| C7 |
| ID: | 1501519904 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 481 (436) | ||
| Sequences: | 1760 (1273.5) | ||
| Seq/Len: | 4.037 | ||
| Nf(neff/√len): | 61.0 |
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: 4.037).
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 |
| 98_N | 101_A | 5.070 | 1.00 |
| 330_Q | 333_E | 4.563 | 1.00 |
| 30_D | 33_E | 4.451 | 1.00 |
| 178_R | 181_E | 4.082 | 1.00 |
| 321_R | 337_D | 4.061 | 1.00 |
| 64_R | 67_E | 3.820 | 1.00 |
| 296_K | 299_D | 3.740 | 1.00 |
| 258_N | 261_L | 3.593 | 1.00 |
| 212_C | 215_K | 3.339 | 1.00 |
| 204_G | 220_F | 3.305 | 1.00 |
| 89_E | 105_S | 3.092 | 1.00 |
| 144_D | 147_K | 3.063 | 1.00 |
| 55_R | 71_D | 2.899 | 1.00 |
| 305_T | 321_R | 2.611 | 1.00 |
| 90_G | 106_F | 2.597 | 1.00 |
| 322_A | 338_Y | 2.444 | 1.00 |
| 73_Q | 89_E | 2.425 | 1.00 |
| 308_V | 318_Y | 2.386 | 1.00 |
| 56_A | 72_A | 2.352 | 1.00 |
| 89_E | 93_H | 2.331 | 1.00 |
| 301_I | 328_T | 2.309 | 1.00 |
| 287_R | 303_D | 2.177 | 1.00 |
| 325_Y | 330_Q | 2.140 | 1.00 |
| 380_S | 383_E | 2.069 | 1.00 |
| 291_N | 299_D | 2.058 | 1.00 |
| 76_V | 86_H | 1.975 | 1.00 |
| 203_R | 219_F | 1.968 | 1.00 |
| 35_Y | 58_T | 1.938 | 1.00 |
| 335_V | 354_L | 1.924 | 1.00 |
| 325_Y | 333_E | 1.914 | 1.00 |
| 325_Y | 337_D | 1.897 | 1.00 |
| 55_R | 59_L | 1.885 | 1.00 |
| 263_Y | 290_V | 1.883 | 1.00 |
| 93_H | 101_A | 1.881 | 1.00 |
| 59_L | 67_E | 1.809 | 1.00 |
| 86_H | 105_S | 1.808 | 1.00 |
| 333_E | 336_R | 1.783 | 0.99 |
| 250_G | 266_Y | 1.772 | 0.99 |
| 74_Q | 77_R | 1.762 | 0.99 |
| 170_A | 186_A | 1.760 | 0.99 |
| 318_Y | 337_D | 1.758 | 0.99 |
| 335_V | 357_A | 1.758 | 0.99 |
| 332_E | 336_R | 1.737 | 0.99 |
| 306_N | 309_K | 1.707 | 0.99 |
| 332_E | 361_L | 1.668 | 0.99 |
| 301_I | 324_C | 1.651 | 0.99 |
| 39_T | 55_R | 1.642 | 0.99 |
| 69_L | 89_E | 1.569 | 0.98 |
| 18_F | 40_K | 1.520 | 0.98 |
| 262_A | 266_Y | 1.517 | 0.98 |
| 391_R | 395_H | 1.516 | 0.98 |
| 338_Y | 353_L | 1.512 | 0.98 |
| 52_Y | 74_Q | 1.504 | 0.98 |
| 187_S | 203_R | 1.499 | 0.98 |
| 93_H | 98_N | 1.491 | 0.97 |
| 35_Y | 62_L | 1.486 | 0.97 |
| 339_E | 358_Q | 1.484 | 0.97 |
| 260_K | 294_L | 1.481 | 0.97 |
| 113_D | 116_N | 1.466 | 0.97 |
| 33_E | 36_N | 1.465 | 0.97 |
| 251_N | 286_N | 1.463 | 0.97 |
| 340_K | 344_T | 1.459 | 0.97 |
| 103_C | 107_Q | 1.458 | 0.97 |
