| BRD7 -force run |
| ID: | 1511621528 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 651 (647) | ||
| Sequences: | 148 (92.4) | ||
| Seq/Len: | 0.229 | ||
| Nf(neff/√len): | 3.6 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 0.229).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 602_P | 614_A | 2.121 | 0.72 |
| 612_R | 615_M | 2.019 | 0.66 |
| 3_K | 6_K | 1.779 | 0.52 |
| 136_L | 143_L | 1.758 | 0.51 |
| 218_Y | 222_K | 1.725 | 0.49 |
| 423_K | 427_D | 1.711 | 0.48 |
| 602_P | 616_G | 1.705 | 0.47 |
| 560_Q | 563_R | 1.701 | 0.47 |
| 602_P | 612_R | 1.691 | 0.46 |
| 156_F | 159_P | 1.686 | 0.46 |
| 206_N | 211_N | 1.684 | 0.46 |
| 42_S | 45_D | 1.671 | 0.45 |
| 203_M | 219_K | 1.661 | 0.45 |
| 529_V | 533_V | 1.642 | 0.43 |
| 200_F | 203_M | 1.641 | 0.43 |
| 602_P | 615_M | 1.623 | 0.42 |
| 139_A | 144_M | 1.599 | 0.41 |
| 433_Y | 464_L | 1.589 | 0.40 |
| 1_M | 5_H | 1.586 | 0.40 |
| 176_M | 180_T | 1.581 | 0.40 |
| 1_M | 6_K | 1.578 | 0.40 |
| 571_N | 575_L | 1.542 | 0.37 |
| 4_K | 7_K | 1.528 | 0.37 |
| 236_R | 377_R | 1.528 | 0.37 |
| 204_C | 219_K | 1.526 | 0.36 |
| 204_C | 208_M | 1.508 | 0.35 |
| 4_K | 8_H | 1.508 | 0.35 |
| 4_K | 9_K | 1.500 | 0.35 |
| 151_D | 166_P | 1.499 | 0.35 |
| 156_F | 165_A | 1.499 | 0.35 |
| 159_P | 165_A | 1.499 | 0.35 |
| 218_Y | 579_S | 1.499 | 0.35 |
| 151_D | 156_F | 1.482 | 0.34 |
| 151_D | 159_P | 1.482 | 0.34 |
| 223_K | 592_N | 1.480 | 0.34 |
| 64_K | 67_K | 1.480 | 0.34 |
| 1_M | 4_K | 1.463 | 0.33 |
| 63_R | 66_R | 1.453 | 0.32 |
| 211_N | 217_Y | 1.446 | 0.32 |
| 121_L | 124_S | 1.440 | 0.32 |
| 468_T | 472_H | 1.437 | 0.31 |
| 162_D | 169_S | 1.428 | 0.31 |
| 2_G | 5_H | 1.420 | 0.31 |
| 206_N | 217_Y | 1.416 | 0.30 |
| 160_V | 165_A | 1.411 | 0.30 |
| 568_P | 579_S | 1.404 | 0.30 |
| 597_A | 605_I | 1.403 | 0.30 |
| 607_S | 614_A | 1.401 | 0.30 |
| 67_K | 71_K | 1.397 | 0.29 |
| 64_K | 71_K | 1.397 | 0.29 |
| 156_F | 166_P | 1.390 | 0.29 |
| 159_P | 166_P | 1.390 | 0.29 |
| 602_P | 607_S | 1.379 | 0.28 |
| 5_H | 9_K | 1.369 | 0.28 |
| 464_L | 472_H | 1.358 | 0.27 |
| 145_R | 240_L | 1.356 | 0.27 |
| 224_L | 391_D | 1.355 | 0.27 |
| 206_N | 210_Y | 1.347 | 0.27 |
| 156_F | 160_V | 1.345 | 0.27 |
| 148_Q | 158_F | 1.334 | 0.26 |
| 200_F | 228_G | 1.334 | 0.26 |
| 612_R | 616_G | 1.328 | 0.26 |
| 601_T | 618_S | 1.328 | 0.26 |
| 322_V | 325_S | 1.323 | 0.26 |
| 165_A | 168_Y | 1.323 | 0.26 |
