# This file is the result of combining several RDB files, specifically # T0375.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0375.t2k.stride-ebghtl.rdb (weight 1.24869) # T0375.t2k.str2.rdb (weight 1.54758) # T0375.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0375.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0375 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0375.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1213 # # ============================================ # Comments from T0375.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0375 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0375.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1213 # # ============================================ # Comments from T0375.t2k.str2.rdb # ============================================ # TARGET T0375 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0375.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1213 # # ============================================ # Comments from T0375.t2k.alpha.rdb # ============================================ # TARGET T0375 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0375.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1213 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0739 0.0321 0.8940 2 S 0.1530 0.0439 0.8031 3 Q 0.4762 0.0258 0.4980 4 I 0.8855 0.0176 0.0970 5 L 0.9160 0.0088 0.0752 6 C 0.9154 0.0064 0.0782 7 V 0.8121 0.0340 0.1539 8 G 0.5589 0.0302 0.4109 9 L 0.4331 0.0912 0.4757 10 V 0.6732 0.0761 0.2507 11 V 0.7357 0.0692 0.1951 12 L 0.7786 0.0545 0.1669 13 D 0.7210 0.0725 0.2065 14 V 0.7161 0.0785 0.2054 15 I 0.7159 0.0584 0.2257 16 S 0.6440 0.0488 0.3072 17 L 0.4536 0.0462 0.5002 18 V 0.2370 0.0688 0.6942 19 D 0.0916 0.1288 0.7796 20 K 0.0899 0.1082 0.8019 21 Y 0.1517 0.0647 0.7837 22 P 0.1441 0.0751 0.7808 23 K 0.1193 0.0712 0.8095 24 E 0.0652 0.1337 0.8011 25 D 0.0664 0.0908 0.8427 26 S 0.2293 0.0832 0.6875 27 E 0.4896 0.0712 0.4392 28 I 0.5581 0.0656 0.3763 29 R 0.5404 0.0625 0.3971 30 C 0.4047 0.1190 0.4764 31 L 0.3358 0.1515 0.5127 32 S 0.3744 0.1524 0.4732 33 Q 0.5363 0.0907 0.3729 34 R 0.6444 0.0577 0.2979 35 W 0.6415 0.0672 0.2914 36 Q 0.4103 0.0664 0.5232 37 R 0.1543 0.1113 0.7344 38 G 0.0601 0.1196 0.8203 39 G 0.0422 0.2307 0.7271 40 N 0.0137 0.7507 0.2356 41 A 0.0060 0.9106 0.0834 42 S 0.0048 0.9505 0.0447 43 N 0.0047 0.9574 0.0379 44 S 0.0047 0.9600 0.0353 45 C 0.0047 0.9605 0.0349 46 T 0.0047 0.9603 0.0350 47 I 0.0047 0.9608 0.0345 48 L 0.0048 0.9576 0.0376 49 S 0.0051 0.9457 0.0491 50 L 0.0064 0.8919 0.1017 51 L 0.0429 0.4125 0.5445 52 G 0.0393 0.0269 0.9338 53 A 0.0769 0.0160 0.9071 54 P 0.3192 0.0223 0.6586 55 C 0.8712 0.0064 0.1225 56 A 0.9055 0.0133 0.0812 57 F 0.9256 0.0050 0.0694 58 M 0.8947 0.0110 0.0943 59 G 0.7843 0.0119 0.2038 60 S 0.5822 0.0303 0.3875 61 M 0.3037 0.0543 0.6420 62 A 0.1253 0.0410 0.8337 63 P 0.0621 0.0634 0.8745 64 G 0.0582 0.1750 0.7668 65 H 0.0074 0.8140 0.1786 66 V 0.0100 0.8616 0.1284 67 A 0.0061 0.9353 0.0585 68 D 0.0051 0.9551 0.0398 69 F 0.0047 0.9581 