# This file is the result of combining several RDB files, specifically # T0528.t04.dssp-ebghstl.rdb (weight 1.53986) # T0528.t04.stride-ebghtl.rdb (weight 1.24869) # T0528.t04.str2.rdb (weight 1.54758) # T0528.t04.alpha.rdb (weight 0.659012) # T0528.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0528.t2k.stride-ebghtl.rdb (weight 1.24869) # T0528.t2k.str2.rdb (weight 1.54758) # T0528.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 T0528.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0528 # 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 T0528.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 1749 # # ============================================ # Comments from T0528.t04.stride-ebghtl.rdb # ============================================ # TARGET T0528 # 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 T0528.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 1749 # # ============================================ # Comments from T0528.t04.str2.rdb # ============================================ # TARGET T0528 # 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 T0528.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 1749 # # ============================================ # Comments from T0528.t04.alpha.rdb # ============================================ # TARGET T0528 # 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 T0528.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 1749 # # ============================================ # Comments from T0528.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0528 # 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 T0528.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 2130 # # ============================================ # Comments from T0528.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0528 # 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 T0528.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 2130 # # ============================================ # Comments from T0528.t2k.str2.rdb # ============================================ # TARGET T0528 # 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 T0528.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 2130 # # ============================================ # Comments from T0528.t2k.alpha.rdb # ============================================ # TARGET T0528 # 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 T0528.