>Seq1

MKTAALAPLFFLPSALATTVYLAGDSTMAKNGGGSGTNGWGEYLASYLSATVVNDAVAGR

SARSYTREGRFENIADVVTAGDYVIVEFGHNDGGSLSTDNGRTDCSGTGAEVCYSVYDGV

NETILTFPAYLENAAKLFTAKGAKVILSSQTPNNPWETGTFVNSPTRFVEYAELAAEVAG

VEYVDHWSYVDSIYETLGNATVNSYFPIDHTHTSPAGAEVVAEAFLKAVVCTGTSLKSVL

TTTSFEGTCL

Is Seq1 a secreted protein ?

Is it a reliable prediction ?

Does it have a propeptide ?

Is it a reliable prediction ?

What is the range of the mature protein

Start:
End:

What is the consequence/reason of a sequence having a

Signal peptide ?
ProPeptide ?

Glycosylated residues (Find NetNglyc & NetOglyc):

N-glycosylated amino acids ?
O-glycosylated amino acids ?

Draw a schematic representation of a neural network with two Input neurons, two hidden neurons and 1 output neuron.

I1 = 5.0

I2 = -3.0

W1,1 = 0.3

W1,2 = -0.45

W2,1 = -6.2

W2,2 = 2.1

V1,1 = 0.15

V2,1 = -0.97

Use the sigmodial function 1/(1+e^-x) to calculate the output value O (check Neural Network lecture for the formula)

O = ?

The Seq1 has been submitted to the NetSurfP program and output is shown below.

What is the most likely class that this protein belongs to: all-a, all-b, a+b, a/b or ‘small’

Explanation of classes:

All-a: Mostly all residues are alpha-helical and coil
All-b: Mostly all residues are beta-strands and coil
a+b: Mixed regions with a-helices and b-strands
a/b: Alternating a-helices and b-strands
small: Mostly all secondary structure elements belong to the Coil category.

