| gp6 -force run |
| ID: | 1473849880 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 660 (579) | ||
| Sequences: | 81 (64) | ||
| Seq/Len: | 0.140 | ||
| Nf(neff/√len): | 2.7 |
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: 0.140).
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 |
| 49_E | 283_A | 2.016 | 0.51 |
| 51_S | 374_I | 1.815 | 0.40 |
| 106_A | 596_N | 1.807 | 0.40 |
| 422_V | 440_I | 1.795 | 0.39 |
| 439_Q | 472_D | 1.792 | 0.39 |
| 33_L | 57_C | 1.784 | 0.39 |
| 61_A | 187_I | 1.655 | 0.32 |
| 415_F | 569_I | 1.645 | 0.32 |
| 149_E | 321_D | 1.611 | 0.30 |
| 105_A | 287_S | 1.601 | 0.30 |
| 313_A | 409_I | 1.551 | 0.27 |
| 43_F | 50_G | 1.536 | 0.27 |
| 123_I | 190_K | 1.535 | 0.27 |
| 147_S | 347_T | 1.527 | 0.26 |
| 169_Q | 436_L | 1.526 | 0.26 |
| 398_D | 501_Y | 1.522 | 0.26 |
| 89_V | 322_I | 1.518 | 0.26 |
| 41_N | 468_V | 1.515 | 0.26 |
| 569_I | 595_I | 1.505 | 0.25 |
| 537_D | 609_I | 1.497 | 0.25 |
| 44_L | 460_A | 1.494 | 0.25 |
| 273_I | 510_M | 1.493 | 0.25 |
| 96_N | 408_I | 1.488 | 0.25 |
| 89_V | 127_R | 1.477 | 0.24 |
| 56_L | 640_I | 1.454 | 0.23 |
| 218_G | 226_M | 1.445 | 0.23 |
| 335_T | 437_E | 1.439 | 0.23 |
| 209_W | 369_P | 1.428 | 0.22 |
| 283_A | 313_A | 1.427 | 0.22 |
| 58_D | 79_F | 1.409 | 0.22 |
| 295_I | 360_V | 1.409 | 0.22 |
| 428_K | 474_S | 1.405 | 0.22 |
| 147_S | 167_L | 1.405 | 0.22 |
| 167_L | 474_S | 1.403 | 0.21 |
| 376_A | 392_I | 1.403 | 0.21 |
| 83_A | 174_R | 1.395 | 0.21 |
| 290_D | 354_G | 1.395 | 0.21 |
| 237_Y | 416_I | 1.394 | 0.21 |
| 187_I | 373_F | 1.389 | 0.21 |
| 362_T | 606_I | 1.387 | 0.21 |
| 405_T | 572_Y | 1.385 | 0.21 |
| 379_K | 432_S | 1.383 | 0.21 |
| 18_P | 42_E | 1.374 | 0.20 |
| 440_I | 466_T | 1.360 | 0.20 |
| 80_M | 329_G | 1.357 | 0.20 |
| 268_I | 278_A | 1.353 | 0.20 |
| 192_I | 465_L | 1.352 | 0.20 |
| 71_G | 539_R | 1.345 | 0.19 |
| 213_S | 611_L | 1.340 | 0.19 |
| 367_T | 510_M | 1.337 | 0.19 |
| 192_I | 602_I | 1.336 | 0.19 |
| 27_A | 346_D | 1.336 | 0.19 |
| 102_S | 183_T | 1.332 | 0.19 |
| 172_I | 322_I | 1.331 | 0.19 |
| 93_A | 392_I | 1.324 | 0.19 |
| 187_I | 275_T | 1.321 | 0.19 |
| 68_Q | 291_T | 1.319 | 0.19 |
| 194_R | 213_S | 1.318 | 0.19 |
| 440_I | 501_Y | 1.315 | 0.18 |
| 287_S | 592_I | 1.311 | 0.18 |
| 223_I | 352_R | 1.307 | 0.18 |
