| bbs_7_full -force run |
| ID: | 1505241655 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 712 (670) | ||
| Sequences: | 299 (218.7) | ||
| Seq/Len: | 0.446 | ||
| Nf(neff/√len): | 8.4 |
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: 0.446).
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 |
| 245_D | 250_G | 3.024 | 0.99 |
| 249_D | 253_D | 2.839 | 0.98 |
| 245_D | 249_D | 2.516 | 0.96 |
| 206_F | 214_G | 2.281 | 0.92 |
| 245_D | 253_D | 2.006 | 0.84 |
| 247_V | 253_D | 1.911 | 0.79 |
| 30_Q | 35_G | 1.778 | 0.72 |
| 166_D | 170_R | 1.767 | 0.71 |
| 256_V | 264_E | 1.683 | 0.66 |
| 30_Q | 42_M | 1.659 | 0.64 |
| 687_K | 705_L | 1.654 | 0.64 |
| 164_C | 172_L | 1.647 | 0.63 |
| 46_M | 51_A | 1.644 | 0.63 |
| 512_F | 516_E | 1.641 | 0.63 |
| 564_S | 570_I | 1.602 | 0.60 |
| 245_D | 257_G | 1.569 | 0.58 |
| 32_V | 43_C | 1.554 | 0.57 |
| 264_E | 349_L | 1.549 | 0.56 |
| 626_L | 647_L | 1.540 | 0.56 |
| 43_C | 79_I | 1.538 | 0.56 |
| 32_V | 81_I | 1.533 | 0.55 |
| 151_P | 159_V | 1.533 | 0.55 |
| 459_E | 491_H | 1.512 | 0.54 |
| 211_G | 214_G | 1.507 | 0.53 |
| 33_V | 79_I | 1.501 | 0.53 |
| 96_Q | 119_F | 1.487 | 0.52 |
| 309_G | 342_L | 1.470 | 0.51 |
| 41_V | 303_V | 1.468 | 0.50 |
| 393_L | 421_S | 1.464 | 0.50 |
| 145_N | 165_Q | 1.456 | 0.50 |
| 33_V | 43_C | 1.454 | 0.49 |
| 371_S | 374_P | 1.452 | 0.49 |
| 144_I | 160_P | 1.434 | 0.48 |
| 80_F | 92_K | 1.417 | 0.47 |
| 358_E | 395_L | 1.410 | 0.46 |
| 207_G | 211_G | 1.406 | 0.46 |
| 110_A | 122_A | 1.399 | 0.45 |
| 30_Q | 258_R | 1.382 | 0.44 |
| 540_F | 612_Y | 1.375 | 0.44 |
| 310_W | 314_L | 1.369 | 0.43 |
| 98_L | 132_C | 1.368 | 0.43 |
| 121_S | 130_C | 1.353 | 0.42 |
| 264_E | 452_E | 1.345 | 0.41 |
| 210_D | 227_W | 1.334 | 0.41 |
| 450_R | 490_L | 1.327 | 0.40 |
| 142_D | 245_D | 1.327 | 0.40 |
| 30_Q | 36_D | 1.326 | 0.40 |
| 334_E | 338_K | 1.323 | 0.40 |
| 66_L | 206_F | 1.321 | 0.40 |
| 41_V | 88_R | 1.319 | 0.39 |
| 245_D | 255_L | 1.319 | 0.39 |
| 229_I | 393_L | 1.316 | 0.39 |
| 77_E | 90_F | 1.309 | 0.39 |
| 617_A | 620_V | 1.307 | 0.39 |
| 504_N | 593_E | 1.306 | 0.39 |
| 163_A | 187_P | 1.304 | 0.38 |
| 89_G | 94_G | 1.304 | 0.38 |
| 229_I | 262_M | 1.296 | 0.38 |
| 41_V | 90_F | 1.296 | 0.38 |
| 92_K | 106_E | 1.280 | 0.37 |
| 55_F | 79_I | 1.280 | 0.37 |
| 47_K | 50_E | 1.272 | 0.36 |
| 71_A | 74_T | 1.270 | 0.36 |
| 123_S | 130_C | 1.269 | 0.36 |
| 255_L | 291_G | 1.267 | 0.36 |
| 485_I | 489_S | 1.266 | 0.36 |
| 148_I | 154_R | 1.266 | 0.36 |
