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. 2013 Jul 13;14:474. doi: 10.1186/1471-2164-14-474

Table 5.

The rate of synonymous (Ks) and non-synonymous (Ka) nucleotide substitution for secretory (signal peptide and mature peptide) and non-secretory proteomes

  Ka (±S. E.) Ks (±S. E.) Ka/Ks (±S. E.)
Frankia ACN/ CcI
  
  
  
Signal Peptide (SP)
 0.897 ± 0.335
 11.698 ± 2. 627
 0.182 ± 0.031
Mature Peptide (MP)
 0.151 ± 0.009
 10.499 ± 3. 11
 0.066 ± 0.005
Secretory Protein (Sec)
 0.105 ± 0.006
 6.893 ± 2. 006
 0.051 ± 0.003
Non-secretory Protein (NSec)
 0.083 ± 0.002
 6.555 ± 0.614
 0.043 ± 0.001
Frankia ACN/ FD
  
  
  
Signal Peptide (SP)
 0.5656 ± 0.2004
 24.4256 ± 14.1669
 0.1952 ± 0.063
Mature Peptide (MP)
 0.2370 ± 0.0328
 12.1243 ± 9.3627
 0.0980 ± 0.028
Secretory Protein (Sec)
 0.2690 ± 0.0255
 27.415 ± 10.51547
 0.077 ± 0.0211
Non-secretory Protein (NSec)
 0.1862 ± 0.0028
 31.77567 ± 1.283
 0.0336 ± 0.001
Frankia ACN/ Ean
  
  
  
Signal Peptide (SP)
 2.14 ± 0.6975
 23.82 ± 4. 32
 0.479 ± 0.262
Mature Peptide (MP)
 0.194 ± 0.0124
 29.85 ± 6. 224
 0.0363 ± 0.005
Secretory Protein (Sec)
 0.183 ± 0.008
 29.785 ± 4. 460
 0.040 ± 0.004
Non-secretory Protein (NSec)
 0.144 ± 0.002
 23.688 ± 1. 120
 0.036 ± 0.001
Frankia ACN/ Eul
  
  
  
Signal Peptide (SP)
 2. 99 ± 0.754
 29. 198 ± 4. 055
 0.568 ± 0.211
Mature Peptide (MP)
 0.258 ± 0.011
 50.244 ± 6. 94
 0.035 ± 0.004
Secretory Protein (Sec)
 0.235 ± 0.008
 36. 971 ± 4. 836
 0.043 ±0.004
Non-secretory Protein (NSec)
 0.178 ± 0.003
 33. 228 ± 1. 306
 0.035 ± 0.001
Frankia CcI/FD
  
  
  
Signal Peptide (SP)
 0.3762 ± 0.0565
 5.4064 ± 2.5889
 0.2136 ± 0.0524
Mature Peptide (MP)
 0.2367 ± 0.0208
 19.3491 ± 9.5834
 0.0581 ± 0.0104
Secretory Protein (Sec)
 0.265 ± 0.02113
 18.01 ± 7.5958
 0.0633 ± 0.0103
Non-secretory Protein (NSec)
 0.1901 ± 0.003
 28.1726 ± 1.158
 0.0334 ± 0.001
Frankia CcI/ Ean
  
  
  
Signal Peptide (SP)
 0.451 ± 0.125
 12.861 ± 6.345
 0.139 ± 0.054
Mature Peptide (MP)
 0.206 ± 0.015
 23.179 ± 10.192
 0.043 ± 0.008
Secretory Protein (Sec)
 0.179 ± 0.010
 35.333 ± 4. 793
 0.027 ± 0.003
Non-secretory Protein (NSec)
 0.147 ± 0.002
 24.320 ± 1. 059
 0.031 ± 0.001
Frankia CcI/ Eu1
  
  
  
Signal Peptide (SP)
 2.202 ± 1. 866
 13.475 ± 8. 425
 0.282 ± 0.111
Mature Peptide (MP)
 0.143 ± 0.025
 21.280 ± 9. 465
 0.070 ± 0.014
Secretory Protein (Sec)
 0.097 ± 0.006
 5.761 ± 2. 462
 0.061 ± 0.005
Non-secretory Protein (NSec)
 0.097 ± 0.015
 5.244 ± 0.511
 0.047 ± 0.001
Frankia FD/ Eu1
  
