| 1DLJA |
| ID: | 1411752343 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 402 (383) | ||
| Sequences: | 3554 (2226.5) | ||
| Seq/Len: | 9.279 | ||
| Nf(neff/√len): | 113.8 |
HHblits Results: (2013_03)
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: 9.279).
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 |
| 32_P | 36_D | 5.475 | 1.00 |
| 125_T | 198_S | 5.188 | 1.00 |
| 311_V | 344_K | 3.075 | 1.00 |
| 2_K | 24_E | 2.974 | 1.00 |
| 37_K | 42_L | 2.903 | 1.00 |
| 4_A | 74_A | 2.885 | 1.00 |
| 195_M | 234_M | 2.845 | 1.00 |
| 66_D | 69_A | 2.839 | 1.00 |
| 314_V | 335_I | 2.768 | 1.00 |
| 226_E | 297_Q | 2.748 | 1.00 |
| 196_G | 199_E | 2.679 | 1.00 |
| 298_I | 378_V | 2.666 | 1.00 |
| 39_N | 63_A | 2.621 | 1.00 |
| 311_V | 346_I | 2.468 | 1.00 |
| 36_D | 40_N | 2.449 | 1.00 |
| 313_G | 374_A | 2.389 | 1.00 |
| 298_I | 376_I | 2.386 | 1.00 |
| 207_A | 239_I | 2.372 | 1.00 |
| 195_M | 203_V | 2.326 | 1.00 |
| 231_N | 234_M | 2.223 | 1.00 |
| 81_T | 84_N | 2.210 | 1.00 |
| 8_S | 27_I | 2.199 | 1.00 |
| 43_S | 54_L | 2.156 | 1.00 |
| 209_T | 217_Y | 2.150 | 1.00 |
| 77_V | 111_A | 2.109 | 1.00 |
| 29_D | 35_V | 2.082 | 1.00 |
| 17_V | 54_L | 2.065 | 1.00 |
| 202_A | 225_A | 2.057 | 1.00 |
| 38_I | 61_I | 2.000 | 1.00 |
| 278_T | 285_S | 1.989 | 1.00 |
| 108_N | 111_A | 1.989 | 1.00 |
| 213_L | 283_I | 1.967 | 1.00 |
| 292_S | 337_I | 1.950 | 1.00 |
| 175_E | 179_L | 1.939 | 1.00 |
| 313_G | 370_F | 1.937 | 1.00 |
| 299_I | 341_K | 1.927 | 1.00 |
| 312_V | 343_I | 1.926 | 1.00 |
| 322_N | 384_N | 1.912 | 1.00 |
| 137_I | 178_A | 1.905 | 1.00 |
| 21_L | 56_S | 1.889 | 1.00 |
| 98_E | 102_K | 1.886 | 1.00 |
| 318_I | 352_L | 1.835 | 1.00 |
| 135_R | 164_E | 1.824 | 1.00 |
| 150_Y | 154_Y | 1.821 | 1.00 |
| 35_V | 63_A | 1.789 | 1.00 |
| 346_I | 374_A | 1.784 | 1.00 |
| 24_E | 62_K | 1.783 | 1.00 |
| 32_P | 65_L | 1.777 | 1.00 |
| 225_A | 232_S | 1.776 | 1.00 |
| 33_S | 36_D | 1.759 | 1.00 |
| 210_Y | 214_R | 1.722 | 1.00 |
| 67_S | 103_E | 1.698 | 1.00 |
| 102_K | 130_K | 1.653 | 1.00 |
| 99_T | 102_K | 1.634 | 1.00 |
| 112_T | 137_I | 1.621 | 1.00 |
| 164_E | 174_A | 1.614 | 1.00 |
| 226_E | 293_Y | 1.585 | 1.00 |
| 28_V | 67_S | 1.570 | 1.00 |
| 210_Y | 246_G | 1.558 | 1.00 |
| 34_K | 44_P | 1.539 | 1.00 |
| 279_L | 286_S | 1.517 | 1.00 |