# Column 1: Class assignment - B for buried or E for Exposed - Threshold: 25% exposure, but not based on RSA

# Column 2: Amino acid

# Column 3: Sequence name

# Column 4: Amino acid number

# Column 5: Relative Surface Accessibility - RSA

# Column 6: Absolute Surface Accessibility

# Column 7: Z-fit score

# Column 8: Probability for Alpha-Helix

# Column 9: Probability for Beta-strand

# Column 10: Probability for Coil

E M Seq1 1 0.569 113.797 -1.139 0.109 0.005 0.886

E K Seq1 2 0.335 68.848 0.249 0.660 0.049 0.291

B T Seq1 3 0.214 29.723 -1.327 0.779 0.100 0.120

B A Seq1 4 0.198 21.776 -0.742 0.751 0.050 0.199

B A Seq1 5 0.162 17.819 -0.799 0.751 0.050 0.199

B L Seq1 6 0.159 29.131 0.323 0.717 0.014 0.269

B A Seq1 7 0.158 17.423 0.209 0.717 0.014 0.269

B P Seq1 8 0.149 21.129 -0.271 0.858 0.002 0.139

B L Seq1 9 0.110 20.196 0.154 0.802 0.014 0.185

B F Seq1 10 0.164 33.015 -1.128 0.782 0.003 0.216

B F Seq1 11 0.175 35.102 -0.660 0.782 0.003 0.216

B L Seq1 12 0.178 32.647 0.039 0.502 0.002 0.495

E P Seq1 13 0.373 52.886 -0.205 0.321 0.003 0.675

E S Seq1 14 0.584 68.421 -0.402 0.109 0.005 0.886

E A Seq1 15 0.484 53.326 0.311 0.053 0.005 0.942

E L Seq1 16 0.682 124.801 0.559 0.018 0.019 0.964

E A Seq1 17 0.463 51.078 0.532 0.005 0.015 0.979

B T Seq1 18 0.256 35.535 0.782 0.005 0.045 0.951

B T Seq1 19 0.152 21.055 1.956 0.002 0.816 0.182

B V Seq1 20 0.019 2.982 1.434 0.001 0.959 0.040

B Y Seq1 21 0.022 4.787 1.592 0.000 0.983 0.017

B L Seq1 22 0.013 2.380 1.711 0.000 0.983 0.017

B A Seq1 23 0.017 1.851 1.517 0.001 0.959 0.040

B G Seq1 24 0.024 1.920 -0.074 0.004 0.616 0.381

B D Seq1 25 0.050 7.234 -0.524 0.018 0.088 0.893

B S Seq1 26 0.031 3.633 -0.497 0.118 0.150 0.732

B T Seq1 27 0.042 5.825 0.604 0.125 0.227 0.648

B M Seq1 28 0.039 7.804 -0.374 0.199 0.152 0.649

B A Seq1 29 0.221 24.310 -0.172 0.113 0.043 0.844

E K Seq1 30 0.342 70.308 -0.758 0.053 0.043 0.903

E N Seq1 31 0.363 53.114 -0.714 0.018 0.047 0.935

E G Seq1 32 0.608 47.857 -2.471 0.018 0.019 0.964

E G Seq1 33 0.499 39.263 -2.306 0.018 0.019 0.964

E G Seq1 34 0.507 39.869 -1.803 0.018 0.019 0.964

E S Seq1 35 0.376 44.020 -0.832 0.058 0.017 0.925

E G Seq1 36 0.307 24.185 -1.598 0.115 0.016 0.868

E T Seq1 37 0.389 53.954 -1.736 0.113 0.043 0.844

E N Seq1 38 0.322 47.112 -1.299 0.113 0.043 0.844

B G Seq1 39 0.128 10.105 -2.730 0.181 0.016 0.803

B W Seq1 40 0.064 15.344 0.161 0.717 0.014 0.269

B G Seq1 41 0.127 9.956 -0.908 0.879 0.010 0.111

E E Seq1 42 0.531 92.748 0.292 0.858 0.002 0.139

B Y Seq1 43 0.166 35.453 -0.069 0.858 0.002 0.139

B L Seq1 44 0.043 7.947 0.368 0.858 0.002 0.139

