| BRD9 FL -force run |
| ID: | 1511620725 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 597 (595) | ||
| Sequences: | 64 (40.2) | ||
| Seq/Len: | 0.108 | ||
| Nf(neff/√len): | 1.6 |
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: 0.108).
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 |
| 3_K | 6_K | 2.471 | 0.66 |
| 1_M | 6_K | 2.289 | 0.58 |
| 1_M | 5_H | 2.167 | 0.51 |
| 1_M | 4_K | 2.067 | 0.46 |
| 69_K | 72_K | 1.997 | 0.43 |
| 2_G | 5_H | 1.891 | 0.38 |
| 69_K | 76_K | 1.854 | 0.36 |
| 68_K | 71_K | 1.806 | 0.34 |
| 142_Q | 150_R | 1.788 | 0.33 |
| 4_K | 8_H | 1.785 | 0.33 |
| 404_D | 454_R | 1.749 | 0.31 |
| 4_K | 7_K | 1.716 | 0.30 |
| 45_S | 48_D | 1.708 | 0.29 |
| 3_K | 7_K | 1.703 | 0.29 |
| 549_N | 553_L | 1.659 | 0.27 |
| 26_K | 41_E | 1.619 | 0.26 |
| 2_G | 6_K | 1.618 | 0.26 |
| 63_H | 73_K | 1.590 | 0.25 |
| 184_G | 229_I | 1.585 | 0.24 |
| 4_K | 9_K | 1.575 | 0.24 |
| 1_M | 7_K | 1.563 | 0.24 |
| 3_K | 9_K | 1.544 | 0.23 |
| 70_K | 76_K | 1.533 | 0.22 |
| 1_M | 8_H | 1.519 | 0.22 |
| 207_L | 443_L | 1.511 | 0.22 |
| 72_K | 76_K | 1.505 | 0.21 |
| 5_H | 9_K | 1.495 | 0.21 |
| 4_K | 11_E | 1.471 | 0.20 |
| 325_Y | 334_L | 1.469 | 0.20 |
| 293_S | 545_R | 1.467 | 0.20 |
| 527_T | 534_L | 1.462 | 0.20 |
| 26_K | 42_L | 1.460 | 0.20 |
| 229_I | 375_E | 1.460 | 0.20 |
| 40_T | 46_G | 1.458 | 0.20 |
| 530_L | 535_H | 1.456 | 0.20 |
| 67_K | 70_K | 1.448 | 0.20 |
| 1_M | 9_K | 1.447 | 0.20 |
| 373_K | 379_K | 1.443 | 0.19 |
| 184_G | 375_E | 1.441 | 0.19 |
| 388_T | 447_I | 1.441 | 0.19 |
| 184_G | 225_L | 1.428 | 0.19 |
| 527_T | 538_Q | 1.404 | 0.18 |
| 580_H | 591_P | 1.394 | 0.18 |
| 349_E | 358_S | 1.379 | 0.17 |
| 352_H | 358_S | 1.375 | 0.17 |
| 63_H | 67_K | 1.374 | 0.17 |
| 63_H | 69_K | 1.372 | 0.17 |
| 204_D | 338_V | 1.353 | 0.17 |
| 68_K | 78_K | 1.351 | 0.17 |
| 227_K | 380_V | 1.347 | 0.17 |
| 416_E | 516_D | 1.344 | 0.16 |
| 573_G | 581_D | 1.330 | 0.16 |
| 54_D | 75_E | 1.327 | 0.16 |
| 343_E | 348_E | 1.323 | 0.16 |
| 38_E | 43_S | 1.322 | 0.16 |
| 36_G | 40_T | 1.321 | 0.16 |
| 300_L | 322_K | 1.319 | 0.16 |
| 3_K | 11_E | 1.313 | 0.16 |
| 471_D | 474_K | 1.310 | 0.16 |
| 546_P | 557_S | 1.309 | 0.15 |
