" 58 " " 54 45 " " 81 16 528 " " 56 113 34 10 " " 57 310 86 49 9 " " 105 29 58 767 5 323 " " 179 137 81 130 59 26 119 " " 27 328 391 112 69 597 26 23 " " 36 22 47 11 17 9 12 6 16 " " 30 38 12 7 23 72 9 6 56 229 " " 35 646 263 26 7 292 181 27 45 21 14 " " 54 44 30 15 31 43 18 14 33 479 388 65 " " 15 5 10 4 78 4 5 5 40 89 248 4 43 " " 194 74 15 15 14 164 18 24 115 10 102 21 16 17 " " 378 101 503 59 223 53 30 201 73 40 59 47 29 92 285 " " 475 64 232 38 42 51 32 33 46 245 25 103 226 12 118 477 " " 9 126 8 4 115 18 10 55 8 9 52 10 24 53 6 35 12 " " 11 20 70 46 209 24 7 8 573 32 24 8 18 536 10 63 21 71 " " 298 17 16 31 62 20 45 47 11 961 180 14 323 62 23 38 112 25 16 " " 0.076748 0.051691 0.042645 0.051544 0.019803 0.040752 0.061830 " " 0.073152 0.022944 0.053761 0.091904 0.058676 0.023826 0.040126 " " 0.050901 0.068765 0.058565 0.014261 0.032102 0.066005 " " Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val " " S_ij = S_ji and PI_i for the Jones model based on the SWISSPROT " " Version 22 data. " " Rate Q_ij=S_ij*PI_j. " " The rest of the file is not used. " " Prepared by Z. Yang, March 1995. " " See the following reference for notation: " " Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid substitution and " " applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611. " " ----------------------------------------------------------------------- " " 426 " " 333 185 " " 596 80 2134 " " 159 214 54 20 " " 332 1203 277 192 14 " " 920 176 286 4497 11 1497 " " 1853 954 470 907 158 144 999 " " 88 716 704 244 58 1027 69 71 " " 286 114 198 59 34 37 72 44 37 " " 394 332 88 62 79 497 101 80 217 2086 " " 294 3606 1209 148 15 1289 1210 215 115 121 140 " " 185 100 56 34 27 78 50 47 33 1129 1567 167 " " 84 21 33 16 115 14 23 28 69 354 1690 17 76 " " 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 " " 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 " " 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 " " 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 " " 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 " " 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 " " A R N D C Q E G H I L K M F P S T W Y V " " Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val " " Accepted point mutations (x10), similar to Figure 80 of Dayhoff et " " al. (1978). SwissProt version 22 data. " " ------------------------------------------------------------------------------ " " 256458 426 333 596 159 332 920 1853 88 286 394 294 185 84 1395 3664 3920 19 49 2771 " " 426 182302 185 80 214 1203 176 954 716 114 332 3606 100 21 360 661 360 171 62 111 " " 333 185 150772 2134 54 277 286 470 704 198 88 1209 56 33 64 2706 1069 9 178 86 " " 596 80 2134 178390 20 192 4497 907 244 59 62 148 34 16 74 390 216 5 142 195 " " 159 214 54 20 68120 14 11 158 58 34 79 15 27 115 27 559 91 60 246 150 " " 332 1203 277 192 14 