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Table 3 Top 20 amino acid pairs of 4 orthologous groups according to differences and ratios in number of forward (non-halophiles to halophiles) and backward (halophiles to non-halophiles) replacements

From: Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes

  Most biased in gain Most biased in ratio
  Pair Ratio Forward no. Reverse no. Gain Pair Ratio Forward no. Reverse no. Gain
Set I (orthologous proteins I→V 1.82 1,632 895 737 C→D 9 27 3 24*
of PLUT and SRUB) I→L 1.85 1,195 647 548 I→D 8.5 34 4 30*
  K→E 4.09 704 172 532 I→P 8.43 59 7 52*
  K→R 2.06 856 416 440 K→D 6.35 438 69 369
  K→D 6.35 438 69 369 I→R 6.18 105 17 88
  E→D 1.39 1,214 874 340 L→D 4.46 107 24 83
  G→D 2.43 485 200 285 K→P 4.38 140 32 108
  S→A 1.53 818 534 284 K→E 4.09 704 172 532
  S→D 2.56 438 171 267 L→W 4.08 49 12 37
  N→D 2.45 431 176 255 M→P 3.43 48 14 34
  K→Q 2.84 330 116 214 M→E 3.28 95 29 66
  S→T 1.52 616 405 211 F→H 3.27 85 26 59
  L→V 1.31 833 635 198 I→E 3.03 94 31 63
  R→D 2.57 308 120 188 M→R 2.95 112 38 74
  S→E 1.82 403 221 182 L→E 2.91 201 69 132
  A→D 1.77 415 235 180 K→Q 2.84 330 116 214
  K→A 2.47 287 116 171 K→G 2.74 167 61 106
  L→R 2.65 252 95 157 L→R 2.65 252 95 157
  K→T 2.64 230 87 143 K→T 2.64 230 87 143
  R→E 1.39 497 357 140 R→D 2.57 308 120 188
Set II (orthologous proteins K→E 5.19 306 59 247 K→D 8.56 214 25 189
of PPUT and HMAR1) I→V 1.62 521 321 200 L→D 5.6 56 10 46
  L→V 1.75 462 264 198 K→E 5.19 306 59 247
  A→E 2.28 351 154 197 Q→D 5.11 189 37 152
  K→D 8.56 214 25 189 K→S 4.92 59 12 47
  A→D 2.93 264 90 174 H→D 4.44 80 18 62
  Q→E 2.44 266 109 157 I→D 4.2 21 5 16
  Q→D 5.11 189 37 152 I→Y 4 40 10 30
  G→D 2.41 210 87 123 P→H 3.8 19 5 14
  R→D 2.71 160 59 101 M→E 3.63 29 8 21
  R→E 1.95 207 106 101 L→P 3.43 48 14 34
  N→D 2.35 169 72 97 Y→D 3.38 27 8 19
  E→D 1.25 429 343 86 K→T 3.29 102 31 71
  S→T 1.46 249 170 79 C→A 3.24 81 25 56
  S→D* 1.9 152 80 72 L→E 3.13 100 32 68
  K→T 3.29 102 31 71 K→G 2.95 65 22 43
  A→T 1.55 198 128 70 A→D 2.93 264 90 174
  P→D 2.82 107 38 69 K→P 2.91 32 11 21
  L→I* 1.25 349 280 69 P→D 2.82 107 38 69
  L→E 3.13 100 32 68 I→E 2.75 44 16 28
Set III (orthologous proteins I→V 2.23 3,368 1,513 1,855 C→Q 10.00 30 3 27*
of MTHP and HMAR1) R→E 2.62 1,836 701 1,135 K→D 7.30 883 121 762
  R→D 4.34 1,306 301 1,005 M→D 7.28 182 25 158
  E→D 1.52 2,576 1,693 883 C→D 5.31 69 13 56
  K→E 4.11 1,162 283 879 I→Q 5.10 148 29 119
  I→L 1.70 2,087 1,230 857 M→Q 4.91 157 32 125
  S→D 2.84 1,312 462 850 C→E 4.86 68 14 54
  K→D 7.30 883 121 762 I→D 4.80 192 40 152
  L→V 1.60 1,978 1,237 741 L→D 4.49 337 75 262
  G→D 2.35 1,183 504 679 M→H 4.44 80 18 62
  S→A 1.61 1,556 967 589 K→Q 4.42 407 92 315
  S→E 2.00 1,054 527 527 R→D 4.34 1,306 301 1,005
  R→A 2.14 978 458 520 K→E 4.11 1,162 283 879
  R→T 3.10 740 239 501 K→G 4.04 331 82 249
  L→A 2.11 946 448 498 C→N 4.00 32 8 24*
  I→A 2.76 756 274 482 I→W 3.88 62 16 46
  I→T 3.84 572 149 423 I→T 3.84 572 149 423
  V→T 1.88 892 475 417 M→E 3.81 259 68 191
  N→D 2.23 753 337 416 K→T 3.79 425 112 313
  R→Q 2.45 697 284 413 W→D 3.69 48 13 35*
Set IV (orthologous proteins I→V 2.58 3,584 1,389 2,195 K→D 12.93 1,461 113 1,348
of UMET and NPHA) K→E 8.72 2,023 232 1,791 K→E 8.72 2,023 232 1,791
  K→D 12.93 1,461 113 1,348 K→A 8.28 993 120 873
  K→R 3.01 1,623 540 1,083 K→G 6.57 519 79 440
  I→L 1.95 2,135 1,096 1,039 M→D 6.50 130 20 110
  K→A 8.28 993 120 873 M→R 5.59 246 44 202
  N→D 3.20 1,024 320 704 K→T 5.44 685 126 559
  S→A 1.65 1,515 920 595 C→R 5.00 60 12 48
  K→T 5.44 685 126 559 K→P 4.92 300 61 239
  I→A 2.78 760 273 487 I→E 4.75 318 67 251
  M→L 1.93 1,000 517 483 I→H 4.48 103 23 80
  G→D 1.85 1,037 561 476 K→S 4.42 570 129 441
  S→D 1.98 915 462 453 I→D 4.05 174 43 131
  I→T 3.88 606 156 450 C→N 4.00 32 8 24*
  K→S 4.42 570 129 441 K→Q 3.95 510 129 381
  K→G 6.57 519 79 440 I→T 3.88 606 156 450
  V→A 1.41 1,464 1,040 424 M→H 3.82 65 17 48
  L→V 1.32 1,753 1,329 424 I→R 3.81 278 73 205
  R→E 1.57 1,136 724 412 M→E 3.48 212 61 151
  E→D 1.23 2,181 1,774 407 M→P 3.41 75 22 53
  1. All the replacements of amino acid pairs are significant at p < 10-3 for set I, p < 10-2 for set II, and p < 10-6 for sets III and IV, except replacements marked with asterisks. Organism abbreviations are listed in Table 1.
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