| 2_G | 7_K | 1.309 | 0.15 |
| 321_G | 531_L | 1.306 | 0.15 |
| 190_I | 193_N | 1.303 | 0.15 |
| 39_V | 43_S | 1.291 | 0.15 |
| 174_S | 441_D | 1.279 | 0.15 |
| 534_L | 538_Q | 1.277 | 0.15 |
| 363_L | 366_G | 1.276 | 0.15 |
| 206_K | 228_K | 1.275 | 0.15 |
| 392_M | 403_S | 1.274 | 0.15 |
| 357_S | 374_D | 1.272 | 0.15 |
| 71_K | 77_E | 1.271 | 0.14 |
| 208_M | 224_K | 1.269 | 0.14 |
| 208_M | 452_H | 1.269 | 0.14 |
| 224_K | 452_H | 1.269 | 0.14 |
| 7_K | 11_E | 1.268 | 0.14 |
| 145_L | 153_Q | 1.266 | 0.14 |
| 219_D | 229_I | 1.265 | 0.14 |
| 221_V | 325_Y | 1.263 | 0.14 |
| 151_Q | 154_R | 1.261 | 0.14 |
| 163_F | 238_S | 1.258 | 0.14 |
| 140_P | 150_R | 1.257 | 0.14 |
| 2_G | 9_K | 1.253 | 0.14 |
| 45_S | 49_S | 1.253 | 0.14 |
| 29_K | 64_K | 1.251 | 0.14 |
| 139_T | 142_Q | 1.251 | 0.14 |
| 42_L | 58_H | 1.245 | 0.14 |
| 236_M | 362_K | 1.238 | 0.14 |
| 58_H | 72_K | 1.236 | 0.14 |
| 51_Y | 333_S | 1.233 | 0.14 |
| 5_H | 8_H | 1.232 | 0.14 |
| 333_S | 539_A | 1.231 | 0.14 |
| 568_S | 580_H | 1.231 | 0.14 |
| 582_P | 588_S | 1.229 | 0.13 |
| 2_G | 8_H | 1.227 | 0.13 |
| 327_K | 341_T | 1.214 | 0.13 |
| 63_H | 71_K | 1.213 | 0.13 |
| 41_E | 49_S | 1.213 | 0.13 |
| 575_Q | 581_D | 1.208 | 0.13 |
| 535_H | 553_L | 1.204 | 0.13 |
| 223_Y | 227_K | 1.201 | 0.13 |
| 1_M | 11_E | 1.198 | 0.13 |
| 583_Y | 588_S | 1.193 | 0.13 |
| 6_K | 9_K | 1.192 | 0.13 |
| 580_H | 588_S | 1.192 | 0.13 |
| 574_E | 592_A | 1.191 | 0.13 |
| 150_R | 153_Q | 1.189 | 0.13 |
| 143_Q | 147_H | 1.188 | 0.13 |
| 66_K | 72_K | 1.186 | 0.12 |
| 43_S | 54_D | 1.183 | 0.12 |
| 5_H | 11_E | 1.178 | 0.12 |
| 526_E | 534_L | 1.178 | 0.12 |
| 361_S | 447_I | 1.176 | 0.12 |
| 34_V | 38_E | 1.175 | 0.12 |
| 341_T | 527_T | 1.173 | 0.12 |
| 168_A | 333_S | 1.172 | 0.12 |
| 217_R | 409_L | 1.170 | 0.12 |
| 470_P | 580_H | 1.169 | 0.12 |
| 376_R | 385_S | 1.169 | 0.12 |
| 415_D | 442_D | 1.169 | 0.12 |
| 412_A | 439_V | 1.168 | 0.12 |
| 87_K | 432_A | 1.168 | 0.12 |
| 488_E | 496_P | 1.168 | 0.12 |
| 576_P | 591_P | 1.168 | 0.12 |
| 43_S | 75_E | 1.167 | 0.12 |
| 170_A | 173_Y | 1.166 | 0.12 |
| 170_A | 220_T | 1.166 | 0.12 |
| 170_A | 222_Y | 1.166 | 0.12 |
| 173_Y | 220_T | 1.166 | 0.12 |