| 35_Y | 59_L | 1.453 | 0.97 |
| 18_F | 37_Y | 1.449 | 0.97 |
| 93_H | 105_S | 1.442 | 0.97 |
| 183_Q | 210_E | 1.430 | 0.97 |
| 72_A | 88_R | 1.422 | 0.96 |
| 305_T | 337_D | 1.417 | 0.96 |
| 106_F | 122_E | 1.402 | 0.96 |
| 291_N | 296_K | 1.397 | 0.96 |
| 25_Y | 33_E | 1.395 | 0.96 |
| 361_L | 364_S | 1.384 | 0.96 |
| 221_V | 225_R | 1.375 | 0.95 |
| 90_G | 109_A | 1.373 | 0.95 |
| 42_I | 52_Y | 1.363 | 0.95 |
| 173_L | 178_R | 1.358 | 0.95 |
| 324_C | 328_T | 1.357 | 0.95 |
| 305_T | 309_K | 1.348 | 0.95 |
| 340_K | 343_Q | 1.343 | 0.95 |
| 301_I | 305_T | 1.336 | 0.94 |
| 35_Y | 55_R | 1.335 | 0.94 |
| 22_G | 37_Y | 1.334 | 0.94 |
| 288_G | 303_D | 1.328 | 0.94 |
| 264_E | 268_E | 1.326 | 0.94 |
| 307_A | 310_L | 1.326 | 0.94 |
| 410_E | 413_K | 1.325 | 0.94 |
| 433_R | 438_Q | 1.321 | 0.94 |
| 38_Y | 54_N | 1.315 | 0.94 |
| 298_D | 328_T | 1.315 | 0.94 |
| 32_N | 62_L | 1.306 | 0.93 |
| 21_Q | 25_Y | 1.306 | 0.93 |
| 169_K | 173_L | 1.303 | 0.93 |
| 103_C | 127_N | 1.292 | 0.93 |
| 204_G | 250_G | 1.289 | 0.93 |
| 67_E | 70_G | 1.283 | 0.93 |
| 298_D | 302_E | 1.280 | 0.93 |
| 391_R | 394_M | 1.272 | 0.92 |
| 319_L | 350_H | 1.264 | 0.92 |
| 422_F | 426_S | 1.257 | 0.92 |
| 267_T | 287_R | 1.254 | 0.92 |
| 266_Y | 286_N | 1.247 | 0.91 |
| 49_A | 75_S | 1.236 | 0.91 |
| 91_K | 106_F | 1.235 | 0.91 |
| 412_E | 416_K | 1.235 | 0.91 |
| 260_K | 264_E | 1.229 | 0.90 |
| 222_Q | 225_R | 1.227 | 0.90 |
| 39_T | 71_D | 1.223 | 0.90 |
| 26_Y | 31_Y | 1.214 | 0.90 |
| 100_M | 130_M | 1.210 | 0.90 |
| 173_L | 181_E | 1.205 | 0.89 |
| 284_Y | 306_N | 1.199 | 0.89 |
| 284_Y | 303_D | 1.194 | 0.89 |
| 431_K | 435_D | 1.193 | 0.89 |
| 190_L | 200_L | 1.192 | 0.89 |
| 86_H | 109_A | 1.189 | 0.88 |
| 22_G | 38_Y | 1.184 | 0.88 |
| 86_H | 108_R | 1.176 | 0.88 |
| 153_D | 169_K | 1.167 | 0.87 |
| 361_L | 365_K | 1.160 | 0.87 |
| 76_V | 85_G | 1.157 | 0.87 |
| 40_K | 43_D | 1.152 | 0.86 |
| 432_T | 436_S | 1.147 | 0.86 |
| 75_S | 85_G | 1.143 | 0.86 |
| 182_A | 206_C | 1.143 | 0.86 |
| 216_A | 220_F | 1.140 | 0.85 |
| 180_P | 210_E | 1.137 | 0.85 |
| 170_A | 189_I | 1.133 | 0.85 |
| 223_A | 233_A | 1.132 | 0.85 |
| 107_Q | 111_E | 1.131 | 0.85 |
| 299_D | 302_E | 1.125 | 0.84 |
| 13_R | 17_T | 1.122 | 0.84 |
| 101_A | 104_R | 1.121 | 0.84 |
| 253_A | 258_N | 1.119 | 0.84 |
