# This file is the result of combining several RDB files, specifically # T0303.t04.dssp-ebghstl.rdb (weight 1.53986) # T0303.t04.stride-ebghtl.rdb (weight 1.24869) # T0303.t04.str2.rdb (weight 1.54758) # T0303.t04.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 T0303.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0303 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0303.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2274 # # ============================================ # Comments from T0303.t04.stride-ebghtl.rdb # ============================================ # TARGET T0303 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0303.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2274 # # ============================================ # Comments from T0303.t04.str2.rdb # ============================================ # TARGET T0303 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0303.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2274 # # ============================================ # Comments from T0303.t04.alpha.rdb # ============================================ # TARGET T0303 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0303.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 2274 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0600 0.0219 0.9181 2 T 0.0785 0.0983 0.8232 3 Q 0.1294 0.0807 0.7898 4 F 0.3042 0.0109 0.6848 5 K 0.4148 0.0338 0.5514 6 L 0.9223 0.0034 0.0743 7 I 0.9322 0.0032 0.0646 8 G 0.9325 0.0032 0.0643 9 F 0.9123 0.0042 0.0835 10 D 0.6532 0.0058 0.3409 11 L 0.2177 0.0525 0.7298 12 D 0.0756 0.0552 0.8692 13 G 0.0754 0.0649 0.8597 14 T 0.2749 0.0649 0.6602 15 L 0.5731 0.0770 0.3499 16 V 0.4171 0.1237 0.4592 17 N 0.2382 0.1003 0.6615 18 S 0.0773 0.1210 0.8016 19 L 0.0291 0.5591 0.4118 20 P 0.0057 0.9153 0.0790 21 D 0.0053 0.9394 0.0554 22 L 0.0048 0.9546 0.0406 23 A 0.0047 0.9587 0.0366 24 L 0.0047 0.9583 0.0370 25 S 0.0047 0.9572 0.0382 26 I 0.0047 0.9588 0.0365 27 N 0.0047 0.9596 0.0358 28 S 0.0047 0.9580 0.0373 29 A 0.0047 0.9567 0.0385 30 L 0.0048 0.9536 0.0416 31 K 0.0052 0.9401 0.0547 32 D 0.0071 0.8792 0.1137 33 V 0.0465 0.5295 0.4240 34 N 0.0426 0.0490 0.9084 35 L 0.0532 0.0147 0.9322 36 P 0.0641 0.0324 0.9035 37 Q 0.0626 0.1102 0.8272 38 A 0.0636 0.0801 0.8563 39 S 0.0602 0.1632 0.7766 40 E 0.0054 0.9340 0.0606 41 N 0.0052 0.9459 0.0489 42 L 0.0055 0.9490 0.0455 43 V 0.0065 0.9501 0.0433 44 M 0.0079 0.9427 0.0495 45 T 0.0091 0.9278 0.0631 46 W 0.0110 0.8983 0.0907 47 I 0.0299 0.7312 0.2389 48 G 0.0330 0.3305 0.6366 49 N 0.0491 0.1819 0.7690 50 G 0.0456 0.2175 0.7370 51 A 0.0242 0.7003 0.2755 52 D 0.0135 0.8824 0.1041 53 V 0.0136 0.9145 0.0720 54 L 0.0180 0.9107 0.0714 55 S 0.0222 0.8941 0.0837 56 Q 0.0210 0.8804 0.0985 57 R 0.0217 0.8484 0.1298 58 A 0.0235 0.8253 0.1512 59 V 0.0346 0.7488 0.2165 60 D 0.0365 0.7334 0.2301 61 W 0.0234 0.8501 0.1265 62 A 0.0290 0.8350 0.1360 63 C 0.0465 0.8004 0.1531 64 T 0.0478 0.7867 0.1655 65 Q 0.0500 0.7414 0.2086 66 A 0.0454 0.6725 0.2821 67 E 0.0441 0.5672 0.3887 68 K 0.0464 0.4652 0.4884 69 E 0.0526 0.2947 0.6526 70 L 0.0906 0.0772 0.8322 71 T 0.0550 0.0491 0.8959 72 E 0.0055 0.9152 0.0794 73 D 0.0052 0.9299 0.0649 74 E 0.0055 0.9297 0.0648 75 F 0.0057 0.9446 0.0497 76 K 0.0051 0.9493 0.0456 77 Y 0.0051 0.9493 0.0456 78 F 0.0051 0.9461 0.0487 79 K 0.0052 0.9486 0.0462 80 R 0.0054 0.9418 0.0528 81 Q 0.0065 0.9299 0.0636 82 F 0.0117 0.9162 0.0721 83 G 0.0087 0.8954 0.0958 84 F 0.0102 0.9044 0.0853 85 Y 0.0118 0.9075 0.0807 86 Y 0.0157 0.8883 0.0960 87 G 0.0138 0.8584 0.1278 88 E 0.0146 0.8104 0.1750 89 N 0.0184 0.7643 0.2172 90 L 0.0299 0.6794 