139546 1497 144 1027 37 497 1289 78 14 629 278 227 20 59 100 " " 920 176 286 4497 11 1497 218432 999 69 72 101 1210 50 23 106 236 217 17 26 336 " " 1853 954 470 907 158 144 999 255274 71 44 80 215 47 28 171 1861 266 106 34 420 " " 88 716 704 244 58 1027 69 71 77124 37 217 115 33 69 249 214 116 5 777 32 " " 286 114 198 59 34 37 72 44 37 191018 2086 121 1129 354 54 274 1420 13 102 6260 " " 394 332 88 62 79 497 101 80 217 2086 319504 140 1567 1690 882 691 256 127 131 2020 " " 294 3606 1209 148 15 1289 1210 215 115 121 140 206568 167 17 117 351 653 16 30 99 " " 185 100 56 34 27 78 50 47 33 1129 1567 167 84670 76 36 89 579 15 25 937 " " 84 21 33 16 115 14 23 28 69 354 1690 17 76 143088 66 468 54 56 1276 307 " " 1395 360 64 74 27 629 106 171 249 54 882 117 36 66 175488 1839 653 8 32 142 " " 3664 661 2706 390 559 278 236 1861 214 274 691 351 89 468 1839 234536 3527 64 259 320 " " 3920 360 1069 216 91 227 217 266 116 1420 256 653 579 54 653 3527 203636 18 73 805 " " 19 171 9 5 60 20 17 106 5 13 127 16 15 56 8 64 18 50486 60 44 " " 49 62 178 142 246 59 26 34 777 102 131 30 25 1276 32 259 73 60 114728 63 " " 2771 111 86 195 150 100 336 420 32 6260 2020 99 937 307 142 320 805 44 63 223724 " " Observed difference counts from pairwise comparisons, with ancestral sequences " " constructed by parsimony. F(t) = PI*P(t). " " Based on the SwissProt 22 data, kindly provided by D. Jones (Jones et al. 1992) " " ------------------------------------------------------------------------------- " " Ala 0.98754 0.00030 0.00023 0.00042 0.00011 0.00023 0.00065 0.00130 0.00006 0.00020 0.00028 0.00021 0.00013 0.00006 0.00098 0.00257 0.00275 0.00001 0.00003 0.00194 " " Arg 0.00044 0.98974 0.00019 0.00008 0.00022 0.00125 0.00018 0.00099 0.00075 0.00012 0.00035 0.00376 0.00010 0.00002 0.00037 0.00069 0.00037 0.00018 0.00006 0.00012 " " Asn 0.00042 0.00023 0.98720 0.00269 0.00007 0.00035 0.00036 0.00059 0.00089 0.00025 0.00011 0.00153 0.00007 0.00004 0.00008 0.00342 0.00135 0.00001 0.00022 0.00011 " " Asp 0.00062 0.00008 0.00223 0.98954 0.00002 0.00020 0.00470 0.00095 0.00025 0.00006 0.00006 0.00015 0.00004 0.00002 0.00008 0.00041 0.00023 0.00001 0.00015 0.00020 " " Cys 0.00043 0.00058 0.00015 0.00005 0.99432 0.00004 0.00003 0.00043 0.00016 0.00009 0.00021 0.00004 0.00007 0.00031 0.00007 0.00152 0.00025 0.00016 0.00067 0.00041 " " Gln 0.00044 0.00159 0.00037 0.00025 0.00002 0.98955 0.00198 0.00019 0.00136 0.00005 0.00066 0.00170 0.00010 0.00002 0.00083 0.00037 0.00030 0.00003 0.00008 0.00013 " " Glu 0.00080 0.00015 0.00025 0.00392 0.00001 0.00130 0.99055 0.00087 0.00006 0.00006 0.00009 0.00105 0.00004 0.00002 0.00009 0.00021 0.00019 0.00001 0.00002 0.00029 " " Gly 0.00136 0.00070 0.00035 0.00067 0.00012 0.00011 0.00074 0.99350 0.00005 0.00003 0.00006 0.00016 0.00003 0.00002 0.00013 0.00137 0.00020 0.00008 0.00003 0.00031 " " His 0.00021 