| 173_Y | 222_Y | 1.166 | 0.12 |
| 41_E | 72_K | 1.164 | 0.12 |
| 356_L | 372_F | 1.164 | 0.12 |
| 152_L | 155_K | 1.160 | 0.12 |
| 42_L | 73_K | 1.159 | 0.12 |
| 26_K | 76_K | 1.151 | 0.12 |
| 188_D | 333_S | 1.149 | 0.12 |
| 184_G | 407_E | 1.147 | 0.12 |
| 249_T | 261_V | 1.146 | 0.12 |
| 40_T | 57_D | 1.145 | 0.12 |
| 360_S | 364_L | 1.143 | 0.12 |
| 571_S | 574_E | 1.142 | 0.12 |
| 66_K | 71_K | 1.140 | 0.11 |
| 58_H | 206_K | 1.140 | 0.11 |
| 375_E | 392_M | 1.138 | 0.11 |
| 42_L | 49_S | 1.137 | 0.11 |
| 63_H | 76_K | 1.135 | 0.11 |
| 42_L | 46_G | 1.134 | 0.11 |
| 35_G | 223_Y | 1.134 | 0.11 |
| 387_T | 594_S | 1.133 | 0.11 |
| 71_K | 78_K | 1.132 | 0.11 |
| 3_K | 8_H | 1.132 | 0.11 |
| 87_K | 387_T | 1.131 | 0.11 |
| 59_E | 62_R | 1.128 | 0.11 |
| 142_Q | 151_Q | 1.127 | 0.11 |
| 94_R | 219_D | 1.126 | 0.11 |
| 163_F | 202_K | 1.123 | 0.11 |
| 57_D | 500_V | 1.121 | 0.11 |
| 326_L | 505_L | 1.121 | 0.11 |
| 196_K | 329_N | 1.120 | 0.11 |
| 67_K | 454_R | 1.120 | 0.11 |
| 78_K | 525_D | 1.115 | 0.11 |
| 66_K | 69_K | 1.115 | 0.11 |
| 382_F | 386_A | 1.113 | 0.11 |
| 204_D | 300_L | 1.110 | 0.11 |
| 2_G | 11_E | 1.110 | 0.11 |
| 170_A | 181_M | 1.109 | 0.11 |
| 173_Y | 181_M | 1.109 | 0.11 |
| 181_M | 220_T | 1.109 | 0.11 |
| 181_M | 222_Y | 1.109 | 0.11 |
| 140_P | 228_K | 1.107 | 0.11 |
| 391_S | 395_N | 1.107 | 0.11 |
| 580_H | 583_Y | 1.107 | 0.11 |
| 38_E | 41_E | 1.105 | 0.11 |
| 574_E | 577_D | 1.104 | 0.11 |
| 58_H | 69_K | 1.104 | 0.11 |
| 470_P | 591_P | 1.103 | 0.11 |
| 244_L | 530_L | 1.103 | 0.11 |
| 293_S | 382_F | 1.100 | 0.11 |
| 27_P | 31_V | 1.099 | 0.11 |
| 35_G | 439_V | 1.099 | 0.11 |
| 435_Y | 443_L | 1.097 | 0.11 |
| 369_T | 379_K | 1.095 | 0.11 |
| 169_I | 413_Y | 1.095 | 0.11 |
| 221_V | 334_L | 1.094 | 0.11 |
| 26_K | 63_H | 1.094 | 0.11 |
| 151_Q | 155_K | 1.093 | 0.11 |
| 310_A | 429_V | 1.091 | 0.10 |
| 66_K | 70_K | 1.090 | 0.10 |
| 144_L | 149_L | 1.089 | 0.10 |
| 5_H | 31_V | 1.089 | 0.10 |
| 364_L | 368_T | 1.088 | 0.10 |
| 229_I | 407_E | 1.087 | 0.10 |
| 88_R | 418_G | 1.086 | 0.10 |
| 63_H | 373_K | 1.085 | 0.10 |
| 197_S | 524_L | 1.084 | 0.10 |
| 176_I | 223_Y | 1.084 | 0.10 |
| 197_S | 454_R | 1.082 | 0.10 |