| 366_D | 369_N | 1.513 | 1.00 |
| 31_L | 34_K | 1.509 | 1.00 |
| 17_V | 61_I | 1.508 | 1.00 |
| 276_P | 281_E | 1.505 | 1.00 |
| 6_A | 100_V | 1.504 | 1.00 |
| 224_Y | 277_Q | 1.501 | 1.00 |
| 279_L | 282_A | 1.491 | 1.00 |
| 18_L | 21_L | 1.488 | 1.00 |
| 223_T | 293_Y | 1.476 | 1.00 |
| 293_Y | 297_Q | 1.473 | 1.00 |
| 199_E | 230_L | 1.470 | 1.00 |
| 337_I | 340_S | 1.468 | 1.00 |
| 223_T | 290_R | 1.459 | 1.00 |
| 213_L | 279_L | 1.457 | 1.00 |
| 36_D | 39_N | 1.457 | 1.00 |
| 175_E | 194_I | 1.439 | 1.00 |
| 181_L | 184_A | 1.430 | 0.99 |
| 256_Y | 284_V | 1.423 | 0.99 |
| 173_D | 181_L | 1.417 | 0.99 |
| 76_L | 112_T | 1.411 | 0.99 |
| 178_A | 182_K | 1.363 | 0.99 |
| 269_L | 281_E | 1.362 | 0.99 |
| 228_R | 273_N | 1.351 | 0.99 |
| 212_A | 284_V | 1.341 | 0.99 |
| 35_V | 65_L | 1.335 | 0.99 |
| 62_K | 69_A | 1.331 | 0.99 |
| 26_T | 62_K | 1.328 | 0.99 |
| 178_A | 181_L | 1.318 | 0.99 |
| 295_A | 334_V | 1.318 | 0.99 |
| 2_K | 26_T | 1.315 | 0.99 |
| 213_L | 217_Y | 1.306 | 0.99 |
| 227_S | 275_I | 1.304 | 0.99 |
| 102_K | 106_S | 1.301 | 0.99 |
| 199_E | 235_I | 1.300 | 0.99 |
| 38_I | 63_A | 1.300 | 0.99 |
| 23_N | 183_S | 1.298 | 0.99 |
| 39_N | 62_K | 1.294 | 0.99 |
| 4_A | 77_V | 1.293 | 0.99 |
| 18_L | 152_N | 1.293 | 0.99 |
| 35_V | 39_N | 1.293 | 0.99 |
| 15_L | 19_L | 1.290 | 0.99 |
| 335_I | 339_K | 1.290 | 0.99 |
| 8_S | 16_G | 1.284 | 0.99 |
| 104_V | 113_L | 1.276 | 0.99 |
| 237_Q | 247_M | 1.257 | 0.98 |
| 206_F | 221_L | 1.256 | 0.98 |
| 332_K | 336_D | 1.254 | 0.98 |
| 317_L | 329_S | 1.251 | 0.98 |
| 54_L | 61_I | 1.245 | 0.98 |
| 333_D | 336_D | 1.243 | 0.98 |
| 24_E | 60_S | 1.241 | 0.98 |
| 64_T | 70_A | 1.234 | 0.98 |
| 79_I | 97_V | 1.234 | 0.98 |
| 298_I | 312_V | 1.232 | 0.98 |
| 37_K | 44_P | 1.229 | 0.98 |
| 172_A | 176_K | 1.223 | 0.98 |
| 17_V | 53_Y | 1.223 | 0.98 |
| 110_H | 135_R | 1.220 | 0.98 |
| 52_Y | 56_S | 1.200 | 0.98 |
| 221_L | 232_S | 1.198 | 0.98 |
| 86_N | 91_Y | 1.198 | 0.98 |
| 113_L | 131_F | 1.193 | 0.97 |
| 218_F | 236_I | 1.193 | 0.97 |
| 317_L | 347_I | 1.186 | 0.97 |
| 107_V | 111_A | 1.180 | 0.97 |
| 338_L | 343_I | 1.176 | 0.97 |
| 101_I | 105_L | 1.172 | 0.97 |
| 367_L | 371_K | 1.170 | 0.97 |
| 313_G | 377_I | 1.166 | 0.97 |
| 53_Y | 149_L | 1.165 | 0.97 |
| 95_Q | 99_T | 1.149 | 0.97 |