| 337_Q | 386_T | 1.307 | 0.18 |
| 273_I | 415_F | 1.306 | 0.18 |
| 46_Y | 51_S | 1.304 | 0.18 |
| 348_F | 440_I | 1.298 | 0.18 |
| 66_Y | 411_P | 1.298 | 0.18 |
| 389_R | 410_S | 1.292 | 0.18 |
| 282_G | 469_D | 1.291 | 0.18 |
| 346_D | 460_A | 1.287 | 0.17 |
| 217_A | 367_T | 1.282 | 0.17 |
| 105_A | 224_Y | 1.282 | 0.17 |
| 47_D | 325_I | 1.280 | 0.17 |
| 68_Q | 130_R | 1.279 | 0.17 |
| 110_I | 414_L | 1.274 | 0.17 |
| 106_A | 569_I | 1.271 | 0.17 |
| 85_L | 187_I | 1.268 | 0.17 |
| 105_A | 420_L | 1.266 | 0.17 |
| 436_L | 486_R | 1.266 | 0.17 |
| 453_E | 502_N | 1.262 | 0.17 |
| 161_Y | 268_I | 1.260 | 0.17 |
| 363_F | 438_G | 1.259 | 0.17 |
| 191_N | 408_I | 1.256 | 0.17 |
| 39_G | 513_N | 1.255 | 0.17 |
| 83_A | 474_S | 1.245 | 0.16 |
| 224_Y | 425_A | 1.244 | 0.16 |
| 191_N | 394_N | 1.242 | 0.16 |
| 150_D | 342_A | 1.240 | 0.16 |
| 273_I | 596_N | 1.236 | 0.16 |
| 223_I | 313_A | 1.233 | 0.16 |
| 151_V | 221_S | 1.229 | 0.16 |
| 578_N | 582_N | 1.227 | 0.16 |
| 51_S | 408_I | 1.227 | 0.16 |
| 463_K | 469_D | 1.227 | 0.16 |
| 41_N | 392_I | 1.224 | 0.16 |
| 572_Y | 575_N | 1.224 | 0.16 |
| 346_D | 362_T | 1.220 | 0.15 |
| 268_I | 465_L | 1.216 | 0.15 |
| 165_L | 434_Q | 1.216 | 0.15 |
| 83_A | 171_R | 1.215 | 0.15 |
| 147_S | 416_I | 1.212 | 0.15 |
| 439_Q | 605_N | 1.212 | 0.15 |
| 149_E | 287_S | 1.211 | 0.15 |
| 80_M | 151_V | 1.210 | 0.15 |
| 432_S | 611_L | 1.207 | 0.15 |
| 37_L | 79_F | 1.206 | 0.15 |
| 523_V | 611_L | 1.204 | 0.15 |
| 93_A | 201_V | 1.204 | 0.15 |
| 236_F | 475_V | 1.201 | 0.15 |
| 172_I | 444_I | 1.199 | 0.15 |
| 89_V | 464_M | 1.198 | 0.15 |
| 440_I | 587_D | 1.197 | 0.15 |
| 27_A | 180_D | 1.195 | 0.15 |
| 110_I | 289_A | 1.191 | 0.15 |
| 385_T | 623_L | 1.187 | 0.15 |
| 56_L | 409_I | 1.183 | 0.14 |
| 484_M | 510_M | 1.183 | 0.14 |
| 444_I | 499_I | 1.182 | 0.14 |
| 472_D | 621_I | 1.173 | 0.14 |
| 64_T | 242_E | 1.173 | 0.14 |
| 117_A | 352_R | 1.173 | 0.14 |
| 268_I | 333_R | 1.172 | 0.14 |
| 213_S | 268_I | 1.171 | 0.14 |
| 242_E | 327_E | 1.170 | 0.14 |
| 322_I | 428_K | 1.168 | 0.14 |
| 268_I | 292_L | 1.166 | 0.14 |
| 496_E | 609_I | 1.166 | 0.14 |
| 50_G | 272_Y | 1.165 | 0.14 |
| 412_N | 637_G | 1.162 | 0.14 |
| 114_C | 298_I | 1.156 | 0.14 |
| 81_R | 221_S | 1.154 | 0.14 |
| 75_V | 606_I | 1.153 | 0.14 |