| 69_L | 92_C | 1.118 | 0.84 |
| 162_C | 165_F | 1.117 | 0.84 |
| 208_Y | 220_F | 1.115 | 0.84 |
| 220_F | 236_A | 1.112 | 0.83 |
| 304_C | 320_R | 1.111 | 0.83 |
| 263_Y | 287_R | 1.109 | 0.83 |
| 289_T | 320_R | 1.106 | 0.83 |
| 149_V | 153_D | 1.102 | 0.83 |
| 34_A | 38_Y | 1.100 | 0.83 |
| 253_A | 261_L | 1.099 | 0.82 |
| 331_Y | 357_A | 1.097 | 0.82 |
| 200_L | 219_F | 1.091 | 0.82 |
| 251_N | 266_Y | 1.090 | 0.82 |
| 26_Y | 57_A | 1.086 | 0.81 |
| 273_D | 276_N | 1.086 | 0.81 |
| 356_N | 360_E | 1.083 | 0.81 |
| 52_Y | 71_D | 1.081 | 0.81 |
| 35_Y | 38_Y | 1.080 | 0.81 |
| 280_N | 284_Y | 1.076 | 0.81 |
| 25_Y | 30_D | 1.076 | 0.81 |
| 260_K | 263_Y | 1.076 | 0.81 |
| 124_K | 322_A | 1.072 | 0.80 |
| 41_A | 75_S | 1.071 | 0.80 |
| 270_L | 280_N | 1.070 | 0.80 |
| 182_A | 186_A | 1.070 | 0.80 |
| 269_A | 283_L | 1.069 | 0.80 |
| 443_E | 446_N | 1.064 | 0.80 |
| 136_A | 152_M | 1.057 | 0.79 |
| 442_E | 445_M | 1.057 | 0.79 |
| 247_K | 251_N | 1.056 | 0.79 |
| 23_N | 54_N | 1.055 | 0.79 |
| 270_L | 284_Y | 1.054 | 0.79 |
| 291_N | 303_D | 1.054 | 0.79 |
| 338_Y | 342_Y | 1.045 | 0.78 |
| 322_A | 341_V | 1.043 | 0.78 |
| 440_L | 443_E | 1.043 | 0.78 |
| 73_Q | 105_S | 1.041 | 0.77 |
| 370_Y | 373_L | 1.041 | 0.77 |
| 144_D | 322_A | 1.039 | 0.77 |
| 42_I | 71_D | 1.039 | 0.77 |
| 285_C | 314_Y | 1.039 | 0.77 |
| 54_N | 57_A | 1.038 | 0.77 |
| 326_M | 338_Y | 1.034 | 0.77 |
| 14_E | 18_F | 1.032 | 0.77 |
| 288_G | 304_C | 1.031 | 0.77 |
| 408_Q | 412_E | 1.026 | 0.76 |
| 339_E | 343_Q | 1.021 | 0.76 |
| 204_G | 223_A | 1.021 | 0.76 |
| 207_L | 215_K | 1.021 | 0.76 |
| 384_I | 388_Y | 1.021 | 0.76 |
| 23_N | 38_Y | 1.020 | 0.75 |
| 296_K | 302_E | 1.013 | 0.75 |
| 59_L | 64_R | 1.006 | 0.74 |
| 365_K | 370_Y | 1.004 | 0.74 |
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 | |
| 2y4tA | 3 | 0.869 | 100 | 0.386 | Contact Map |
| 1w3bA | 2 | 0.7672 | 100 | 0.532 | Contact Map |
| 3iegA | 2 | 0.738 | 100 | 0.55 | Contact Map |
| 4ui9C | 2 | 0 | 100 | 0.568 | Contact Map |
| 3fp2A | 1 | 0.7734 | 100 | 0.577 | Contact Map |
| 2gw1A | 2 | 0.7963 | 100 | 0.581 | Contact Map |
| 4ui9J | 1 | 0 | 100 | 0.583 | Contact Map |
| 4ui9X | 2 | 0 | 100 | 0.591 | Contact Map |
| 4rg9A | 2 | 0.7089 | 100 | 0.592 | Contact Map |
| 4ui9F | 2 | 0 | 100 | 0.593 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)