  
  
Signal Peptide (SP)
 0.450 ± 0.125
 12.86 ± 6.34
 0.138 ± 0.053
Mature Peptide (MP)
 0.205 ± 0.015
 23.179 ± 10.19
 0.0429 ± 0.008
Secretory Protein (Sec)
 0.307 ± 0.015
 30.9 ± 10.99
 0.0502 ± 0.0125
Non-secretory Protein (NSec)
 0.189 ± 0.002
 25.7 ± 1.32
 0.0288 ± 0.009
Frankia FD/ Ean
  
  
  
Signal Peptide (SP)
 2.202 ± 1.865
 13.475 ± 8.4
 0.282 ± 0.11
Mature Peptide (MP)
 0.143 ± 0.022
 21.28 ± 5.96
 0.070 ± 0.011
Secretory Protein (Sec)
 0.329 ± 0.016
 29.094 ±10.111
 0.053 ± 0.011
Non-secretory Protein (NSec)
 0.203 ± .002
 23.128 ± 8.98
 0.028 ± .009
Frankia Ean/ Eul
  
  
  
Signal Peptide (SP)
 0.677 ± 0.037
 20.845 ± 8. 942
 0.321 ± 0.034
Mature Peptide (MP)
 0.235 ± 0.021
 23.780 ± 7. 688
 0.065 ± 0.005
Secretory Protein (Sec)
 0.230 ± 0.009
 51.172 ± 5. 025
 0.033 ± 0.001
Non-secretory Protein (NSec)
 0.201 ± 0.013
 32.649 ± 1. 250
 0.032 ± 0.004
S. coelicolor/S. avermitilis
  
  
  
Signal Peptide (SP)
 0.483 ± 0.157
 10.529 ± 2. 48
 0.166 ±0.016
Mature Peptide (MP)
 0.144 ± 0.005
 11.029 ± 3. 42
 0.061 ± 0.003
Secretory Protein (Sec)
 0.142 ± 0.005
 13.460 ± 3. 072
 0.066 ± 0.003
Non-secretory Protein (NSec)
 0.109 ± 0.002
 10.344 ± 0.601
 0.052 ± 0.001
S. coelicolor/S. griseus
  
  
  
Signal Peptide (SP)
 0.952 ± 0.229
 26.889 ± 3.260
 0.157 ± 0.0250
Mature Peptide (MP)
 0.210 ± 0.007
 28.96 ± 5.938
 0.049 ±0.003
Secretory Protein (Sec)
 0.226 ± 0.007
 39.273 ± 4.598
 0.048 ± 0.004
Non-secretory Protein (NSec)
 0.166 ± 0.002
 27.224 ± 0.941
 0.043 ± 0.001
S. coelicolor- S. somaliensis
  
  
  
Signal Peptide (SP)
 1.648 ± 0.439
 26.224 ± 5.183
 0.324 ± 0.113
Mature Peptide (MP)
 0.227 ± 0.009
 35.567 ± 3.675
 0.033 ± 0.005
Secretory Protein (Sec)
 0.235 ± 0.005
 45.582 ± 7.275
 0.041 ± 0.005
Non-secretory Protein (NSec)
 0.151 ± 0.002
 26.060 ± 1.209
 0.040 ± 0.001
S. coelicolor- S. scabiei
  
  
  
Signal Peptide (SP)
 0.585 ± 0.126
 15.974 ± 2.126
 0.177 ± 0.016
Mature Peptide (MP)
 0.172 ± 0.005
 18.214 ± 3.100
 0.057 ± 0.003
Secretory Protein (Sec)
 0.159 ± 0.008
 15.480 ± 4.913
 0.067 ± 0.005
Non-secretory Protein (NSec)
 0.103 ± 0.002
 10.699 ± 0.802
 0.050 ± 0.001
S. avermitilis- S. somaliensis
  
  
  
Signal Peptide (SP)
 0.634 ± 0.101
 23.098 ± 4.180
 0.347 ± 0.088
Mature Peptide (MP)
 0.233 ± 0.009
 43.112 ± 6.251
 0.040 ± 0.005
Secretory Protein (Sec)
 0.236 ± 0.008
 41.932 ± 6.196
 0.042 ± 0.005
Non-secretory Protein (NSec)
 0.147 ± 0.002
 27.533 ± 1.286
 0.036 ± 0.001
S. avermitilis- S. scabiei
  