| 268_I | 594_E | 1.152 | 0.14 |
| 349_V | 517_F | 1.152 | 0.14 |
| 307_D | 375_A | 1.151 | 0.14 |
| 113_T | 165_L | 1.150 | 0.14 |
| 411_P | 637_G | 1.150 | 0.14 |
| 61_A | 162_F | 1.149 | 0.14 |
| 282_G | 503_N | 1.149 | 0.14 |
| 447_Y | 469_D | 1.147 | 0.13 |
| 165_L | 619_Q | 1.145 | 0.13 |
| 332_K | 572_Y | 1.144 | 0.13 |
| 43_F | 48_F | 1.143 | 0.13 |
| 152_I | 197_V | 1.142 | 0.13 |
| 282_G | 353_F | 1.140 | 0.13 |
| 461_K | 484_M | 1.137 | 0.13 |
| 525_N | 534_V | 1.136 | 0.13 |
| 322_I | 335_T | 1.134 | 0.13 |
| 75_V | 536_Y | 1.134 | 0.13 |
| 87_S | 94_Q | 1.133 | 0.13 |
| 152_I | 440_I | 1.130 | 0.13 |
| 104_S | 383_Y | 1.129 | 0.13 |
| 595_I | 602_I | 1.127 | 0.13 |
| 34_I | 308_P | 1.126 | 0.13 |
| 233_N | 279_D | 1.126 | 0.13 |
| 38_N | 150_D | 1.125 | 0.13 |
| 386_T | 438_G | 1.124 | 0.13 |
| 62_Y | 128_G | 1.122 | 0.13 |
| 30_K | 37_L | 1.121 | 0.13 |
| 83_A | 392_I | 1.120 | 0.13 |
| 220_T | 394_N | 1.117 | 0.13 |
| 58_D | 235_E | 1.115 | 0.13 |
| 349_V | 503_N | 1.114 | 0.13 |
| 220_T | 268_I | 1.114 | 0.13 |
| 30_K | 48_F | 1.114 | 0.13 |
| 212_K | 408_I | 1.114 | 0.13 |
| 184_P | 214_M | 1.113 | 0.13 |
| 186_I | 464_M | 1.111 | 0.13 |
| 247_A | 307_D | 1.109 | 0.13 |
| 178_I | 610_N | 1.108 | 0.13 |
| 114_C | 416_I | 1.108 | 0.13 |
| 80_M | 575_N | 1.107 | 0.13 |
| 57_C | 167_L | 1.105 | 0.12 |
| 112_L | 284_V | 1.104 | 0.12 |
| 99_L | 187_I | 1.100 | 0.12 |
| 268_I | 444_I | 1.099 | 0.12 |
| 217_A | 595_I | 1.098 | 0.12 |
| 113_T | 293_T | 1.096 | 0.12 |
| 165_L | 472_D | 1.096 | 0.12 |
| 216_H | 268_I | 1.096 | 0.12 |
| 355_S | 619_Q | 1.096 | 0.12 |
| 43_F | 272_Y | 1.095 | 0.12 |
| 169_Q | 369_P | 1.094 | 0.12 |
| 195_N | 602_I | 1.093 | 0.12 |
| 58_D | 63_N | 1.092 | 0.12 |
| 218_G | 410_S | 1.092 | 0.12 |
| 236_F | 508_R | 1.089 | 0.12 |
| 96_N | 376_A | 1.089 | 0.12 |
| 72_N | 98_Y | 1.088 | 0.12 |
| 72_N | 281_N | 1.088 | 0.12 |
| 98_Y | 281_N | 1.088 | 0.12 |
| 58_D | 424_Y | 1.088 | 0.12 |
| 105_A | 391_D | 1.086 | 0.12 |
| 90_V | 360_V | 1.086 | 0.12 |
| 394_N | 469_D | 1.085 | 0.12 |
| 346_D | 606_I | 1.084 | 0.12 |
| 512_S | 621_I | 1.083 | 0.12 |
| 106_A | 280_A | 1.081 | 0.12 |
| 90_V | 228_E | 1.080 | 0.12 |
| 280_A | 419_N | 1.079 | 0.12 |
| 29_I | 468_V | 1.077 | 0.12 |
| 187_I | 197_V | 1.076 | 0.12 |
| 57_C | 207_I | 1.075 | 0.12 |
