| bbs_2_full -force run |
| ID: | 1505240139 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 721 (683) | ||
| Sequences: | 291 (216.4) | ||
| Seq/Len: | 0.426 | ||
| Nf(neff/√len): | 8.3 |
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: 0.426).
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 |
| 251_D | 256_G | 2.768 | 0.98 |
| 255_D | 259_E | 2.585 | 0.96 |
| 24_Y | 32_A | 2.471 | 0.95 |
| 251_D | 255_D | 2.320 | 0.92 |
| 219_Y | 227_G | 2.238 | 0.90 |
| 253_N | 259_E | 1.744 | 0.69 |
| 251_D | 259_E | 1.739 | 0.68 |
| 77_C | 120_A | 1.651 | 0.62 |
| 691_K | 710_L | 1.637 | 0.61 |
| 402_L | 427_S | 1.584 | 0.58 |
| 90_D | 101_L | 1.555 | 0.55 |
| 262_T | 270_D | 1.540 | 0.54 |
| 105_V | 110_D | 1.530 | 0.54 |
| 296_D | 301_G | 1.528 | 0.54 |
| 15_S | 18_M | 1.524 | 0.53 |
| 90_D | 95_G | 1.522 | 0.53 |
| 185_D | 189_R | 1.503 | 0.52 |
| 505_E | 509_R | 1.492 | 0.51 |
| 621_I | 648_Y | 1.478 | 0.50 |
| 183_S | 191_F | 1.469 | 0.49 |
| 161_D | 251_D | 1.467 | 0.49 |
| 100_L | 306_I | 1.466 | 0.49 |
| 182_G | 206_I | 1.461 | 0.49 |
| 223_N | 236_W | 1.454 | 0.48 |
| 3_Q | 37_A | 1.452 | 0.48 |
| 18_M | 75_V | 1.446 | 0.47 |
| 558_T | 564_A | 1.441 | 0.47 |
| 93_L | 136_A | 1.432 | 0.46 |
| 92_L | 102_A | 1.429 | 0.46 |
| 8_L | 28_H | 1.416 | 0.45 |
| 461_V | 484_Y | 1.416 | 0.45 |
| 102_A | 136_A | 1.408 | 0.45 |
| 26_G | 29_P | 1.400 | 0.44 |
| 65_D | 83_L | 1.398 | 0.44 |
| 92_L | 138_I | 1.393 | 0.44 |
| 6_F | 31_L | 1.392 | 0.43 |
| 654_L | 679_I | 1.382 | 0.43 |
| 564_A | 580_L | 1.377 | 0.42 |
| 455_L | 600_V | 1.373 | 0.42 |
| 402_L | 535_F | 1.370 | 0.42 |
| 675_V | 678_A | 1.369 | 0.42 |
| 34_A | 37_A | 1.366 | 0.42 |
| 170_D | 178_E | 1.365 | 0.42 |
| 90_D | 264_W | 1.364 | 0.41 |
| 21_V | 295_G | 1.353 | 0.41 |
| 607_H | 610_L | 1.350 | 0.40 |
| 270_D | 355_Y | 1.349 | 0.40 |
| 93_L | 102_A | 1.345 | 0.40 |
| 312_G | 348_L | 1.340 | 0.40 |
| 289_I | 352_L | 1.338 | 0.40 |
| 43_H | 81_G | 1.325 | 0.39 |
| 226_V | 289_I | 1.314 | 0.38 |
| 673_K | 685_L | 1.307 | 0.37 |
| 570_S | 586_F | 1.304 | 0.37 |
| 26_G | 81_G | 1.301 | 0.37 |
| 221_L | 227_G | 1.296 | 0.37 |