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 2130 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0213 0.8731 0.1056 2 T 0.0203 0.9194 0.0603 3 A 0.0145 0.9226 0.0629 4 T 0.0135 0.9239 0.0626 5 A 0.0120 0.9136 0.0744 6 V 0.0104 0.8992 0.0905 7 A 0.0105 0.8598 0.1297 8 L 0.0130 0.8092 0.1778 9 A 0.0178 0.7250 0.2572 10 T 0.0213 0.6822 0.2965 11 T 0.0231 0.6644 0.3125 12 A 0.0246 0.6417 0.3337 13 V 0.0291 0.5840 0.3870 14 H 0.0358 0.5062 0.4580 15 A 0.0548 0.3441 0.6012 16 A 0.0519 0.1505 0.7976 17 D 0.0824 0.0539 0.8636 18 D 0.3393 0.0242 0.6365 19 L 0.7895 0.0074 0.2032 20 K 0.8851 0.0053 0.1096 21 I 0.9008 0.0078 0.0914 22 A 0.8855 0.0078 0.1067 23 L 0.9003 0.0054 0.0944 24 I 0.8298 0.0141 0.1561 25 Y 0.6358 0.0170 0.3472 26 G 0.3354 0.0729 0.5917 27 K 0.1772 0.1174 0.7054 28 T 0.1350 0.1126 0.7524 29 G 0.0779 0.1379 0.7842 30 P 0.0667 0.3835 0.5499 31 L 0.0566 0.5742 0.3692 32 E 0.0421 0.6420 0.3159 33 A 0.0425 0.5873 0.3701 34 Y 0.0363 0.5077 0.4560 35 A 0.0317 0.4745 0.4937 36 K 0.0161 0.7837 0.2002 37 Q 0.0148 0.8513 0.1339 38 T 0.0073 0.9330 0.0598 39 E 0.0054 0.9514 0.0432 40 T 0.0049 0.9541 0.0410 41 G 0.0047 0.9565 0.0388 42 L 0.0047 0.9603 0.0350 43 M 0.0047 0.9606 0.0347 44 M 0.0047 0.9592 0.0362 45 G 0.0047 0.9578 0.0375 46 L 0.0047 0.9572 0.0381 47 E 0.0047 0.9553 0.0400 48 Y 0.0048 0.9477 0.0474 49 A 0.0072 0.9292 0.0636 50 T 0.0114 0.8752 0.1134 51 K 0.0114 0.7405 0.2481 52 G 0.0414 0.3592 0.5994 53 T 0.0539 0.1344 0.8117 54 M 0.1170 0.1012 0.7818 55 T 0.2657 0.1230 0.6113 56 L 0.3138 0.1035 0.5827 57 D 0.1347 0.0744 0.7908 58 G 0.0929 0.0458 0.8614 59 R 0.3263 0.0113 0.6625 60 K 0.6913 0.0043 0.3045 61 I 0.8423 0.0044 0.1533 62 V 0.8938 0.0043 0.1020 63 V 0.9146 0.0032 0.0822 64 I 0.8917 0.0041 0.1042 65 T 0.8270 0.0053 0.1676 66 K 0.5874 0.0158 0.3968 67 D 0.2062 0.0214 0.7724 68 D 0.0354 0.1255 0.8391 69 Q 0.0375 0.0924 0.8701 70 S 0.0419 0.0671 0.8910 71 K 0.0732 0.0477 0.8791 72 P 0.0137 0.8755 0.1108 73 D 0.0060 0.9422 0.0519 74 L 0.0053 0.9513 0.0434 75 S 0.0047 0.9561 0.0391 76 K 0.0047 0.9598 0.0355 77 A 0.0047 0.9596 0.0357 78 A 0.0047 0.9589 0.0364 79 L 0.0047 0.9586 0.0367 80 A 0.0047 0.9577 0.0376 81 E 0.0048 0.9516 0.0436 82 A 0.0048 0.9422 0.0530 83 Y 0.0054 0.9278 0.0668 84 Q 0.0069 0.8574 0.1357 85 D 0.0225 0.5525 0.4250 86 D 0.0433 0.1962 0.7605 87 G 0.0488 0.0484 0.9028 88 A 0.2507 0.0079 0.7414 89 D 0.5973 0.0251 0.3776 90 I 0.9196 0.0041 0.0763 91 A 0.9273 0.0035 0.0693 92 I 0.8842 0.0159 0.0999 93 G 0.7512 0.0150 0.2339 94 T 0.2678 0.0378 0.6944 95 S 0.0821 0.0877 0.8302 96 S 0.0688 0.1234 0.8077 97 S 0.0507 0.2962 0.6530 98 A 0.0128 0.8001 0.1871 99 A 0.0081 0.8699 0.1220 100 A 0.0081 0.9145 0.0774 101 L 0.0076 0.9253 0.0671 102 A 0.0087 