| 203_M | 208_M | 1.321 | 0.26 |
| 258_D | 288_K | 1.318 | 0.25 |
| 151_D | 165_A | 1.312 | 0.25 |
| 160_V | 166_P | 1.308 | 0.25 |
| 42_S | 46_S | 1.307 | 0.25 |
| 185_I | 188_N | 1.306 | 0.25 |
| 204_C | 228_G | 1.302 | 0.25 |
| 220_A | 224_L | 1.302 | 0.25 |
| 178_F | 217_Y | 1.301 | 0.25 |
| 204_C | 207_A | 1.300 | 0.25 |
| 203_M | 211_N | 1.296 | 0.24 |
| 250_L | 354_L | 1.294 | 0.24 |
| 207_A | 210_Y | 1.293 | 0.24 |
| 6_K | 9_K | 1.293 | 0.24 |
| 2_G | 6_K | 1.292 | 0.24 |
| 464_L | 468_T | 1.292 | 0.24 |
| 209_I | 421_I | 1.291 | 0.24 |
| 155_F | 162_D | 1.291 | 0.24 |
| 208_M | 218_Y | 1.289 | 0.24 |
| 165_A | 175_P | 1.284 | 0.24 |
| 3_K | 7_K | 1.280 | 0.24 |
| 37_L | 43_G | 1.277 | 0.24 |
| 203_M | 206_N | 1.275 | 0.23 |
| 321_I | 325_S | 1.272 | 0.23 |
| 206_N | 215_T | 1.271 | 0.23 |
| 586_A | 593_L | 1.271 | 0.23 |
| 35_T | 43_G | 1.270 | 0.23 |
| 171_I | 175_P | 1.265 | 0.23 |
| 314_E | 318_L | 1.264 | 0.23 |
| 346_D | 468_T | 1.261 | 0.23 |
| 200_F | 204_C | 1.261 | 0.23 |
| 312_E | 315_Q | 1.259 | 0.23 |
| 556_L | 560_Q | 1.257 | 0.23 |
| 465_D | 468_T | 1.257 | 0.23 |
| 166_P | 175_P | 1.254 | 0.22 |
| 203_M | 228_G | 1.254 | 0.22 |
| 21_K | 37_L | 1.252 | 0.22 |
| 52_K | 55_H | 1.248 | 0.22 |
| 177_D | 180_T | 1.247 | 0.22 |
| 390_E | 393_R | 1.246 | 0.22 |
| 211_N | 215_T | 1.244 | 0.22 |
| 404_Y | 412_P | 1.243 | 0.22 |
| 564_L | 582_E | 1.243 | 0.22 |
| 564_L | 569_P | 1.242 | 0.22 |
| 219_K | 228_G | 1.242 | 0.22 |
| 162_D | 167_G | 1.241 | 0.22 |
| 21_K | 36_E | 1.239 | 0.22 |
| 144_M | 157_S | 1.236 | 0.22 |
| 208_M | 228_G | 1.235 | 0.22 |
| 1_M | 7_K | 1.234 | 0.22 |
| 433_Y | 468_T | 1.234 | 0.22 |
| 165_A | 176_M | 1.233 | 0.22 |
| 50_E | 56_D | 1.230 | 0.21 |
| 137_Q | 152_P | 1.230 | 0.21 |
| 37_L | 55_H | 1.228 | 0.21 |
| 66_R | 72_Q | 1.226 | 0.21 |
| 607_S | 615_M | 1.222 | 0.21 |
| 1_M | 9_K | 1.221 | 0.21 |
| 208_M | 219_K | 1.220 | 0.21 |
| 391_D | 394_N | 1.220 | 0.21 |
| 219_K | 226_H | 1.220 | 0.21 |
| 51_D | 70_E | 1.218 | 0.21 |
| 156_F | 175_P | 1.214 | 0.21 |
| 159_P | 175_P | 1.214 | 0.21 |
| 3_K | 9_K | 1.210 | 0.21 |
| 160_V | 175_P | 1.209 | 0.21 |
| 177_D | 184_K | 1.206 | 0.20 |
| 546_L | 556_L | 1.205 | 0.20 |
| 405_G | 412_P | 1.204 | 0.20 |
| 39_T | 51_D | 1.203 | 0.20 |
| 65_K | 71_K | 1.202 | 0.20 |
| 409_S | 412_P | 1.202 | 0.20 |
| 42_S | 55_H | 1.197 | 0.20 |
| 137_Q | 145_R | 1.196 | 0.20 |