| 26_T | 64_T | 1.140 | 0.96 |
| 313_G | 346_I | 1.138 | 0.96 |
| 69_A | 73_E | 1.138 | 0.96 |
| 292_S | 296_K | 1.136 | 0.96 |
| 234_M | 237_Q | 1.133 | 0.96 |
| 92_F | 120_P | 1.130 | 0.96 |
| 223_T | 227_S | 1.121 | 0.96 |
| 277_Q | 280_I | 1.120 | 0.96 |
| 2_K | 73_E | 1.120 | 0.96 |
| 214_R | 218_F | 1.115 | 0.96 |
| 26_T | 74_A | 1.115 | 0.96 |
| 98_E | 127_M | 1.113 | 0.96 |
| 143_L | 148_A | 1.113 | 0.96 |
| 126_E | 130_K | 1.103 | 0.95 |
| 99_T | 103_E | 1.101 | 0.95 |
| 26_T | 73_E | 1.094 | 0.95 |
| 125_T | 197_A | 1.092 | 0.95 |
| 129_Q | 136_I | 1.090 | 0.95 |
| 75_E | 111_A | 1.089 | 0.95 |
| 172_A | 175_E | 1.085 | 0.95 |
| 243_D | 248_H | 1.081 | 0.95 |
| 51_E | 55_K | 1.080 | 0.95 |
| 28_V | 64_T | 1.078 | 0.95 |
| 1_M | 23_N | 1.072 | 0.94 |
| 4_A | 28_V | 1.067 | 0.94 |
| 295_A | 341_K | 1.061 | 0.94 |
| 174_A | 181_L | 1.060 | 0.94 |
| 3_I | 19_L | 1.059 | 0.94 |
| 321_S | 382_Y | 1.058 | 0.94 |
| 317_L | 326_F | 1.056 | 0.94 |
| 225_A | 235_I | 1.055 | 0.94 |
| 289_V | 296_K | 1.053 | 0.94 |
| 29_D | 65_L | 1.050 | 0.94 |
| 34_K | 37_K | 1.047 | 0.94 |
| 177_F | 181_L | 1.045 | 0.93 |
| 355_L | 359_D | 1.041 | 0.93 |
| 337_I | 341_K | 1.041 | 0.93 |
| 147_K | 150_Y | 1.038 | 0.93 |
| 354_K | 357_S | 1.035 | 0.93 |
| 128_R | 163_E | 1.032 | 0.93 |
| 30_I | 96_H | 1.029 | 0.93 |
| 364_V | 369_N | 1.027 | 0.93 |
| 370_F | 374_A | 1.026 | 0.93 |
| 265_T | 280_I | 1.024 | 0.93 |
| 76_L | 114_I | 1.023 | 0.92 |
| 4_A | 70_A | 1.011 | 0.92 |
| 162_C | 175_E | 1.011 | 0.92 |
| 8_S | 29_D | 1.010 | 0.92 |
| 176_K | 179_L | 1.009 | 0.92 |
| 326_F | 331_I | 1.009 | 0.92 |
| 10_Y | 327_R | 1.003 | 0.92 |
| 30_I | 103_E | 1.002 | 0.91 |
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 | |
| 1dljA | 1 | 1 | 100 | 0.254 | Contact Map |
| 3pidA | 1 | 0.9378 | 100 | 0.268 | Contact Map |
| 2y0cA | 4 | 0.9876 | 100 | 0.305 | Contact Map |
| 3gg2A | 4 | 0.9776 | 100 | 0.333 | Contact Map |
| 4a7pA | 2 | 0.9652 | 100 | 0.336 | Contact Map |
| 3vtfA | 1 | 0.9677 | 100 | 0.338 | Contact Map |
| 1mv8A | 4 | 0.9577 | 100 | 0.345 | Contact Map |
| 2q3eA | 12 | 0.9851 | 100 | 0.346 | Contact Map |
| 2o3jA | 3 | 0.9851 | 100 | 0.346 | Contact Map |
| 3g79A | 2 | 0.9627 | 100 | 0.348 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)