| 2_G | 31_V | 1.082 | 0.10 |
| 183_F | 209_C | 1.082 | 0.10 |
| 141_I | 148_F | 1.081 | 0.10 |
| 66_K | 76_K | 1.078 | 0.10 |
| 150_R | 154_R | 1.077 | 0.10 |
| 140_P | 206_K | 1.077 | 0.10 |
| 361_S | 388_T | 1.075 | 0.10 |
| 63_H | 70_K | 1.073 | 0.10 |
| 357_S | 403_S | 1.073 | 0.10 |
| 531_L | 541_R | 1.071 | 0.10 |
| 87_K | 259_V | 1.070 | 0.10 |
| 408_L | 534_L | 1.069 | 0.10 |
| 194_E | 252_E | 1.067 | 0.10 |
| 41_E | 58_H | 1.067 | 0.10 |
| 139_T | 150_R | 1.066 | 0.10 |
| 460_K | 577_D | 1.065 | 0.10 |
| 524_L | 534_L | 1.064 | 0.10 |
| 202_K | 238_S | 1.064 | 0.10 |
| 76_K | 373_K | 1.061 | 0.10 |
| 418_G | 422_A | 1.060 | 0.10 |
| 28_L | 230_L | 1.059 | 0.10 |
| 162_A | 310_A | 1.059 | 0.10 |
| 30_L | 33_K | 1.055 | 0.10 |
| 26_K | 35_G | 1.055 | 0.10 |
| 583_Y | 594_S | 1.054 | 0.10 |
| 297_E | 531_L | 1.052 | 0.10 |
| 561_Q | 579_T | 1.051 | 0.10 |
| 260_P | 591_P | 1.050 | 0.10 |
| 69_K | 75_E | 1.047 | 0.10 |
| 184_G | 387_T | 1.046 | 0.10 |
| 353_P | 358_S | 1.046 | 0.10 |
| 528_T | 537_A | 1.045 | 0.10 |
| 329_N | 399_G | 1.044 | 0.10 |
| 58_H | 76_K | 1.043 | 0.10 |
| 42_L | 54_D | 1.042 | 0.10 |
| 159_G | 418_G | 1.041 | 0.10 |
| 190_I | 422_A | 1.041 | 0.10 |
| 375_E | 447_I | 1.040 | 0.10 |
| 388_T | 574_E | 1.039 | 0.10 |
| 159_G | 239_K | 1.038 | 0.10 |
| 538_Q | 560_D | 1.038 | 0.10 |
| 144_L | 362_K | 1.038 | 0.10 |
| 34_V | 43_S | 1.038 | 0.10 |
| 230_L | 398_F | 1.037 | 0.10 |
| 372_F | 375_E | 1.037 | 0.10 |
| 40_T | 43_S | 1.036 | 0.09 |
| 366_G | 372_F | 1.035 | 0.09 |
| 357_S | 521_H | 1.035 | 0.09 |
| 29_K | 183_F | 1.035 | 0.09 |
| 526_E | 538_Q | 1.035 | 0.09 |
| 26_K | 238_S | 1.035 | 0.09 |
| 325_Y | 394_N | 1.034 | 0.09 |
| 359_L | 422_A | 1.034 | 0.09 |
| 189_K | 205_F | 1.034 | 0.09 |
| 198_V | 580_H | 1.033 | 0.09 |
| 399_G | 447_I | 1.032 | 0.09 |
| 170_A | 377_R | 1.031 | 0.09 |
| 173_Y | 377_R | 1.031 | 0.09 |
| 220_T | 377_R | 1.031 | 0.09 |
| 222_Y | 377_R | 1.031 | 0.09 |
| 586_L | 591_P | 1.031 | 0.09 |
| 229_I | 392_M | 1.030 | 0.09 |
| 366_G | 375_E | 1.030 | 0.09 |
| 64_K | 67_K | 1.030 | 0.09 |
| 581_D | 587_Q | 1.029 | 0.09 |
| 139_T | 228_K | 1.029 | 0.09 |
| 255_V | 425_L | 1.029 | 0.09 |
| 256_P | 360_S | 1.029 | 0.09 |