  
  
Signal Peptide (SP)
 0.554 ± 0.146
 12.172 ± 1.912
 0.268 ± 0.038
Mature Peptide (MP)
 0.164 ± 0.005
 13.605 ± 2.619
 0.068 ± 0.003
Secretory Protein (Sec)
 0.134 ± 0.006
 3.663 ± 1.879
 0.084 ± 0.005
Non-secretory Protein (NSec)
 0.096 ± 0.002
 7.412 ± 0.719
 0.055 ± 0.001
S. avermitilis/ S. griseus
  
  
  
Signal Peptide (SP)
 1.359 ± 0.326
 21.298 ± 2.755
 0.504 ± 0.036
Mature Peptide (MP)
 0.210 ± 0.007
 48.403 ± 6.312
 0.037 ± 0.003
Secretory Protein (Sec)
 0.234 ± 0.006
 44. 581 ± 4.500
 0.047 ± 0.005
Non-secretory Protein (NSec)
 0.158 ± 0.002
 26. 284 ± 0.889
 0.040 ± 0.001
S. somaliensis- S. scabiei
  
  
  
Signal Peptide (SP)
 1.346 ± 0.450
 25.264 ± 4.391
 0.492 ± 0.283
Mature Peptide (MP)
 0.223 ± 0.007
 24.696 ± 5.321
 0.032 ± 0.004
Secretory Protein (Sec)
 0.232 ± 0.008
 42.124 ± 6.385
 0.056 ± 0.006
Non-secretory Protein (NSec)
 0.151 ± 0.002
 27.537 ± 1.294
 0.035 ± 0.004
S. somaliensis- S. griseus
  
  
  
Signal Peptide (SP)
 0.565 ± 0.145
 20.919 ± 3.434
 0.170 ± 0.026
Mature Peptide (MP)
 0.220 ± 0.009
 42.007 ± 6.413
 0.034 ± 0.004
Secretory Protein (Sec)
 0.197 ± 0.006
 38.510 ± 6.153
 0.043 ± 0.005
Non-secretory Protein (NSec)
 0.157 ± 0.039
 20.710 ± 3.643
 0.041 ± 0.003
S. scabiei- S. griseus
  
  
  
Signal Peptide (SP)
 0.734 ± 0.178
 22.970 ± 2.788
 0.743 ± 0.256
Mature Peptide (MP)
 0.216 ± 0.007
 49.319 ± 6.226
 0.037 ± 0.003
Secretory Protein (Sec)
 0.211 ± 0.008
 36.526 ± 6.828
 0.046 ± 0.005
Non-secretory Protein (NSec)
 0.148 ± 0.002
 24.148 ± 1.233
 0.040 ± 0.001
M. tuberculosis/M. leprae
  
  
  
Signal Peptide (SP)
 0.414 ± 0.0408
 12.978 ± 6.284
 0.165 ± 0.069
Mature Peptide (MP)
 0.111 ± 0.011
 1.406 ± 0.055
 0.079 ± 0.008
Secretory Protein (Sec)
 0.137 ± 0.009
 1.4109 ± 0.076
 0.099 ± 0.008
Non-secretory Protein (NSec)
 0.122 ± 0.002
 2.173 ± 0.288
 0.088 ± 0.001
M. tuberculosis/M. smegmatis
  
  
  
Signal Peptide (SP)
 1.059 ± 0.273
 30.888 ± 8.194
 0.098 ± 0.031
Mature Peptide (MP)
 0.199 ± 0.021
 23.071 ± 10.099
 0.043 ± 0.014
Secretory Protein (Sec)
 0.239 ± 0.017
 39.868 ± 9.856
 0.032 ± 0.0105
Non-secretory Protein (NSec)
 0.163 ± 0.003
 28.329 ± 1.413
 0.030 ± 0.001
M. tuberculosis/ M. ulcerans
  
  
  