| 138_Y | 172_L | 1.264 | 0.36 |
| 98_L | 101_E | 1.258 | 0.35 |
| 610_L | 618_K | 1.257 | 0.35 |
| 531_K | 604_K | 1.254 | 0.35 |
| 282_L | 302_I | 1.254 | 0.35 |
| 32_V | 79_I | 1.248 | 0.34 |
| 257_G | 261_G | 1.248 | 0.34 |
| 650_A | 654_Q | 1.246 | 0.34 |
| 373_V | 376_F | 1.245 | 0.34 |
| 502_P | 565_D | 1.243 | 0.34 |
| 253_D | 257_G | 1.242 | 0.34 |
| 663_H | 671_I | 1.241 | 0.34 |
| 78_K | 82_A | 1.238 | 0.34 |
| 204_L | 230_R | 1.238 | 0.34 |
| 653_L | 676_I | 1.235 | 0.34 |
| 303_V | 306_T | 1.234 | 0.34 |
| 614_L | 646_I | 1.233 | 0.33 |
| 164_C | 170_R | 1.227 | 0.33 |
| 67_E | 246_I | 1.223 | 0.33 |
| 169_L | 209_S | 1.222 | 0.33 |
| 104_L | 134_D | 1.221 | 0.33 |
| 454_K | 465_L | 1.221 | 0.33 |
| 208_T | 214_G | 1.220 | 0.33 |
| 163_A | 173_Q | 1.218 | 0.32 |
| 91_T | 98_L | 1.211 | 0.32 |
| 652_H | 655_E | 1.211 | 0.32 |
| 140_S | 143_K | 1.211 | 0.32 |
| 105_T | 108_I | 1.210 | 0.32 |
| 80_F | 90_F | 1.204 | 0.32 |
| 667_L | 676_I | 1.203 | 0.32 |
| 44_F | 49_G | 1.202 | 0.31 |
| 113_I | 122_A | 1.199 | 0.31 |
| 306_T | 310_W | 1.199 | 0.31 |
| 118_L | 125_I | 1.196 | 0.31 |
| 414_L | 420_N | 1.189 | 0.31 |
| 172_L | 207_G | 1.188 | 0.31 |
| 521_V | 552_E | 1.188 | 0.31 |
| 100_F | 132_C | 1.188 | 0.31 |
| 456_R | 673_D | 1.187 | 0.30 |
| 306_T | 610_L | 1.187 | 0.30 |
| 127_N | 134_D | 1.184 | 0.30 |
| 669_G | 673_D | 1.184 | 0.30 |
| 177_V | 265_V | 1.183 | 0.30 |
| 139_L | 163_A | 1.182 | 0.30 |
| 140_S | 164_C | 1.182 | 0.30 |
| 447_N | 468_Y | 1.181 | 0.30 |
| 577_L | 622_L | 1.179 | 0.30 |
| 238_I | 253_D | 1.178 | 0.30 |
| 175_S | 262_M | 1.178 | 0.30 |
| 453_L | 508_L | 1.177 | 0.30 |
| 21_L | 30_Q | 1.176 | 0.30 |
| 681_F | 684_T | 1.175 | 0.30 |
| 29_T | 87_I | 1.173 | 0.30 |
| 40_I | 57_T | 1.173 | 0.30 |
| 32_V | 51_A | 1.172 | 0.30 |
| 700_Y | 708_F | 1.171 | 0.29 |
| 112_H | 151_P | 1.168 | 0.29 |
| 387_D | 591_S | 1.166 | 0.29 |
| 137_Y | 180_E | 1.165 | 0.29 |
| 673_D | 677_D | 1.162 | 0.29 |
| 479_Q | 486_K | 1.162 | 0.29 |
| 161_V | 194_N | 1.162 | 0.29 |
| 249_D | 257_G | 1.159 | 0.29 |
| 287_T | 294_V | 1.159 | 0.29 |
| 205_L | 208_T | 1.152 | 0.28 |
| 237_G | 275_V | 1.151 | 0.28 |
| 542_F | 565_D | 1.150 | 0.28 |
| 165_Q | 263_V | 1.146 | 0.28 |
| 156_L | 159_V | 1.145 | 0.28 |
| 345_E | 370_K | 1.145 | 0.28 |
| 293_C | 298_G | 1.143 | 0.28 |
| 656_E | 705_L | 1.143 | 0.28 |
| 85_S | 140_S | 1.142 | 0.28 |
| 521_V | 641_P | 1.142 | 0.28 |
| 513_S | 586_I | 1.142 | 0.28 |
| 609_K | 687_K | 1.142 | 0.28 |
| 376_F | 479_Q | 1.139 | 0.28 |