0.0372 70 V 0.0047 0.9580 0.0373 71 L 0.0047 0.9591 0.0362 72 D 0.0048 0.9588 0.0364 73 D 0.0048 0.9580 0.0372 74 L 0.0048 0.9563 0.0389 75 R 0.0050 0.9455 0.0496 76 R 0.0056 0.9029 0.0915 77 Y 0.0423 0.3697 0.5880 78 S 0.0401 0.0269 0.9331 79 V 0.0967 0.0147 0.8886 80 D 0.2271 0.0200 0.7529 81 L 0.3020 0.2594 0.4387 82 R 0.3287 0.3052 0.3661 83 Y 0.5642 0.1355 0.3003 84 T 0.7130 0.0222 0.2648 85 V 0.7127 0.0187 0.2686 86 F 0.6300 0.0288 0.3412 87 Q 0.3237 0.0392 0.6371 88 T 0.0851 0.0786 0.8363 89 T 0.0747 0.0494 0.8758 90 G 0.1616 0.0340 0.8044 91 S 0.2639 0.0336 0.7024 92 V 0.4459 0.0232 0.5309 93 P 0.6317 0.0183 0.3501 94 I 0.8551 0.0065 0.1385 95 A 0.9113 0.0036 0.0851 96 T 0.9266 0.0032 0.0703 97 V 0.9257 0.0034 0.0709 98 I 0.9143 0.0038 0.0819 99 I 0.8793 0.0059 0.1148 100 N 0.4634 0.0117 0.5249 101 E 0.0429 0.0970 0.8601 102 A 0.0448 0.0388 0.9164 103 S 0.0673 0.0474 0.8853 104 G 0.2693 0.0262 0.7046 105 S 0.7303 0.0128 0.2569 106 R 0.8460 0.0103 0.1437 107 T 0.8848 0.0073 0.1079 108 I 0.8657 0.0092 0.1252 109 L 0.7744 0.0167 0.2089 110 Y 0.4975 0.0319 0.4707 111 Y 0.1413 0.1182 0.7405 112 D 0.0604 0.1819 0.7576 113 R 0.0462 0.3607 0.5931 114 S 0.0449 0.4488 0.5063 115 L 0.0298 0.5312 0.4390 116 P 0.0302 0.5200 0.4498 117 D 0.0365 0.4915 0.4720 118 V 0.0519 0.4112 0.5369 119 S 0.0500 0.4316 0.5184 120 A 0.0229 0.6019 0.3751 121 T 0.0226 0.6228 0.3546 122 D 0.0225 0.6469 0.3306 123 F 0.0273 0.6277 0.3449 124 E 0.0273 0.6488 0.3239 125 K 0.0125 0.7823 0.2052 126 V 0.0127 0.7849 0.2024 127 D 0.0134 0.7785 0.2081 128 L 0.0219 0.7163 0.2618 129 T 0.0217 0.5626 0.4157 130 Q 0.0365 0.2965 0.6670 131 F 0.1032 0.0743 0.8226 132 K 0.1047 0.0811 0.8142 133 W 0.7913 0.0179 0.1908 134 I 0.9151 0.0065 0.0784 135 H 0.9238 0.0054 0.0709 136 I 0.9008 0.0085 0.0907 137 E 0.7081 0.0338 0.2581 138 G 0.3264 0.0523 0.6212 139 R 0.1964 0.0846 0.7191 140 N 0.1449 0.0982 0.7570 141 A 0.0641 0.0883 0.8476 142 S 0.0511 0.1197 0.8293 143 E 0.0147 0.6365 0.3487 144 Q 0.0086 0.8401 0.1512 145 V 0.0088 0.8764 0.1148 146 K 0.0066 0.9305 0.0629 147 M 0.0058 0.9498 0.0444 148 L 0.0047 0.9567 0.0386 149 Q 0.0047 0.9572 0.0380 150 R 0.0047 0.9567 0.0386 151 I 0.0048 0.9558 0.0394 152 D 0.0049 0.9544 0.0408 153 A 0.0052 0.9496 0.0452 154 H 0.0057 0.9276 0.0666 155 N 0.0077 0.8531 0.1392 156 T 0.0468 0.2613 0.6918 157 R 0.0403 0.0170 0.9426 158 Q 0.1282 0.0083 0.8634 159 P 0.6574 0.0047 0.3379 160 P 0.8802 0.0042 0.1156 161 E 0.8853 0.0043 0.1104 162 Q 0.8413 0.0070 0.1517 163 K 0.5387 0.0120 0.4492 164 I 0.1351 0.1240 0.7410 165 R 0.0765 0.1328 0.7907 166 V 0.0475 0.2595 0.6931 167 S 0.0512 0.3103 0.6385 168 V 0.0421 0.5153 0.4426 169 E 0.0372 0.5618 0.4010 170 V 0.0271 0.6458 0.3271 171 E 0.0181 0.7102 0.2717 172 K 0.0185 0.7084 0.2731 173 P 0.0209 0.6985 0.2806 174 R 0.0127 0.8097 0.1776 175 E 0.0086 0.8476 0.1438 176 E 0.0082 0.8632 0.1286 177 L 0.0078 0.8918 0.1005 178 F 0.0062 0.8908 0.1030 179 Q 0.0061 0.8751 0.1188 180 L 0.0102 0.8277 0.1621 181 F 0.0329 0.7134 0.2536 182 G 0.0133 0.5246 0.4621 183 Y 0.0347 0.3384 0.6269 