| Tim23-Tim50 Whole -force run |
| ID: | 1488651922 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 559 (549) | ||
| Sequences: | 177 (129.2) | ||
| Seq/Len: | 0.322 | ||
| Nf(neff/√len): | 5.5 |
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: 0.322).
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 |
| 494_K | 498_E | 3.078 | 0.98 |
| 27_N | 40_T | 2.629 | 0.94 |
| 362_L | 369_L | 2.418 | 0.91 |
| 279_I | 284_F | 2.323 | 0.88 |
| 433_N | 436_E | 2.263 | 0.86 |
| 252_T | 256_E | 2.046 | 0.78 |
| 374_I | 382_Y | 2.036 | 0.77 |
| 91_A | 106_S | 1.995 | 0.75 |
| 382_Y | 391_P | 1.965 | 0.73 |
| 363_S | 385_Q | 1.917 | 0.71 |
| 194_K | 197_N | 1.764 | 0.61 |
| 382_Y | 392_M | 1.761 | 0.61 |
| 448_K | 451_G | 1.742 | 0.60 |
| 508_E | 511_G | 1.727 | 0.59 |
| 87_A | 279_I | 1.699 | 0.57 |
| 286_V | 294_H | 1.692 | 0.57 |
| 121_K | 322_S | 1.686 | 0.56 |
| 25_L | 41_V | 1.636 | 0.53 |
| 339_H | 507_Q | 1.616 | 0.51 |
| 402_K | 433_N | 1.612 | 0.51 |
| 373_I | 456_G | 1.609 | 0.51 |
| 120_K | 124_L | 1.573 | 0.48 |
| 475_K | 483_E | 1.565 | 0.48 |
| 19_S | 23_Q | 1.556 | 0.47 |
| 87_A | 392_M | 1.551 | 0.47 |
| 490_L | 497_E | 1.548 | 0.47 |
| 357_V | 383_K | 1.537 | 0.46 |
| 172_E | 279_I | 1.521 | 0.45 |
| 304_A | 508_E | 1.520 | 0.45 |
| 26_Q | 447_D | 1.518 | 0.45 |
| 375_I | 406_L | 1.500 | 0.44 |
| 426_N | 429_E | 1.499 | 0.43 |
| 266_P | 273_R | 1.498 | 0.43 |
| 286_V | 517_L | 1.496 | 0.43 |
| 26_Q | 508_E | 1.493 | 0.43 |
| 179_K | 182_R | 1.457 | 0.41 |
| 186_T | 372_V | 1.436 | 0.39 |
| 258_P | 499_E | 1.435 | 0.39 |
| 41_V | 114_A | 1.433 | 0.39 |
| 354_K | 384_L | 1.430 | 0.39 |
| 365_L | 372_V | 1.421 | 0.38 |
| 87_A | 110_A | 1.419 | 0.38 |
| 456_G | 460_A | 1.405 | 0.37 |
| 204_L | 390_I | 1.387 | 0.36 |
| 83_I | 110_A | 1.385 | 0.36 |
| 428_F | 485_G | 1.382 | 0.36 |
| 88_L | 285_L | 1.377 | 0.35 |
| 186_T | 435_A | 1.376 | 0.35 |
| 530_E | 533_K | 1.362 | 0.35 |
| 82_S | 87_A | 1.357 | 0.34 |
| 23_Q | 41_V | 1.356 | 0.34 |
| 56_A | 362_L | 1.348 | 0.34 |
| 204_L | 374_I | 1.339 | 0.33 |
| 453_H | 474_T | 1.324 | 0.32 |
| 317_I | 497_E | 1.314 | 0.32 |
| 19_S | 44_H | 1.314 | 0.32 |
| 61_L | 278_V | 1.313 | 0.32 |
| 314_Y | 485_G | 1.310 | 0.31 |
| 311_L | 337_P | 1.299 | 0.31 |
| 499_E | 502_K | 1.295 | 0.31 |
| 83_I | 494_K | 1.294 | 0.30 |
| 269_P | 272_Q | 1.294 | 0.30 |
| 11_L | 454_K | 1.290 | 0.30 |
| 438_F | 485_G | 1.287 | 0.30 |
| 333_E | 344_Y | 1.284 | 0.30 |
| 412_Y | 449_F | 1.283 | 0.30 |
| 29_P | 32_S | 1.283 | 0.30 |
