# This file is the result of combining several RDB files, specifically # T0611.t04.dssp-ebghstl.rdb (weight 1.53986) # T0611.t04.stride-ebghtl.rdb (weight 1.24869) # T0611.t04.str2.rdb (weight 1.54758) # T0611.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 T0611.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0611 # Using neural net t04-2621-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 T0611.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 1880 # # ============================================ # Comments from T0611.t04.stride-ebghtl.rdb # ============================================ # TARGET T0611 # 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 T0611.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 1880 # # ============================================ # Comments from T0611.t04.str2.rdb # ============================================ # TARGET T0611 # Using neural net t04-2621-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 T0611.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 1880 # # ============================================ # Comments from T0611.t04.alpha.rdb # ============================================ # TARGET T0611 # 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 T0611.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 1880 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0550 0.0194 0.9255 2 T 0.0537 0.0484 0.8978 3 M 0.0306 0.3691 0.6003 4 K 0.0275 0.5360 0.4365 5 T 0.0279 0.7016 0.2705 6 R 0.0049 0.9523 0.0428 7 D 0.0048 0.9600 0.0352 8 K 0.0047 0.9609 0.0345 9 I 0.0047 0.9609 0.0344 10 L 0.0047 0.9608 0.0346 11 L 0.0047 0.9610 0.0343 12 S 0.0047 0.9600 0.0352 13 S 0.0048 0.9585 0.0367 14 L 0.0047 0.9598 0.0355 15 E 0.0047 0.9607 0.0347 16 L 0.0047 0.9594 0.0359 17 F 0.0047 0.9545 0.0408 18 N 0.0051 0.9298 0.0652 19 D 0.0078 0.8488 0.1434 20 K 0.0436 0.4428 0.5136 21 G 0.0357 0.1335 0.8308 22 E 0.0546 0.2300 0.7154 23 R 0.0687 0.3428 0.5884 24 N 0.1051 0.2548 0.6401 25 I 0.2218 0.1129 0.6653 26 T 0.1814 0.1545 0.6641 27 T 0.0068 0.9524 0.0408 28 N 0.0064 0.9574 0.0362 29 H 0.0054 0.9592 0.0354 30 I 0.0051 0.9598 0.0351 31 A 0.0047 0.9580 0.0373 32 A 0.0057 0.9433 0.0510 33 H 0.0090 0.9010 0.0900 34 L 0.0527 0.4610 0.4864 35 A 0.0421 0.0600 0.8979 36 I 0.0971 0.0251 0.8778 37 S 0.0690 0.0261 0.9049 38 P 0.0357 0.3047 0.6596 39 G 0.0677 0.2699 0.6624 40 N 0.1865 0.3763 0.4372 41 L 0.3160 0.4372 0.2468 42 Y 0.3921 0.3891 0.2188 43 Y 0.3911 0.3033 