| 444_C | 491_H | 1.139 | 0.28 |
| 536_E | 576_V | 1.136 | 0.27 |
| 87_I | 306_T | 1.135 | 0.27 |
| 201_G | 219_T | 1.135 | 0.27 |
| 57_T | 63_I | 1.133 | 0.27 |
| 77_E | 138_Y | 1.132 | 0.27 |
| 213_L | 250_G | 1.132 | 0.27 |
| 116_S | 130_C | 1.132 | 0.27 |
| 215_L | 257_G | 1.131 | 0.27 |
| 225_H | 228_E | 1.129 | 0.27 |
| 99_S | 124_Y | 1.127 | 0.27 |
| 54_V | 78_K | 1.126 | 0.27 |
| 439_L | 444_C | 1.125 | 0.27 |
| 102_T | 108_I | 1.125 | 0.27 |
| 119_F | 130_C | 1.124 | 0.27 |
| 677_D | 680_K | 1.122 | 0.27 |
| 22_P | 30_Q | 1.122 | 0.27 |
| 672_T | 681_F | 1.122 | 0.27 |
| 121_S | 124_Y | 1.120 | 0.26 |
| 266_Y | 274_P | 1.120 | 0.26 |
| 476_K | 627_K | 1.119 | 0.26 |
| 201_G | 254_L | 1.114 | 0.26 |
| 90_F | 286_V | 1.113 | 0.26 |
| 437_F | 453_L | 1.113 | 0.26 |
| 246_I | 249_D | 1.112 | 0.26 |
| 82_A | 120_L | 1.112 | 0.26 |
| 62_K | 160_P | 1.112 | 0.26 |
| 56_K | 63_I | 1.111 | 0.26 |
| 409_D | 415_L | 1.111 | 0.26 |
| 454_K | 473_I | 1.111 | 0.26 |
| 145_N | 166_D | 1.110 | 0.26 |
| 263_V | 392_S | 1.109 | 0.26 |
| 210_D | 231_N | 1.107 | 0.26 |
| 172_L | 188_T | 1.107 | 0.26 |
| 18_M | 139_L | 1.107 | 0.26 |
| 445_Q | 448_T | 1.106 | 0.26 |
| 568_S | 611_E | 1.105 | 0.26 |
| 20_L | 49_G | 1.105 | 0.26 |
| 47_K | 146_D | 1.104 | 0.26 |
| 256_V | 265_V | 1.103 | 0.25 |
| 528_V | 608_P | 1.103 | 0.25 |
| 565_D | 648_E | 1.103 | 0.25 |
| 175_S | 183_V | 1.103 | 0.25 |
| 57_T | 78_K | 1.101 | 0.25 |
| 213_L | 244_F | 1.100 | 0.25 |
| 450_R | 564_S | 1.098 | 0.25 |
| 159_V | 163_A | 1.098 | 0.25 |
| 62_K | 125_I | 1.097 | 0.25 |
| 86_E | 96_Q | 1.097 | 0.25 |
| 214_G | 227_W | 1.097 | 0.25 |
| 684_T | 696_I | 1.096 | 0.25 |
| 34_V | 213_L | 1.093 | 0.25 |
| 141_G | 164_C | 1.091 | 0.25 |
| 375_S | 453_L | 1.090 | 0.25 |
| 510_G | 586_I | 1.090 | 0.25 |
| 496_F | 521_V | 1.090 | 0.25 |
| 55_F | 138_Y | 1.089 | 0.25 |
| 653_L | 667_L | 1.088 | 0.25 |
| 261_G | 309_G | 1.088 | 0.25 |
| 44_F | 231_N | 1.085 | 0.24 |
| 452_E | 467_A | 1.085 | 0.24 |
| 166_D | 169_L | 1.085 | 0.24 |
| 163_A | 174_G | 1.084 | 0.24 |
| 78_K | 89_G | 1.084 | 0.24 |
| 292_G | 626_L | 1.084 | 0.24 |
| 238_I | 255_L | 1.084 | 0.24 |
| 513_S | 516_E | 1.082 | 0.24 |
| 573_L | 588_L | 1.082 | 0.24 |
| 493_R | 581_A | 1.081 | 0.24 |
| 460_G | 463_G | 1.080 | 0.24 |
| 124_Y | 137_Y | 1.079 | 0.24 |
| 295_G | 311_I | 1.079 | 0.24 |
| 241_V | 301_E | 1.078 | 0.24 |
| 77_E | 92_K | 1.077 | 0.24 |
| 669_G | 680_K | 1.077 | 0.24 |
| 311_I | 701_D | 1.076 | 0.24 |
