| pgp |
| ID: | 1486135290 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 417 (400) | ||
| Sequences: | 36620 (24346.8) | ||
| Seq/Len: | 91.550 | ||
| Nf(neff/√len): | 1217.3 |
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: 91.550).
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 |
| 297_H | 307_Y | 4.189 | 1.00 |
| 178_T | 201_E | 4.021 | 1.00 |
| 384_L | 396_H | 3.904 | 1.00 |
| 203_K | 206_Q | 3.901 | 1.00 |
| 267_C | 271_E | 3.832 | 1.00 |
| 206_Q | 384_L | 3.817 | 1.00 |
| 181_E | 197_G | 3.774 | 1.00 |
| 176_N | 201_E | 3.601 | 1.00 |
| 180_G | 235_K | 3.547 | 1.00 |
| 292_K | 297_H | 3.512 | 1.00 |
| 180_G | 237_L | 3.489 | 1.00 |
| 270_A | 284_Q | 3.454 | 1.00 |
| 297_H | 301_E | 3.230 | 1.00 |
| 399_H | 409_Y | 3.117 | 1.00 |
| 235_K | 242_E | 3.075 | 1.00 |
| 270_A | 308_S | 2.970 | 1.00 |
| 410_F | 414_S | 2.842 | 1.00 |
| 196_Q | 392_R | 2.788 | 1.00 |
| 270_A | 274_A | 2.782 | 1.00 |
| 193_P | 196_Q | 2.673 | 1.00 |
| 183_V | 197_G | 2.669 | 1.00 |
| 291_A | 307_Y | 2.620 | 1.00 |
| 289_R | 293_E | 2.563 | 1.00 |
| 222_V | 340_L | 2.560 | 1.00 |
| 254_H | 337_H | 2.511 | 1.00 |
| 178_T | 237_L | 2.467 | 1.00 |
| 179_F | 182_V | 2.466 | 1.00 |
| 284_Q | 288_V | 2.315 | 1.00 |
| 283_S | 286_E | 2.310 | 1.00 |
| 273_I | 291_A | 2.283 | 1.00 |
| 270_A | 287_I | 2.279 | 1.00 |
| 176_N | 203_K | 2.253 | 1.00 |
| 386_V | 396_H | 2.237 | 1.00 |
| 288_V | 297_H | 2.219 | 1.00 |
| 222_V | 372_I | 2.213 | 1.00 |
| 406_K | 410_F | 2.211 | 1.00 |
| 183_V | 193_P | 2.199 | 1.00 |
| 247_N | 250_W | 2.181 | 1.00 |
| 185_N | 193_P | 2.178 | 1.00 |
| 398_T | 401_Q | 2.167 | 1.00 |
| 200_L | 386_V | 2.156 | 1.00 |
| 335_Q | 367_R | 2.153 | 1.00 |
| 183_V | 233_A | 2.135 | 1.00 |
| 227_R | 230_D | 2.128 | 1.00 |
| 202_V | 208_L | 2.097 | 1.00 |
| 305_N | 309_T | 2.097 | 1.00 |
| 230_D | 244_K | 2.029 | 1.00 |
| 397_G | 401_Q | 2.021 | 1.00 |
| 256_G | 336_P | 2.011 | 1.00 |
| 288_V | 292_K | 1.982 | 1.00 |
| 395_E | 407_G | 1.980 | 1.00 |
| 361_D | 381_N | 1.977 | 1.00 |
| 176_N | 204_K | 1.950 | 1.00 |
| 296_I | 299_F | 1.921 | 1.00 |
| 207_T | 382_A | 1.914 | 1.00 |
| 389_Q | 408_I | 1.911 | 1.00 |
| 277_D | 281_V | 1.851 | 1.00 |
| 288_V | 301_E | 1.841 | 1.00 |
| 277_D | 286_E | 1.835 | 1.00 |
| 353_E | 375_R | 1.822 | 1.00 |
| 179_F | 200_L | 1.798 | 1.00 |
| 202_V | 370_I | 1.793 | 1.00 |
| 151_I | 155_E | 1.787 | 1.00 |
