| DegP |
| ID: | 1513765045 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 474 (432) | ||
| Sequences: | 2836 (1780.8) | ||
| Seq/Len: | 6.565 | ||
| Nf(neff/√len): | 85.7 |
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: 6.565).
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 |
| 242_N | 246_E | 6.301 | 1.00 |
| 46_E | 185_R | 6.089 | 1.00 |
| 367_L | 376_V | 4.897 | 1.00 |
| 338_S | 366_G | 4.318 | 1.00 |
| 184_L | 248_I | 4.088 | 1.00 |
| 139_I | 153_M | 3.925 | 1.00 |
| 149_F | 167_I | 3.757 | 1.00 |
| 180_D | 183_A | 3.423 | 1.00 |
| 177_K | 246_E | 3.280 | 1.00 |
| 208_V | 225_I | 3.252 | 1.00 |
| 164_L | 281_V | 3.227 | 1.00 |
| 322_N | 326_A | 3.217 | 1.00 |
| 130_N | 156_K | 3.173 | 1.00 |
| 182_D | 271_N | 3.140 | 1.00 |
| 51_S | 175_A | 3.080 | 1.00 |
| 231_I | 265_G | 2.897 | 1.00 |
| 120_D | 123_K | 2.891 | 1.00 |
| 443_N | 446_E | 2.844 | 1.00 |
| 152_K | 168_Q | 2.815 | 1.00 |
| 436_A | 447_L | 2.783 | 1.00 |
| 180_D | 271_N | 2.773 | 1.00 |
| 118_I | 143_L | 2.769 | 1.00 |
| 404_N | 444_I | 2.738 | 1.00 |
| 340_N | 357_M | 2.726 | 1.00 |
| 316_V | 336_I | 2.681 | 1.00 |
| 413_V | 427_L | 2.668 | 1.00 |
| 364_T | 375_N | 2.565 | 1.00 |
| 339_L | 354_V | 2.532 | 1.00 |
| 337_T | 368_L | 2.521 | 1.00 |
| 40_S | 188_D | 2.452 | 1.00 |
| 42_A | 185_R | 2.450 | 1.00 |
| 151_A | 165_I | 2.392 | 1.00 |
| 362_K | 377_N | 2.376 | 1.00 |
| 330_I | 365_L | 2.341 | 1.00 |
| 127_V | 277_T | 2.323 | 1.00 |
| 58_E | 138_V | 2.310 | 1.00 |
| 42_A | 188_D | 2.303 | 1.00 |
| 431_D | 464_R | 2.272 | 1.00 |
| 176_I | 241_V | 2.253 | 1.00 |
| 362_K | 379_E | 2.227 | 1.00 |
| 239_A | 247_L | 2.223 | 1.00 |
| 127_V | 273_V | 2.212 | 1.00 |
| 184_L | 208_V | 2.164 | 1.00 |
| 117_V | 247_L | 2.148 | 1.00 |
| 316_V | 330_I | 2.144 | 1.00 |
| 125_Y | 154_V | 2.119 | 1.00 |
| 330_I | 367_L | 2.113 | 1.00 |
| 442_K | 446_E | 2.111 | 1.00 |
| 138_V | 150_D | 2.105 | 1.00 |
| 339_L | 357_M | 2.088 | 1.00 |
| 125_Y | 164_L | 2.087 | 1.00 |
| 291_L | 378_L | 2.027 | 1.00 |
| 119_I | 277_T | 2.015 | 1.00 |
| 125_Y | 281_V | 1.992 | 1.00 |
| 48_V | 176_I | 1.987 | 1.00 |
| 404_N | 411_V | 1.963 | 1.00 |
| 41_L | 189_Y | 1.940 | 1.00 |
| 43_P | 185_R | 1.894 | 1.00 |
| 117_V | 239_A | 1.892 | 1.00 |
| 152_K | 166_Q | 1.831 | 1.00 |
| 402_M | 447_L | 1.819 | 1.00 |
| 364_T | 377_N | 1.813 | 1.00 |
| 126_V | 167_I | 1.808 | 1.00 |
| 366_G | 375_N | 1.802 | 1.00 |