| 610_L | 671_I | 1.076 | 0.24 |
| 63_I | 265_V | 1.076 | 0.24 |
| 98_L | 105_T | 1.076 | 0.24 |
| 77_E | 80_F | 1.076 | 0.24 |
| 87_I | 207_G | 1.076 | 0.24 |
| 622_L | 628_E | 1.076 | 0.24 |
| 510_G | 516_E | 1.075 | 0.24 |
| 661_P | 673_D | 1.074 | 0.24 |
| 79_I | 95_K | 1.073 | 0.24 |
| 21_L | 204_L | 1.073 | 0.24 |
| 55_F | 66_L | 1.073 | 0.24 |
| 277_R | 671_I | 1.071 | 0.24 |
| 491_H | 572_I | 1.070 | 0.24 |
| 643_Y | 676_I | 1.069 | 0.24 |
| 601_H | 608_P | 1.069 | 0.24 |
| 80_F | 93_R | 1.068 | 0.24 |
| 44_F | 145_N | 1.066 | 0.23 |
| 183_V | 225_H | 1.065 | 0.23 |
| 510_G | 628_E | 1.064 | 0.23 |
| 127_N | 137_Y | 1.063 | 0.23 |
| 64_A | 188_T | 1.063 | 0.23 |
| 510_G | 513_S | 1.063 | 0.23 |
| 303_V | 422_A | 1.063 | 0.23 |
| 255_L | 292_G | 1.063 | 0.23 |
| 169_L | 291_G | 1.062 | 0.23 |
| 108_I | 129_Y | 1.062 | 0.23 |
| 617_A | 632_H | 1.061 | 0.23 |
| 91_T | 141_G | 1.061 | 0.23 |
| 579_K | 675_F | 1.061 | 0.23 |
| 449_T | 525_M | 1.061 | 0.23 |
| 476_K | 686_V | 1.060 | 0.23 |
| 643_Y | 667_L | 1.059 | 0.23 |
| 450_R | 459_E | 1.058 | 0.23 |
| 108_I | 121_S | 1.058 | 0.23 |
| 243_S | 282_L | 1.057 | 0.23 |
| 110_A | 121_S | 1.055 | 0.23 |
| 212_K | 228_E | 1.055 | 0.23 |
| 684_T | 694_L | 1.055 | 0.23 |
| 138_Y | 164_C | 1.054 | 0.23 |
| 562_F | 608_P | 1.052 | 0.23 |
| 45_G | 78_K | 1.052 | 0.23 |
| 114_S | 120_L | 1.052 | 0.23 |
| 306_T | 309_G | 1.050 | 0.23 |
| 672_T | 698_D | 1.050 | 0.23 |
| 380_D | 483_Y | 1.050 | 0.23 |
| 21_L | 116_S | 1.049 | 0.23 |
| 254_L | 263_V | 1.048 | 0.22 |
| 444_C | 448_T | 1.047 | 0.22 |
| 57_T | 97_F | 1.047 | 0.22 |
| 105_T | 109_K | 1.046 | 0.22 |
| 31_K | 38_D | 1.045 | 0.22 |
| 253_D | 305_S | 1.044 | 0.22 |
| 255_L | 453_L | 1.044 | 0.22 |
| 463_G | 490_L | 1.044 | 0.22 |
| 351_Y | 358_E | 1.043 | 0.22 |
| 50_E | 92_K | 1.043 | 0.22 |
| 99_S | 130_C | 1.042 | 0.22 |
| 608_P | 647_L | 1.041 | 0.22 |
| 114_S | 126_Y | 1.040 | 0.22 |
| 201_G | 239_L | 1.040 | 0.22 |
| 635_N | 640_I | 1.040 | 0.22 |
| 656_E | 659_K | 1.039 | 0.22 |
| 402_D | 408_S | 1.039 | 0.22 |
| 380_D | 481_R | 1.037 | 0.22 |
| 385_N | 401_I | 1.036 | 0.22 |
| 415_L | 420_N | 1.035 | 0.22 |
| 416_D | 564_S | 1.035 | 0.22 |
| 161_V | 318_P | 1.035 | 0.22 |
| 97_F | 100_F | 1.034 | 0.22 |
| 64_A | 105_T | 1.034 | 0.22 |
| 151_P | 346_L | 1.034 | 0.22 |
| 306_T | 444_C | 1.033 | 0.22 |
| 84_G | 124_Y | 1.031 | 0.22 |
| 420_N | 442_Y | 1.031 | 0.22 |
| 477_T | 634_G | 1.031 | 0.22 |
| 250_G | 257_G | 1.030 | 0.22 |
| 100_F | 103_N | 1.030 | 0.22 |