0.3055 44 H 0.3263 0.2396 0.4341 45 F 0.1430 0.0735 0.7835 46 R 0.0714 0.0951 0.8335 47 N 0.0847 0.0686 0.8467 48 K 0.0053 0.9432 0.0515 49 S 0.0053 0.9549 0.0398 50 D 0.0050 0.9565 0.0385 51 I 0.0048 0.9592 0.0360 52 I 0.0047 0.9608 0.0346 53 Y 0.0046 0.9615 0.0339 54 E 0.0046 0.9615 0.0339 55 I 0.0047 0.9599 0.0354 56 F 0.0047 0.9594 0.0359 57 Q 0.0047 0.9599 0.0354 58 E 0.0048 0.9568 0.0384 59 Y 0.0048 0.9528 0.0423 60 E 0.0048 0.9538 0.0414 61 K 0.0048 0.9523 0.0429 62 L 0.0051 0.9420 0.0528 63 V 0.0062 0.9290 0.0647 64 D 0.0077 0.8995 0.0929 65 Y 0.0095 0.8773 0.1132 66 Y 0.0158 0.7943 0.1899 67 L 0.0525 0.5620 0.3854 68 D 0.0574 0.3602 0.5824 69 I 0.0691 0.1637 0.7672 70 P 0.0521 0.2943 0.6537 71 E 0.0536 0.3261 0.6203 72 D 0.0660 0.2164 0.7176 73 R 0.0781 0.0590 0.8629 74 P 0.0722 0.0610 0.8667 75 I 0.1125 0.0349 0.8526 76 T 0.0767 0.0201 0.9032 77 L 0.0050 0.9306 0.0644 78 E 0.0047 0.9593 0.0360 79 D 0.0048 0.9582 0.0369 80 M 0.0047 0.9603 0.0351 81 T 0.0046 0.9612 0.0342 82 F 0.0046 0.9616 0.0338 83 Y 0.0046 0.9614 0.0340 84 L 0.0047 0.9599 0.0354 85 E 0.0047 0.9605 0.0348 86 S 0.0047 0.9602 0.0351 87 V 0.0048 0.9565 0.0387 88 F 0.0049 0.9546 0.0406 89 D 0.0050 0.9529 0.0422 90 G 0.0052 0.9429 0.0519 91 L 0.0063 0.9248 0.0689 92 W 0.0086 0.8789 0.1125 93 S 0.0131 0.7496 0.2374 94 Y 0.0281 0.5997 0.3722 95 R 0.0093 0.8010 0.1897 96 F 0.0100 0.8390 0.1510 97 F 0.0118 0.8832 0.1051 98 H 0.0165 0.9030 0.0805 99 R 0.0203 0.9064 0.0733 100 D 0.0233 0.9099 0.0668 101 L 0.0122 0.9302 0.0576 102 E 0.0120 0.9216 0.0664 103 Y 0.0119 0.9052 0.0829 104 L 0.0145 0.8517 0.1338 105 L 0.0352 0.6431 0.3217 106 D 0.0289 0.3587 0.6124 107 S 0.0310 0.1510 0.8180 108 D 0.0821 0.0345 0.8835 109 P 0.0055 0.8510 0.1434 110 R 0.0061 0.8835 0.1105 111 L 0.0064 0.8989 0.0947 112 R 0.0062 0.9196 0.0742 113 Q 0.0051 0.9409 0.0540 114 D 0.0052 0.9409 0.0539 115 Y 0.0048 0.9540 0.0412 116 R 0.0047 0.9578 0.0375 117 E 0.0047 0.9580 0.0373 118 F 0.0048 0.9546 0.0406 119 T 0.0048 0.9559 0.0393 120 N 0.0049 0.9563 0.0388 121 R 0.0047 0.9576 0.0377 122 C 0.0047 0.9571 0.0381 123 L 0.0047 0.9610 0.0343 124 A 0.0047 0.9615 0.0338 125 A 0.0046 0.9615 0.0339 126 I 0.0046 0.9612 0.0342 127 N 0.0046 0.9615 0.0339 128 R 0.0046 0.9614 0.0339 129 I 0.0047 0.9606 0.0347 130 F 0.0047 0.9604 0.0349 131 A 0.0046 0.9565 0.0389 132 K 0.0046 0.9444 0.0509 133 L 0.0047 0.9302 0.0651 134 A 0.0055 0.8755 0.1190 135 D 0.0073 0.8045 0.1883 136 A 0.0423 0.3528 