E A Seq1 45 0.439 48.378 0.828 0.782 0.003 0.216

E S Seq1 46 0.733 85.908 0.635 0.694 0.003 0.303

E Y Seq1 47 0.280 59.772 -0.044 0.502 0.002 0.495

B L Seq1 48 0.172 31.493 0.383 0.181 0.016 0.803

E S Seq1 49 0.778 91.158 1.273 0.005 0.015 0.979

B A Seq1 50 0.141 15.538 0.368 0.004 0.138 0.858

E T Seq1 51 0.496 68.851 1.306 0.003 0.718 0.279

B V Seq1 52 0.041 6.332 0.030 0.001 0.959 0.040

B V Seq1 53 0.196 30.171 0.765 0.001 0.959 0.040

B N Seq1 54 0.072 10.526 -2.948 0.001 0.900 0.099

B D Seq1 55 0.223 32.105 0.273 0.004 0.514 0.481

B A Seq1 56 0.078 8.585 -3.514 0.004 0.420 0.576

B V Seq1 57 0.239 36.765 0.258 0.005 0.336 0.660

E A Seq1 58 0.293 32.256 -1.072 0.018 0.088 0.893

B G Seq1 59 0.216 17.039 -2.423 0.018 0.019 0.964

E R Seq1 60 0.323 73.944 -1.114 0.115 0.016 0.868

B S Seq1 61 0.166 19.467 -0.668 0.257 0.016 0.727

B A Seq1 62 0.062 6.854 -0.876 0.522 0.016 0.462

E R Seq1 63 0.409 93.615 -0.108 0.522 0.016 0.462

E S Seq1 64 0.373 43.680 -0.043 0.430 0.016 0.555

B Y Seq1 65 0.144 30.666 -0.717 0.430 0.016 0.555

E T Seq1 66 0.280 38.864 0.080 0.522 0.016 0.462

E R Seq1 67 0.518 118.599 -1.196 0.522 0.016 0.462

E E Seq1 68 0.438 76.484 -0.842 0.522 0.016 0.462

E G Seq1 69 0.367 28.859 -0.393 0.430 0.016 0.555

B R Seq1 70 0.194 44.540 0.592 0.522 0.016 0.462

B F Seq1 71 0.061 12.323 1.044 0.858 0.002 0.139

E E Seq1 72 0.459 80.187 1.279 0.923 0.002 0.076

E N Seq1 73 0.478 69.935 1.551 0.923 0.002 0.076

B I Seq1 74 0.051 9.342 0.632 0.923 0.002 0.076

B A Seq1 75 0.063 6.899 0.610 0.923 0.002 0.076

E D Seq1 76 0.600 86.532 1.247 0.858 0.002 0.139

E V Seq1 77 0.493 75.820 1.005 0.694 0.003 0.303

B V Seq1 78 0.122 18.705 -0.341 0.502 0.002 0.495

E T Seq1 79 0.504 69.974 0.626 0.109 0.005 0.886

E A Seq1 80 0.563 62.010 0.581 0.016 0.005 0.979

B G Seq1 81 0.178 14.009 0.072 0.005 0.015 0.979

E D Seq1 82 0.248 35.737 0.291 0.005 0.045 0.951

B Y Seq1 83 0.043 9.210 0.904 0.002 0.816 0.182

B V Seq1 84 0.015 2.336 1.753 0.001 0.959 0.040

B I Seq1 85 0.018 3.330 1.752 0.000 0.983 0.017

B V Seq1 86 0.016 2.413 1.456 0.000 0.983 0.017

B E Seq1 87 0.024 4.123 0.750 0.001 0.900 0.099

B F Seq1 88 0.023 4.556 0.972 0.004 0.514 0.481

B G Seq1 89 0.022 1.708 0.110 0.021 0.279 0.699

B H Seq1 90 0.049 8.877 -0.579 0.020 0.205 0.775

B N Seq1 91 0.030 4.465 -0.676 0.053 0.043 0.903

B D Seq1 92 0.039 5.605 -1.391 0.115 0.016 0.868

B G Seq1 93 0.169 13.308 -1.849 0.181 0.016 0.803

E G Seq1 94 0.300 23.634 -0.446 0.109 0.005 0.886

E S Seq1 95 0.332 38.934 -0.467 0.053 0.005 0.942

E L Seq1 96 0.596 109.183 -1.570 0.058 0.017 0.925