| 164_H | 184_E | 1.294 | 0.37 |
| 611_S | 614_M | 1.294 | 0.37 |
| 188_I | 222_S | 1.289 | 0.36 |
| 156_W | 199_E | 1.287 | 0.36 |
| 220_A | 224_G | 1.287 | 0.36 |
| 184_E | 269_V | 1.287 | 0.36 |
| 124_V | 252_L | 1.286 | 0.36 |
| 217_F | 239_K | 1.285 | 0.36 |
| 82_V | 87_L | 1.285 | 0.36 |
| 515_N | 519_L | 1.281 | 0.36 |
| 685_L | 688_G | 1.277 | 0.35 |
| 291_G | 306_I | 1.273 | 0.35 |
| 379_A | 383_H | 1.271 | 0.35 |
| 18_M | 67_S | 1.268 | 0.35 |
| 423_F | 426_E | 1.268 | 0.35 |
| 71_I | 75_V | 1.267 | 0.35 |
| 103_Y | 108_N | 1.263 | 0.34 |
| 217_F | 234_R | 1.260 | 0.34 |
| 146_G | 151_G | 1.258 | 0.34 |
| 157_T | 191_F | 1.252 | 0.34 |
| 163_V | 179_L | 1.251 | 0.34 |
| 270_D | 454_D | 1.249 | 0.34 |
| 514_L | 642_N | 1.247 | 0.33 |
| 664_N | 672_L | 1.246 | 0.33 |
| 680_Q | 684_H | 1.246 | 0.33 |
| 156_W | 202_E | 1.240 | 0.33 |
| 651_N | 655_L | 1.239 | 0.33 |
| 688_G | 699_R | 1.237 | 0.33 |
| 269_V | 401_E | 1.234 | 0.33 |
| 613_D | 636_D | 1.232 | 0.32 |
| 18_M | 22_G | 1.229 | 0.32 |
| 452_P | 483_M | 1.228 | 0.32 |
| 158_V | 182_G | 1.228 | 0.32 |
| 495_P | 559_D | 1.227 | 0.32 |
| 251_D | 263_G | 1.226 | 0.32 |
| 11_R | 44_N | 1.224 | 0.32 |
| 238_I | 402_L | 1.224 | 0.32 |
| 123_I | 219_Y | 1.224 | 0.32 |
| 519_L | 567_I | 1.221 | 0.32 |
| 5_V | 13_K | 1.220 | 0.32 |
| 506_R | 509_R | 1.215 | 0.31 |
| 227_G | 236_W | 1.215 | 0.31 |
| 26_G | 33_A | 1.214 | 0.31 |
| 13_K | 32_A | 1.214 | 0.31 |
| 40_V | 72_N | 1.213 | 0.31 |
| 179_L | 202_E | 1.212 | 0.31 |
| 673_K | 703_R | 1.211 | 0.31 |
| 4_P | 26_G | 1.210 | 0.31 |
| 202_E | 234_R | 1.209 | 0.31 |
| 223_N | 240_S | 1.207 | 0.31 |
| 100_L | 147_F | 1.205 | 0.31 |
| 10_L | 34_A | 1.205 | 0.31 |
| 340_E | 344_K | 1.203 | 0.31 |
| 644_Y | 679_I | 1.203 | 0.31 |
| 137_I | 149_H | 1.200 | 0.30 |
| 560_D | 569_Q | 1.197 | 0.30 |
| 4_P | 35_T | 1.193 | 0.30 |
| 25_D | 35_T | 1.191 | 0.30 |
| 296_D | 345_K | 1.191 | 0.30 |
| 17_R | 29_P | 1.189 | 0.30 |
| 14_I | 21_V | 1.188 | 0.30 |
| 37_A | 635_R | 1.187 | 0.30 |
| 114_R | 120_A | 1.187 | 0.30 |
| 518_F | 644_Y | 1.184 | 0.29 |
| 313_E | 317_Y | 1.183 | 0.29 |
| 4_P | 24_Y | 1.183 | 0.29 |