0.6049 137 G 0.0326 0.0441 0.9233 138 I 0.1308 0.0368 0.8324 139 I 0.3534 0.0174 0.6292 140 Q 0.1699 0.0194 0.8106 141 P 0.1103 0.0539 0.8358 142 Q 0.0639 0.0566 0.8795 143 P 0.0589 0.1346 0.8065 144 E 0.0148 0.9048 0.0805 145 D 0.0225 0.9109 0.0665 146 L 0.0066 0.9491 0.0442 147 R 0.0050 0.9582 0.0368 148 S 0.0047 0.9602 0.0352 149 A 0.0047 0.9602 0.0350 150 M 0.0047 0.9599 0.0354 151 S 0.0047 0.9588 0.0364 152 L 0.0047 0.9587 0.0366 153 N 0.0047 0.9578 0.0375 154 V 0.0047 0.9567 0.0386 155 W 0.0047 0.9581 0.0372 156 L 0.0047 0.9587 0.0366 157 V 0.0051 0.9559 0.0390 158 I 0.0063 0.9473 0.0463 159 T 0.0105 0.9314 0.0582 160 N 0.0161 0.8945 0.0893 161 W 0.0190 0.8638 0.1172 162 M 0.0271 0.8378 0.1351 163 A 0.0380 0.7680 0.1940 164 F 0.0469 0.6317 0.3214 165 L 0.0683 0.3987 0.5330 166 K 0.0720 0.2410 0.6870 167 T 0.0927 0.1852 0.7220 168 A 0.0955 0.1267 0.7778 169 H 0.0733 0.0715 0.8552 170 A 0.0154 0.6546 0.3299 171 A 0.0163 0.6355 0.3482 172 E 0.0252 0.6575 0.3173 173 E 0.0381 0.5848 0.3771 174 P 0.0178 0.7750 0.2073 175 A 0.0123 0.8582 0.1295 176 S 0.0150 0.8808 0.1042 177 L 0.0241 0.8838 0.0922 178 S 0.0092 0.9252 0.0656 179 L 0.0047 0.9552 0.0401 180 T 0.0047 0.9607 0.0346 181 E 0.0047 0.9600 0.0353 182 L 0.0047 0.9573 0.0380 183 K 0.0049 0.9501 0.0450 184 Q 0.0069 0.8969 0.0962 185 G 0.0094 0.7219 0.2688 186 I 0.0260 0.6604 0.3136 187 Y 0.0805 0.5821 0.3374 188 Q 0.1006 0.5508 0.3486 189 V 0.1114 0.4835 0.4051 190 L 0.1109 0.4180 0.4711 191 T 0.1140 0.3484 0.5376 192 L 0.1201 0.2475 0.6324 193 E 0.1207 0.1772 0.7022 194 V 0.1010 0.0544 0.8446 195 P 0.0996 0.0748 0.8256 196 Y 0.1236 0.0706 0.8057 197 L 0.1112 0.0233 0.8655 198 T 0.0567 0.0124 0.9309 199 P 0.0059 0.8687 0.1255 200 E 0.0057 0.8980 0.0963 201 Y 0.0058 0.9169 0.0773 202 R 0.0050 0.9515 0.0435 203 E 0.0049 0.9574 0.0377 204 R 0.0047 0.9555 0.0398 205 V 0.0049 0.9548 0.0403 206 L 0.0047 0.9535 0.0418 207 A 0.0051 0.9412 0.0537 208 L 0.0054 0.9182 0.0764 209 R 0.0076 0.8946 0.0978 210 E 0.0074 0.8494 0.1432 211 K 0.0109 0.7423 0.2468 212 Y 0.0484 0.5106 0.4409 213 R 0.0741 0.1193 0.8066 214 P 0.0414 0.1679 0.7907 215 T 0.0623 0.1470 0.7907 216 L 0.0789 0.0850 0.8360 217 P 0.0618 0.1993 0.7388 218 E 0.0570 0.3201 0.6229 219 A 0.0582 0.3234 0.6184 220 Q 0.0630 0.2380 0.6989 221 G 0.0597 0.1241 0.8162 222 I 0.1050 0.1171 0.7779 223 S 0.0889 0.1249 0.7862 224 G 0.0527 0.1386 0.8087 225 V 0.0729 0.1154 0.8117 226 E 0.0779 0.1011 0.8210 227 A 0.0532 0.1079 0.8389