| 402_K | 436_E | 1.280 | 0.30 |
| 319_L | 342_V | 1.278 | 0.30 |
| 317_I | 404_V | 1.277 | 0.29 |
| 488_N | 508_E | 1.276 | 0.29 |
| 85_A | 527_S | 1.275 | 0.29 |
| 93_F | 464_L | 1.272 | 0.29 |
| 222_E | 282_E | 1.267 | 0.29 |
| 357_V | 380_N | 1.263 | 0.29 |
| 45_I | 189_D | 1.262 | 0.29 |
| 415_T | 438_F | 1.260 | 0.29 |
| 344_Y | 503_I | 1.255 | 0.28 |
| 197_N | 200_Y | 1.254 | 0.28 |
| 179_K | 183_K | 1.244 | 0.28 |
| 3_Y | 246_R | 1.244 | 0.28 |
| 252_T | 255_Q | 1.241 | 0.27 |
| 428_F | 481_I | 1.239 | 0.27 |
| 446_K | 479_D | 1.236 | 0.27 |
| 216_R | 246_R | 1.233 | 0.27 |
| 434_L | 439_D | 1.231 | 0.27 |
| 47_K | 280_T | 1.229 | 0.27 |
| 92_L | 464_L | 1.225 | 0.27 |
| 187_S | 196_A | 1.220 | 0.26 |
| 519_D | 523_G | 1.218 | 0.26 |
| 212_I | 394_P | 1.215 | 0.26 |
| 23_Q | 47_K | 1.215 | 0.26 |
| 107_A | 373_I | 1.215 | 0.26 |
| 308_L | 317_I | 1.213 | 0.26 |
| 165_E | 463_A | 1.208 | 0.26 |
| 519_D | 522_E | 1.204 | 0.25 |
| 18_F | 428_F | 1.199 | 0.25 |
| 87_A | 206_A | 1.199 | 0.25 |
| 88_L | 224_E | 1.192 | 0.25 |
| 122_R | 282_E | 1.192 | 0.25 |
| 319_L | 521_V | 1.191 | 0.25 |
| 271_Y | 344_Y | 1.190 | 0.25 |
| 362_L | 374_I | 1.184 | 0.24 |
| 542_V | 546_F | 1.183 | 0.24 |
| 50_P | 314_Y | 1.181 | 0.24 |
| 119_V | 173_P | 1.181 | 0.24 |
| 273_R | 394_P | 1.179 | 0.24 |
| 5_T | 53_G | 1.178 | 0.24 |
| 38_L | 475_K | 1.178 | 0.24 |
| 69_T | 347_F | 1.176 | 0.24 |
| 249_S | 508_E | 1.176 | 0.24 |
| 191_K | 405_R | 1.174 | 0.24 |
| 481_I | 485_G | 1.173 | 0.24 |
| 237_S | 394_P | 1.171 | 0.24 |
| 230_I | 394_P | 1.171 | 0.24 |
| 108_M | 111_A | 1.169 | 0.24 |
| 35_K | 61_L | 1.169 | 0.24 |
| 196_A | 200_Y | 1.169 | 0.24 |
| 61_L | 70_I | 1.167 | 0.24 |
| 375_I | 428_F | 1.161 | 0.23 |
| 50_P | 441_R | 1.156 | 0.23 |
| 368_D | 372_V | 1.154 | 0.23 |
| 272_Q | 414_A | 1.145 | 0.23 |
| 198_W | 201_I | 1.144 | 0.22 |
| 105_S | 272_Q | 1.142 | 0.22 |
| 71_D | 254_F | 1.142 | 0.22 |
| 68_S | 95_S | 1.141 | 0.22 |
| 81_G | 446_K | 1.141 | 0.22 |
| 108_M | 112_A | 1.140 | 0.22 |
| 92_L | 454_K | 1.139 | 0.22 |
| 100_K | 413_L | 1.138 | 0.22 |
| 496_I | 519_D | 1.135 | 0.22 |
| 113_C | 116_W | 1.134 | 0.22 |
| 70_I | 530_E | 1.133 | 0.22 |
| 545_L | 548_E | 1.132 | 0.22 |
| 233_G | 238_L | 1.132 | 0.22 |
| 220_P | 223_S | 1.131 | 0.22 |
| 447_D | 451_G | 1.130 | 0.22 |
| 282_E | 347_F | 1.130 | 0.22 |
| 50_P | 485_G | 1.129 | 0.22 |
| 205_S | 209_G | 1.129 | 0.22 |
| 88_L | 92_L | 1.128 | 0.22 |
| 438_F | 474_T | 1.127 | 0.22 |