| 36_E | 42_S | 1.195 | 0.20 |
| 35_T | 38_S | 1.193 | 0.20 |
| 222_K | 228_G | 1.191 | 0.20 |
| 45_D | 55_H | 1.190 | 0.20 |
| 213_P | 549_T | 1.186 | 0.20 |
| 36_E | 55_H | 1.186 | 0.20 |
| 140_L | 143_L | 1.183 | 0.20 |
| 138_E | 142_Q | 1.182 | 0.20 |
| 146_Q | 150_K | 1.181 | 0.19 |
| 408_S | 467_L | 1.181 | 0.19 |
| 87_E | 92_R | 1.180 | 0.19 |
| 202_L | 206_N | 1.178 | 0.19 |
| 61_R | 67_K | 1.177 | 0.19 |
| 156_F | 172_I | 1.176 | 0.19 |
| 159_P | 172_I | 1.176 | 0.19 |
| 405_G | 414_Y | 1.176 | 0.19 |
| 372_G | 390_E | 1.174 | 0.19 |
| 225_L | 228_G | 1.174 | 0.19 |
| 602_P | 613_K | 1.173 | 0.19 |
| 60_D | 69_G | 1.172 | 0.19 |
| 61_R | 66_R | 1.171 | 0.19 |
| 158_F | 173_K | 1.165 | 0.19 |
| 585_L | 589_V | 1.164 | 0.19 |
| 219_K | 388_F | 1.164 | 0.19 |
| 556_L | 582_E | 1.163 | 0.19 |
| 58_H | 68_K | 1.163 | 0.19 |
| 37_L | 47_S | 1.162 | 0.19 |
| 160_V | 172_I | 1.162 | 0.19 |
| 383_N | 571_N | 1.160 | 0.19 |
| 367_C | 426_S | 1.159 | 0.19 |
| 404_Y | 411_A | 1.159 | 0.19 |
| 202_L | 211_N | 1.159 | 0.19 |
| 579_S | 597_A | 1.158 | 0.19 |
| 140_L | 169_S | 1.157 | 0.19 |
| 161_T | 164_I | 1.156 | 0.19 |
| 35_T | 82_R | 1.154 | 0.18 |
| 160_V | 168_Y | 1.151 | 0.18 |
| 230_K | 393_R | 1.149 | 0.18 |
| 62_K | 65_K | 1.149 | 0.18 |
| 151_D | 160_V | 1.149 | 0.18 |
| 38_S | 51_D | 1.149 | 0.18 |
| 203_M | 210_Y | 1.148 | 0.18 |
| 433_Y | 472_H | 1.146 | 0.18 |
| 603_G | 606_V | 1.145 | 0.18 |
| 200_F | 208_M | 1.145 | 0.18 |
| 146_Q | 149_R | 1.144 | 0.18 |
| 363_E | 605_I | 1.143 | 0.18 |
| 552_L | 557_Q | 1.140 | 0.18 |
| 465_D | 472_H | 1.139 | 0.18 |
| 607_S | 616_G | 1.138 | 0.18 |
| 191_Q | 467_L | 1.137 | 0.18 |
| 340_F | 349_T | 1.135 | 0.18 |
| 34_V | 38_S | 1.135 | 0.18 |
| 183_E | 197_K | 1.122 | 0.17 |
| 4_K | 11_D | 1.119 | 0.17 |
| 602_P | 606_V | 1.113 | 0.17 |
| 200_F | 217_Y | 1.113 | 0.17 |
| 549_T | 556_L | 1.112 | 0.17 |
| 412_P | 415_D | 1.112 | 0.17 |
| 32_N | 45_D | 1.111 | 0.17 |
| 168_Y | 175_P | 1.111 | 0.17 |
| 200_F | 371_L | 1.110 | 0.17 |
| 553_L | 576_L | 1.109 | 0.17 |
| 5_H | 8_H | 1.106 | 0.17 |
| 89_K | 92_R | 1.104 | 0.17 |
| 225_L | 393_R | 1.103 | 0.17 |
| 134_T | 137_Q | 1.103 | 0.17 |
| 280_G | 283_E | 1.103 | 0.17 |
| 382_V | 572_M | 1.101 | 0.17 |
| 342_R | 350_T | 1.101 | 0.17 |
| 36_E | 43_G | 1.101 | 0.17 |
| 61_R | 64_K | 1.100 | 0.16 |
| 313_R | 322_V | 1.100 | 0.16 |