E S Seq1 97 0.481 56.397 -1.006 0.058 0.017 0.925

E T Seq1 98 0.393 54.440 -1.525 0.115 0.016 0.868

E D Seq1 99 0.584 84.097 -2.015 0.181 0.016 0.803

E N Seq1 100 0.495 72.483 -0.895 0.257 0.016 0.727

E G Seq1 101 0.310 24.428 -1.751 0.257 0.016 0.727

E R Seq1 102 0.350 80.104 -1.196 0.339 0.016 0.645

E T Seq1 103 0.392 54.343 -1.357 0.354 0.048 0.598

E D Seq1 104 0.375 54.052 -1.262 0.354 0.048 0.598

B C Seq1 105 0.265 37.220 -0.908 0.268 0.043 0.689

E S Seq1 106 0.419 49.119 -0.867 0.268 0.043 0.689

E G Seq1 107 0.435 34.219 -1.628 0.268 0.043 0.689

E T Seq1 108 0.386 53.566 -1.369 0.354 0.048 0.598

E G Seq1 109 0.433 34.046 -1.298 0.268 0.043 0.689

E A Seq1 110 0.468 51.596 -1.416 0.354 0.048 0.598

E E Seq1 111 0.444 77.584 -0.835 0.278 0.093 0.628

B V Seq1 112 0.257 39.578 -0.959 0.307 0.165 0.527

E C Seq1 113 0.292 40.983 -0.449 0.307 0.165 0.527

E Y Seq1 114 0.453 96.806 -0.832 0.307 0.165 0.527

E S Seq1 115 0.334 39.157 -1.278 0.307 0.165 0.527

E V Seq1 116 0.318 48.877 -1.400 0.278 0.093 0.628

E Y Seq1 117 0.445 95.011 -1.242 0.268 0.043 0.689

E D Seq1 118 0.543 78.232 -1.506 0.268 0.043 0.689

E G Seq1 119 0.426 33.495 -1.102 0.191 0.086 0.723

E V Seq1 120 0.462 71.025 -1.037 0.118 0.150 0.732

E N Seq1 121 0.535 78.383 -0.362 0.056 0.142 0.802

B E Seq1 122 0.260 45.405 0.200 0.018 0.088 0.893

E T Seq1 123 0.256 35.549 0.541 0.052 0.084 0.864

B I Seq1 124 0.153 28.342 0.137 0.802 0.014 0.185

E L Seq1 125 0.583 106.692 0.788 0.879 0.010 0.111

E T Seq1 126 0.352 48.892 1.687 0.938 0.007 0.055

B F Seq1 127 0.032 6.382 0.458 0.970 0.001 0.030

E P Seq1 128 0.285 40.498 1.312 0.970 0.001 0.030

E A Seq1 129 0.529 58.318 1.557 0.970 0.001 0.030

B Y Seq1 130 0.129 27.546 0.960 0.970 0.001 0.030

B L Seq1 131 0.014 2.545 1.743 0.988 0.000 0.012

E E Seq1 132 0.354 61.809 2.002 0.988 0.000 0.012

E N Seq1 133 0.411 60.200 2.264 0.988 0.000 0.012

B A Seq1 134 0.032 3.482 1.047 0.970 0.001 0.030

B A Seq1 135 0.021 2.347 1.192 0.970 0.001 0.030

E K Seq1 136 0.529 108.795 1.939 0.988 0.000 0.012

E L Seq1 137 0.281 51.433 1.669 0.970 0.001 0.030

B F Seq1 138 0.021 4.275 0.859 0.970 0.001 0.030

E T Seq1 139 0.421 58.434 1.601 0.923 0.002 0.076

E A Seq1 140 0.791 87.124 0.899 0.782 0.003 0.216

E K Seq1 141 0.476 97.810 1.130 0.176 0.004 0.820

E G Seq1 142 0.669 52.666 -0.246 0.003 0.003 0.994

B A Seq1 143 0.074 8.210 -0.154 0.005 0.015 0.979

E K Seq1 144 0.351 72.242 1.450 0.004 0.514 0.481

B V Seq1 145 0.041 6.332 0.717 0.001 0.900 0.099

B I Seq1 146 0.018 3.349 1.395 0.000 0.983 0.017

B L Seq1 147 0.020 3.735 0.878 0.000 0.983 0.017