| 540_K | 544_A | 1.124 | 0.22 |
| 94_K | 288_S | 1.123 | 0.22 |
| 12_G | 108_M | 1.123 | 0.22 |
| 275_L | 445_L | 1.122 | 0.21 |
| 45_I | 172_E | 1.121 | 0.21 |
| 15_I | 463_A | 1.120 | 0.21 |
| 231_D | 392_M | 1.120 | 0.21 |
| 105_S | 109_V | 1.119 | 0.21 |
| 476_F | 506_Q | 1.117 | 0.21 |
| 94_K | 437_E | 1.115 | 0.21 |
| 497_E | 500_K | 1.108 | 0.21 |
| 273_R | 329_D | 1.107 | 0.21 |
| 187_S | 282_E | 1.106 | 0.21 |
| 45_I | 249_S | 1.105 | 0.21 |
| 192_R | 273_R | 1.102 | 0.21 |
| 428_F | 446_K | 1.102 | 0.21 |
| 468_N | 510_M | 1.101 | 0.21 |
| 202_F | 205_S | 1.101 | 0.21 |
| 206_A | 425_L | 1.099 | 0.20 |
| 352_V | 380_N | 1.099 | 0.20 |
| 188_T | 191_K | 1.098 | 0.20 |
| 450_Y | 505_I | 1.097 | 0.20 |
| 282_E | 358_H | 1.094 | 0.20 |
| 330_K | 505_I | 1.093 | 0.20 |
| 269_P | 372_V | 1.091 | 0.20 |
| 269_P | 368_D | 1.090 | 0.20 |
| 92_L | 260_P | 1.090 | 0.20 |
| 440_H | 444_K | 1.089 | 0.20 |
| 92_L | 212_I | 1.089 | 0.20 |
| 26_Q | 240_Y | 1.087 | 0.20 |
| 414_A | 481_I | 1.086 | 0.20 |
| 100_K | 218_W | 1.085 | 0.20 |
| 206_A | 379_P | 1.082 | 0.20 |
| 546_F | 549_E | 1.081 | 0.20 |
| 261_D | 265_P | 1.079 | 0.20 |
| 278_V | 358_H | 1.079 | 0.20 |
| 86_G | 216_R | 1.078 | 0.19 |
| 183_K | 494_K | 1.078 | 0.19 |
| 182_R | 196_A | 1.077 | 0.19 |
| 21_M | 73_L | 1.077 | 0.19 |
| 286_V | 304_A | 1.075 | 0.19 |
| 106_S | 438_F | 1.074 | 0.19 |
| 22_M | 507_Q | 1.071 | 0.19 |
| 432_K | 459_W | 1.070 | 0.19 |
| 243_F | 520_Y | 1.069 | 0.19 |
| 243_F | 247_F | 1.067 | 0.19 |
| 250_M | 279_I | 1.067 | 0.19 |
| 279_I | 447_D | 1.066 | 0.19 |
| 304_A | 308_L | 1.065 | 0.19 |
| 187_S | 191_K | 1.065 | 0.19 |
| 209_G | 354_K | 1.064 | 0.19 |
| 119_V | 123_L | 1.060 | 0.19 |
| 412_Y | 427_S | 1.060 | 0.19 |
| 84_G | 392_M | 1.059 | 0.19 |
| 478_L | 481_I | 1.059 | 0.19 |
| 58_I | 434_L | 1.058 | 0.19 |
| 284_F | 354_K | 1.058 | 0.19 |
| 502_K | 506_Q | 1.058 | 0.19 |
| 329_D | 414_A | 1.056 | 0.19 |
| 45_I | 240_Y | 1.056 | 0.19 |
| 314_Y | 479_D | 1.054 | 0.18 |
| 62_S | 66_I | 1.054 | 0.18 |
| 102_M | 291_S | 1.053 | 0.18 |
| 449_F | 498_E | 1.052 | 0.18 |
| 204_L | 260_P | 1.052 | 0.18 |
| 59_L | 308_L | 1.051 | 0.18 |
| 100_K | 363_S | 1.051 | 0.18 |
| 256_E | 312_S | 1.051 | 0.18 |
| 194_K | 200_Y | 1.050 | 0.18 |
| 12_G | 234_Y | 1.049 | 0.18 |
| 212_I | 419_K | 1.048 | 0.18 |
| 3_Y | 216_R | 1.048 | 0.18 |
| 65_I | 342_V | 1.048 | 0.18 |
| 252_T | 330_K | 1.048 | 0.18 |
| 401_D | 405_R | 1.047 | 0.18 |
| 323_N | 352_V | 1.045 | 0.18 |
| 475_K | 479_D | 1.045 | 0.18 |
