside: from residue 1 to 226
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