B S Seq1 148 0.020 2.391 0.667 0.001 0.900 0.099

B S Seq1 149 0.027 3.153 -0.004 0.004 0.420 0.576

B Q Seq1 150 0.049 8.734 -0.304 0.019 0.141 0.840

B T Seq1 151 0.107 14.896 -0.193 0.020 0.205 0.775

B P Seq1 152 0.179 25.457 -1.121 0.019 0.141 0.840

B N Seq1 153 0.235 34.419 -1.091 0.018 0.088 0.893

E N Seq1 154 0.328 48.078 -1.224 0.018 0.047 0.935

E P Seq1 155 0.483 68.524 -1.448 0.058 0.017 0.925

E W Seq1 156 0.258 62.073 -0.866 0.058 0.017 0.925

E E Seq1 157 0.679 118.709 -1.238 0.053 0.005 0.942

E T Seq1 158 0.733 101.625 -1.811 0.053 0.005 0.942

E G Seq1 159 0.433 34.085 -1.725 0.058 0.017 0.925

E T Seq1 160 0.519 71.944 0.082 0.053 0.043 0.903

B F Seq1 161 0.173 34.661 -0.078 0.113 0.043 0.844

E V Seq1 162 0.364 56.008 -0.398 0.113 0.043 0.844

E N Seq1 163 0.537 78.631 -1.278 0.181 0.016 0.803

E S Seq1 164 0.339 39.789 0.175 0.181 0.016 0.803

B P Seq1 165 0.101 14.289 -0.016 0.858 0.002 0.139

E T Seq1 166 0.515 71.486 1.041 0.923 0.002 0.076

E R Seq1 167 0.431 98.791 1.400 0.923 0.002 0.076

B F Seq1 168 0.031 6.242 0.701 0.970 0.001 0.030

B V Seq1 169 0.086 13.203 0.604 0.970 0.001 0.030

E E Seq1 170 0.537 93.744 1.844 0.988 0.000 0.012

B Y Seq1 171 0.063 13.378 1.299 0.970 0.001 0.030

B A Seq1 172 0.017 1.862 1.571 0.988 0.000 0.012

E E Seq1 173 0.307 53.598 1.955 0.988 0.000 0.012

E L Seq1 174 0.464 84.995 2.011 0.988 0.000 0.012

B A Seq1 175 0.032 3.559 0.717 0.970 0.001 0.030

B A Seq1 176 0.019 2.127 0.286 0.970 0.001 0.030

E E Seq1 177 0.639 111.546 1.584 0.923 0.002 0.076

E V Seq1 178 0.611 93.880 1.004 0.858 0.002 0.139

E A Seq1 179 0.281 30.955 1.465 0.321 0.003 0.675

E G Seq1 180 0.778 61.236 1.058 0.003 0.003 0.994

B V Seq1 181 0.050 7.700 0.990 0.005 0.045 0.951

B E Seq1 182 0.278 48.602 0.656 0.004 0.420 0.576

B Y Seq1 183 0.065 13.869 0.634 0.001 0.900 0.099

B V Seq1 184 0.056 8.638 1.478 0.001 0.900 0.099

B D Seq1 185 0.154 22.177 -0.223 0.004 0.616 0.381

B H Seq1 186 0.082 14.861 -0.307 0.056 0.142 0.802

B W Seq1 187 0.203 48.846 0.383 0.257 0.016 0.727

E S Seq1 188 0.426 49.904 0.569 0.782 0.003 0.216

E Y Seq1 189 0.280 59.772 0.156 0.858 0.002 0.139

B V Seq1 190 0.037 5.625 -0.555 0.858 0.002 0.139

B D Seq1 191 0.213 30.693 0.858 0.970 0.001 0.030

E S Seq1 192 0.537 62.983 1.061 0.970 0.001 0.030

B I Seq1 193 0.110 20.387 0.727 0.970 0.001 0.030

B Y Seq1 194 0.053 11.283 -0.183 0.923 0.002 0.076

E E Seq1 195 0.586 102.339 0.962 0.923 0.002 0.076

E T Seq1 196 0.626 86.882 0.460 0.782 0.003 0.216

B L Seq1 197 0.187 34.185 -0.507 0.502 0.002 0.495

E G Seq1 198 0.322 25.310 -0.671 0.176 0.004 0.820

E N Seq1 199 0.516 75.498 0.013 0.321 0.003 0.675