0.00168 0.00165 0.00057 0.00014 0.00241 0.00016 0.00017 0.98864 0.00009 0.00051 0.00027 0.00008 0.00016 0.00058 0.00050 0.00027 0.00001 0.00182 0.00008 " " Ile 0.00029 0.00011 0.00020 0.00006 0.00003 0.00004 0.00007 0.00004 0.00004 0.98729 0.00209 0.00012 0.00113 0.00035 0.00005 0.00027 0.00142 0.00001 0.00010 0.00627 " " Leu 0.00023 0.00019 0.00005 0.00004 0.00005 0.00029 0.00006 0.00005 0.00013 0.00122 0.99330 0.00008 0.00092 0.00099 0.00052 0.00040 0.00015 0.00007 0.00008 0.00118 " " Lys 0.00027 0.00331 0.00111 0.00014 0.00001 0.00118 0.00111 0.00020 0.00011 0.00011 0.00013 0.99100 0.00015 0.00002 0.00011 0.00032 0.00060 0.00001 0.00003 0.00009 " " Met 0.00042 0.00023 0.00013 0.00008 0.00006 0.00018 0.00011 0.00011 0.00007 0.00255 0.00354 0.00038 0.98818 0.00017 0.00008 0.00020 0.00131 0.00003 0.00006 0.00212 " " Phe 0.00011 0.00003 0.00004 0.00002 0.00015 0.00002 0.00003 0.00004 0.00009 0.00047 0.00227 0.00002 0.00010 0.99360 0.00009 0.00063 0.00007 0.00008 0.00171 0.00041 " " Pro 0.00148 0.00038 0.00007 0.00008 0.00003 0.00067 0.00011 0.00018 0.00026 0.00006 0.00093 0.00012 0.00004 0.00007 0.99270 0.00194 0.00069 0.00001 0.00003 0.00015 " " Ser 0.00287 0.00052 0.00212 0.00031 0.00044 0.00022 0.00018 0.00146 0.00017 0.00021 0.00054 0.00027 0.00007 0.00037 0.00144 0.98556 0.00276 0.00005 0.00020 0.00025 " " Thr 0.00360 0.00033 0.00098 0.00020 0.00008 0.00021 0.00020 0.00024 0.00011 0.00131 0.00024 0.00060 0.00053 0.00005 0.00060 0.00324 0.98665 0.00002 0.00007 0.00074 " " Trp 0.00007 0.00065 0.00003 0.00002 0.00023 0.00008 0.00006 0.00040 0.00002 0.00005 0.00048 0.00006 0.00006 0.00021 0.00003 0.00024 0.00007 0.99686 0.00023 0.00017 " " Tyr 0.00008 0.00010 0.00030 0.00024 0.00041 0.00010 0.00004 0.00006 0.00130 0.00017 0.00022 0.00005 0.00004 0.00214 0.00005 0.00043 0.00012 0.00010 0.99392 0.00011 " " Val 0.00226 0.00009 0.00007 0.00016 0.00012 0.00008 0.00027 0.00034 0.00003 0.00511 0.00165 0.00008 0.00076 0.00025 0.00012 0.00026 0.00066 0.00004 0.00005 0.98761 " " P(0.01), amino acid exchange data generated from SWISSPROT Release 22.0 " " Ref. Jones D.T., Taylor W.R. and Thornton J.M. (1992) CABIOS 8:275-282 " " Usable sequences: 23824 " " Final alignments: 5437 " " Accepted point mutations: 92883 " " A R N D C Q E G H I L K M F P S T W Y V " " 0.0767477 100 " " 0.0516907 82.3263 " " 0.0426448 102.697 " " 0.0515445 83.8924 " " 0.0198027 45.6097 " " 0.0407523 83.8825 " " 0.0618296 75.7914 " " 0.0731516 52.1273 " " 0.0229438 91.1374 " " 0.0537609 101.99 " " 0.0919042 53.7672 " " 0.0586762 72.2308 " " 0.0238262 94.8144 " " 0.0401265 51.3146 " " 0.0509007 58.5874 " " 0.0687652 115.899 " " 0.0585647 107.092 " " 0.0142613 25.2297 " " 0.0321015 48.7629 " " 0.0660051 99.4571 " " " " Normalized Relative " " frequency mutabilities " " (SUM m*f) = 80.240436 " " ------------------------------------------- "