0.9051 0.0861 103 D 0.0081 0.9086 0.0833 104 L 0.0091 0.9344 0.0565 105 P 0.0052 0.9486 0.0461 106 V 0.0051 0.9552 0.0397 107 A 0.0050 0.9530 0.0419 108 E 0.0055 0.9364 0.0580 109 E 0.0074 0.8550 0.1376 110 N 0.0488 0.3370 0.6142 111 K 0.0365 0.0266 0.9369 112 K 0.1104 0.0091 0.8805 113 I 0.5060 0.0076 0.4864 114 L 0.8362 0.0098 0.1540 115 I 0.8818 0.0088 0.1094 116 V 0.8149 0.0095 0.1755 117 E 0.6013 0.0393 0.3594 118 P 0.2157 0.0635 0.7208 119 A 0.0975 0.0997 0.8028 120 V 0.0931 0.0890 0.8179 121 A 0.0971 0.1382 0.7647 122 D 0.0747 0.3185 0.6068 123 Q 0.1430 0.3461 0.5109 124 I 0.2204 0.2574 0.5222 125 T 0.1916 0.1790 0.6294 126 G 0.1179 0.1580 0.7241 127 E 0.0681 0.2064 0.7255 128 K 0.0709 0.1576 0.7715 129 W 0.1062 0.1089 0.7849 130 N 0.1278 0.0442 0.8280 131 R 0.1194 0.0920 0.7886 132 Y 0.3425 0.0662 0.5913 133 I 0.7680 0.0197 0.2124 134 F 0.8543 0.0122 0.1335 135 R 0.8335 0.0103 0.1561 136 T 0.6773 0.0204 0.3023 137 G 0.3210 0.0251 0.6539 138 R 0.1199 0.0404 0.8397 139 N 0.0681 0.0374 0.8945 140 S 0.0206 0.6031 0.3762 141 S 0.0060 0.8518 0.1422 142 Q 0.0054 0.9012 0.0934 143 D 0.0058 0.9037 0.0905 144 A 0.0057 0.9330 0.0613 145 I 0.0053 0.9507 0.0440 146 S 0.0050 0.9529 0.0421 147 N 0.0050 0.9529 0.0421 148 A 0.0048 0.9533 0.0419 149 V 0.0048 0.9500 0.0452 150 A 0.0053 0.9410 0.0538 151 I 0.0077 0.9142 0.0781 152 G 0.0136 0.8058 0.1806 153 K 0.0302 0.3033 0.6664 154 Q 0.0375 0.0634 0.8991 155 G 0.0643 0.0225 0.9132 156 V 0.1679 0.0243 0.8078 157 T 0.8166 0.0044 0.1790 158 I 0.9257 0.0036 0.0707 159 A 0.9299 0.0034 0.0667 160 T 0.9258 0.0034 0.0707 161 L 0.8589 0.0079 0.1332 162 A 0.4858 0.0106 0.5036 163 Q 0.1121 0.0770 0.8110 164 D 0.0623 0.0810 0.8567 165 Y 0.0476 0.1803 0.7721 166 A 0.0294 0.4292 0.5415 167 F 0.0385 0.4707 0.4908 168 G 0.0292 0.5986 0.3722 169 R 0.0173 0.8341 0.1486 170 D 0.0133 0.8756 0.1112 171 G 0.0070 0.9229 0.0701 172 V 0.0051 0.9491 0.0458 173 A 0.0048 0.9537 0.0415 174 A 0.0047 0.9571 0.0382 175 F 0.0047 0.9579 0.0374 176 K 0.0047 0.9593 0.0360 177 E 0.0047 0.9594 0.0359 178 A 0.0047 0.9588 0.0365 179 L 0.0047 0.9563 0.0390 180 A 0.0049 0.9432 0.0519 181 K 0.0062 0.8737 0.1201 182 T 0.0424 0.3078 0.6498 183 G 0.0391 0.0174 0.9434 184 A 0.1338 0.0090 0.8572 185 T 0.7237 0.0059 0.2704 186 L 0.8691 0.0040 0.1270 187 A 0.8632 0.0143 0.1225 188 T 0.8199 0.0087 0.1713 189 E 0.7720 0.0162 0.2118 190 E 0.7618 0.0152 0.2230 191 Y 0.7203 0.0177 0.2620 192 V 0.5363 0.0172 0.4465 193 P 0.2257 0.0225 0.7517 194 T 0.0500 0.0968 0.8533 195 T 0.0328 0.0754 0.8918 196 T 0.0884 0.1254 0.7863 197 T 0.0909 0.1922 0.7168 