| 455_Y | 463_L | 1.099 | 0.16 |
| 493_L | 636_E | 1.098 | 0.16 |
| 423_K | 565_S | 1.095 | 0.16 |
| 340_F | 411_A | 1.093 | 0.16 |
| 560_Q | 582_E | 1.092 | 0.16 |
| 218_Y | 568_P | 1.091 | 0.16 |
| 602_P | 610_G | 1.091 | 0.16 |
| 1_M | 8_H | 1.090 | 0.16 |
| 434_G | 468_T | 1.090 | 0.16 |
| 207_A | 211_N | 1.089 | 0.16 |
| 43_G | 82_R | 1.089 | 0.16 |
| 151_D | 175_P | 1.088 | 0.16 |
| 52_K | 57_K | 1.088 | 0.16 |
| 3_K | 11_D | 1.088 | 0.16 |
| 67_K | 70_E | 1.086 | 0.16 |
| 168_Y | 176_M | 1.086 | 0.16 |
| 225_L | 387_G | 1.086 | 0.16 |
| 156_F | 162_D | 1.085 | 0.16 |
| 159_P | 162_D | 1.085 | 0.16 |
| 155_F | 167_G | 1.084 | 0.16 |
| 244_I | 460_A | 1.083 | 0.16 |
| 562_E | 575_L | 1.083 | 0.16 |
| 397_T | 401_Y | 1.083 | 0.16 |
| 435_E | 465_D | 1.081 | 0.16 |
| 203_M | 217_Y | 1.080 | 0.16 |
| 351_L | 404_Y | 1.079 | 0.16 |
| 203_M | 214_E | 1.078 | 0.16 |
| 162_D | 166_P | 1.077 | 0.16 |
| 7_K | 11_D | 1.076 | 0.16 |
| 40_G | 43_G | 1.075 | 0.16 |
| 642_D | 649_G | 1.074 | 0.16 |
| 37_L | 42_S | 1.073 | 0.16 |
| 21_K | 30_G | 1.072 | 0.16 |
| 351_L | 411_A | 1.071 | 0.16 |
| 148_Q | 154_A | 1.069 | 0.15 |
| 2_G | 8_H | 1.069 | 0.15 |
| 58_H | 71_K | 1.068 | 0.15 |
| 567_R | 581_R | 1.065 | 0.15 |
| 176_M | 190_Y | 1.064 | 0.15 |
| 416_S | 465_D | 1.064 | 0.15 |
| 2_G | 7_K | 1.064 | 0.15 |
| 41_S | 45_D | 1.063 | 0.15 |
| 553_L | 600_V | 1.062 | 0.15 |
| 414_Y | 423_K | 1.062 | 0.15 |
| 423_K | 426_S | 1.058 | 0.15 |
| 61_R | 65_K | 1.055 | 0.15 |
| 342_R | 391_D | 1.054 | 0.15 |
| 355_H | 398_P | 1.054 | 0.15 |
| 308_S | 567_R | 1.053 | 0.15 |
| 55_H | 69_G | 1.051 | 0.15 |
| 203_M | 226_H | 1.050 | 0.15 |
| 435_E | 440_P | 1.050 | 0.15 |
| 156_F | 190_Y | 1.049 | 0.15 |
| 159_P | 190_Y | 1.049 | 0.15 |
| 341_E | 442_D | 1.049 | 0.15 |
| 434_G | 464_L | 1.048 | 0.15 |
| 56_D | 79_G | 1.047 | 0.15 |
| 87_E | 91_K | 1.047 | 0.15 |
| 610_G | 614_A | 1.046 | 0.15 |
| 332_R | 419_A | 1.046 | 0.15 |
| 567_R | 601_T | 1.045 | 0.15 |
| 10_S | 15_Y | 1.045 | 0.15 |
| 608_T | 612_R | 1.044 | 0.15 |
| 601_T | 608_T | 1.044 | 0.15 |
| 37_L | 68_K | 1.044 | 0.15 |
| 463_L | 472_H | 1.043 | 0.15 |
| 348_T | 592_N | 1.043 | 0.15 |
| 36_E | 39_T | 1.042 | 0.15 |
| 162_D | 165_A | 1.042 | 0.15 |
| 35_T | 54_D | 1.040 | 0.15 |
| 385_L | 393_R | 1.040 | 0.15 |
| 38_S | 50_E | 1.040 | 0.15 |
| 21_K | 58_H | 1.039 | 0.14 |
| 601_T | 604_D | 1.037 | 0.14 |