Signal Peptide (SP)
 0.685 ± 0.258
 8.146 ± 3.966
 0.436 ± 0.159
Mature Peptide (MP)
 0.109 ± 0.014
 5.997 ± 4.625
 0.069 ± 0.010
Secretory Protein (Sec)
 0.127 ± 0.012
 1.48434 ± 0.077
 0.0864 ± 0.007
Non-secretory Protein (NSec)
 0.096 ± 0.002
 2.616 ± 0.353
 0.065 ± 0.001
M. tuberculosis/ M. vanbaalenii
  
  
  
Signal Peptide (SP)
 0.821 ± 0.083
 13.294 ± 5.633
 0.247 ± 0.072
Mature Peptide (MP)
 0.226 ± 0.018
 21.208 ± 9.415
 0.053 ± 0.012
Secretory Protein (Sec)
 0.247 ± 0.015
 20.711 ± 7.419
 0.049 ± 0.009
Non-secretory Protein (NSec)
 0.168 ± 0.003
 26.060 ± 1.344
 0.032 ± 0.001
M. leprae/ M. smegmatis
  
  
  
Signal Peptide (SP)
 1.003 ± 0.129
 20.464 ± 6.323
 0.207 ± 0.062
Mature Peptide (MP)
 0.247 ± 0.025
 16.558 ± 5.325
 0.0278 ± 0.005
Secretory Protein (Sec)
 0.281 ± 0.018
 34.78545 ± 6.822
 0.02763 ± 0.006
Non-secretory Protein (NSec)
 0.188 ± 0.003
 28.210 ± 1.291
 0.026 ± 0.001
M. leprae/ M. ulcerans
  
  
  
Signal Peptide (SP)
 0.462 ± 0.056
 14.975 ± 6.791
 0.273 ± 0.080
Mature Peptide (MP)
 0.158 ± 0.021
 6.794 ± 4.753
 0.0731 ± 0.009
Secretory Protein (Sec)
 0.176 ± 0.020
 5.359 ± 3.338
 0.081 ± 0.007
Non-secretory Protein (NSec)
 0.132 ± 0.003
 2.877 ± 0.312
 0.070 ± 0.002
M. leprae/ M. vanbalanii
  
  
  
Signal Peptide (SP)
 1.322 ± 0.349
 33.707 ± 8.948
 0.115 ± 0.048
Mature Peptide (MP)
 0.278 ± 0.0267
 17.136 ± 6.912
 0.038 ± 0.006
Secretory Protein (Sec)
 0.302 ± 0.021
 25.442 ± 6.775
 0.041 ± 0.008
Non-secretory Protein (NSec)
 0.193 ± 0.004
 25.629 ± 1.238
 0.029 ± 0.001
M. smegmatis / M. ulcerans
  
  
  
Signal Peptide (SP)
 1.409 ± 0.415
 18.212 ± 5.189
 0.293 ± 0.138
Mature Peptide (MP)
 0.225 ± 0.0184
 18.889 ± 7.0584
 0.041947 ± 0.007
Secretory Protein (Sec)
 0.257 ± 0.017
 27.432 ± 6.438
 0.037 ± 0.006
Non-secretory Protein (NSec)
 0.163 ± 0.003
 28.286 ± 1.443
 0.030008 ± 0.001
M. smegmatis / M. vanbaalenii
  
  
  
Signal Peptide (SP)
 3.458 ± 1.548
 19.415 ± 5.519
 0.668 ± 0.356
Mature Peptide (MP)
 0.1737 ± 0.014936
 19.717 ± 8.35107
 0.0518 ± 0.0084
Secretory Protein (Sec)
 0.2046 ± 0.01668
 23.418 ± 7.994028
 0.0621 ± 0.0111
Non-secretory Protein (NSec)
 0.1252 ± 0.0027
 16.09933 ± 1.215
 0.0416 ± 0.0014
M. ulcerans / M. vanbaalenii
  
  
  
Signal Peptide (SP)
 1.640 ± 0.833
 20.487 ± 5.451
 0.1985 ± 0.0625
Mature Peptide (MP)
 0.2575 ± 0.017255
 13.6171 ± 4.540
 0.0524 ± 0.0084
Secretory Protein (Sec)
 0.2721 ± 0.0158
 24.692 ± 6.523
 0.0438 ± 0.0071
Non-secretory Protein (NSec) 0.165 ± 0.0031 27.909 ± 1.427 0.0309 ± 0.0011