| 14_I | 17_R | 1.183 | 0.29 |
| 390_S | 412_I | 1.181 | 0.29 |
| 214_G | 232_T | 1.177 | 0.29 |
| 94_V | 226_V | 1.176 | 0.29 |
| 688_G | 698_C | 1.172 | 0.29 |
| 480_R | 622_R | 1.170 | 0.29 |
| 672_L | 686_R | 1.169 | 0.28 |
| 119_G | 179_L | 1.169 | 0.28 |
| 217_F | 229_Y | 1.164 | 0.28 |
| 115_E | 120_A | 1.162 | 0.28 |
| 19_V | 23_R | 1.160 | 0.28 |
| 182_G | 192_K | 1.157 | 0.28 |
| 688_G | 701_A | 1.157 | 0.28 |
| 4_P | 32_A | 1.156 | 0.28 |
| 34_A | 76_S | 1.155 | 0.28 |
| 113_Y | 157_T | 1.155 | 0.28 |
| 194_D | 268_K | 1.152 | 0.27 |
| 263_G | 267_G | 1.152 | 0.27 |
| 251_D | 261_I | 1.148 | 0.27 |
| 221_L | 229_Y | 1.147 | 0.27 |
| 180_L | 213_Y | 1.147 | 0.27 |
| 28_H | 44_N | 1.147 | 0.27 |
| 314_I | 706_N | 1.147 | 0.27 |
| 234_R | 237_R | 1.145 | 0.27 |
| 4_P | 9_K | 1.145 | 0.27 |
| 417_I | 425_G | 1.144 | 0.27 |
| 591_E | 598_V | 1.144 | 0.27 |
| 217_F | 221_L | 1.144 | 0.27 |
| 92_L | 110_D | 1.143 | 0.27 |
| 44_N | 67_S | 1.143 | 0.27 |
| 151_G | 155_F | 1.141 | 0.27 |
| 21_V | 80_A | 1.140 | 0.27 |
| 455_L | 501_F | 1.138 | 0.27 |
| 379_A | 385_T | 1.138 | 0.27 |
| 285_F | 305_L | 1.136 | 0.27 |
| 4_P | 25_D | 1.135 | 0.26 |
| 21_V | 29_P | 1.134 | 0.26 |
| 5_V | 32_A | 1.133 | 0.26 |
| 76_S | 138_I | 1.132 | 0.26 |
| 4_P | 12_H | 1.131 | 0.26 |
| 33_A | 67_S | 1.131 | 0.26 |
| 261_I | 455_L | 1.131 | 0.26 |
| 159_T | 183_S | 1.129 | 0.26 |
| 252_L | 255_D | 1.128 | 0.26 |
| 90_D | 96_T | 1.127 | 0.26 |
| 21_V | 34_A | 1.127 | 0.26 |
| 179_L | 194_D | 1.127 | 0.26 |
| 443_I | 447_P | 1.124 | 0.26 |
| 18_M | 44_N | 1.122 | 0.26 |
| 191_F | 220_A | 1.122 | 0.26 |
| 71_I | 94_V | 1.121 | 0.26 |
| 170_D | 352_L | 1.120 | 0.26 |
| 108_N | 341_L | 1.120 | 0.26 |
| 103_Y | 164_H | 1.120 | 0.26 |
| 76_S | 80_A | 1.118 | 0.26 |
| 229_Y | 234_R | 1.118 | 0.26 |
| 682_A | 686_R | 1.116 | 0.25 |
| 421_G | 425_G | 1.115 | 0.25 |
| 673_K | 686_R | 1.115 | 0.25 |
| 100_L | 145_Q | 1.115 | 0.25 |
| 26_G | 75_V | 1.112 | 0.25 |
| 175_G | 178_E | 1.112 | 0.25 |
| 268_K | 291_G | 1.111 | 0.25 |
| 514_L | 545_Y | 1.111 | 0.25 |
| 668_L | 679_I | 1.109 | 0.25 |
| 236_W | 348_L | 1.108 | 0.25 |