| 328_L | 486_R | 1.074 | 0.12 |
| 385_T | 419_N | 1.072 | 0.12 |
| 33_L | 440_I | 1.071 | 0.12 |
| 56_L | 348_F | 1.067 | 0.12 |
| 89_V | 347_T | 1.067 | 0.12 |
| 18_P | 637_G | 1.066 | 0.12 |
| 133_A | 571_P | 1.065 | 0.12 |
| 56_L | 143_Y | 1.064 | 0.12 |
| 347_T | 596_N | 1.064 | 0.12 |
| 145_F | 474_S | 1.063 | 0.11 |
| 339_C | 482_I | 1.063 | 0.11 |
| 351_E | 534_V | 1.062 | 0.11 |
| 114_C | 153_A | 1.062 | 0.11 |
| 416_I | 596_N | 1.062 | 0.11 |
| 65_L | 371_Y | 1.060 | 0.11 |
| 105_A | 110_I | 1.059 | 0.11 |
| 165_L | 432_S | 1.059 | 0.11 |
| 48_F | 272_Y | 1.059 | 0.11 |
| 165_L | 171_R | 1.058 | 0.11 |
| 312_G | 464_M | 1.056 | 0.11 |
| 525_N | 581_A | 1.056 | 0.11 |
| 412_N | 440_I | 1.056 | 0.11 |
| 38_N | 122_Y | 1.055 | 0.11 |
| 507_D | 510_M | 1.054 | 0.11 |
| 156_D | 389_R | 1.054 | 0.11 |
| 347_T | 439_Q | 1.054 | 0.11 |
| 105_A | 113_T | 1.053 | 0.11 |
| 191_N | 226_M | 1.052 | 0.11 |
| 57_C | 398_D | 1.051 | 0.11 |
| 97_G | 378_P | 1.051 | 0.11 |
| 241_G | 480_A | 1.050 | 0.11 |
| 409_I | 464_M | 1.050 | 0.11 |
| 68_Q | 218_G | 1.050 | 0.11 |
| 190_K | 618_V | 1.050 | 0.11 |
| 147_S | 422_V | 1.050 | 0.11 |
| 171_R | 471_A | 1.049 | 0.11 |
| 231_D | 345_Y | 1.047 | 0.11 |
| 105_A | 465_L | 1.045 | 0.11 |
| 82_T | 497_A | 1.043 | 0.11 |
| 167_L | 590_Y | 1.042 | 0.11 |
| 323_E | 499_I | 1.042 | 0.11 |
| 178_I | 182_L | 1.042 | 0.11 |
| 342_A | 402_A | 1.042 | 0.11 |
| 273_I | 346_D | 1.042 | 0.11 |
| 216_H | 426_L | 1.040 | 0.11 |
| 224_Y | 513_N | 1.040 | 0.11 |
| 44_L | 247_A | 1.040 | 0.11 |
| 394_N | 598_P | 1.039 | 0.11 |
| 63_N | 515_F | 1.039 | 0.11 |
| 123_I | 285_G | 1.039 | 0.11 |
| 174_R | 349_V | 1.037 | 0.11 |
| 338_R | 512_S | 1.036 | 0.11 |
| 365_D | 600_D | 1.035 | 0.11 |
| 329_G | 410_S | 1.034 | 0.11 |
| 44_L | 61_A | 1.034 | 0.11 |
| 335_T | 463_K | 1.034 | 0.11 |
| 224_Y | 605_N | 1.033 | 0.11 |
| 462_S | 469_D | 1.033 | 0.11 |
| 30_K | 280_A | 1.032 | 0.11 |
| 132_L | 389_R | 1.032 | 0.11 |
| 51_S | 282_G | 1.031 | 0.11 |
| 47_D | 333_R | 1.030 | 0.11 |
| 325_I | 512_S | 1.030 | 0.11 |
| 144_N | 476_I | 1.030 | 0.11 |
| 268_I | 433_E | 1.030 | 0.11 |
| 26_F | 62_Y | 1.029 | 0.11 |
| 62_Y | 462_S | 1.028 | 0.11 |
| 181_K | 335_T | 1.028 | 0.11 |
| 441_I | 478_S | 1.028 | 0.11 |
| 145_F | 243_I | 1.027 | 0.11 |