198 D 0.1310 0.2091 0.6599 199 F 0.0170 0.8219 0.1611 200 T 0.0103 0.9081 0.0816 201 A 0.0066 0.9373 0.0561 202 V 0.0061 0.9458 0.0481 203 G 0.0064 0.9351 0.0585 204 Q 0.0061 0.9156 0.0782 205 R 0.0054 0.9066 0.0881 206 L 0.0070 0.9058 0.0872 207 F 0.0066 0.8982 0.0951 208 D 0.0060 0.8572 0.1369 209 A 0.0074 0.8048 0.1878 210 L 0.0104 0.7245 0.2651 211 K 0.0148 0.5625 0.4228 212 D 0.0514 0.3135 0.6351 213 K 0.0687 0.0381 0.8932 214 P 0.0993 0.0151 0.8856 215 G 0.1936 0.0560 0.7504 216 K 0.9238 0.0044 0.0719 217 K 0.9336 0.0032 0.0632 218 I 0.9298 0.0033 0.0669 219 I 0.9039 0.0060 0.0901 220 W 0.5957 0.0234 0.3810 221 V 0.2126 0.0355 0.7519 222 I 0.1140 0.0625 0.8235 223 W 0.0547 0.1797 0.7656 224 A 0.0175 0.5963 0.3862 225 G 0.0118 0.7168 0.2714 226 G 0.0068 0.8851 0.1081 227 G 0.0051 0.9438 0.0511 228 D 0.0048 0.9525 0.0427 229 P 0.0047 0.9574 0.0379 230 L 0.0047 0.9587 0.0366 231 T 0.0047 0.9593 0.0360 232 K 0.0047 0.9594 0.0359 233 L 0.0048 0.9578 0.0375 234 Q 0.0050 0.9470 0.0480 235 D 0.0054 0.9140 0.0806 236 M 0.0401 0.4158 0.5441 237 D 0.0339 0.0306 0.9355 238 P 0.0661 0.0272 0.9066 239 K 0.1233 0.0365 0.8402 240 R 0.2434 0.0542 0.7024 241 Y 0.5321 0.0438 0.4241 242 G 0.7865 0.0226 0.1909 243 I 0.8037 0.0259 0.1704 244 E 0.7219 0.0412 0.2369 245 L 0.5757 0.0672 0.3571 246 S 0.3609 0.1056 0.5335 247 T 0.2162 0.1500 0.6338 248 G 0.1820 0.1618 0.6563 249 G 0.1551 0.1418 0.7031 250 N 0.0818 0.1746 0.7436 251 I 0.0088 0.8638 0.1275 252 L 0.0065 0.9116 0.0818 253 P 0.0057 0.9290 0.0653 254 A 0.0067 0.9279 0.0653 255 L 0.0080 0.9089 0.0831 256 A 0.0100 0.8557 0.1342 257 A 0.0338 0.6886 0.2775 258 Y 0.0350 0.5135 0.4515 259 K 0.0265 0.5929 0.3806 260 R 0.0288 0.5894 0.3818 261 L 0.0704 0.4673 0.4623 262 P 0.0856 0.3184 0.5959 263 G 0.1404 0.1534 0.7062 264 M 0.4066 0.0956 0.4978 265 E 0.7574 0.0416 0.2010 266 G 0.8172 0.0310 0.1518 267 A 0.7445 0.0396 0.2158 268 T 0.5532 0.0604 0.3864 269 Y 0.3465 0.0860 0.5675 270 Y 0.2580 0.1056 0.6364 271 Y 0.1923 0.1269 0.6807 272 Y 0.1335 0.1712 0.6954 273 D 0.0695 0.2419 0.6886 274 I 0.0608 0.1967 0.7425 275 P 0.0461 0.1780 0.7760 276 K 0.0388 0.1433 0.8179 277 N 0.0567 0.1012 0.8421 278 P 0.0132 0.7936 0.1931 279 I 0.0096 0.8378 0.1526 280 N 0.0067 0.9062 0.0871 281 E 0.0050 0.9510 0.0440 282 W 0.0047 0.9562 0.0390 283 L 0.0047 0.9588 0.0365 284 V 0.0047 0.9604 0.0349 285 T 0.0047 0.9594 0.0359 286 E 0.0047 0.9588 0.0365 287 H 0.0047 0.9575 0.0378 288 Q 0.0049 0.9451 0.0500 289 K 0.0057 0.9200 0.0743 290 R 0.0114 0.8406 0.1480 291 F 0.0493 0.5270 0.4237 292 N 0.0410 0.0797 0.8793 293 A 0.0584 