| 600_V | 618_S | 1.108 | 0.25 |
| 11_R | 20_A | 1.107 | 0.25 |
| 7_T | 16_P | 1.107 | 0.25 |
| 701_A | 713_I | 1.107 | 0.25 |
| 167_A | 173_G | 1.106 | 0.25 |
| 5_V | 11_R | 1.106 | 0.25 |
| 214_G | 245_M | 1.106 | 0.25 |
| 587_P | 628_A | 1.105 | 0.25 |
| 19_V | 338_I | 1.105 | 0.25 |
| 670_G | 684_H | 1.104 | 0.25 |
| 250_F | 305_L | 1.104 | 0.25 |
| 688_G | 695_I | 1.102 | 0.25 |
| 21_V | 33_A | 1.102 | 0.25 |
| 420_E | 468_Q | 1.101 | 0.25 |
| 170_D | 175_G | 1.100 | 0.25 |
| 694_V | 706_N | 1.100 | 0.25 |
| 4_P | 39_K | 1.099 | 0.24 |
| 261_I | 294_E | 1.099 | 0.24 |
| 238_I | 268_K | 1.099 | 0.24 |
| 159_T | 162_N | 1.096 | 0.24 |
| 29_P | 33_A | 1.095 | 0.24 |
| 5_V | 21_V | 1.095 | 0.24 |
| 37_A | 74_T | 1.094 | 0.24 |
| 515_N | 537_S | 1.091 | 0.24 |
| 226_V | 256_G | 1.091 | 0.24 |
| 143_A | 153_D | 1.091 | 0.24 |
| 219_Y | 351_E | 1.090 | 0.24 |
| 153_D | 156_W | 1.088 | 0.24 |
| 95_G | 108_N | 1.088 | 0.24 |
| 576_A | 633_L | 1.086 | 0.24 |
| 146_G | 412_I | 1.086 | 0.24 |
| 137_I | 287_S | 1.085 | 0.24 |
| 424_A | 482_S | 1.084 | 0.24 |
| 13_K | 24_Y | 1.084 | 0.24 |
| 9_K | 17_R | 1.082 | 0.24 |
| 622_R | 660_I | 1.081 | 0.23 |
| 255_D | 289_I | 1.080 | 0.23 |
| 679_I | 701_A | 1.080 | 0.23 |
| 41_F | 71_I | 1.075 | 0.23 |
| 20_A | 74_T | 1.074 | 0.23 |
| 11_R | 71_I | 1.074 | 0.23 |
| 34_A | 42_I | 1.073 | 0.23 |
| 103_Y | 240_S | 1.073 | 0.23 |
| 679_I | 686_R | 1.073 | 0.23 |
| 634_M | 683_G | 1.072 | 0.23 |
| 70_N | 73_Q | 1.071 | 0.23 |
| 10_L | 13_K | 1.071 | 0.23 |
| 629_E | 651_N | 1.071 | 0.23 |
| 247_I | 250_F | 1.071 | 0.23 |
| 68_L | 80_A | 1.071 | 0.23 |
| 405_S | 408_N | 1.071 | 0.23 |
| 144_L | 309_S | 1.070 | 0.23 |
| 604_H | 647_L | 1.069 | 0.23 |
| 139_G | 272_R | 1.069 | 0.23 |
| 74_T | 82_V | 1.069 | 0.23 |
| 217_F | 272_R | 1.069 | 0.23 |
| 255_D | 263_G | 1.068 | 0.23 |
| 462_G | 479_P | 1.066 | 0.23 |
| 520_L | 544_L | 1.065 | 0.23 |
| 178_E | 182_G | 1.065 | 0.23 |
| 36_Q | 68_L | 1.064 | 0.23 |
| 8_L | 31_L | 1.064 | 0.23 |
| 204_E | 287_S | 1.063 | 0.23 |
| 4_P | 43_H | 1.063 | 0.23 |
| 137_I | 633_L | 1.063 | 0.23 |
| 21_V | 65_D | 1.060 | 0.22 |