| 285_G | 304_P | 1.027 | 0.11 |
| 110_I | 273_I | 1.026 | 0.11 |
| 364_T | 600_D | 1.026 | 0.11 |
| 292_L | 379_K | 1.026 | 0.11 |
| 346_D | 423_T | 1.023 | 0.11 |
| 224_Y | 404_I | 1.023 | 0.11 |
| 397_K | 488_V | 1.022 | 0.11 |
| 224_Y | 390_E | 1.021 | 0.11 |
| 229_T | 447_Y | 1.021 | 0.11 |
| 62_Y | 228_E | 1.019 | 0.11 |
| 74_A | 640_I | 1.019 | 0.11 |
| 483_Q | 507_D | 1.018 | 0.11 |
| 26_F | 30_K | 1.018 | 0.11 |
| 44_L | 203_G | 1.017 | 0.10 |
| 129_T | 474_S | 1.017 | 0.10 |
| 176_E | 618_V | 1.017 | 0.10 |
| 143_Y | 602_I | 1.017 | 0.10 |
| 130_R | 435_W | 1.016 | 0.10 |
| 221_S | 472_D | 1.015 | 0.10 |
| 123_I | 187_I | 1.014 | 0.10 |
| 53_L | 323_E | 1.014 | 0.10 |
| 89_V | 596_N | 1.014 | 0.10 |
| 142_P | 389_R | 1.013 | 0.10 |
| 128_G | 338_R | 1.013 | 0.10 |
| 459_F | 572_Y | 1.013 | 0.10 |
| 408_I | 422_V | 1.011 | 0.10 |
| 177_I | 270_I | 1.011 | 0.10 |
| 159_N | 210_T | 1.011 | 0.10 |
| 104_S | 374_I | 1.010 | 0.10 |
| 355_S | 480_A | 1.010 | 0.10 |
| 71_G | 179_Y | 1.010 | 0.10 |
| 104_S | 471_A | 1.009 | 0.10 |
| 296_T | 299_N | 1.009 | 0.10 |
| 226_M | 451_D | 1.009 | 0.10 |
| 364_T | 372_A | 1.009 | 0.10 |
| 401_L | 479_S | 1.008 | 0.10 |
| 73_A | 438_G | 1.008 | 0.10 |
| 225_Y | 275_T | 1.008 | 0.10 |
| 120_R | 415_F | 1.008 | 0.10 |
| 82_T | 213_S | 1.007 | 0.10 |
| 227_R | 640_I | 1.006 | 0.10 |
| 173_V | 296_T | 1.005 | 0.10 |
| 236_F | 510_M | 1.005 | 0.10 |
| 374_I | 535_L | 1.005 | 0.10 |
| 80_M | 347_T | 1.003 | 0.10 |
| 128_G | 228_E | 1.003 | 0.10 |
| 460_A | 510_M | 1.002 | 0.10 |
| 30_K | 79_F | 1.002 | 0.10 |
| 219_S | 592_I | 1.001 | 0.10 |
| 217_A | 270_I | 1.001 | 0.10 |
| 38_N | 44_L | 1.001 | 0.10 |
| 203_G | 468_V | 1.000 | 0.10 |
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 | |
| 3h2tA | 2 | 0.4864 | 100 | 0.586 | Contact Map |
| 4txdA | 1 | 0.1167 | 17.3 | 0.989 | Contact Map |
| 1x0pA | 10 | 0.1 | 12.8 | 0.989 | Contact Map |
| 3j7aG | 1 | 0.0758 | 9.7 | 0.99 | Contact Map |
| 1j8uA | 1 | 0.0864 | 8.5 | 0.99 | Contact Map |
| 2z6vA | 1 | 0.1561 | 8.2 | 0.99 | Contact Map |
| 3a1gB | 2 | 0.0576 | 5.9 | 0.991 | Contact Map |
| 1tvmA | 1 | 0.0576 | 5.6 | 0.991 | Contact Map |
| 1dp7P | 1 | 0.1121 | 5.3 | 0.991 | Contact Map |
| 1uxcA | 1 | 0.0712 | 5.2 | 0.991 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)