| 378_N | 534_L | 1.029 | 0.09 |
| 366_G | 378_N | 1.026 | 0.09 |
| 536_E | 549_N | 1.025 | 0.09 |
| 403_S | 543_G | 1.024 | 0.09 |
| 29_K | 67_K | 1.023 | 0.09 |
| 57_D | 83_E | 1.021 | 0.09 |
| 526_E | 536_E | 1.019 | 0.09 |
| 214_T | 401_L | 1.018 | 0.09 |
| 334_L | 395_N | 1.018 | 0.09 |
| 166_T | 541_R | 1.018 | 0.09 |
| 142_Q | 147_H | 1.018 | 0.09 |
| 184_G | 392_M | 1.018 | 0.09 |
| 204_D | 420_Q | 1.018 | 0.09 |
| 219_D | 459_L | 1.017 | 0.09 |
| 6_K | 11_E | 1.016 | 0.09 |
| 65_E | 74_S | 1.015 | 0.09 |
| 43_S | 53_D | 1.014 | 0.09 |
| 227_K | 333_S | 1.014 | 0.09 |
| 68_K | 72_K | 1.014 | 0.09 |
| 157_P | 228_K | 1.014 | 0.09 |
| 217_R | 239_K | 1.014 | 0.09 |
| 115_K | 128_A | 1.013 | 0.09 |
| 41_E | 50_S | 1.013 | 0.09 |
| 409_L | 440_V | 1.013 | 0.09 |
| 359_L | 417_T | 1.012 | 0.09 |
| 41_E | 46_G | 1.012 | 0.09 |
| 198_V | 338_V | 1.011 | 0.09 |
| 402_K | 447_I | 1.011 | 0.09 |
| 63_H | 72_K | 1.010 | 0.09 |
| 574_E | 593_A | 1.009 | 0.09 |
| 368_T | 549_N | 1.009 | 0.09 |
| 228_K | 531_L | 1.008 | 0.09 |
| 322_K | 454_R | 1.008 | 0.09 |
| 124_R | 127_R | 1.008 | 0.09 |
| 69_K | 73_K | 1.007 | 0.09 |
| 137_E | 142_Q | 1.006 | 0.09 |
| 329_N | 390_L | 1.006 | 0.09 |
| 159_G | 409_L | 1.006 | 0.09 |
| 327_K | 370_L | 1.004 | 0.09 |
| 297_E | 445_D | 1.003 | 0.09 |
| 390_L | 542_G | 1.003 | 0.09 |
| 578_V | 594_S | 1.002 | 0.09 |
| 82_D | 260_P | 1.002 | 0.09 |
| 204_D | 359_L | 1.002 | 0.09 |
| 50_S | 73_K | 1.002 | 0.09 |
| 26_K | 379_K | 1.000 | 0.09 |
| 181_M | 541_R | 1.000 | 0.09 |
| 77_E | 252_E | 1.000 | 0.09 |
| 201_F | 430_K | 1.000 | 0.09 |
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 | |
| 4uitA | 1 | 0 | 100 | 0.895 | Contact Map |
| 4xy8A | 1 | 0.1893 | 100 | 0.898 | Contact Map |
| 2i7kA | 1 | 0.196 | 100 | 0.9 | Contact Map |
| 4lc2A | 1 | 0.191 | 99.9 | 0.909 | Contact Map |
| 5ameA | 2 | 0.206 | 99.9 | 0.91 | Contact Map |
| 4qb3A | 1 | 0 | 99.9 | 0.911 | Contact Map |
| 3mb4A | 2 | 0.1843 | 99.9 | 0.912 | Contact Map |
| 4q0nA | 8 | 0.1792 | 99.9 | 0.913 | Contact Map |
| 5c4qA | 2 | 0 | 99.9 | 0.913 | Contact Map |
| 3nxbA | 2 | 0.1692 | 99.9 | 0.914 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)