| 151_V | 211_A | 1.044 | 0.18 |
| 311_L | 315_Y | 1.044 | 0.18 |
| 269_P | 508_E | 1.043 | 0.18 |
| 222_E | 347_F | 1.043 | 0.18 |
| 186_T | 434_L | 1.041 | 0.18 |
| 87_A | 359_I | 1.041 | 0.18 |
| 8_V | 445_L | 1.041 | 0.18 |
| 333_E | 428_F | 1.041 | 0.18 |
| 532_M | 540_K | 1.040 | 0.18 |
| 298_T | 312_S | 1.040 | 0.18 |
| 325_M | 341_F | 1.040 | 0.18 |
| 92_L | 168_E | 1.037 | 0.18 |
| 12_G | 92_L | 1.036 | 0.18 |
| 123_L | 425_L | 1.036 | 0.18 |
| 81_G | 504_R | 1.036 | 0.18 |
| 288_S | 372_V | 1.035 | 0.18 |
| 27_N | 44_H | 1.033 | 0.18 |
| 543_D | 547_E | 1.033 | 0.18 |
| 312_S | 415_T | 1.032 | 0.18 |
| 69_T | 72_A | 1.030 | 0.18 |
| 484_E | 500_K | 1.030 | 0.18 |
| 79_T | 121_K | 1.028 | 0.17 |
| 102_M | 106_S | 1.027 | 0.17 |
| 194_K | 198_W | 1.026 | 0.17 |
| 94_K | 206_A | 1.026 | 0.17 |
| 370_S | 373_I | 1.025 | 0.17 |
| 80_A | 87_A | 1.025 | 0.17 |
| 490_L | 498_E | 1.025 | 0.17 |
| 88_L | 217_D | 1.024 | 0.17 |
| 59_L | 332_A | 1.022 | 0.17 |
| 298_T | 309_G | 1.021 | 0.17 |
| 312_S | 341_F | 1.020 | 0.17 |
| 191_K | 352_V | 1.020 | 0.17 |
| 502_K | 505_I | 1.020 | 0.17 |
| 63_Y | 242_R | 1.020 | 0.17 |
| 542_V | 545_L | 1.019 | 0.17 |
| 120_K | 266_P | 1.019 | 0.17 |
| 272_Q | 481_I | 1.018 | 0.17 |
| 70_I | 289_E | 1.018 | 0.17 |
| 374_I | 389_A | 1.016 | 0.17 |
| 108_M | 471_G | 1.015 | 0.17 |
| 549_E | 556_A | 1.014 | 0.17 |
| 352_V | 499_E | 1.014 | 0.17 |
| 239_M | 358_H | 1.010 | 0.17 |
| 155_G | 158_K | 1.009 | 0.17 |
| 47_K | 176_K | 1.009 | 0.17 |
| 251_F | 324_Y | 1.004 | 0.17 |
| 5_T | 10_L | 1.004 | 0.17 |
| 487_K | 508_E | 1.004 | 0.17 |
| 539_Q | 542_V | 1.003 | 0.16 |
| 536_L | 540_K | 1.002 | 0.16 |
| 19_S | 47_K | 1.002 | 0.16 |
| 219_E | 260_P | 1.002 | 0.16 |
| 282_E | 383_K | 1.002 | 0.16 |
| 47_K | 58_I | 1.002 | 0.16 |
| 280_T | 431_K | 1.001 | 0.16 |
| 372_V | 417_Q | 1.001 | 0.16 |
| 197_N | 204_L | 1.001 | 0.16 |
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 | |
| 3qleA | 1 | 0.3256 | 100 | 0.831 | Contact Map |
| 3shqA | 1 | 0.5009 | 100 | 0.876 | Contact Map |
| 2ghtA | 2 | 0.2934 | 99.9 | 0.9 | Contact Map |
| 2hhlA | 4 | 0.297 | 99.9 | 0.908 | Contact Map |
| 4xpzA | 1 | 0.4651 | 99.8 | 0.924 | Contact Map |
| 3ef1A | 1 | 0.3345 | 99.8 | 0.925 | Contact Map |
| 4um7A | 4 | 0.2952 | 92.8 | 0.978 | Contact Map |
| 2obbA | 1 | 0.2147 | 90.1 | 0.979 | Contact Map |
| 2i33A | 2 | 0.3363 | 88.8 | 0.98 | Contact Map |
| 2no4A | 2 | 0.2755 | 87.9 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)