E A Seq1 200 0.652 71.839 -0.242 0.430 0.016 0.555

E T Seq1 201 0.481 66.673 -0.431 0.339 0.016 0.645

B V Seq1 202 0.229 35.182 -0.284 0.339 0.016 0.645

E N Seq1 203 0.428 62.659 0.159 0.184 0.043 0.773

E S Seq1 204 0.604 70.754 0.632 0.113 0.043 0.844

B Y Seq1 205 0.145 31.072 -0.093 0.184 0.043 0.773

B F Seq1 206 0.111 22.258 0.091 0.052 0.084 0.864

E P Seq1 207 0.342 48.572 -0.417 0.053 0.043 0.903

E I Seq1 208 0.514 94.998 -0.666 0.018 0.019 0.964

B D Seq1 209 0.113 16.312 -2.243 0.018 0.019 0.964

B H Seq1 210 0.211 38.326 -0.787 0.018 0.047 0.935

B T Seq1 211 0.069 9.515 -1.066 0.004 0.085 0.910

B H Seq1 212 0.070 12.788 0.761 0.004 0.085 0.910

B T Seq1 213 0.124 17.240 -0.010 0.005 0.045 0.951

E S Seq1 214 0.237 27.730 1.227 0.016 0.005 0.979

E P Seq1 215 0.549 77.917 -0.046 0.858 0.002 0.139

E A Seq1 216 0.444 48.940 1.503 0.923 0.002 0.076

B G Seq1 217 0.025 1.952 -0.409 0.970 0.001 0.030

B A Seq1 218 0.054 5.929 0.351 0.970 0.001 0.030

E E Seq1 219 0.367 64.167 1.549 0.970 0.001 0.030

B V Seq1 220 0.104 15.923 1.395 0.970 0.001 0.030

B V Seq1 221 0.026 4.012 1.060 0.970 0.001 0.030

B A Seq1 222 0.024 2.623 0.947 0.970 0.001 0.030

E E Seq1 223 0.322 56.271 1.603 0.970 0.001 0.030

B A Seq1 224 0.097 10.689 1.215 0.988 0.000 0.012

B F Seq1 225 0.028 5.559 0.845 0.988 0.000 0.012

B L Seq1 226 0.057 10.363 1.158 0.988 0.000 0.012

E K Seq1 227 0.473 97.399 2.155 0.988 0.000 0.012

B A Seq1 228 0.118 12.982 0.627 0.970 0.001 0.030

B V Seq1 229 0.039 5.994 -0.263 0.970 0.001 0.030

E V Seq1 230 0.422 64.861 1.407 0.923 0.002 0.076

E C Seq1 231 0.763 107.139 0.865 0.694 0.003 0.303

E T Seq1 232 0.329 45.618 0.100 0.406 0.004 0.590

E G Seq1 233 0.380 29.898 0.226 0.176 0.004 0.820

E T Seq1 234 0.385 53.427 -0.183 0.321 0.003 0.675

E S Seq1 235 0.494 57.897 0.535 0.522 0.016 0.462

B L Seq1 236 0.042 7.709 -0.400 0.717 0.014 0.269

E K Seq1 237 0.287 59.056 1.487 0.717 0.014 0.269

E S Seq1 238 0.695 81.407 1.201 0.717 0.014 0.269

B V Seq1 239 0.262 40.331 0.740 0.622 0.015 0.363

B L Seq1 240 0.066 12.085 -0.334 0.430 0.016 0.555

E T Seq1 241 0.510 70.709 0.725 0.181 0.016 0.803

E T Seq1 242 0.538 74.593 1.148 0.113 0.043 0.844

E T Seq1 243 0.563 78.088 -0.656 0.115 0.016 0.868

E S Seq1 244 0.559 65.527 -0.382 0.058 0.017 0.925

B F Seq1 245 0.171 34.340 -0.222 0.053 0.005 0.942

E E Seq1 246 0.469 81.899 -0.251 0.053 0.005 0.942

E G Seq1 247 0.605 47.629 -1.763 0.018 0.019 0.964

E T Seq1 248 0.498 69.142 0.615 0.053 0.043 0.903

E C Seq1 249 0.396 55.641 -1.112 0.053 0.043 0.903

E L Seq1 250 0.569 104.239 -0.833 0.003 0.003 0.994