| 189_Y | 205_S | 1.780 | 1.00 |
| 297_E | 347_F | 1.763 | 1.00 |
| 285_Q | 382_Q | 1.745 | 1.00 |
| 278_S | 282_E | 1.740 | 1.00 |
| 338_S | 341_G | 1.733 | 1.00 |
| 208_V | 248_I | 1.720 | 1.00 |
| 367_L | 374_V | 1.714 | 1.00 |
| 140_K | 148_K | 1.694 | 1.00 |
| 463_Q | 466_D | 1.691 | 1.00 |
| 51_S | 176_I | 1.666 | 1.00 |
| 321_P | 326_A | 1.654 | 1.00 |
| 312_R | 343_P | 1.635 | 1.00 |
| 338_S | 343_P | 1.612 | 1.00 |
| 427_L | 462_I | 1.608 | 1.00 |
| 250_I | 273_V | 1.596 | 1.00 |
| 118_I | 173_L | 1.593 | 1.00 |
| 289_G | 380_L | 1.588 | 1.00 |
| 298_L | 308_V | 1.588 | 1.00 |
| 302_L | 306_M | 1.569 | 0.99 |
| 125_Y | 166_Q | 1.565 | 0.99 |
| 181_S | 271_N | 1.554 | 0.99 |
| 441_V | 450_V | 1.540 | 0.99 |
| 162_I | 250_I | 1.534 | 0.99 |
| 178_M | 274_K | 1.512 | 0.99 |
| 45_L | 203_V | 1.512 | 0.99 |
| 48_V | 241_V | 1.511 | 0.99 |
| 287_K | 382_Q | 1.501 | 0.99 |
| 134_D | 158_P | 1.499 | 0.99 |
| 233_R | 257_P | 1.485 | 0.99 |
| 446_E | 449_K | 1.479 | 0.99 |
| 337_T | 366_G | 1.470 | 0.99 |
| 439_Q | 450_V | 1.465 | 0.99 |
| 176_I | 247_L | 1.460 | 0.99 |
| 126_V | 165_I | 1.452 | 0.99 |
| 296_T | 302_L | 1.439 | 0.99 |
| 403_S | 414_N | 1.432 | 0.99 |
| 330_I | 376_V | 1.431 | 0.99 |
| 312_R | 345_S | 1.421 | 0.99 |
| 130_N | 134_D | 1.409 | 0.99 |
| 446_E | 450_V | 1.406 | 0.99 |
| 145_D | 149_F | 1.404 | 0.99 |
| 401_E | 415_N | 1.404 | 0.99 |
| 444_I | 448_R | 1.403 | 0.99 |
| 184_L | 225_I | 1.394 | 0.98 |
| 342_K | 353_Q | 1.389 | 0.98 |
| 117_V | 176_I | 1.388 | 0.98 |
| 164_L | 277_T | 1.383 | 0.98 |
| 291_L | 323_S | 1.383 | 0.98 |
| 178_M | 270_S | 1.380 | 0.98 |
| 203_V | 207_I | 1.356 | 0.98 |
| 357_M | 380_L | 1.350 | 0.98 |
| 340_N | 363_L | 1.350 | 0.98 |
| 340_N | 361_S | 1.340 | 0.98 |
| 117_V | 241_V | 1.334 | 0.98 |
| 162_I | 270_S | 1.332 | 0.98 |
| 294_M | 318_Q | 1.324 | 0.98 |
| 411_V | 444_I | 1.317 | 0.98 |
| 118_I | 167_I | 1.310 | 0.98 |
| 55_I | 141_V | 1.299 | 0.97 |
| 160_S | 276_L | 1.295 | 0.97 |
| 57_V | 113_L | 1.292 | 0.97 |
| 441_V | 446_E | 1.284 | 0.97 |
| 327_K | 381_Q | 1.279 | 0.97 |
| 143_L | 149_F | 1.271 | 0.97 |
| 44_M | 241_V | 1.268 | 0.97 |
| 48_V | 193_I | 1.264 | 0.97 |
| 283_Y | 287_K | 1.259 | 0.97 |
| 302_L | 305_A | 1.258 | 0.97 |
| 363_L | 380_L | 1.256 | 0.97 |
| 357_M | 361_S | 1.247 | 0.96 |
| 56_N | 112_A | 1.245 | 0.96 |
| 274_K | 278_S | 1.240 | 0.96 |
| 358_P | 361_S | 1.234 | 0.96 |