| 616_D | 686_R | 1.059 | 0.22 |
| 306_I | 309_S | 1.059 | 0.22 |
| 657_G | 660_I | 1.058 | 0.22 |
| 79_T | 82_V | 1.058 | 0.22 |
| 22_G | 35_T | 1.058 | 0.22 |
| 503_I | 577_I | 1.058 | 0.22 |
| 103_Y | 140_G | 1.057 | 0.22 |
| 194_D | 202_E | 1.057 | 0.22 |
| 224_G | 227_G | 1.056 | 0.22 |
| 44_N | 65_D | 1.055 | 0.22 |
| 148_N | 160_G | 1.054 | 0.22 |
| 92_L | 136_A | 1.054 | 0.22 |
| 569_Q | 582_V | 1.053 | 0.22 |
| 14_I | 19_V | 1.052 | 0.22 |
| 28_H | 613_D | 1.052 | 0.22 |
| 142_C | 159_T | 1.051 | 0.22 |
| 682_A | 685_L | 1.051 | 0.22 |
| 119_G | 223_N | 1.051 | 0.22 |
| 21_V | 154_L | 1.051 | 0.22 |
| 237_R | 282_K | 1.050 | 0.22 |
| 419_A | 456_H | 1.049 | 0.22 |
| 25_D | 28_H | 1.049 | 0.22 |
| 32_A | 80_A | 1.049 | 0.22 |
| 244_A | 259_E | 1.048 | 0.22 |
| 16_P | 44_N | 1.048 | 0.22 |
| 523_D | 533_V | 1.046 | 0.22 |
| 533_V | 541_G | 1.046 | 0.22 |
| 25_D | 29_P | 1.046 | 0.22 |
| 104_D | 108_N | 1.045 | 0.22 |
| 157_T | 183_S | 1.044 | 0.22 |
| 688_G | 717_G | 1.044 | 0.22 |
| 78_L | 467_T | 1.044 | 0.22 |
| 105_V | 108_N | 1.042 | 0.21 |
| 627_Q | 630_D | 1.041 | 0.21 |
| 452_P | 461_V | 1.041 | 0.21 |
| 96_T | 108_N | 1.041 | 0.21 |
| 99_N | 115_E | 1.041 | 0.21 |
| 268_K | 305_L | 1.040 | 0.21 |
| 164_H | 185_D | 1.040 | 0.21 |
| 218_G | 221_L | 1.040 | 0.21 |
| 226_V | 261_I | 1.040 | 0.21 |
| 357_E | 427_S | 1.040 | 0.21 |
| 259_E | 263_G | 1.040 | 0.21 |
| 193_E | 270_D | 1.038 | 0.21 |
| 110_D | 139_G | 1.036 | 0.21 |
| 705_N | 713_I | 1.036 | 0.21 |
| 21_V | 66_V | 1.035 | 0.21 |
| 106_Y | 109_S | 1.034 | 0.21 |
| 559_D | 565_G | 1.033 | 0.21 |
| 90_D | 108_N | 1.032 | 0.21 |
| 240_S | 425_G | 1.032 | 0.21 |
| 306_I | 428_H | 1.031 | 0.21 |
| 664_N | 679_I | 1.029 | 0.21 |
| 23_R | 44_N | 1.029 | 0.21 |
| 117_A | 133_S | 1.027 | 0.21 |
| 139_G | 146_G | 1.027 | 0.21 |
| 481_F | 586_F | 1.025 | 0.21 |
| 25_D | 31_L | 1.025 | 0.21 |
| 14_I | 39_K | 1.025 | 0.21 |
| 104_D | 204_E | 1.024 | 0.21 |
| 250_F | 336_D | 1.024 | 0.21 |
| 8_L | 32_A | 1.024 | 0.21 |
| 9_K | 21_V | 1.023 | 0.21 |
| 19_V | 33_A | 1.023 | 0.21 |
| 458_K | 674_A | 1.023 | 0.21 |
| 673_K | 688_G | 1.022 | 0.21 |