| 315_Q | 329_L | 1.037 | 0.14 |
| 135_P | 145_R | 1.037 | 0.14 |
| 390_E | 407_Y | 1.035 | 0.14 |
| 25_L | 28_K | 1.035 | 0.14 |
| 172_I | 175_P | 1.034 | 0.14 |
| 63_R | 75_G | 1.034 | 0.14 |
| 151_D | 177_D | 1.034 | 0.14 |
| 31_G | 35_T | 1.034 | 0.14 |
| 582_E | 586_A | 1.032 | 0.14 |
| 200_F | 219_K | 1.031 | 0.14 |
| 356_P | 401_Y | 1.031 | 0.14 |
| 210_Y | 217_Y | 1.030 | 0.14 |
| 37_L | 52_K | 1.030 | 0.14 |
| 328_K | 420_N | 1.030 | 0.14 |
| 140_L | 162_D | 1.029 | 0.14 |
| 218_Y | 454_D | 1.027 | 0.14 |
| 152_P | 161_T | 1.025 | 0.14 |
| 636_E | 644_A | 1.025 | 0.14 |
| 156_F | 161_T | 1.025 | 0.14 |
| 38_S | 56_D | 1.025 | 0.14 |
| 355_H | 401_Y | 1.024 | 0.14 |
| 147_L | 166_P | 1.023 | 0.14 |
| 557_Q | 600_V | 1.022 | 0.14 |
| 607_S | 612_R | 1.020 | 0.14 |
| 386_Q | 552_L | 1.019 | 0.14 |
| 249_D | 605_I | 1.018 | 0.14 |
| 164_I | 433_Y | 1.018 | 0.14 |
| 147_L | 160_V | 1.018 | 0.14 |
| 316_E | 329_L | 1.017 | 0.14 |
| 223_K | 231_I | 1.017 | 0.14 |
| 42_S | 52_K | 1.016 | 0.14 |
| 565_S | 569_P | 1.015 | 0.14 |
| 630_D | 633_E | 1.015 | 0.14 |
| 119_K | 124_S | 1.015 | 0.14 |
| 2_G | 9_K | 1.014 | 0.14 |
| 43_G | 51_D | 1.013 | 0.14 |
| 355_H | 400_L | 1.013 | 0.14 |
| 464_L | 470_G | 1.013 | 0.14 |
| 140_L | 148_Q | 1.010 | 0.14 |
| 219_K | 230_K | 1.010 | 0.14 |
| 608_T | 615_M | 1.009 | 0.14 |
| 208_M | 211_N | 1.008 | 0.14 |
| 78_K | 81_K | 1.008 | 0.14 |
| 351_L | 412_P | 1.008 | 0.14 |
| 58_H | 62_K | 1.007 | 0.14 |
| 445_I | 458_V | 1.007 | 0.14 |
| 54_D | 80_R | 1.007 | 0.14 |
| 22_P | 26_V | 1.006 | 0.13 |
| 61_R | 71_K | 1.005 | 0.13 |
| 42_S | 51_D | 1.005 | 0.13 |
| 60_D | 67_K | 1.005 | 0.13 |
| 22_P | 25_L | 1.004 | 0.13 |
| 36_E | 69_G | 1.003 | 0.13 |
| 498_E | 505_E | 1.003 | 0.13 |
| 394_N | 556_L | 1.002 | 0.13 |
| 122_T | 125_L | 1.000 | 0.13 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4xy8A | 1 | 0.1736 | 100 | 0.884 | Contact Map |
| 4uitA | 1 | 0 | 100 | 0.889 | Contact Map |
| 2i7kA | 1 | 0.1797 | 100 | 0.895 | Contact Map |
| 5ameA | 2 | 0.1889 | 99.9 | 0.899 | Contact Map |
| 4lc2A | 1 | 0.1751 | 99.9 | 0.902 | Contact Map |
| 4ldfA | 2 | 0.1644 | 99.9 | 0.905 | Contact Map |
| 3uv4A | 2 | 0.1889 | 99.9 | 0.905 | Contact Map |
| 4qb3A | 1 | 0 | 99.9 | 0.906 | Contact Map |
| 4qspA | 1 | 0.1935 | 99.9 | 0.906 | Contact Map |
| 4uydA | 1 | 0.1905 | 99.9 | 0.906 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)