| 670_M | 680_K | 1.030 | 0.22 |
| 620_V | 646_I | 1.030 | 0.22 |
| 204_L | 225_H | 1.029 | 0.21 |
| 641_P | 688_T | 1.028 | 0.21 |
| 445_Q | 478_C | 1.028 | 0.21 |
| 171_V | 176_D | 1.028 | 0.21 |
| 450_R | 476_K | 1.027 | 0.21 |
| 238_I | 254_L | 1.027 | 0.21 |
| 443_R | 558_G | 1.027 | 0.21 |
| 30_Q | 185_G | 1.026 | 0.21 |
| 664_L | 668_Y | 1.025 | 0.21 |
| 278_F | 292_G | 1.025 | 0.21 |
| 408_S | 454_K | 1.025 | 0.21 |
| 43_C | 52_V | 1.024 | 0.21 |
| 21_L | 104_L | 1.023 | 0.21 |
| 104_L | 122_A | 1.023 | 0.21 |
| 518_H | 555_Y | 1.023 | 0.21 |
| 62_K | 98_L | 1.022 | 0.21 |
| 204_L | 266_Y | 1.022 | 0.21 |
| 34_V | 240_C | 1.022 | 0.21 |
| 35_G | 41_V | 1.021 | 0.21 |
| 30_Q | 104_L | 1.021 | 0.21 |
| 59_P | 78_K | 1.020 | 0.21 |
| 137_Y | 183_V | 1.019 | 0.21 |
| 416_D | 478_C | 1.018 | 0.21 |
| 679_F | 682_K | 1.018 | 0.21 |
| 89_G | 261_G | 1.017 | 0.21 |
| 627_K | 685_N | 1.017 | 0.21 |
| 620_V | 633_E | 1.017 | 0.21 |
| 31_K | 77_E | 1.016 | 0.21 |
| 678_K | 687_K | 1.016 | 0.21 |
| 289_I | 393_L | 1.015 | 0.21 |
| 566_N | 575_D | 1.014 | 0.21 |
| 675_F | 678_K | 1.013 | 0.21 |
| 410_V | 419_K | 1.013 | 0.21 |
| 382_F | 385_N | 1.011 | 0.21 |
| 99_S | 121_S | 1.009 | 0.20 |
| 490_L | 546_F | 1.008 | 0.20 |
| 110_A | 117_D | 1.008 | 0.20 |
| 689_K | 693_L | 1.008 | 0.20 |
| 241_V | 244_F | 1.008 | 0.20 |
| 82_A | 116_S | 1.008 | 0.20 |
| 81_I | 245_D | 1.007 | 0.20 |
| 151_P | 156_L | 1.007 | 0.20 |
| 80_F | 265_V | 1.005 | 0.20 |
| 253_D | 265_V | 1.005 | 0.20 |
| 374_P | 380_D | 1.004 | 0.20 |
| 211_G | 261_G | 1.004 | 0.20 |
| 122_A | 144_I | 1.004 | 0.20 |
| 87_I | 229_I | 1.004 | 0.20 |
| 81_I | 87_I | 1.004 | 0.20 |
| 32_V | 88_R | 1.003 | 0.20 |
| 241_V | 252_K | 1.002 | 0.20 |
| 263_V | 283_S | 1.002 | 0.20 |
| 82_A | 121_S | 1.001 | 0.20 |
| 188_T | 581_A | 1.000 | 0.20 |
| 459_E | 488_L | 1.000 | 0.20 |
| 55_F | 260_D | 1.000 | 0.20 |
| 99_S | 104_L | 1.000 | 0.20 |
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 | 0.4003 | 99.4 | 0.933 | Contact Map |
| 4czxA | 1 | 0.4017 | 99.3 | 0.933 | Contact Map |
| 2pbiB | 2 | 0.4031 | 99.3 | 0.936 | Contact Map |
| 4u7aA | 1 | 0 | 99.2 | 0.938 | Contact Map |
| 3sfzA | 1 | 0.389 | 99.1 | 0.94 | Contact Map |
| 1gxrA | 2 | 0.3455 | 99.1 | 0.94 | Contact Map |
| 4d0kA | 1 | 0.4031 | 99.1 | 0.941 | Contact Map |
| 4pswB | 1 | 0.3708 | 99.1 | 0.941 | Contact Map |
| 4zoxA | 1 | 0 | 99 | 0.942 | Contact Map |
| 4yvdA | 1 | 0.389 | 99 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)