| 185_N | 232_L | 1.777 | 1.00 |
| 290_A | 294_A | 1.765 | 1.00 |
| 38_G | 41_K | 1.750 | 1.00 |
| 395_E | 405_Q | 1.740 | 1.00 |
| 273_I | 287_I | 1.739 | 1.00 |
| 293_E | 362_K | 1.720 | 1.00 |
| 15_A | 52_E | 1.713 | 1.00 |
| 207_T | 371_V | 1.694 | 1.00 |
| 389_Q | 394_K | 1.691 | 1.00 |
| 286_E | 335_Q | 1.691 | 1.00 |
| 208_L | 384_L | 1.688 | 1.00 |
| 295_N | 355_V | 1.676 | 1.00 |
| 89_V | 93_M | 1.665 | 1.00 |
| 206_Q | 383_D | 1.654 | 1.00 |
| 208_L | 386_V | 1.653 | 1.00 |
| 175_G | 239_D | 1.651 | 1.00 |
| 395_E | 406_K | 1.627 | 1.00 |
| 221_V | 388_F | 1.622 | 1.00 |
| 394_K | 408_I | 1.621 | 1.00 |
| 354_K | 358_E | 1.610 | 1.00 |
| 274_A | 284_Q | 1.605 | 1.00 |
| 274_A | 287_I | 1.570 | 1.00 |
| 299_F | 322_Q | 1.562 | 1.00 |
| 386_V | 393_V | 1.559 | 1.00 |
| 181_E | 199_S | 1.558 | 1.00 |
| 209_A | 382_A | 1.552 | 1.00 |
| 284_Q | 308_S | 1.545 | 1.00 |
| 289_R | 292_K | 1.495 | 1.00 |
| 266_D | 310_K | 1.489 | 1.00 |
| 403_L | 413_V | 1.487 | 1.00 |
| 22_V | 49_N | 1.484 | 1.00 |
| 174_E | 239_D | 1.477 | 1.00 |
| 293_E | 332_L | 1.476 | 1.00 |
| 210_L | 386_V | 1.444 | 1.00 |
| 195_L | 198_L | 1.415 | 1.00 |
| 176_N | 239_D | 1.413 | 1.00 |
| 226_E | 257_I | 1.408 | 1.00 |
| 242_E | 245_R | 1.403 | 0.99 |
| 312_G | 317_Q | 1.399 | 0.99 |
| 177_V | 370_I | 1.396 | 0.99 |
| 184_F | 220_T | 1.372 | 0.99 |
| 184_F | 224_L | 1.370 | 0.99 |
| 288_V | 307_Y | 1.367 | 0.99 |
| 303_L | 309_T | 1.364 | 0.99 |
| 408_I | 411_S | 1.361 | 0.99 |
| 286_E | 289_R | 1.346 | 0.99 |
| 213_S | 389_Q | 1.343 | 0.99 |
| 184_F | 229_Y | 1.340 | 0.99 |
| 93_M | 97_D | 1.339 | 0.99 |
| 305_N | 310_K | 1.329 | 0.99 |
| 210_L | 221_V | 1.325 | 0.99 |
| 285_E | 288_V | 1.319 | 0.99 |
| 97_D | 105_K | 1.313 | 0.99 |
| 348_L | 356_V | 1.303 | 0.99 |
| 203_K | 384_L | 1.297 | 0.99 |
| 15_A | 56_I | 1.291 | 0.99 |
| 291_A | 300_I | 1.289 | 0.99 |
| 182_V | 231_P | 1.288 | 0.99 |
| 34_I | 39_Q | 1.287 | 0.99 |
| 183_V | 196_Q | 1.279 | 0.99 |
| 380_Q | 400_Q | 1.278 | 0.99 |
| 291_A | 297_H | 1.274 | 0.99 |
| 209_A | 379_I | 1.269 | 0.99 |
| 175_G | 204_K | 1.261 | 0.99 |
| 373_A | 378_T | 1.259 | 0.99 |
| 173_L | 239_D | 1.250 | 0.99 |
| 298_A | 301_E | 1.249 | 0.99 |
| 200_L | 221_V | 1.248 | 0.99 |
| 179_F | 225_L | 1.246 | 0.98 |
| 395_E | 410_F | 1.244 | 0.98 |
| 224_L | 236_V | 1.238 | 0.98 |
| 286_E | 333_V | 1.235 | 0.98 |
| 162_S | 247_N | 1.230 | 0.98 |