| 653_D | 656_N | 1.022 | 0.21 |
| 613_D | 683_G | 1.021 | 0.20 |
| 562_D | 601_D | 1.020 | 0.20 |
| 241_K | 264_W | 1.020 | 0.20 |
| 25_D | 43_H | 1.020 | 0.20 |
| 316_G | 340_E | 1.018 | 0.20 |
| 4_P | 8_L | 1.017 | 0.20 |
| 644_Y | 668_L | 1.017 | 0.20 |
| 17_R | 42_I | 1.017 | 0.20 |
| 95_G | 155_F | 1.017 | 0.20 |
| 13_K | 73_Q | 1.016 | 0.20 |
| 41_F | 76_S | 1.015 | 0.20 |
| 157_T | 160_G | 1.015 | 0.20 |
| 137_I | 147_F | 1.014 | 0.20 |
| 685_L | 695_I | 1.014 | 0.20 |
| 17_R | 33_A | 1.014 | 0.20 |
| 575_F | 582_V | 1.013 | 0.20 |
| 480_R | 690_P | 1.012 | 0.20 |
| 589_Y | 592_E | 1.011 | 0.20 |
| 559_D | 649_D | 1.011 | 0.20 |
| 28_H | 35_T | 1.011 | 0.20 |
| 113_Y | 136_A | 1.011 | 0.20 |
| 654_L | 668_L | 1.011 | 0.20 |
| 10_L | 412_I | 1.011 | 0.20 |
| 21_V | 67_S | 1.010 | 0.20 |
| 371_D | 415_V | 1.009 | 0.20 |
| 671_S | 684_H | 1.009 | 0.20 |
| 96_T | 449_K | 1.009 | 0.20 |
| 20_A | 36_Q | 1.009 | 0.20 |
| 100_L | 160_G | 1.008 | 0.20 |
| 95_G | 100_L | 1.008 | 0.20 |
| 684_H | 687_V | 1.008 | 0.20 |
| 312_G | 316_G | 1.006 | 0.20 |
| 687_V | 698_C | 1.006 | 0.20 |
| 448_P | 452_P | 1.005 | 0.20 |
| 3_Q | 9_K | 1.005 | 0.20 |
| 355_Y | 358_N | 1.005 | 0.20 |
| 239_K | 268_K | 1.004 | 0.20 |
| 20_A | 266_N | 1.004 | 0.20 |
| 65_D | 80_A | 1.002 | 0.20 |
| 380_N | 383_H | 1.002 | 0.20 |
| 20_A | 32_A | 1.002 | 0.20 |
| 142_C | 156_W | 1.001 | 0.20 |
| 43_H | 80_A | 1.001 | 0.20 |
| 269_V | 327_N | 1.000 | 0.19 |
| 121_S | 207_T | 1.000 | 0.19 |
| 225_T | 237_R | 1.000 | 0.19 |
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 | |
| 3odtA | 2 | 0.3939 | 99.4 | 0.935 | Contact Map |
| 4g56B | 2 | 0.3883 | 99.4 | 0.937 | Contact Map |
| 1gxrA | 2 | 0.4022 | 99.3 | 0.94 | Contact Map |
| 4yvdA | 1 | 0.3939 | 99.2 | 0.941 | Contact Map |
| 2hesX | 1 | 0.3717 | 99.2 | 0.941 | Contact Map |
| 2pbiB | 2 | 0.4008 | 99.2 | 0.941 | Contact Map |
| 4e54B | 1 | 0.3953 | 99.2 | 0.941 | Contact Map |
| 4zoyA | 1 | 0 | 99.2 | 0.941 | Contact Map |
| 1r5mA | 1 | 0.3731 | 99.2 | 0.942 | Contact Map |
| 4gqbB | 1 | 0.3981 | 99.2 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)