0.2907 91 C 0.0426 0.5413 0.4161 92 N 0.0353 0.4711 0.4936 93 I 0.0644 0.3904 0.5452 94 S 0.1489 0.1920 0.6591 95 R 0.1825 0.1447 0.6728 96 L 0.1681 0.0984 0.7335 97 Y 0.0841 0.0528 0.8632 98 P 0.0162 0.3531 0.6307 99 N 0.0182 0.3656 0.6162 100 V 0.0073 0.8650 0.1277 101 K 0.0055 0.9475 0.0470 102 E 0.0054 0.9559 0.0388 103 T 0.0052 0.9570 0.0378 104 L 0.0047 0.9611 0.0342 105 E 0.0046 0.9607 0.0346 106 A 0.0046 0.9609 0.0344 107 L 0.0047 0.9594 0.0360 108 K 0.0048 0.9515 0.0437 109 A 0.0055 0.9078 0.0867 110 Q 0.0419 0.2471 0.7110 111 G 0.0372 0.0146 0.9482 112 Y 0.0819 0.0078 0.9103 113 I 0.6907 0.0054 0.3039 114 L 0.9239 0.0039 0.0722 115 A 0.9322 0.0033 0.0645 116 V 0.9316 0.0032 0.0652 117 V 0.8899 0.0061 0.1040 118 T 0.4961 0.0122 0.4917 119 N 0.0635 0.0445 0.8920 120 K 0.0642 0.0400 0.8958 121 P 0.0585 0.1578 0.7837 122 T 0.0228 0.5903 0.3869 123 K 0.0185 0.6978 0.2837 124 H 0.0176 0.7699 0.2125 125 V 0.0157 0.8672 0.1171 126 Q 0.0078 0.9324 0.0598 127 P 0.0058 0.9508 0.0434 128 I 0.0049 0.9579 0.0372 129 L 0.0047 0.9571 0.0382 130 T 0.0049 0.9443 0.0508 131 A 0.0056 0.9021 0.0923 132 F 0.0427 0.4604 0.4969 133 G 0.0455 0.0314 0.9231 134 I 0.0421 0.1092 0.8487 135 D 0.0396 0.3956 0.5648 136 H 0.0451 0.5432 0.4117 137 L 0.0610 0.5375 0.4016 138 F 0.1864 0.2859 0.5277 139 S 0.1442 0.3049 0.5509 140 E 0.5743 0.2251 0.2006 141 M 0.7118 0.1741 0.1140 142 L 0.6758 0.1597 0.1645 143 G 0.3927 0.0802 0.5271 144 G 0.1260 0.1597 0.7143 145 Q 0.0751 0.2159 0.7090 146 S 0.1085 0.2344 0.6571 147 L 0.1011 0.1358 0.7631 148 P 0.0708 0.2122 0.7170 149 E 0.0856 0.2045 0.7099 150 I 0.1330 0.1027 0.7643 151 K 0.1051 0.0257 0.8691 152 P 0.0968 0.0326 0.8707 153 H 0.0836 0.0231 0.8933 154 P 0.0314 0.6781 0.2905 155 A 0.0195 0.8730 0.1074 156 P 0.0068 0.9387 0.0545 157 F 0.0056 0.9519 0.0425 158 Y 0.0047 0.9588 0.0365 159 Y 0.0048 0.9586 0.0366 160 L 0.0047 0.9590 0.0363 161 C 0.0048 0.9574 0.0379 162 G 0.0051 0.9481 0.0468 163 K 0.0066 0.9087 0.0847 164 F 0.0439 0.4476 0.5085 165 G 0.0332 0.0215 0.9453 166 L 0.0678 0.0078 0.9245 167 Y 0.0900 0.0096 0.9004 168 P 0.0457 0.5846 0.3697 169 K 0.0919 0.5528 0.3553 170 Q 0.2270 0.4107 0.3623 171 I 0.8678 0.0161 0.1161 172 L 0.8991 0.0141 0.0868 173 F 0.9183 0.0053 0.0764 174 V 0.8554 0.0224 0.1222 175 G 0.5322 0.0214 0.4464 176 D 0.1866 0.0215 0.7919 177 S 0.0673 0.0657 0.8670 178 Q 0.0095 0.7296 0.2609 179 N 0.0113 0.8216 0.1671 180 D 0.0109 0.8542 0.1349 181 I 0.0060 0.9504 0.0436 182 F 0.0053 0.9553 0.0394 183 A 0.0052 0.9577 0.0371 184 A 0.0048 0.9574 0.0378 185 H 0.0050 0.9507 0.0444 186 S 0.0065 0.8974 0.0961 187 A 0.0457 0.3428 0.6115 188 G 0.0438 0.0217 0.9345 189 C 0.1032 0.0081 0.8887 190 A 0.3732 0.0198 0.6070 191 V 0.9080 0.0042 0.0878 192 V 0.9188 0.0061 0.0751 193 G 0.9217 0.0045 0.0738 194 L 0.8656 0.0089 0.1255 195 T 0.5430 0.0145 0.4425 196 Y 0.1956 0.0417 0.7628 197 G 0.0865 0.0492 0.8642 198 Y 0.0905 0.0911 0.8184 199 N 0.0933 0.1072 0.7995 200 Y 0.0884 0.1303 0.7813 201 N 0.0956 0.1152 0.7892 202 I 0.1429 0.0958 0.7612 203 P 0.1865 0.1460 0.6676 204 I 0.1092 0.4669 0.4239 205 A 0.0732 0.5202 0.4066 206 Q 0.0642 0.4206 0.5151 207 S 0.0955 0.1741 0.7303 208 K 0.0961 0.0381 0.8657 209 P 0.1157 0.0518 0.8326 210 D 0.2359 0.0896 0.6745 211 W 0.7395 0.0438 0.2167 212 I 0.8167 0.0369 0.1463 213 F 0.6823 0.0388 0.2789 214 D 0.2990 0.0786 0.6224 215 D 0.1339 0.0584 0.8077 216 F 0.0071 0.9014 0.0915 217 A 0.0058 0.9319 0.0623 218 D 0.0052 0.9436 0.0511 219 I 0.0051 0.9439 0.0510 220 L 0.0053 0.9337 0.0610 221 K 0.0062 0.8885 0.1053 222 I 0.0095 0.7623 0.2282 223 T 0.0374 0.3840 0.5787 224 Q 0.0208 0.0790 0.9002