| 18_K | 52_E | 1.227 | 0.98 |
| 256_G | 331_A | 1.225 | 0.98 |
| 311_V | 318_L | 1.223 | 0.98 |
| 26_V | 42_E | 1.217 | 0.98 |
| 29_A | 263_I | 1.216 | 0.98 |
| 262_P | 327_A | 1.202 | 0.98 |
| 294_A | 329_A | 1.202 | 0.98 |
| 358_E | 362_K | 1.192 | 0.98 |
| 273_I | 333_V | 1.185 | 0.98 |
| 198_L | 221_V | 1.179 | 0.98 |
| 197_G | 392_R | 1.170 | 0.97 |
| 225_L | 370_I | 1.163 | 0.97 |
| 296_I | 300_I | 1.152 | 0.97 |
| 214_S | 352_S | 1.149 | 0.97 |
| 15_A | 18_K | 1.145 | 0.97 |
| 258_V | 331_A | 1.144 | 0.97 |
| 250_W | 253_A | 1.137 | 0.97 |
| 179_F | 236_V | 1.130 | 0.97 |
| 241_K | 246_L | 1.121 | 0.97 |
| 371_V | 382_A | 1.115 | 0.96 |
| 364_R | 369_C | 1.108 | 0.96 |
| 147_A | 151_I | 1.104 | 0.96 |
| 179_F | 221_V | 1.098 | 0.96 |
| 241_K | 245_R | 1.096 | 0.96 |
| 295_N | 352_S | 1.095 | 0.96 |
| 11_K | 56_I | 1.093 | 0.96 |
| 269_I | 326_I | 1.090 | 0.96 |
| 216_C | 388_F | 1.089 | 0.96 |
| 213_S | 408_I | 1.088 | 0.96 |
| 248_V | 252_R | 1.087 | 0.96 |
| 236_V | 243_I | 1.078 | 0.95 |
| 10_D | 148_A | 1.074 | 0.95 |
| 207_T | 369_C | 1.073 | 0.95 |
| 400_Q | 404_A | 1.073 | 0.95 |
| 291_A | 296_I | 1.072 | 0.95 |
| 299_F | 303_L | 1.071 | 0.95 |
| 290_A | 332_L | 1.068 | 0.95 |
| 224_L | 231_P | 1.066 | 0.95 |
| 362_K | 365_E | 1.063 | 0.95 |
| 285_E | 289_R | 1.052 | 0.95 |
| 282_V | 333_V | 1.042 | 0.94 |
| 301_E | 306_K | 1.037 | 0.94 |
| 193_P | 232_L | 1.037 | 0.94 |
| 22_V | 45_R | 1.028 | 0.94 |
| 163_Y | 245_R | 1.024 | 0.93 |
| 180_G | 199_S | 1.021 | 0.93 |
| 231_P | 243_I | 1.013 | 0.93 |
| 373_A | 379_I | 1.012 | 0.93 |
| 46_Y | 50_L | 1.011 | 0.93 |
| 18_K | 49_N | 1.011 | 0.93 |
| 107_T | 110_A | 1.010 | 0.93 |
| 42_E | 275_Y | 1.009 | 0.93 |
| 284_Q | 287_I | 1.006 | 0.93 |
| 288_V | 291_A | 1.000 | 0.92 |
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 | |
| 4ry2A | 2 | 0 | 100 | 0.027 | Contact Map |
| 4a82A | 4 | 0.952 | 100 | 0.066 | Contact Map |
| 4f4cA | 1 | 0.9329 | 100 | 0.082 | Contact Map |
| 4q4hB | 1 | 0.9472 | 100 | 0.114 | Contact Map |
| 4mrsA | 2 | 0.9496 | 100 | 0.118 | Contact Map |
| 4mycA | 3 | 0.9472 | 100 | 0.119 | Contact Map |
| 4q9hA | 1 | 0.9568 | 100 | 0.119 | Contact Map |
| 3b5xA | 2 | 0.9472 | 100 | 0.124 | Contact Map |
| 3b60A | 4 | 0.9472 | 100 | 0.124 | Contact Map |
| 3zdqA | 1 | 0.9281 | 100 | 0.126 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)