184 G 0.1702 0.0389 0.7909 185 D 0.2285 0.0625 0.7089 186 V 0.8918 0.0082 0.1000 187 V 0.9091 0.0042 0.0866 188 F 0.8787 0.0042 0.1171 189 V 0.5924 0.0087 0.3989 190 S 0.1773 0.0090 0.8137 191 K 0.0054 0.8885 0.1060 192 D 0.0050 0.9320 0.0629 193 V 0.0050 0.9449 0.0500 194 A 0.0048 0.9488 0.0464 195 K 0.0051 0.9384 0.0565 196 H 0.0061 0.9056 0.0883 197 L 0.0109 0.8232 0.1659 198 G 0.0467 0.4953 0.4580 199 F 0.0354 0.1350 0.8296 200 Q 0.0572 0.0717 0.8711 201 S 0.0412 0.1494 0.8094 202 A 0.0480 0.2901 0.6619 203 E 0.0163 0.7522 0.2315 204 E 0.0086 0.8544 0.1370 205 A 0.0074 0.8943 0.0983 206 L 0.0066 0.9230 0.0704 207 R 0.0057 0.9280 0.0664 208 G 0.0056 0.9304 0.0640 209 L 0.0054 0.9344 0.0603 210 Y 0.0050 0.9393 0.0557 211 G 0.0056 0.9278 0.0666 212 R 0.0066 0.8954 0.0980 213 V 0.0135 0.7456 0.2408 214 R 0.0411 0.3276 0.6313 215 K 0.0453 0.0296 0.9251 216 G 0.0960 0.0084 0.8957 217 A 0.2047 0.0379 0.7574 218 V 0.9121 0.0037 0.0842 219 L 0.9305 0.0033 0.0662 220 V 0.9311 0.0032 0.0657 221 C 0.9114 0.0043 0.0843 222 A 0.7222 0.0104 0.2674 223 W 0.3074 0.0310 0.6617 224 A 0.1232 0.0512 0.8256 225 E 0.0641 0.1433 0.7926 226 E 0.0960 0.0871 0.8169 227 G 0.3245 0.0482 0.6273 228 A 0.7143 0.0139 0.2718 229 D 0.8958 0.0066 0.0976 230 A 0.9087 0.0063 0.0850 231 L 0.8866 0.0081 0.1054 232 G 0.6524 0.0165 0.3310 233 P 0.0763 0.0975 0.8262 234 D 0.0588 0.0392 0.9020 235 G 0.1356 0.0463 0.8181 236 K 0.3797 0.0308 0.5895 237 L 0.7033 0.0214 0.2753 238 L 0.7545 0.0177 0.2278 239 H 0.7496 0.0162 0.2342 240 S 0.6185 0.0169 0.3646 241 D 0.4129 0.0173 0.5698 242 A 0.3189 0.0190 0.6621 243 F 0.2495 0.0199 0.7306 244 P 0.2262 0.0162 0.7576 245 P 0.3671 0.0170 0.6159 246 P 0.4795 0.0212 0.4993 247 R 0.6681 0.0122 0.3196 248 V 0.6979 0.0162 0.2859 249 V 0.6668 0.0211 0.3121 250 D 0.4907 0.0210 0.4883 251 T 0.2017 0.1223 0.6759 252 L 0.1285 0.0990 0.7725 253 G 0.0699 0.1522 0.7778 254 A 0.0365 0.4018 0.5617 255 G 0.0187 0.5658 0.4156 256 D 0.0069 0.8502 0.1429 257 T 0.0048 0.9344 0.0608 258 F 0.0048 0.9536 0.0416 259 N 0.0047 0.9567 0.0385 260 A 0.0047 0.9589 0.0364 261 S 0.0047 0.9601 0.0352 262 V 0.0047 0.9607 0.0346 263 I 0.0047 0.9598 0.0355 264 F 0.0047 0.9581 0.0372 265 S 0.0049 0.9548 0.0404 266 L 0.0057 0.9326 0.0616 267 S 0.0089 0.7920 0.1991 268 Q 0.0393 0.2595 0.7012 269 G 0.0351 0.0305 0.9344 270 R 0.0769 0.0150 0.9081 271 S 0.1160 0.0256 0.8585 272 V 0.0068 0.9226 0.0705 273 Q 0.0048 0.9478 0.0474 274 E 0.0049 0.9457 0.0494 275 A 0.0048 0.9500 0.0452 276 L 0.0051 0.9480 0.0469 277 R 0.0051 0.9473 0.0476 278 F 0.0049 0.9453 0.0498 279 G 0.0052 0.9411 0.0537 280 C 0.0052 0.9493 0.0455 281 Q 0.0053 0.9525 0.0422 282 V 0.0056 0.9521 0.0423 283 A 0.0068 0.9450 0.0482 284 G 0.0090 0.9383 0.0527 285 K 0.0163 0.9191 0.0646 286 K 0.0377 0.8749 0.0873 287 C 0.0796 0.7738 0.1466 288 G 0.1045 0.5988 0.2966 289 L 0.1233 0.4143 0.4623 290 Q 0.0846 0.2727 0.6428 291 G 0.0750 0.1418 0.7831 292 F 0.1090 0.1231 0.7679 293 D 0.1027 0.1281 0.7692 294 G 0.1384 0.1346 0.7270 295 I 0.1258 0.1087 0.7654 296 V 0.0614 0.0231 0.9155