| 59_G | 110_F | 1.234 | 0.96 |
| 123_K | 166_Q | 1.225 | 0.96 |
| 50_P | 174_T | 1.220 | 0.96 |
| 298_L | 311_Q | 1.218 | 0.96 |
| 178_M | 273_V | 1.217 | 0.96 |
| 293_I | 314_A | 1.208 | 0.95 |
| 299_N | 302_L | 1.206 | 0.95 |
| 328_A | 378_L | 1.206 | 0.95 |
| 90_Q | 94_F | 1.193 | 0.95 |
| 190_T | 248_I | 1.184 | 0.95 |
| 41_L | 205_S | 1.182 | 0.95 |
| 229_A | 265_G | 1.181 | 0.95 |
| 296_T | 317_S | 1.180 | 0.95 |
| 44_M | 191_V | 1.164 | 0.94 |
| 419_G | 423_A | 1.164 | 0.94 |
| 127_V | 270_S | 1.161 | 0.94 |
| 345_S | 349_A | 1.155 | 0.94 |
| 295_G | 350_L | 1.135 | 0.93 |
| 339_L | 365_L | 1.133 | 0.93 |
| 195_N | 253_A | 1.124 | 0.93 |
| 191_V | 243_L | 1.121 | 0.92 |
| 290_E | 320_L | 1.120 | 0.92 |
| 411_V | 441_V | 1.107 | 0.92 |
| 227_T | 240_L | 1.105 | 0.92 |
| 72_F | 75_F | 1.103 | 0.92 |
| 169_N | 173_L | 1.089 | 0.91 |
| 45_L | 191_V | 1.083 | 0.91 |
| 331_K | 370_D | 1.083 | 0.91 |
| 278_S | 281_V | 1.081 | 0.91 |
| 273_V | 277_T | 1.077 | 0.90 |
| 435_G | 461_N | 1.075 | 0.90 |
| 318_Q | 332_A | 1.069 | 0.90 |
| 49_M | 201_E | 1.067 | 0.90 |
| 136_A | 139_I | 1.066 | 0.90 |
| 291_L | 380_L | 1.064 | 0.90 |
| 140_K | 150_D | 1.062 | 0.89 |
| 159_R | 383_S | 1.057 | 0.89 |
| 413_V | 431_D | 1.056 | 0.89 |
| 130_N | 158_P | 1.046 | 0.89 |
| 306_M | 335_V | 1.044 | 0.88 |
| 117_V | 250_I | 1.041 | 0.88 |
| 40_S | 43_P | 1.039 | 0.88 |
| 143_L | 147_R | 1.038 | 0.88 |
| 409_Q | 442_K | 1.038 | 0.88 |
| 445_A | 449_K | 1.026 | 0.87 |
| 344_I | 353_Q | 1.022 | 0.87 |
| 155_G | 280_M | 1.022 | 0.87 |
| 334_D | 369_R | 1.019 | 0.87 |
| 211_L | 225_I | 1.018 | 0.87 |
| 90_Q | 93_P | 1.017 | 0.87 |
| 257_P | 262_I | 1.011 | 0.86 |
| 324_S | 381_Q | 1.008 | 0.86 |
| 54_S | 112_A | 1.008 | 0.86 |
| 183_A | 244_N | 1.005 | 0.86 |
| 57_V | 112_A | 1.001 | 0.85 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1ky9A | 2 | 0.8418 | 100 | 0.401 | Contact Map |
| 3pv2A | 4 | 0.7996 | 100 | 0.431 | Contact Map |
| 4a8cA | 12 | 0.8249 | 100 | 0.455 | Contact Map |
| 3stjA | 12 | 0.6308 | 100 | 0.545 | Contact Map |
| 4flnA | 3 | 0.8059 | 100 | 0.546 | Contact Map |
| 4ic6A | 3 | 0.6667 | 100 | 0.598 | Contact Map |
| 1lcyA | 1 | 0.6118 | 100 | 0.598 | Contact Map |
| 3qo6A | 3 | 0.6646 | 100 | 0.601 | Contact Map |
| 4ri0A | 3 | 0.6435 | 100 | 0.613 | Contact Map |
| 1te0A | 2 | 0.6646 | 100 | 0.622 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)