0.0683 0.8734 294 P 0.0673 0.0450 0.8877 295 P 0.0684 0.1217 0.8099 296 D 0.0530 0.1682 0.7788 297 F 0.0270 0.6199 0.3531 298 F 0.0160 0.7932 0.1907 299 T 0.0100 0.8736 0.1164 300 A 0.0057 0.9328 0.0615 301 G 0.0055 0.9346 0.0599 302 G 0.0048 0.9534 0.0418 303 F 0.0047 0.9582 0.0371 304 S 0.0047 0.9598 0.0355 305 A 0.0047 0.9606 0.0347 306 A 0.0047 0.9609 0.0345 307 M 0.0047 0.9608 0.0345 308 A 0.0046 0.9614 0.0339 309 V 0.0047 0.9601 0.0352 310 V 0.0047 0.9597 0.0356 311 T 0.0047 0.9595 0.0358 312 A 0.0048 0.9580 0.0372 313 V 0.0049 0.9520 0.0431 314 Q 0.0054 0.9346 0.0600 315 K 0.0076 0.8550 0.1373 316 A 0.0449 0.4345 0.5207 317 K 0.0335 0.0524 0.9141 318 S 0.0669 0.0405 0.8925 319 T 0.0687 0.0667 0.8646 320 D 0.1057 0.0468 0.8475 321 T 0.0069 0.8890 0.1041 322 E 0.0052 0.9486 0.0463 323 K 0.0048 0.9562 0.0391 324 L 0.0048 0.9571 0.0381 325 I 0.0047 0.9561 0.0392 326 A 0.0048 0.9506 0.0446 327 A 0.0052 0.9333 0.0615 328 M 0.0098 0.9016 0.0885 329 E 0.0069 0.6958 0.2973 330 G 0.0166 0.2846 0.6988 331 M 0.0792 0.0695 0.8513 332 E 0.1786 0.0552 0.7662 333 F 0.2652 0.0577 0.6771 334 D 0.2318 0.0827 0.6855 335 T 0.1791 0.0680 0.7530 336 P 0.1544 0.0905 0.7551 337 K 0.1574 0.0819 0.7608 338 G 0.2200 0.0523 0.7278 339 K 0.4121 0.0298 0.5581 340 M 0.7775 0.0119 0.2105 341 V 0.8451 0.0117 0.1433 342 F 0.8421 0.0102 0.1477 343 R 0.5149 0.0137 0.4714 344 K 0.1025 0.0984 0.7991 345 E 0.0210 0.1046 0.8744 346 D 0.0500 0.0657 0.8843 347 H 0.1136 0.0466 0.8398 348 Q 0.4112 0.0495 0.5392 349 A 0.5340 0.0570 0.4089 350 L 0.4864 0.0445 0.4690 351 Q 0.4178 0.0355 0.5466 352 S 0.5352 0.0200 0.4448 353 M 0.8147 0.0066 0.1787 354 Y 0.9116 0.0034 0.0850 355 H 0.9255 0.0034 0.0710 356 F 0.9185 0.0041 0.0774 357 K 0.9207 0.0035 0.0758 358 V 0.8905 0.0056 0.1039 359 K 0.7170 0.0221 0.2609 360 V 0.2758 0.0401 0.6840 361 D 0.0473 0.0584 0.8943 362 P 0.1014 0.0651 0.8335 363 A 0.5097 0.0323 0.4580 364 V 0.7913 0.0101 0.1986 365 A 0.8175 0.0114 0.1711 366 W 0.7761 0.0100 0.2139 367 A 0.6555 0.0209 0.3236 368 V 0.4382 0.0692 0.4926 369 L 0.3344 0.1402 0.5254 370 E 0.3207 0.1141 0.5652 371 P 0.3227 0.0862 0.5911 372 V 0.4720 0.0341 0.4940 373 R 0.5059 0.0257 0.4684 374 E 0.3717 0.0245 0.6037 375 L 0.2018 0.0238 0.7744 376 K 0.1623 0.0333 0.8044 377 I 0.1306 0.0376 0.8318 378 E 0.1049 0.1682 0.7269 379 E 0.0655 0.3642 0.5703 380 M 0.0804 0.4547 0.4649 381 N 0.0983 0.3919 0.5098 382 I 0.1152 0.2227 0.6621 383 P 0.1158 0.1122 0.7720 384 I 0.0884 0.1133 0.7983 385 K 0.0633 0.1640 0.7727 386 N 0.0616 0.1530 0.7854 387 K 0.0633 0.1243 0.8124 388 K 0.0400 0.0662 0.8939